ChemWiki - User contributions [en]

Talk:Mod:Hunt Research Group/ion pair scan

2014-11-21T18:50:24Z

Gd2613: /* How to... conduct a systematic conformational analysis for an ion pair dimer */

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:ScanAngles.png‎|500px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one of the atom coordinates is altered all the other atoms referred to it follows that atom; Notwithstanding, the first three atoms declared are an exception as they has to be referred to atoms external to the molecule. To obtain uniquely the rotation of the molecule around the other these three atoms were referred to a set of dummy atoms. To execute a 2D rotational scan 4 dummy atoms has been used. Two of them are static trough the scan whereas the other two rotates around the two static ones. Thinking thoughtfully to the system can be understood why 4 atoms are used.
To define a point in the space by a Z-matrix you define it in relation to other points previously defined.
Three parameters are used to define a point in the space : the interatomic distance, the angle, and the dihedral angle. The first two parameters can be defined respectively to the two static dummy atoms. Because the rotation of the other two atoms is in plane with the two static dummy atoms it does not affect a dihedral angle defined by the use of rotating atom as one of the terminal atoms of the dihedral angle.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’. The two molecules will respectively move in 2 perpendicular planes of rotation, which will allow to carry out the spheric scan of the interactions between the two molecules.

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

S 30 1.72774347 31 122.85100226 1 1.94989600 0

</pre>

The first atom (atom 30 in this case) is set so that the sample-probe distance is determined by the variable B1, then the angle defines that the atom will be positioned approximatively in line with the atom 1 and 3 so that moving 3 will inherently move this atom and the dihedral angle defines the plane perpendicular to the 1 2 3 atoms plane where the atom 30 will lay(notice that the plane containing 1 2 3 will change through the scan with the movement of the atom 3).

The second atom (atom 31 in this case) is defined with respect to the previous atom for the interatomic distance. Because 1 is the center of the system the angle 1 30 31 will be constant therefore is a good way to define the atom 31 position. Dihedral angle is defined but left variable so that the molecule can tilt respect to the 30-1 axis. The atom 2 is not modified through the scan so it is a good place holder to be used to define the dihedral angle and the variation of the 30 atom position with respect to the movement of the atom 3 does not affect the 31 30 1 2 dihedral angle because it doesn't vary the plane defined by the atoms 30 1 2.

The third atom is defined for the interatomic distance and the angle with respect of the two other atoms defined before. The dihedral angle is defined with respect of the atom 1 that being the centre of the system does not make the dihedral angle trough the scan (plane defined by 30 31 and 1 does not vary trough the scan)

All the remaining atoms of the molecule are defined with respect to these three atoms defined here so that when these three atoms move all the molecule moves coherently. THis can be imposed by the button in gaussview with the letter 'A' that allows to change the coordinates.

The first three atoms of the sample molecule are defined as it follows :

<pre>

C 1 1.15771466 2 90.00000000 4 90.00000000 0

N 1 1.17242544 5 71.45544166 2 83.48309458 0

N 1 1.13616026 5 69.80539566 6 -173.48309458 0

</pre>

The position of the molecule is fixed but the first of the three atoms defines the dihedral angle with respect of the coordinates of the atoms C(5) 1 2 4 therefore the rotation of the dummy atom 4 will result in the inherent rotation of the C atom (the dihedral angle that defines the position of the atom 4 is a variable).
The other two atoms are defined with the atoms 1 and 2 that does not move during the scan.

<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the butyl chain causes to the script to do not converge.
In my case I have tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I have tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more conformational freedom, carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I have added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-10-10T17:32:38Z

Gd2613:

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:ScanAngles.png‎|500px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one of the atom coordinates is altered all the other atoms referred to it follows that atom; Notwithstanding, the first three atoms declared are an exception as they has to be referred to atoms external to the molecule. To obtain uniquely the rotation of the molecule around the other these three atoms were referred to a set of dummy atoms. To execute a 2D rotational scan 4 dummy atoms has been used. Two of them are static trough the scan whereas the other two rotates around the two static ones. Thinking thoughtfully to the system can be understood why 4 atoms are used.
To define a point in the space by a Z-matrix you define it in relation to other points previously defined.
Three parameters are used to define a point in the space : the interatomic distance, the angle, and the dihedral angle. The first two parameters can be defined respectively to the two static dummy atoms. Because the rotation of the other two atoms is in plane with the two static dummy atoms it does not affect a dihedral angle defined by the use of rotating atom as one of the terminal atoms of the dihedral angle.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

S 30 1.72774347 31 122.85100226 1 1.94989600 0

</pre>

The first atom (atom 30 in this case) is set so that the sample-probe distance is determined by the variable B1, then the angle defines that the atom will be positioned approximatively in line with the atom 1 and 3 so that moving 3 will inherently move this atom and the dihedral angle defines the plane perpendicular to the 1 2 3 atoms plane where the atom 30 will lay(notice that the plane containing 1 2 3 will change through the scan with the movement of the atom 3).

The second atom (atom 31 in this case) is defined with respect to the previous atom for the interatomic distance. Because 1 is the center of the system the angle 1 30 31 will be constant therefore is a good way to define the atom 31 position. Dihedral angle is defined but left variable so that the molecule can tilt respect to the 30-1 axis. The atom 2 is not modified through the scan so it is a good place holder to be used to define the dihedral angle and the variation of the 30 atom position with respect to the movement of the atom 3 does not affect the 31 30 1 2 dihedral angle because it doesn't vary the plane defined by the atoms 30 1 2.

The third atom is defined for the interatomic distance and the angle with respect of the two other atoms defined before. The dihedral angle is defined with respect of the atom 1 that being the centre of the system does not make the dihedral angle trough the scan (plane defined by 30 31 and 1 does not vary trough the scan)

All the remaining atoms of the molecule are defined with respect to these three atoms defined here so that when these three atoms move all the molecule moves coherently.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-10-06T15:32:58Z

Gd2613:

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:ScanAngles.png‎|500px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

S 30 1.72774347 31 122.85100226 1 1.94989600 0

</pre>

The first atom (atom 30 in this case) is set so that the sample-probe distance is determined by the variable B1, then the angle defines that the atom will be positioned approximatively in line with the atom 1 and 3 so that moving 3 will inherently move this atom and the dihedral angle defines the plane perpendicular to the 1 2 3 atoms plane where the atom 30 will lay(notice that the plane containing 1 2 3 will change through the scan with the movement of the atom 3).

The second atom (atom 31 in this case) is defined with respect to the previous atom for the interatomic distance. Because 1 is the center of the system the angle 1 30 31 will be constant therefore is a good way to define the atom 31 position. Dihedral angle is defined but left variable so that the molecule can tilt respect to the 30-1 axis. The atom 2 is not modified through the scan so it is a good place holder to be used to define the dihedral angle and the variation of the 30 atom position with respect to the movement of the atom 3 does not affect the 31 30 1 2 dihedral angle because it doesn't vary the plane defined by the atoms 30 1 2.

The third atom is defined for the interatomic distance and the angle with respect of the two other atoms defined before. The dihedral angle is defined with respect of the atom 1 that being the centre of the system does not make the dihedral angle trough the scan (plane defined by 30 31 and 1 does not vary trough the scan)

All the remaining atoms of the molecule are defined with respect to these three atoms defined here so that when these three atoms move all the molecule moves coherently.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-09T15:36:51Z

Gd2613:

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:ScanAngles.png‎|500px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-09T15:30:42Z

Gd2613: /* How to... conduct a systematic conformational analysis for an ion pair dimer */

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:Spherical_scan.png|150px| ]]
</td>
<tr>
<td>
</td>
<td>
[[Image:ScanAngles.png‎|500px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-09T15:30:09Z

Gd2613: /* How to... conduct a systematic conformational analysis for an ion pair dimer */

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:Spherical_scan.png|150px| ]]
</td>
<tr>
<td>
[[Image:ScanAngles.png‎|500px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-09T15:29:47Z

Gd2613: /* How to... conduct a systematic conformational analysis for an ion pair dimer */

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:Spherical_scan.png|150px| ]]
</td>
<tr>
<td>
[[Image:ScanAngles.png‎|300px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-09T15:29:28Z

Gd2613: /* How to... conduct a systematic conformational analysis for an ion pair dimer */

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:Spherical_scan.png|150px| ]]
</td>
<tr>
<td>
</td>
<td>
[[Image:ScanAngles.png‎|300px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

File:ScanAngles.png

2014-09-09T15:27:02Z

Gd2613:

File:Test IN OP top.gif

2014-09-09T15:27:01Z

Gd2613:

File:Test IN OP in plane.gif

2014-09-09T15:27:00Z

Gd2613:

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-09T15:22:27Z

Gd2613:

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:Spherical_scan.png|150px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814

A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000

D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-09T15:20:32Z

Gd2613:

== How to... conduct a systematic conformational analysis for an ion pair dimer ==

<table>
<tr>
<td>
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.
</td>
<td>
[[Image:Spherical_scan.png|150px| ]]
</td>
</tr>

</table>

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<pre>
%nprocshared=8
%mem=14400MB
%chk=test_IN_ON_90.chk
# opt=z-matrix b3lyp/6-31g nosymm geom=connectivity empiricaldispersion=gd3

BMIM

0 1
X
X 1 2.00000000
X 1 3.00000000 2 A1
X 1 3.00000000 2 90.00000000 3 D1 0
C 1 1.15771466 2 90.00000000 4 90.00000000 0
N 1 1.17242544 5 71.45544166 2 83.48309458 0
N 1 1.13616026 5 69.80539566 6 -173.48309458 0
C 6 2.20589881 7 36.75204317 5 179.62354220 0
C 7 2.20741318 6 36.76548810 5 -179.76966396 0
H 8 3.24571830 6 41.19810842 7 -0.35958291 0
C 6 1.47006172 5 126.67015792 7 179.44651575 0
C 7 1.48214358 6 161.27267589 8 170.17035599 0
H 8 1.07651940 6 167.56517796 7 179.25571448 0
H 9 1.07678623 6 122.06766763 7 179.41091048 0
H 11 1.08952723 6 109.31735900 7 121.89721467 0
H 11 1.08956200 6 109.42948493 7 -117.41092715 0
H 11 1.08825013 6 109.03687137 7 2.28983614 0
C 12 1.53044333 6 112.70900607 7 88.75485300 0
H 12 1.09089731 6 115.47545821 7 -41.55756898 0
H 12 1.09150376 6 96.58931706 7 -154.92737321 0
C 18 1.53159261 12 114.02466815 7 60.21093562 0
H 18 1.09474130 12 106.71484623 7 -178.13510738 0
H 18 1.09574182 12 109.46847196 7 -63.61295391 0
C 21 1.53133717 18 112.36924430 12 177.24888774 0
H 21 1.09703026 18 109.68946719 12 -61.12025577 0
H 21 1.09729776 18 109.24326164 12 55.39969468 0
H 24 1.09178867 21 111.10805048 18 179.79823172 0
H 24 1.09323755 21 111.08215903 18 -60.23501784 0
H 24 1.09375708 21 111.13297855 18 59.78378948 0
C 1 B1 3 178.99999509 2 -72.98467412 0
S 30 1.72416943 1 58.52894245 2 D2 0
S 30 1.72774347 31 122.85100226 1 1.94989600 0
N 30 1.38649628 31 118.69787900 32 179.88857349 0
C 33 1.46198199 30 122.51211282 32 176.69344464 0
C 33 1.46194880 30 122.67895299 34 -179.91918915 0
H 34 1.09727882 33 107.79539191 30 -147.02448390 0
H 34 1.08972480 33 108.19170344 30 -30.07257517 0
C 34 1.53221816 33 112.70644243 30 91.09689577 0
H 35 1.09729025 33 107.78009396 30 -147.24569440 0
H 35 1.08967434 33 108.19965873 30 -30.30969788 0
C 35 1.53224904 33 112.72406370 30 90.88083173 0
H 38 1.09170104 34 108.92193675 33 -62.10201645 0
H 38 1.09523444 34 111.32513550 33 57.95875345 0
H 38 1.09666295 34 110.72033274 33 178.37187932 0
H 41 1.09519819 35 111.31213651 33 57.80156920 0
H 41 1.09171890 35 108.94832172 33 -62.26011562 0
H 41 1.09664056 35 110.70985861 33 178.21143471 0

B1 5.86611814
A1 90.00000000 S 9 -9.90000
D1 90.00000000 S 9 -10.00000
D2 -90.00000000

1 2 1.5 3 2.0 6 1.0
2 5 1.0 7 1.0
3 4 1.5 8 1.0
4 5 2.0 9 1.0
5 10 1.0
6
7 11 1.0 12 1.0 13 1.0
8 14 1.0 15 1.0 16 1.0
9
10
11
12
13
14 17 1.0 18 1.0 19 1.0
15
16
17 20 1.0 21 1.0 22 1.0
18
19
20 23 1.0 24 1.0 25 1.0
21
22
23
24
25
26 27 1.0 28 1.0 29 1.0
27
28
29 30 1.0 31 1.0
30 32 1.0 33 1.0 34 1.0
31 35 1.0 36 1.0 37 1.0
32
33
34 38 1.0 39 1.0 40 1.0
35
36
37 41 1.0 42 1.0 43 1.0
38
39
40
41
42
43
</pre>

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-05T15:10:13Z

Gd2613: /* How to... conduct a systematic conformational analysis for an ion pair dimer */

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-05T15:03:15Z

Gd2613:

== How to... conduct a systematic conformational analysis for an ion pair dimer ==
[[File:spherical_scan.jpg]]This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

File:Spherical scan.png

2014-09-05T15:02:15Z

Gd2613:

Mod:Hunt Research Group

2014-09-05T15:01:28Z

Gd2613: /* Research Notes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD'''
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Systematic conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-05T14:57:12Z

Gd2613:

== How to... conduct a systematic conformational analysis for an ion pair dimer ==
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

'''[under development]'''
<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-05T14:55:16Z

Gd2613:

== How to... conduct a systematic conformational analysis for an ion pair dimer ==
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has to be self-referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Talk:Mod:Hunt Research Group/ion pair scan

2014-09-05T14:52:29Z

Gd2613: Created page with "== How to... conduct a systematic conformational analysis for an ion pair dimer == This is a tutorial about a simple procedure to spherical scan of the potential energy surface o..."

== How to... conduct a systematic conformational analysis for an ion pair dimer ==
This is a tutorial about a simple procedure to spherical scan of the potential energy surface of one molecule sampled by another molecule used as a probe. For this scan would be convenient to have a referiment atom in the centre of the sphere but not often the centre of the sphere is occupied by an atom and Gaussian do not allow us to use dummy atoms as referiments for relaxed angle scan (keyword: modredundant). To do that we have to define a coordinate system with some dummy atoms and operate a Z-matrix scan on the coordinates by using the keyword opt=z-matrix in the route.

Herein, I’ll show step by step what I’ve done to set the PES scan for the [C1C4Im][C2C2DTC] ion pair.

<h2>1 - Set the referiment system of your scan</h2>

As first step you’ll introduce these four dummy atoms reported below as the first four atoms of your z-matrix.

<pre>

0 1

X

X 1 3.00000000

X 1 3.00000000 2 A1

X 1 3.00000000 2 90.00000000 3 D1 0

</pre>
These atoms are set to allow us to rotate X3 and X4 in 2 perpendicular planes by modifying A1 and D1 variables.

<h2>2 – Define your molecules</h2>

Now we have to define the molecules involved in the scan. Each molecule has tobe self referred. This means that its atoms are referred to atoms inside the same molecule so that when one atom coordinates are altered all the other atoms referred to it follows that atom. The first three atom declared are an exception, they has to be referred to atoms external to the molecule. These atoms will be the dummy atoms set before.

This is the hard point of the creation of the .com file because you have to set the coordinates of the first three atoms thoughtfully to allow the rotation of the molecule without affecting the coordinates of these atoms during it. This can be checked by rotating the angle in gaussview and seeing if the result is what expected. Hopefully, the procedure described hereafter should work but I do not have occasion to check it onto molecules other than the one displayed.

In order to proceed, we have to distinguish the role of the 2 molecules, one will be our ‘probe’ and the other will be our ‘sample’. The ‘sample’ will rotate on itself whereas the ‘probe’ will move around the ‘sample’

The dummy atoms 1 and 2 must be included in the axis of rotation of the ‘sample’ and 1 will be the ‘centre of inversion’ of the sphere.

The first three atoms of the probe must be set like this :

<pre>

C 1 B1 3 178.99999509 2 -72.98467412 0

S 30 1.72416943 1 58.52894245 2 D2 0

</pre>

The bond of the first atom is set as a variable so that it can vary during the optimization and the dihedral angle of the second atom is also set as a variable, varying the attack angle of the probe. The atom respect to whom the coordinates are set must be respected. The ‘30’ atom is the carbon atom just set in the line before.

<h2>3 – Set the scan</h2>

After the z-matrix a white line must be left and then we will set our variables :

<pre>

B1 5.86611814

A1 90.00000000 S 9 -9.90000

D1 -90.00000000 S 9 +10.00000

D2 -90.00000000

</pre>

Obviously your values will be different but the scan amongst the angle A1 should rotate the probe over and under the plane formed by the atoms 1,3,4 and D1 should rotate the probe in the plane formed by 1,2,3. It is important to remember that Gaussian has some issues with the limiting angles therefore is better to scan until ~179 or ~1 to avoid script faults. Remember to set the opt=z-matrix in the script route.

<h2>4 – What can go wrong</h2>

Personally, I suggest to do multiple ‘little’ scans because in the scan fails the output will not be formatted by gaussview as a X, Y, Z table that is useful for further elaboration. For example, I have done eight scans but two have failed because the buthyl chain causes to the script to do not converge.
In my case I’ve tried to add the keyword in the route INT=ultrafine opt=(z-matrix, tight, maxcycles=250) but this does not solve my problem. I’ve tried to reduce the freedom of the molecule fixing the D2 angle but also that does not deserve to anything. The solution has been to unfreeze the butyl chain. A similar issue can happen also to you and for me the solution has been more freedom carefully given where needed.

<h2>5 – Further elaboration</h2>

After gain your data you have to plot them in a graph. Matlab is a big, heavy and powerful suite of mathematical elaboration scripts that is really useful to produce automatized procedures to output your data as a surface plot by the command surf(). If you would like to try to use this software suite I’ve added a an help page that should help you to plot your scans output.(link available soon) Otherwise you can use a simple plotting software but I think that matlab allows you to have a workspace extremely useful. For example it can produce derivatives of your data spotting out the minimum and maximum of your data.

Mod:Hunt Research Group

2014-09-05T14:48:21Z

Gd2613: /* Research Notes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD'''
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ion_pair_scan link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group

2014-09-05T14:47:14Z

Gd2613: /* Research Notes */

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===HPC Resources===
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#HPC servers and run scripts [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc link]
#Setting up a connection to HPC if you have a PC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_connections link]
#How to fix Windows files under UNIX [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Windowsfiles link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#How to set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to use gaussview directly on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gview link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#How to connect to HPC directory on desktop for file transfers [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc_Directory_on_desktop link]
#How to set up cx2 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cx2 link]

===Visualisation===
*'''ESPs'''
#Instructions for visualizing electrostatic potentials (Gaussview)[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials link]
#Electrostatic Potentials II (Molden) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/electrostatic_potentials_2 link]
*'''VMD'''
#Beginners guide to VMD: a molecular dynamics visualisation package [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#Visualising your Simulation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VisualisingyourSimulation link]
#How to turn a Gaussian optimization into a VMD movie [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/VMDmovie link]
#How to make VMD trajectory repeated periodically [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/vmd link]
*'''JMol'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]
*'''EMO Code'''
#How to use Ling's emo plot code[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emoplot link]
#How to plot EMOs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emo link]

===Gaussian General===
#A database of common errors encountered when running Gaussian jobs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gaussian_errors link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#How to include dispersion [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dispersion link]
#Basic ONIOM (Mechanical Embedding) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/basiconiom link]
#M0n and DFT-D [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/DFTD link]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]

===Setup and Running Ab-Initio MD Simulations===
#CPMD: Car-Parrinello Molecular Dynamics [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd link]
#How to run CPMD to study aqueous solutions [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/cpmd_water link]
#How to run CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k_how link]
#[bmim]Cl using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cpmd link]
#[bmim]Cl using CP2K [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/bmimCl_cp2k link]
#mman using CPMD and Gaussian [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/mman link]
#[emim]SCN using CP2K[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/emimscn link]
#CP2K Donts [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/cp2k link]

===Setup and Running Classical MD Simulations===
#DLPOLY a MD simulation package, Installation on an IMac (old needs to be updated) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/dlpoly_install link]
#DL_POLY FAQs [http://www.stfc.ac.uk/cse/DL_POLY/ccp1gui/38621.aspx] from DL_POLY webpage.
#Packmol for generating starting configurations [http://www.ime.unicamp.br/~martinez/packmol/] from Packmol webpage.
#Getting started: generating a solvated structure and "relaxing" it [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#local [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_to_dlpoly_scripts packmol to dlpoly] conversion scripts
#Getting the Force Field [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Wheretostart link]
#Choosing an Ensemble [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Ensembles link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#Energy Drift [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EnergyDrift link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids link]
#How to equilibrate an MD run[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/equilibration link]
#Equilibration of [bmim][BF4] and [bmim][NO3][https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/BmimBF4_equilibration link]
#Summary of discussions with Ruth[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Aug09QtoRuth link]

===Running QM/MM Simulations in ChemShell===
#ChemShell official website which contains the manual and a tutorial [http://www.stfc.ac.uk/CSE/randd/ccg/36254.aspx link]
#Introduction to ChemShell - Copper in water [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Introduction link]
#Defining the system: Cu2+ and its first 2 solvation shells [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_System_Aqeuous_Cu(II) link]
#Defining the force field parameters [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_Force_Field_Parameters_Aqueous_Cu(II) link]
#Single point QM/MM energy calculation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_SP_Aqeuous_Cu(II) link]
#QM/MM Optimisation [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_OPT_Aqeuous_Cu(II) link]
#QM/MM Molecular Dynamics [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/QMMM_MD_Aqeuous_Cu(II) link]

===Research Notes===
#Cl- in water [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/wannier_centre link]
#The use of Legendre time correlation functions to study reorientational dynamics in liquids[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/legendre link]
#Functional for ILs using CPMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/IL_cpmd_functional link]
#Solving the angular part of the Schrödinger equation for a hydrogen atom [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link] (notes by Vincent)
#Conformational scan for ion-pair dimers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/angular_schrodinger link]

===Installing and using other packages===
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#How to install Geomview [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/geomview link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===Admin Stuff===
#Not used to writing a wiki, make your test runs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/testing on this page]
#How to set-up new macs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_setup link]
#How to set-up remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#[https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/calendar Calendar]
#Demonstrating in the 3rd year computational chemistry lab [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/compchemlab Timetable]
#How to switch the printer HP CP3525dn duplex on and off [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/printing link]

Mod:Hunt Research Group/pimpQSUB

2014-08-04T13:19:40Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=15800
MAXDISK=400
WALLT="499:00:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
GREEN='\033[0;32m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD";
echo "2.# $#";
echo "3.* $*";
echo "4.OPTARG ${OPTARG}";
echo "5.OPTIND ${OPTIND}";
echo "6.CUE ${CUE}";
echo "7.CORE ${CORE}";
echo "8.MEM ${MEM}";
echo "9.WALLTIME ${WALLT}";
echo "10.MAXDISK ${MAXDISK}";
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
save save the list of the current jobs
load call the list of the jobs saved and highlight in red the ended ones
verify.date[mm_dd_yy]
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${FL}
if [[ ${FL} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=499:00:00
#PBS -l select=1:ncpus=8:mem=15800MB:tmpspace=400GB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;15800MB;499:00:00;d01;400GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;15800MB;499:00:00;d01;400GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
else
MAXDISK=${OPTARG-"400"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"15800"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
else
MAXDISK=${PRESET[5]-"400"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"15800"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
q=$(qstat);
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
done < "$WLOG"
elif [[ ${OPTARG} =~ 'save' ]]
then
q=$(qstat);
rm ~/$(date +'.%m_%d_%y')
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $q =~ $n ]]
then
echo -e "$line" >> ~/$(date +'.%m_%d_%y')
fi
done < "$WLOG"
cp ~/$(date +'.%m_%d_%y') ~/.current
elif [[ ${OPTARG} =~ 'load' ]]
then
q=$(qstat);
v=$(cat ~/.current)
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $v =~ $n ]]
then
if [[ ! $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
fi
done < "$WLOG"
elif [[ ${OPTARG} =~ 'verify' ]]
then
q=$(qstat);
v=$(cat ~/${OPTARG#verify})
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $v =~ $n ]]
then
if [[ ! $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
fi
done < "$WLOG"
elif [[ ${OPTARG} == 'edit' ]]
then
vi $WLOG;
else

q=$(qstat);
sed -n "/${OPTARG}/p" $WLOG | while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
done
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -l select=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}GB/" "${SFILE}"
else
sed -i "s/#PBS -l select=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" "${SFILE}"
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" "${SFILE}"
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}"

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" "${SFILE}"
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
FL=${1}
ID=$(ID ${FL});
FNT=${ID}'.com'
if [[ -f ${FNT} && ${#FNT} -gt 4 ]]
then
FL=${ID}.com
fi

NMFL=${FL%.com}
NMFL=${NMFL##*/}
DIR=${1%/*}
echo $DIR
PD=$(pwd)
cd $DIR

if [[ ! -f ${FL} ]]
then
echo "\"${FL}\" does not exists."
exit
elif [[ ! ${FL} =~ .*'.com' ]]
then
echo "\"${FL}\" is not a com file."
exit
fi
echo $FL

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} - 50*CORE))
gmem=$(grep -i -c "%mem=.*/" ${FL})
gpshar=$(grep -i -c "%nprocshared=.*/" ${FL})
gchk=$(grep -i -c "%chk=./" ${FL})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${FL}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${FL}
sed -i "s/%chk=.*chk/%chk=$CD${NMFL}.chk/" ${FL}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}GB/" ${FL##*/}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${FL}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=$RED${NMFL%.com}$NC ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOG
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
cd $PD
shift
done

</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-08-04T12:52:57Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=15800
MAXDISK=400
WALLT="499:00:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
GREEN='\033[0;32m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD";
echo "2.# $#";
echo "3.* $*";
echo "4.OPTARG ${OPTARG}";
echo "5.OPTIND ${OPTIND}";
echo "6.CUE ${CUE}";
echo "7.CORE ${CORE}";
echo "8.MEM ${MEM}";
echo "9.WALLTIME ${WALLT}";
echo "10.MAXDISK ${MAXDISK}";
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
save save the list of the current jobs
load call the list of the jobs saved and highlight in red the ended ones
verify.date[mm_dd_yy]
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${FL}
if [[ ${FL} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=499:00:00
#PBS -l select=1:ncpus=8:mem=15800MB:tmpspace=400GB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;15800MB;499:00:00;d01;400GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;15800MB;499:00:00;d01;400GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
else
MAXDISK=${OPTARG-"400"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"15800"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
else
MAXDISK=${PRESET[5]-"400"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"15800"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
q=$(qstat);
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
done < "$WLOG"
elif [[ ${OPTARG} =~ 'save' ]]
then
q=$(qstat);
rm ~/$(date +'.%m_%d_%y')
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $q =~ $n ]]
then
echo -e "$line" >> ~/$(date +'.%m_%d_%y')
fi
done < "$WLOG"
cp ~/$(date +'.%m_%d_%y') ~/.current
elif [[ ${OPTARG} =~ 'load' ]]
then
q=$(qstat);
v=$(cat ~/.current)
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $v =~ $n ]]
then
if [[ ! $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
fi
done < "$WLOG"
elif [[ ${OPTARG} =~ 'verify' ]]
then
q=$(qstat);
v=$(cat ~/${OPTARG#verify})
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $v =~ $n ]]
then
if [[ ! $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
fi
done < "$WLOG"
elif [[ ${OPTARG} == 'edit' ]]
then
vi $WLOG;
else

q=$(qstat);
sed -n "/${OPTARG}/p" $WLOG | while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
done < "$WLOG"
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -l select=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}GB/" "${SFILE}"
else
sed -i "s/#PBS -l select=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" "${SFILE}"
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" "${SFILE}"
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}"

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" "${SFILE}"
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
FL=${1}
ID=$(ID ${FL});
FNT=${ID}'.com'
if [[ -f ${FNT} && ${#FNT} -gt 4 ]]
then
FL=${ID}.com
fi

NMFL=${FL%.com}
NMFL=${NMFL##*/}
DIR=${1%/*}
echo $DIR
PD=$(pwd)
cd $DIR

if [[ ! -f ${FL} ]]
then
echo "\"${FL}\" does not exists."
exit
elif [[ ! ${FL} =~ .*'.com' ]]
then
echo "\"${FL}\" is not a com file."
exit
fi
echo $FL

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} - 50*CORE))
gmem=$(grep -i -c "%mem=.*/" ${FL})
gpshar=$(grep -i -c "%nprocshared=.*/" ${FL})
gchk=$(grep -i -c "%chk=./" ${FL})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${FL}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${FL}
sed -i "s/%chk=.*chk/%chk=$CD${NMFL}.chk/" ${FL}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}GB/" ${FL##*/}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${FL}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=$RED${NMFL%.com}$NC ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOG
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
cd $PD
shift
done

</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-08-04T10:48:15Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=15800
MAXDISK=400
WALLT="499:00:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD";
echo "2.# $#";
echo "3.* $*";
echo "4.OPTARG ${OPTARG}";
echo "5.OPTIND ${OPTIND}";
echo "6.CUE ${CUE}";
echo "7.CORE ${CORE}";
echo "8.MEM ${MEM}";
echo "9.WALLTIME ${WALLT}";
echo "10.MAXDISK ${MAXDISK}";
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${FL}
if [[ ${FL} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=499:00:00
#PBS -l select=1:ncpus=8:mem=15800MB:tmpspace=400GB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;15800MB;499:00:00;d01;400GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;15800MB;499:00:00;d01;400GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
else
MAXDISK=${OPTARG-"400"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"15800"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
else
MAXDISK=${PRESET[5]-"400"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"15800"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
q=$(qstat);
rm ~/$(date +'.%m_%d_%y')
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $q =~ $n ]]
then
echo -e "$RED$line"
echo -e "$line" >> ~/$(date +'.%m_%d_%y')
else
echo -e "$NC$line"
fi
done < "$WLOG"
elif [[ ${OPTARG} =~ 'verify' ]]
then
q=$(qstat);
v=$(cat ~/${OPTARG#verify})
while read line
do
n=${line%.cx1b*}
n=${n##* | }
if [[ $v =~ $n ]]
then
if [[ ! $q =~ $n ]]
then
echo -e "$RED$line"
else
echo -e "$NC$line"
fi
fi
done < "$WLOG"
elif [[ ${OPTARG} == 'edit' ]]
then
vi $WLOG;
else
sed -n "/${OPTARG}/p" $WLOG | while read x; do echo -e $x; done;
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -l select=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}GB/" "${SFILE}"
else
sed -i "s/#PBS -l select=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" "${SFILE}"
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" "${SFILE}"
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}"

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" "${SFILE}"
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
FL=${1}
ID=$(ID ${FL});
FNT=${ID}'.com'
if [[ -f ${FNT} && ${#FNT} -gt 4 ]]
then
FL=${ID}.com
fi

NMFL=${FL%.com}
NMFL=${NMFL##*/}
DIR=${1%/*}
echo $DIR
PD=$(pwd)
cd $DIR

if [[ ! -f ${FL} ]]
then
echo "\"${FL}\" does not exists."
exit
elif [[ ! ${FL} =~ .*'.com' ]]
then
echo "\"${FL}\" is not a com file."
exit
fi
echo $FL

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} - 50*CORE))
gmem=$(grep -i -c "%mem=.*/" ${FL})
gpshar=$(grep -i -c "%nprocshared=.*/" ${FL})
gchk=$(grep -i -c "%chk=./" ${FL})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${FL}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${FL}
sed -i "s/%chk=.*chk/%chk=$CD${NMFL}.chk/" ${FL}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}GB/" ${FL##*/}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${FL}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=$RED${NMFL%.com}$NC ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOG
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
cd $PD
shift
done

</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/calendar

2014-07-31T13:36:09Z

Gd2613: /* Calendar */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th </td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Richard F - paper)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away) (Patricia away)</td>
<td>5th CECAM workshop Claire away (Patricia away) (Giacomo Away) (Richard F away)</td>
<td>6th CECAM workshop Claire away (Patricia away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Matt - paper)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th LIBLICE conference-Gabriel </td>
<td>17th '''(Hakim-presentation practice)''' LIBLICE conference-Gabriel </td>
<td>18th LIBLICE conference-Gabriel </td>
<td>19th LIBLICE conference-Gabriel </td>
<td>20th LIBLICE conference-Gabriel </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th '''(Talk practice)'''</td>
<td bgcolor="#FFA500">27th '''End of term''' Richard F away</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th (Richard F away)</td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}} (Richard F away)</td>
<td>2nd (Richard F away)</td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th Bryan Away EUCHEM-Richard&Claire</td>
<td>8th Bryan Away EUCHEM-Richard & Claire</td>
<td>9th Bryan Away EUCHEM-Richard & Claire</td>
<td>10th Bryan Away EUCHEM-Richard & Claire</td>
<td>11th Bryan Away EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Bryan Away Richard away Claire away</td>
<td>15th Bryan Away Richard away Claire away</td>
<td>16th Bryan Away Richard away Claire away Vincent away</td>
<td>17th Bryan Away Richard away Matthew Away Claire away Vincent away</td>
<td>18th Bryan Away Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st Liquid Matter-Gabriel Vincent away</td>
<td>22nd Liquid Matter-Gabriel</td>
<td>23rd Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel</td>
<td>24th Gaussian workshop - Claire & Bryan Liquid Matter-Gabriel </td>
<td>25th Liquid Matter-Gabriel jacq away </td>
<td bgcolor="#CCCCCC">26th jacq away </td>
<td bgcolor="#CCCCCC">27th jacq away </td>
</tr>
<tr valign="top">
<td>28th Matthew Away jacq away </td>
<td>29th Matthew Away </td>
<td>30th Matthew Away </td>
<td>31st Bryan Away Matthew Away </td>
<td bgcolor="#4357CFF">1st August Bryan Away Matthew Away </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th Bryan on hiatus Matthew Away </td>
<td>5th Bryan on hiatus Matthew Away </td>
<td>6th Bryan on hiatus Matthew Away </td>
<td>7th Bryan on hiatus Matthew Away </td>
<td>8th Bryan on hiatus Matthew Away </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th Bryan on hiatus Matthew Away </td>
<td>12th Bryan on hiatus </td>
<td>13th Bryan on hiatus </td>
<td>14th Bryan on hiatus </td>
<td>15th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th Bryan on hiatus </td>
<td>19th Bryan on hiatus </td>
<td>20th Bryan on hiatus </td>
<td>21st Bryan on hiatus </td>
<td>22nd Bryan on hiatus </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th Bryan on hiatus </td>
<td>27th Bryan on hiatus </td>
<td>28th Bryan on hiatus </td>
<td>39th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September Bryan on hiatus </td>
<td>2nd Bryan on hiatus </td>
<td>3rd Bryan on hiatus </td>
<td>4th Bryan on hiatus </td>
<td>5th Bryan on hiatus </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/mac remote

2014-07-31T13:35:52Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]
==== set-up system preferences on your office mac ====
:This only works without a firewall
:System Preferences -> Sharing -> Remote Management.
::Allow access for "only these users" and set appropriate limits
:You can then access the remote mac through the Finder on the sidebar under the Shared browser.
::This will show you all the machines on your local network that have sharing on. Click on the mac you want to connect to, don't worry that is "connects" you only as guest when you use the share screen button this will connect you as a particular user and not guest.

==== screen sharing through a firewall ====
:you need a VNC viewer on your home mac
:: common client is chicken of the VNC (free) http://sourceforge.net/projects/cotvnc/
: start up a VNC client (and thats all you need to do!)
:: in Applications "Chicken of the VNC.app"
:you may need the IP address of your office mac
:: in which case ssh into the machine
:: type "/sbin/ifconfig"
:: in the list that follows you want the number after "inet"
:so you went to fullscreen and cannot recover supposedly (none of these worked for me)
::ctrl+alt+cmd+'
::or ctrl+alt+cmd+shift+'
::or ctrl+alt+cmd+§
:so the remote screen is much larger than your current screen, use window zoom and then try to resize
::the green dot in the mac window will resize any window to the whole screen if you loose the edges (if its not working as in iTunes, hold the option key and then the green button)

==== to start an application remotely using ssh ====
:use the terminal application
:ssh in, ie user@mac.ch.ic.ac.uk
::enter password
:then cd to Applications and type "open application"
::the application will then run on the remote mac

==== screen sharing without setting up system pref beforehand ====
: CAREFUL! only do this if you know about using terminal commands
: ssh into the remote (office) mac with an admin login
: enable the remote management via the kickstart utility
: for help
:: <code>$ sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart -help</code>
:options (uninstall/install, deactivate/activate, configure, stop/restart)
:these then have sub-options
:: use "-restart -agent" to restart
::: "-agent" restarts the ARD agent and helper
::: "-console" restarts the console application
::: "-menu" restarts the menu extra
:to set the configure options
:: use "-configure -access -on" to enable access for all users
:: use "-configure -access -off" to disable access for all users
:access privlages (delete files, control and observe, open and quit applications etc)
:: use "-users admin -privs -all" to enable all access privileges for all admin users
:: use "-users guest -privs -none" to disable all access privileges for specified user=guest
:access options
:: use "-allowAccessFor -specifiedUsers" grant access to users with privileges
:: use "-clientopts -setvnclegacy -vnclegacy yes" allow VNC legacy password mode
:: use "-clientopts -setvncpw -vncpw mypasswd" set VNC legacy password, this should be a new password not your login one.

:Activate Remote Desktop Sharing, enable access privileges for all users, restart ARD Agent
:::<code>$ sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart -activate -configure -access -on -privs -all -restart -agent</code>
:Activate Remote Desktop Sharing, enable access privileges for the users "admin", grant full privileges for the users "admin", restart ARD Agent and Menu extra
:::<code>$ sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart -activate -configure -access -on -users admin -privs -all -restart -agent -menu</code>

:turn on the screen sharing
::<code>$ sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart -activate -configure -access -on -users admin -clientopts -setvnclegacy -vnclegacy yes -clientopts -setvncpw -vncpw mypasswd -privs -all -restart -agent</code>

:when you are done turn off the screen sharing
::<code>$ sudo /System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Resources/kickstart -deactivate -configure -access -off</code>

Mod:Hunt Research Group/mac setup

2014-07-31T13:35:21Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

==== make a group ====
::open accounts in system prefs
::click on the + button
::choose groups on pulldown menu
::type in a name and add those users you want to belong to the group
::in this case call the group "hunt_group"
::exit

==== set-up the terminal ====
::create the file ".bash_profile"
::copy and paste the following into it
<pre>
#echo "bash_profile"
. ~/.bashrc
</pre>
::create the file ".bashrc"
::copy and paste the following into it
<pre>
# .bashrc
# WARNING: had to make .bash_profile and added execute to this file
#
# important stuff
#
# tells the computer where to look for personal scripts
export PATH=$PATH:/Users/$USER/bin:/usr/local/bin
#
# change the prompt
export PS1="[\$USER@\h]\$PWD \$ "
#
# control-R lets you search backward through history
HISTSIZE=100
HISTCONTROL=erasedups
HISTIGNORE="cd:exit"
EDITOR=vi
export EDITOR
#
# gaussian
#
# where to fine the executable
export g09root="/Applications"
# set the default memory
export GAUSS_MEMDEF="500MB"
# where to put the LARGE temporary files when running gaussian
export GAUSS_SCRDIR="/Users/$USER/Work/Jobs/tmp"
# script which sets many variables for gaussian
source $g09root/g09/bsd/g09.profile
#
# gaussview
#
# where to find gaussview
export GV_DIR="/Applications/gv"
# libraries
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${GV_DIR}/lib
# allow start from the comand line in mac terminal
alias gv="open $GV_DIR/gview.app"
#
# alias definitions
#
alias home="cd"
alias force="grep -i 'Maximum Force'"
alias dist="grep -i 'Maximum Disp'"
alias rm='rm -I'
#
</pre>

::create the file ".login"
::this is needed because gaussview looks for csh stuff
::copy and paste the following into it
<pre>
setenv g09root /Applications
source $g09root/g09/bsd/g09.login
setenv GAUSS_SCRDIR /Users/$USER/Work/Jobs/tmp
setenv GV_DIR /Applications/gv
setenv GAUSS_EXEDIR /Applications/g09
</pre>
::of course replace my name with your name (or directory structure)
::and the directory tmp should exist before you run any jobs.

==== set-up working directories ====
::make a directory called "work", keep ALL your files here
::inside work make a directory called "jobs", keep all your gaussian jobs here
::inside work make a directory called "testing" ie full path is /Users/name/work/jobs/testing
::vi a file "test.com" and copy and paste the following into it
::ps don't forget the last line must be blank
<pre>
%chk=test.chk
%mem=500MB
%nproc=1
# hf/3-21g geom=connectivity

Title Card Required

0 1
C
H 1 B1
H 1 B2 2 A1
H 1 B3 3 A2 2 D1
H 1 B4 3 A3 2 D2

B1 1.07000000
B2 1.07000000
B3 1.07000000
B4 1.07000000
A1 109.47120255
A2 109.47125080
A3 109.47121829
D1 -119.99998525
D2 120.00000060

1 2 1.0 3 1.0 4 1.0 5 1.0
2
3
4
5

</pre>

==== install gaussian ====
::insert the CD
::double click on the .dmg file
::a CDROM disk icon will appear
::in a terminal window cd /Volumes/CDROM (or name of CD)
::read the "readme" file
::change to the cshell
<pre>
csh
</pre>
::tell the script where gaussian (G09) is to be installed
<pre>
setenv g09root "/Applications"
</pre>
::now goto the g03root directory
<pre>
cd $g09root
</pre>
::read the CD
<pre>
cat /Volumes/CDROM/tar/*.tgz | zcat | tar xvf -
</pre>
::this will unpack and copy the contents of the CD, you should see a stream of file names, when this stops and the prompt returns
::ensure that the group permissions are set
<pre>
chgrp -R gaussian g09
</pre>
::check this has worked, type "ls -al"
::you should see a list with the following
<pre>
drwxr-x--- 154 name hunt_group 5236 1 Nov 2007 g09
</pre>
::goto the gaussian directory and run the install script
<pre>
cd g09
./bsd/install
</pre>
::eject the disk
::you are not quite ready to run as the variables g09root, GAUSS_SCRDIR and the g09.login script need to be set in your .bashrc file ... this was done in the terminal instructions above
:: you may also want to get rid of the pesky error "-bash: ulimit: open files: cannot modify limit: Invalid argument" which shows up because you have asked "source $g09root/g09/bsd/g09.profile" in your .bashrc
:::goto the direcotry g09/bsd
:::edit the file g09.profile, goto the end and hash out the following command
<pre>
#turned off by tricia to stop error message
#ulimit -n hard
</pre>
::now you are ready to run a test job
:::nohup means don't stop if you logout
:::the trailing & means run in the background
<pre>
cd work/jobs/testing
nohup g09 test &
</pre>
::ls to see that the job is running and that test.chk and test.log files are being generated.
::check that the job finishes ok

==== install gaussview ====
=====getting ready=====
::insert the CD
::double click on the .dmg file
::a CDROM disk icon will appear
::in a terminal window cd /Volumes/CDROM (or name of CD)
::read the "readme" file

=====do the install=====
::change to the cshell
::tell the script where the cd is mounted
<pre>
csh
setenv g09root "/Applications"
cd $g09root
</pre>
::now read and unpack the CD
<pre>
cat /Volumes/CDROM/tar/*.tgz | zcat | tar xvf -
</pre>
::change the group premisions to the same as those for g09
<pre>
chgrp -R gaussian gv
</pre>
::eject the disk

::gaussview uses csh, so you need to have a .login if you want to run from the launcher
::check that you have the following in your .login
<pre>
setenv g09root /Applications
source $g09root/g09/bsd/g09.login
setenv GAUSS_SCRDIR /Users/tricia/Work/tmp
setenv GV_DIR /Applications/gv
setenv GAUSS_EXEDIR /Applications/g09
</pre>

=====set-up quick starting of gaussview=====
::goto the Applications folder and click on the gv folder
::drag the gaussview icon into the launcher
::double click to start gaussview
::if you get an error saying that it cannot find gaussian directories then
:::cd to the gv directory
:::cd into the data directory
:::edit the gpath.txt file (and give the correct path to the g03 application)
<pre>
/Applications/g09
</pre>
:::quit gaussview and then restart it, your problem should be fixed

=====set-up preferences=====
::now we need to set some directories in the preferences of gaussview
::click on preferences
::choose the "File?Directory" option
::under the starting directory, choose Specify, click on the "..." button and pick your work/jobs directory
::under the scratch directory, choose "Use GAUSS_SCRDIR"
=====test run a job=====
::start X11 (this is in Applications/Utilities folder, drag the X11 app to a launcher)
::type "gv" in the window (and press return)
::choose "open" and goto your /work/jobs/testing directory, open your test.com file
::submit it to run (save as test_1.com) so that you don't overwrite the other test job
::check that it finishes OK
::open your test molecule's com file

==== set-up easy remote connections ====
::create the file "config" in your home/.ssh directory
::see heiko's notes for what to put in it.

Mod:Hunt Research Group/mac setup

2014-07-31T13:33:26Z

Gd2613: /* set-up the terminal */

==== make a group ====
::open accounts in system prefs
::click on the + button
::choose groups on pulldown menu
::type in a name and add those users you want to belong to the group
::in this case call the group "hunt_group"
::exit

==== set-up the terminal ====
::create the file ".bash_profile"
::copy and paste the following into it
<pre>
#echo "bash_profile"
. ~/.bashrc
</pre>
::create the file ".bashrc"
::copy and paste the following into it
<pre>
# .bashrc
# WARNING: had to make .bash_profile and added execute to this file
#
# important stuff
#
# tells the computer where to look for personal scripts
export PATH=$PATH:/Users/$USER/bin:/usr/local/bin
#
# change the prompt
export PS1="[\$USER@\h]\$PWD \$ "
#
# control-R lets you search backward through history
HISTSIZE=100
HISTCONTROL=erasedups
HISTIGNORE="cd:exit"
EDITOR=vi
export EDITOR
#
# gaussian
#
# where to fine the executable
export g09root="/Applications"
# set the default memory
export GAUSS_MEMDEF="500MB"
# where to put the LARGE temporary files when running gaussian
export GAUSS_SCRDIR="/Users/$USER/Work/Jobs/tmp"
# script which sets many variables for gaussian
source $g09root/g09/bsd/g09.profile
#
# gaussview
#
# where to find gaussview
export GV_DIR="/Applications/gv"
# libraries
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${GV_DIR}/lib
# allow start from the comand line in mac terminal
alias gv="open $GV_DIR/gview.app"
#
# alias definitions
#
alias home="cd"
alias force="grep -i 'Maximum Force'"
alias dist="grep -i 'Maximum Disp'"
alias rm='rm -I'
#
</pre>

::create the file ".login"
::this is needed because gaussview looks for csh stuff
::copy and paste the following into it
<pre>
setenv g09root /Applications
source $g09root/g09/bsd/g09.login
setenv GAUSS_SCRDIR /Users/$USER/Work/Jobs/tmp
setenv GV_DIR /Applications/gv
setenv GAUSS_EXEDIR /Applications/g09
</pre>
::of course replace my name with your name (or directory structure)
::and the directory tmp should exist before you run any jobs.

==== set-up working directories ====
::make a directory called "work", keep ALL your files here
::inside work make a directory called "jobs", keep all your gaussian jobs here
::inside work make a directory called "testing" ie full path is /Users/name/work/jobs/testing
::vi a file "test.com" and copy and paste the following into it
::ps don't forget the last line must be blank
<pre>
%chk=test.chk
%mem=500MB
%nproc=1
# hf/3-21g geom=connectivity

Title Card Required

0 1
C
H 1 B1
H 1 B2 2 A1
H 1 B3 3 A2 2 D1
H 1 B4 3 A3 2 D2

B1 1.07000000
B2 1.07000000
B3 1.07000000
B4 1.07000000
A1 109.47120255
A2 109.47125080
A3 109.47121829
D1 -119.99998525
D2 120.00000060

1 2 1.0 3 1.0 4 1.0 5 1.0
2
3
4
5

</pre>

==== install gaussian ====
::insert the CD
::double click on the .dmg file
::a CDROM disk icon will appear
::in a terminal window cd /Volumes/CDROM (or name of CD)
::read the "readme" file
::change to the cshell
<pre>
csh
</pre>
::tell the script where gaussian (G09) is to be installed
<pre>
setenv g09root "/Applications"
</pre>
::now goto the g03root directory
<pre>
cd $g09root
</pre>
::read the CD
<pre>
cat /Volumes/CDROM/tar/*.tgz | zcat | tar xvf -
</pre>
::this will unpack and copy the contents of the CD, you should see a stream of file names, when this stops and the prompt returns
::ensure that the group permissions are set
<pre>
chgrp -R gaussian g09
</pre>
::check this has worked, type "ls -al"
::you should see a list with the following
<pre>
drwxr-x--- 154 name hunt_group 5236 1 Nov 2007 g09
</pre>
::goto the gaussian directory and run the install script
<pre>
cd g09
./bsd/install
</pre>
::eject the disk
::you are not quite ready to run as the variables g09root, GAUSS_SCRDIR and the g09.login script need to be set in your .bashrc file ... this was done in the terminal instructions above
:: you may also want to get rid of the pesky error "-bash: ulimit: open files: cannot modify limit: Invalid argument" which shows up because you have asked "source $g09root/g09/bsd/g09.profile" in your .bashrc
:::goto the direcotry g09/bsd
:::edit the file g09.profile, goto the end and hash out the following command
<pre>
#turned off by tricia to stop error message
#ulimit -n hard
</pre>
::now you are ready to run a test job
:::nohup means don't stop if you logout
:::the trailing & means run in the background
<pre>
cd work/jobs/testing
nohup g09 test &
</pre>
::ls to see that the job is running and that test.chk and test.log files are being generated.
::check that the job finishes ok

==== install gaussview ====
=====getting ready=====
::insert the CD
::double click on the .dmg file
::a CDROM disk icon will appear
::in a terminal window cd /Volumes/CDROM (or name of CD)
::read the "readme" file

=====do the install=====
::change to the cshell
::tell the script where the cd is mounted
<pre>
csh
setenv g09root "/Applications"
cd $g09root
</pre>
::now read and unpack the CD
<pre>
cat /Volumes/CDROM/tar/*.tgz | zcat | tar xvf -
</pre>
::change the group premisions to the same as those for g09
<pre>
chgrp -R gaussian gv
</pre>
::eject the disk

::gaussview uses csh, so you need to have a .login if you want to run from the launcher
::check that you have the following in your .login
<pre>
setenv g09root /Applications
source $g09root/g09/bsd/g09.login
setenv GAUSS_SCRDIR /Users/tricia/Work/tmp
setenv GV_DIR /Applications/gv
setenv GAUSS_EXEDIR /Applications/g09
</pre>

=====set-up quick starting of gaussview=====
::goto the Applications folder and click on the gv folder
::drag the gaussview icon into the launcher
::double click to start gaussview
::if you get an error saying that it cannot find gaussian directories then
:::cd to the gv directory
:::cd into the data directory
:::edit the gpath.txt file (and give the correct path to the g03 application)
<pre>
/Applications/g09
</pre>
:::quit gaussview and then restart it, your problem should be fixed

=====set-up preferences=====
::now we need to set some directories in the preferences of gaussview
::click on preferences
::choose the "File?Directory" option
::under the starting directory, choose Specify, click on the "..." button and pick your work/jobs directory
::under the scratch directory, choose "Use GAUSS_SCRDIR"
=====test run a job=====
::start X11 (this is in Applications/Utilities folder, drag the X11 app to a launcher)
::type "gv" in the window (and press return)
::choose "open" and goto your /work/jobs/testing directory, open your test.com file
::submit it to run (save as test_1.com) so that you don't overwrite the other test job
::check that it finishes OK
::open your test molecule's com file

==== set-up easy remote connections ====
::create the file "config" in your home/.ssh directory
::see heiko's notes for what to put in it.

Mod:Hunt Research Group/pimpQSUB

2014-07-31T13:26:57Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=15800
MAXDISK=400
WALLT="499:00:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${FL}
if [[ ${FL} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=499:00:00
#PBS -l select=1:ncpus=8:mem=15800MB:tmpspace=400GB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;15800MB;499:00:00;d01;400GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;15800MB;499:00:00;d01;400GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
else
MAXDISK=${OPTARG-"400"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"15800"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
else
MAXDISK=${PRESET[5]-"400"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"15800"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
while read line
do
echo $"$line"
done < "$WLOG"
elif [[ ${OPTARG} == 'edit' ]]
then
vi $WLOG;
else
sed -n "/${OPTARG}/p" $WLOG;
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -l select=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}GB/" "${SFILE}"
else
sed -i "s/#PBS -l select=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" "${SFILE}"
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" "${SFILE}"
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}"

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" "${SFILE}"
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
FL=${1}
ID=$(ID ${FL});
if [[ -f ${ID}'.com' ]]
then
FL=${ID}.com
fi

NMFL=${FL%.com}
NMFL=${NMFL##*/}
DIR=${1%/*}
echo $DIR
PD=$(pwd)
cd $DIR

if [[ ! -f ${FL} ]]
then
echo "\"${FL}\" does not exists."
exit
elif [[ ! ${FL} =~ .*'.com' ]]
then
echo "\"${FL}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} - 50*CORE))
gmem=$(grep -i -c "%mem=.*/" ${FL})
gpshar=$(grep -i -c "%nprocshared=.*/" ${FL})
gchk=$(grep -i -c "%chk=./" ${FL})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${FL}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${FL}
sed -i "s/%chk=.*chk/%chk=$CD${NMFL}.chk/" ${FL}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}GB/" ${FL##*/}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${FL}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=$RED${NMFL%.com}$NC ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOG
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
cd $PD
shift
done

</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-07-29T12:12:41Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
while read line
do
echo $"$line"
done < "$WLOG"
elif [[ ${OPTARG} == 'edit' ]]
then
vi $WLOG;
else
sed -n "/${OPTARG}/p" $WLOG;
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#Gaussian is greedy !!!
MEM=$((${MEM} - 50*CORE))

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" "${SFILE}"
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" "${SFILE}"
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" "${SFILE}"
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}"

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" "${SFILE}"
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}
NMFL=${NMFL##*/}
DIR=${1%/*}
echo $DIR
PD=$(pwd)
cd $DIR

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=${MEM}
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=./" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=$CD${NMFL}.chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1##*/}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=$RED${NMFL%.com}$NC ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOG
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
cd $PD
shift
done

</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-07-03T13:32:01Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
cat $WLOG;
elif [[ ${OPTARG} == 'edit' ]]
then
vi $WLOG;
else
sed -n "/${OPTARG}/p" $WLOG;
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" "${SFILE}"
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" "${SFILE}"
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" "${SFILE}"
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}"

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" "${SFILE}"
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}
NMFL=${NMFL##*/}
DIR=${1%/*}
echo $DIR
PD=$(pwd)
cd $DIR

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=./" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=$CD${NMFL}.chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1##*/}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=$RED${NMFL%.com}$NC ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOG
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/$USER/jobs}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
cd $PD
shift
done

</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-07-03T13:29:32Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
cat $WLOG;
elif [[ ${OPTARG} == 'edit' ]]
then
vi $WLOG;
else
sed -n "/${OPTARG}/p" $WLOG;
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" "${SFILE}"
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" "${SFILE}"
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" "${SFILE}"
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}"

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" "${SFILE}"
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}
NMFL=${NMFL##*/}
DIR=${1%/*}
echo $DIR
PD=$(pwd)
cd $DIR

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=./" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=$CD${NMFL}.chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1##*/}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=$RED${NMFL%.com}$NC ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/gd2613/jobs}" >> $WLOG
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/gd2613/jobs}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
cd $PD
shift
done

</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-06-27T13:26:14Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
cat $WLOG;
else
sed -n "/${OPTARG}/p" $WLOG;
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" "${SFILE}"
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" "${SFILE}"
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" "${SFILE}"
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" "${SFILE}"

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" "${SFILE}"
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}
NMFL=${NMFL##*/}
DIR=${1%/*}
echo $DIR
PD=$(pwd)
cd $DIR

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=./" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=$CD${NMFL}.chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1##*/}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=$RED${NMFL%.com}$NC ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${NMFL%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/gd2613/jobs/}" >> $WLOG
echo "$(date +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/gd2613/jobs/}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi
cd $PD
shift
done
</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-05-28T13:23:07Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
WLOGf="$HOME/bin/.wulog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
FRC=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC} [select]
select =
all
work ID (e.g. '7197851')
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts fhnsc:d:g:l:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
f)
FRC=1;
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
if [[ ${OPTARG} == 'all' ]]
then
cat $WLOG;
else
sed -n "/${OPTARG}/p" $WLOG;
fi
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" ${SFILE}
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
CD=$(pwd)
CD=${CD//\//\\\/}'\/'
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=./" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=$CD${1%com}chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
if [[ $FRC=1 ]]
then
out=$(qsub -p 100 -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng);
else
out=$(qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng);
fi
cp="$(pwd)"
if [[ -n $out ]]
then
echo "$(date -u +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/gd2613/jobs/}" >> $WLOG
echo "$(date -u +'%d/%m - %H:%M') | $out | $NMFL | ${cp#/work/gd2613/jobs/}" >> $WLOGf
fi
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/calendar

2014-05-27T13:29:19Z

Gd2613:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Tricia away Richard away Precious away Giacomo away Gabriel away </td>
<td>24th Richard away Giacomo away Gabriel away Precious away </td>
<td>25th Richard away Giacomo away Precious away Gabriel away </td>
<td bgcolor="#FFA500">26th '''Start of term''' Giacomo away </td>
<td bgcolor="#CCCCCC">27th Giacomo away </td>
</tr>
<tr valign="top">
<td>28th Giacomo away </td>
<td >29th '''(Vincent & Gabriel)'''</td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th '''(Kevin)'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th '''(Richard)'''</td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th Careers course - Vincent, Gabriel</td>
<td >20th '''(Precious)''' Careers course - Vincent, Gabriel</td>
<td>21st Careers course - Vincent, Gabriel</td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th '''(Pat)'''</td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Giacomo)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away)</td>
<td>5th CECAM workshop Claire away (Giacomo Away)</td>
<td>6th CECAM workshop Claire away </td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Gabriel)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th '''(Hakim-presentation practice)'''</td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th '''(Bryan)'''</td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th EUCHEM-Richard&Claire</td>
<td>8th '''(Richard F)''' EUCHEM-Richard & Claire</td>
<td>9th EUCHEM-Richard & Claire</td>
<td>10th EUCHEM-Richard & Claire</td>
<td>11th EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away Claire away</td>
<td>15th '''(Matthew)''' Richard away Claire away</td>
<td>16th Richard away Claire away</td>
<td>17th Richard away Claire away</td>
<td>18th Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd '''(Vincent)'''</td>
<td>23rd Gaussian workshop - Claire & Bryan</td>
<td>24th Gaussian workshop - Claire & Bryan</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>39th </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-05-27T13:28:49Z

Gd2613:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Tricia away Richard away Precious away Giacomo away Gabriel away </td>
<td>24th Richard away Giacomo away Gabriel away Precious away </td>
<td>25th Richard away Giacomo away Precious away Gabriel away </td>
<td bgcolor="#FFA500">26th '''Start of term''' Giacomo away </td>
<td bgcolor="#CCCCCC">27th Giacomo away </td>
</tr>
<tr valign="top">
<td>28th Giacomo away </td>
<td >29th '''(Vincent & Gabriel)'''</td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th '''(Kevin)'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th '''(Richard)'''</td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th Careers course - Vincent, Gabriel</td>
<td >20th '''(Precious)''' Careers course - Vincent, Gabriel</td>
<td>21st Careers course - Vincent, Gabriel</td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th '''(Pat)'''</td>
<td>28th </td>
<td>29th </td>
<td>30th (Giacomo Away)</td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June (Giacomo Away) </td>
</tr>
<tr valign="top">
<td>2nd (Giacomo Away)</td>
<td>3rd '''(Giacomo)''' (Giacomo Away)</td>
<td>4th CECAM workshop Claire away (Giacomo Away)</td>
<td>5th CECAM workshop Claire away (Giacomo Away)</td>
<td>6th CECAM workshop Claire away (Giacomo Away)</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Gabriel)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th '''(Hakim-presentation practice)'''</td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th '''(Bryan)'''</td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th </td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th EUCHEM-Richard&Claire</td>
<td>8th '''(Richard F)''' EUCHEM-Richard & Claire</td>
<td>9th EUCHEM-Richard & Claire</td>
<td>10th EUCHEM-Richard & Claire</td>
<td>11th EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away Claire away</td>
<td>15th '''(Matthew)''' Richard away Claire away</td>
<td>16th Richard away Claire away</td>
<td>17th Richard away Claire away</td>
<td>18th Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd '''(Vincent)'''</td>
<td>23rd Gaussian workshop - Claire & Bryan</td>
<td>24th Gaussian workshop - Claire & Bryan</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>39th </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/calendar

2014-05-27T13:26:55Z

Gd2613:

== Calendar ==

*Tricia (Not Done)
*Abdihakim Hassan (Not Done)
*Bryan Ward (Not Done)
*Claire Ashworth (Not Done)
*Matthew Clough (Not Done)
*Precious Ugbomah (Not Done)
*Richard Matthews (Not Done)
*Vincent Chen (Not Done)
*Gabriel Lau (Not Done)
*Rebecca Rowe (Not Done)
*Patricia Ho (Not Done)
*Giacomo Damilano (Not Done)
*Richard Fogarty (Not Done)

<table border="1" cellpadding="5" width="1190">
<tr bgcolor="#66CCFF">
<th width="170px">Mon</th>
<th width="170px">Tues</th>
<th width="170px">Wed</th>
<th width="170px">Thur</th>
<th width="170px">Fri</th>
<th width="170px" bgcolor="#CCCCCC">Sat</th>
<th width="170px" bgcolor="#CCCCCC">Sun</th>
<tr valign="top">
<td bgcolor="#339933">21st '''College Closed'''</td>
<td bgcolor="#339933" >22nd '''College Closed'''</td>
<td>23rd Tricia away Richard away Precious away Giacomo away Gabriel away </td>
<td>24th Richard away Giacomo away Gabriel away Precious away </td>
<td>25th Richard away Giacomo away Precious away Gabriel away </td>
<td bgcolor="#FFA500">26th '''Start of term''' Giacomo away </td>
<td bgcolor="#CCCCCC">27th Giacomo away </td>
</tr>
<tr valign="top">
<td>28th Giacomo away </td>
<td >29th '''(Vincent & Gabriel)'''</td>
<td>30th </td>
<td bgcolor="#4357CFF">1st May </td>
<td>2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
<td bgcolor="#CCCCCC">4th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">5th '''College Closed''' '''Bank holiday'''</td>
<td >6th '''(Kevin)'''</td>
<td>7th </td>
<td>8th </td>
<td>9th </td>
<td bgcolor="#CCCCCC">10th </td>
<td bgcolor="#CCCCCC">11th </td>
</tr>
<tr valign="top">
<td >12th </td>
<td >13th '''(Richard)'''</td>
<td>14th </td>
<td>15th </td>
<td>16th </td>
<td bgcolor="#CCCCCC">17th </td>
<td bgcolor="#CCCCCC">18th </td>
</tr>
<tr valign="top">
<td >19th Careers course - Vincent, Gabriel</td>
<td >20th '''(Precious)''' Careers course - Vincent, Gabriel</td>
<td>21st Careers course - Vincent, Gabriel</td>
<td>22nd </td>
<td>23rd </td>
<td bgcolor="#CCCCCC">24th </td>
<td bgcolor="#CCCCCC">25th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">26th '''College closed''' '''Bank holiday'''</td>
<td >27th '''(Pat)'''</td>
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td bgcolor="#CCCCCC">31st </td>
<td bgcolor="#4357CFF">1st June </td>
</tr>
<tr valign="top">
<td>2nd </td>
<td>3rd '''(Giacomo)'''</td>
<td>4th CECAM workshop Claire away</td>
<td>5th CECAM workshop Claire away</td>
<td>6th CECAM workshop Claire away</td>
<td bgcolor="#CCCCCC">7th </td>
<td bgcolor="#CCCCCC">8th </td>
</tr>
<tr valign="top">
<td>9th </td>
<td>10th '''(Gabriel)'''</td>
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td bgcolor="#CCCCCC">14th </td>
<td bgcolor="#CCCCCC">15th </td>
</tr>
<tr valign="top">
<td>16th </td>
<td>17th '''(Hakim-presentation practice)'''</td>
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td bgcolor="#CCCCCC">21st </td>
<td bgcolor="#CCCCCC">22nd </td>
</tr>
<tr valign="top">
<td>23rd </td>
<td>24th '''(Bryan)'''</td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#FFA500">27th '''End of term'''</td>
<td bgcolor="#CCCCCC">28th </td>
<td bgcolor="#CCCCCC">29th </td>
</tr>
<tr valign="top">
<td>30th (Giacomo Away)</td>
<td bgcolor="#4357CFF" >1st July {{fontcolor|#FFD700|'''PhD Symposium (Chem.)'''}}</td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td bgcolor="#CCCCCC">5th </td>
<td bgcolor="#CCCCCC">6th EUCHEM-Richard & Claire</td>
</tr>
<tr valign="top">
<td>7th EUCHEM-Richard&Claire</td>
<td>8th '''(Richard F)''' EUCHEM-Richard & Claire</td>
<td>9th EUCHEM-Richard & Claire</td>
<td>10th EUCHEM-Richard & Claire</td>
<td>11th EUCHEM-Richard & Claire</td>
<td bgcolor="#CCCCCC">12th </td>
<td bgcolor="#CCCCCC">13th </td>
</tr>
<tr valign="top">
<td>14th Richard away Claire away</td>
<td>15th '''(Matthew)''' Richard away Claire away</td>
<td>16th Richard away Claire away</td>
<td>17th Richard away Claire away</td>
<td>18th Richard away Claire away</td>
<td bgcolor="#CCCCCC">19th </td>
<td bgcolor="#CCCCCC">20th </td>
</tr>
<tr valign="top">
<td>21st </td>
<td>22nd '''(Vincent)'''</td>
<td>23rd Gaussian workshop - Claire & Bryan</td>
<td>24th Gaussian workshop - Claire & Bryan</td>
<td>25th </td>
<td bgcolor="#CCCCCC">26th </td>
<td bgcolor="#CCCCCC">27th </td>
</tr>
<tr valign="top">
<td>28th </td>
<td>29th </td>
<td>30th </td>
<td>31st </td>
<td bgcolor="#4357CFF">1st August </td>
<td bgcolor="#CCCCCC">2nd </td>
<td bgcolor="#CCCCCC">3rd </td>
</tr>
<tr valign="top">
<td>4th </td>
<td>5th </td>
<td>6th </td>
<td>7th </td>
<td>8th </td>
<td bgcolor="#CCCCCC">9th </td>
<td bgcolor="#CCCCCC">10th </td>
</tr>
<tr valign="top">
<td>11th </td>
<td>12th </td>
<td>13th </td>
<td>14th </td>
<td>15th </td>
<td bgcolor="#CCCCCC">16th </td>
<td bgcolor="#CCCCCC">17th </td>
</tr>
<tr valign="top">
<td>18th </td>
<td>19th </td>
<td>20th </td>
<td>21st </td>
<td>22nd </td>
<td bgcolor="#CCCCCC">23rd </td>
<td bgcolor="#CCCCCC">24th </td>
</tr>
<tr valign="top">
<td bgcolor="#339933">25th '''College closed''' '''Bank holiday'''</td>
<td>26th </td>
<td>27th </td>
<td>28th </td>
<td>39th </td>
<td bgcolor="#CCCCCC">30th </td>
<td bgcolor="#CCCCCC">31st </td>
</tr>
<tr valign="top">
<td bgcolor="#4357CFF">1st September </td>
<td>2nd </td>
<td>3rd </td>
<td>4th </td>
<td>5th </td>
<td bgcolor="#CCCCCC">6th </td>
<td bgcolor="#CCCCCC">7th </td>
</tr>
<tr valign="top">
<td>8th </td>
<td>9th </td>
<td>10th </td>
<td>11th </td>
<td>12th </td>
<td bgcolor="#CCCCCC">13th </td>
<td bgcolor="#CCCCCC">14th </td>
</tr>
<tr valign="top">
<td>15th </td>
<td>16th </td>
<td>17th </td>
<td>18th </td>
<td>19th </td>
<td bgcolor="#CCCCCC">20th </td>
<td bgcolor="#CCCCCC">21st </td>
</tr>
<tr valign="top">
<td>22nd </td>
<td>23rd </td>
<td>24th </td>
<td>25th </td>
<td>26th </td>
<td bgcolor="#CCCCCC">27th </td>
<td bgcolor="#CCCCCC">28th </td>
</tr>
<tr valign="top">
<td>29th </td>
<td>30th </td>
<td bgcolor="#4357CFF">1st October </td>
<td> </td>
<td> </td>
<td bgcolor="#CCCCCC"> </td>
<td bgcolor="#CCCCCC"> </td>
</tr>
</table>

Mod:Hunt Research Group/pimpQSUB

2014-05-09T15:44:02Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC}
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts chlnsd:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
cat $WLOG;
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" ${SFILE}
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
out=$(qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng)
echo "$(date -u +'%d/%m - %H:%M') | $NMFL | $out" >> $WLOG
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>
write and quit
<pre>:wq</pre>
and then set the file as executable file
<pre>chmod +x gf</pre>
I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-05-08T14:40:46Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC}
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts chlnsd:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
cat $WLOG;
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" ${SFILE}
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores: $CORE; Memory: $MEM; Cue: $CUE; Walltime: $WALLT; Gaussian-version: $GAUSS; Maxdisk: $MAXDISK"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
out=$(qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng)
echo "$(date -u +'%d/%m - %H:%M') | $NMFL | $out" >> $WLOG
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-05-08T14:37:43Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC}
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts chlnsd:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-10"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
cat $WLOG;
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" ${SFILE}
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
out=$(qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng)
echo "$(date -u +'%d/%m - %H:%M') | $NMFL | $out" >> $WLOG
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-05-08T13:41:28Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
WLOG="$HOME/bin/.wlog"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
QUIET=0
CORRECTION=1
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-l${NC}
prints the log of the jobs sent
${BLUE}-h${NC}
help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts chlnsd:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION=0;
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET=1;
;;
l)
cat $WLOG;
;;
?)
usage;
exit;
;;
esac
done

if [[ $# -eq 0 ]]
then
usage
exit
fi

shift $OPT

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" ${SFILE}
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION -eq 1 ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1}
fi
fi

if [[ $QUIET -eq 1 ]]
then
response="y"
else
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
out=$(qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng)
echo "$(date -u +'%d/%m - %H:%M') | $NMFL | $out" >> $WLOG
echo $out
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-04-02T18:21:48Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
SKIP="TRUE"
QUIET="FALSE"
CORRECTION="TRUE"
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-h${NC} help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB:tmpspace=400gb
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts chns:d:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION="FALSE";
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET="TRUE";
;;
?)
usage;
exit;
;;
esac
done
shift $OPT

if [[ $# -eq 0 ]]
then
usage
exit
fi

#########################################################################################
# Correcting the script file #
#########################################################################################
if [[ -n $MAXDISK ]]
then
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB:tmpspace=${MAXDISK}MB/" ${SFILE}
else
sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
fi
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
if [[ -n $MAXDISK ]]
then
sed -i "s/maxdisk=.*B/maxdisk=${MAXDISK}MB/" ${1}
fi
fi

if [[ !$QUIET ]]
then
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
else
response="y"
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-04-02T18:09:40Z

Gd2613: /* How to... speed up your job cueing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
SKIP="TRUE"
QUIET="FALSE"
CORRECTION="TRUE"
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-h${NC} help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

WHITESTRIPES="Preset not charged";

while getopts chns:d:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION="FALSE";
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET="TRUE";
;;
?)
usage;
exit;
;;
esac
done
shift $OPT

if [[ $# -eq 0 ]]
then
usage
exit
fi

#########################################################################################
# Correcting the script file #
#########################################################################################

sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
fi

if [[ !$QUIET ]]
then
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
else
response="y"
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-04-02T18:09:20Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
SKIP="TRUE"
QUIET="FALSE"
CORRECTION="TRUE"
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-h${NC} help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################
WHITESTRIPES="Preset not charged";
while getopts chns:d:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION="FALSE";
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET="TRUE";
;;
?)
usage;
exit;
;;
esac
done
shift $OPT

if [[ $# -eq 0 ]]
then
usage
exit
fi

#########################################################################################
# Correcting the script file #
#########################################################################################

sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
fi

if [[ !$QUIET ]]
then
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
else
response="y"
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-04-02T17:10:59Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
SKIP="TRUE"
QUIET="FALSE"
CORRECTION="TRUE"
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use (MB or GB)
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-p${NC} [preset]
preset =
[0-9] load a preset
show list the saved preset
set open the editor to set the preset
${BLUE}-d${NC} [max disk]
set the maxdisk
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-h${NC} help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts chns:d:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION="FALSE";
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET="TRUE";
;;
?)
usage;
exit;
;;
esac
done
shift $OPT

if [[ $# -eq 0 ]]
then
usage
exit
fi

#########################################################################################
# Correcting the script file #
#########################################################################################

sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
fi

if [[ !$QUIET ]]
then
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
else
response="y"
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-04-02T17:04:58Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cueing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash

#########################################################################################
# Default Variables #
#########################################################################################

DIR=$PWD
SFILE="$HOME/bin/.rng"
PFILE="$HOME/bin/.presets"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
SKIP="TRUE"
QUIET="FALSE"
CORRECTION="TRUE"
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

#########################################################################################
# Debugging Function #
#########################################################################################

debug(){
echo "1.PWD $PWD"
echo "2.# $#"
echo "3.* $*"
echo "4.OPTARG ${OPTARG}"
echo "5.OPTIND ${OPTIND}"
echo "6.CUE ${CUE}"
echo "7.CORE ${CORE}"
echo "8.MEM ${MEM}"
echo "9.WALLTIME ${WALLT}"
echo "10.MAXDISK ${MAXDISK}"
}

#########################################################################################
# Help output #
#########################################################################################

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use, the memory must be inputed as MB, 16000MB are set as default
${BLUE}-w${NC} [walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-h${NC} help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

bytechunker(){
local __resultvar=${1}
if [[ ${1} =~ .*"MB" ]];
then
local MBYTES=${1%MB};
elif [[ $1 =~ .*"GB" ]]
then
local MBYTES=${1%GB};
let "MBYTES=MBYTES*1000";
else
local MBYTES=${1-"800000"};
fi
echo $MBYTES;

eval $__resultvar="'$MBYTES'"
}

#########################################################################################
# Creating/Verifing the existence of some files used by the function #
#########################################################################################

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${SFILE} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${SFILE}"
chmod a+x "${SFILE}"
fi

if [[ ! -f ${PFILE} ]]
then
echo '## Here is where to list the preset for gaussian calculations
## Each line is a preset and it is written in this way :
## [CUE];[CORES];[MEMORY];[WALLTIME];[GAUSSIAN VERSION];[MAXDISK]
## e.g pqph;8;14400MB;119:59:00;d01;800GB
##
##
##-----------------------------------------------------------------------------
##
## presets starts from next line
pqph;8;14400MB;119:59:00;d01;800GB' > "${PFILE}"
fi

#########################################################################################
# Retriving inputted options #
#########################################################################################

while getopts chns:d:g:m:p:q:w: OPTION
do
if [[ $OPT -lt $OPTIND ]]
then
let "OPT=OPTIND - 1"
fi

case $OPTION in
d)
if [[ $OPTARG =~ .*"MB" ]];
then
MAXDISK=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MAXDISK=${OPTARG%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${OPTARG-"16000"};
fi
;;
p)
if [[ $OPTARG =~ [0-9] ]]
then
i=0;
while read VAR
do
let "m=i-9"
if [[ $m == $OPTARG ]]
then
echo $VAR
IFS=";" read -ra PRESET <<< "$VAR"
CUE=${PRESET[0]};
CORE=${PRESET[1]};

if [[ ${PRESET[2]} =~ .*"MB" ]];
then
MEM=${PRESET[2]%MB};
elif [[ ${PRESET[2]} =~ .*"GB" ]]
then
$MEM=${PRESET[2]%GB}
let "MEM=MEM*1000";
else
MEM=${PRESET[2]-"16000"};
fi
WALLT=${PRESET[3]};
GAUSS=${PRESET[4]};
if [[ ${PRESET[5]} =~ .*"MB" ]];
then
MAXDISK=${PRESET[5]%MB};
elif [[ ${PRESET[5]} =~ .*"GB" ]]
then
MAXDISK=${PRESET[5]%GB};
let "MAXDISK=MAXDISK*1000";
else
MAXDISK=${PRESET[5]-"16000"};
fi
fi
((i++))
done < $PFILE;
elif [[ $OPTARG == "show" ]]
then
i=1;
while read VAR
do
if [[ $i -gt 9 ]]
then
IFS=";" read -ra PRESET <<< "$VAR"
let "m=i-9"
echo "$m - cue: ${PRESET[0]} cores:${PRESET[1]} memory: ${PRESET[2]} walltime: ${PRESET[3]} gaussian version: ${PRESET[4]} max disk: ${PRESET[5]}";
fi
((i++))
done < $PFILE
exit
elif [[ $OPTARG == "set" ]]
then
vi $PFILE
exit
fi
WHITESTRIPES="Charged preset : $CUE $CORE $MEM $WALLT $GAUSS $MAXDISK";
;;
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB};
let "MEM=MEM*1000";
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION="FALSE";
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET="TRUE";
;;
?)
usage;
exit;
;;
esac
done
shift $OPT

if [[ $# -eq 0 ]]
then
usage
exit
fi

#########################################################################################
# Correcting the script file #
#########################################################################################

sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${SFILE}
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${SFILE}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${SFILE}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${SFILE}
fi

#########################################################################################
# Pushing the job to the HPC #
#########################################################################################

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION ]]
then
GMEM=$((${MEM} * 9 / 10))
gmem=$(grep -i -c "%mem=.*/" ${1})
gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
fi

if [[ !$QUIET ]]
then
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e $YELLOW$WHITESTRIPES$NC
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
else
response="y"
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-04-01T16:35:20Z

Gd2613:

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cuing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash
DIR=$PWD
BIN="$HOME/bin/.rng"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
SKIP="TRUE"
QUIET="FALSE"
CORRECTION="TRUE"
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
OPT=0

debug(){
echo $PWD
echo $#
echo $*
echo ${OPTARG}
echo ${OPTIND}
}

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use, the memory must be inputed as MB, 16000MB are set as default
${BLUE}-w${NC}[walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-h${NC} help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

while getopts hnsw:g:c:m:q: OPTION
do
if [[ $OPT<$OPTIND ]]
then
OPT=$OPTIND
fi
case $OPTION in
h)
usage;
exit;
;;
q)
CUE=${OPTARG-"pqph"};
;;
c)
CORE=${OPTARG-"8"};
;;
m)
if [[ $OPTARG =~ .*"MB" ]];
then
MEM=${OPTARG%MB};
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB}*1000;
else
MEM=${OPTARG-"16000"};
fi
;;
n)
CORRECTION="FALSE";
;;
g)
GAUSS=${OPTARG};
;;
w)
WALLT=${OPTARG};
;;
s)
QUIET="TRUE";
;;
?)
usage;
exit;
;;
esac
done

shift $OPT

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${BIN} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${BIN}"
chmod a+x "${BIN}"
fi

sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${BIN}
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${BIN}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${BIN}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${BIN}
fi

if [[ $# -eq 0 ]]
then
usage
exit
fi

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists."
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "\"${1}\" is not a com file."
exit
fi

if [[ $CORRECTION ]]
then
GMEM=$((${MEM} * 9 / 10))
$gmem=$(grep -i -c "%mem=.*/" ${1})
$gpshar=$(grep -i -c "%nprocshared=.*/" ${1})
$gchk=$(grep -i -c "%chk=.*/" ${1})
echo $gmem $gpshar $gchk
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
fi

if [[ !$QUIET ]]
then
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
more ${1}
echo -e "${RED}--------------------------------------------------------------------------------\n\n${NC}"
echo -e "qsub -N${NMFL:0:15} -v in=${RED}${1}${NC} ~/bin/.rng"
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}------------------------------Are you sure? [y/N]-------------------------------${NC}"
read -r -p " " response
else
response="y"
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-03-31T10:46:53Z

Gd2613: /* How to... speed up your job cuing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cuing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash
DIR=$PWD
BIN="$HOME/bin/.rng"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
SKIP="TRUE"
QUIET="FALSE"
CORRECTION="TRUE"
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
debug(){
echo $PWD
echo $#
echo $*
}

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use, the memory must be inputed as MB, 16000MB are set as default
${BLUE}-w${NC}[walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-h${NC} help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

while getopts “:hq:nw:g:c:m:s” OPTION
do
case $OPTION in
h)
usage
exit
;;
q)
CUE=${OPTARG-"pqph"}
;;
c)
CORE=${OPTARG-"8"}
;;
m)
if [[ $OPTARG =~ .*"MB" ]]
then
MEM=${OPTARG%MB}
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB}*1000
else
MEM=${OPTARG-"16000"}
fi
;;
n)
CORRECTION="FALSE"
;;
g)
GAUSS=${OPTARG}
;;
w)
WALLT=${OPTARG}
;;
s)
QUIET="TRUE"
;;
?)
usage
exit
;;
esac
done

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${BIN} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${BIN}"
chmod a+x "${BIN}"
fi

sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${BIN}
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${BIN}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${BIN}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${BIN}
fi

if [[ $# -eq 0 ]]
then
usage
exit
fi

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists"
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "This is not a com file"
exit
fi

if [[ $CORRECTION ]]
then
GMEM=$((${MEM} * 9 / 10))
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
fi

if [[ !$QUIET ]]
then
echo -e "${RED}------------------------------------------------ \n\n${NC}"
more ${1}
echo -e "${RED}------------------------------------------------ \n\n${NC}"
echo qsub -N${NMFL:0:15} -v in=${1} ~/bin/.rng
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}--------------Are you sure? [y/N]--------------- ${NC}"
read -r -p " " response
else
response="y"
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 3 alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.

Mod:Hunt Research Group/pimpQSUB

2014-03-31T10:46:11Z

Gd2613: /* How to... speed up your job cuing */

Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== How to... speed up your job cuing ==
This is a little function that reduce the time spent in sending job to the hpc. It has also some useful auto-correction part that automatically sets your chk, your processors and your memory in the input file if not coherent with the terminal input. Write in the hpc terminal
<pre>vi ~/bin/gf</pre>
and copy and paste this:
<pre>
#!/bin/bash
DIR=$PWD
BIN="$HOME/bin/.rng"
CUE="pqph"
CORE=8
MEM=16000
WALLT="119:59:00"
SKIP="TRUE"
QUIET="FALSE"
CORRECTION="TRUE"
RED='\033[0;31m'
NC='\033[m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
debug(){
echo $PWD
echo $#
echo $*
}

usage(){
echo -e "gaussian function v1.2

${RED}NAME${NC}
gfunc

${RED}SYNOPSIS${NC}
gf [jobfilename.com]

${RED}OPTIONS${NC}
${BLUE}-q${NC} [cue]
set the cue for the job, default is pqph
${BLUE}-c${NC} [cores]
sets the number of cores, 8 is set as default
${BLUE}-m${NC} [memory]
sets the quantity of memory to use, the memory must be inputed as MB, 16000MB are set as default
${BLUE}-w${NC}[walltime]
set the walltime
${BLUE}-g${NC} [gaussian version]
sets the version of gaussian in use (e.g. d01)
${BLUE}-s${NC} silent
send directly the job
${BLUE}-n${NC} no correction
no correction of the input file
${BLUE}-h${NC} help

${RED}DESCRIPTION${NC}
This function sends the jobs to the HPC.
It also corrects the settings of your file automatically.
In the input file the checkpoint filename is set equally to the input filename, the number of cores is set coherently to the input as the memory. This automatic correction can be disabled by -n option
This function relies on a modified version of a script files given me by Claire (thanks Claire) that have to be placed in ~/bin.
Next function that is projected to be added is the correction of the input file settings even if they are not written at all in the input file.
Enjoy!!"
}

while getopts “:hq:nw:g:c:m:s” OPTION
do
case $OPTION in
h)
usage
exit
;;
q)
CUE=${OPTARG-"pqph"}
;;
c)
CORE=${OPTARG-"8"}
;;
m)
if [[ $OPTARG =~ .*"MB" ]]
then
MEM=${OPTARG%MB}
elif [[ $OPTARG =~ .*"GB" ]]
then
MEM=${OPTARG%GB}*1000
else
MEM=${OPTARG-"16000"}
fi
;;
n)
CORRECTION="FALSE"
;;
g)
GAUSS=${OPTARG}
;;
w)
WALLT=${OPTARG}
;;
s)
QUIET="TRUE"
;;
?)
usage
exit
;;
esac
done

if [[ ! -d ~/bin ]]
then
mkdir ~/bin
fi

if [[ ! -f ${BIN} ]]
then
echo '#!/bin/sh

# submit jobs to the que with this script using the following command:
# rng4 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in%.com}
#
# qsub rng -N jobname -v in=name

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=8:mem=16000MB
#PBS -j oe
#PBS -q pqph
#PBS -m ae

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submited.
test -r $PBS_O_WORKDIR/${in%.com}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in%.com}.chk"
cp $PBS_O_WORKDIR/${in%.com}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in%.com}.chk"
fi
#
# run gaussian
#
g09 $PBS_O_WORKDIR/${in}
cp $TMPDIR/${in%.com}.chk /$PBS_O_WORKDIR/.
cp $TMPDIR/${in%.com}.wfx /$PBS_O_WORKDIR/.
# cp *.chk /$PBS_O_WORKDIR/pbs_${in%.com}.chk
# test -r $TMPDIR/fort.7
# if [ $? -eq 0 ]
# then
# cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in%.com}.mos
# fi
# exit' > "${BIN}"
chmod a+x "${BIN}"
fi

sed -i "s/#PBS -lselect=1:ncpus=.*/#PBS -lselect=1:ncpus=${CORE}:mem=${MEM}MB/" ${BIN}
sed -i "s/#PBS -l walltime=.*/#PBS -l walltime=${WALLT}/" ${BIN}
sed -i "s/#PBS -q .*/#PBS -q ${CUE}/" ${BIN}

if [[ -n $GAUSS ]]
then
sed -i "s/module load gaussian.*/module load gaussian/g09-${GAUSS}/" ${BIN}
fi

if [[ $# -eq 0 ]]
then
usage
exit
fi

while [ $# -gt 0 ]
do
NMFL=${1%.com}

if [[ ! -f ${1} ]]
then
echo "\"${1}\" does not exists"
exit
elif [[ ! ${1} =~ .*'.com' ]]
then
echo "This is not a com file"
exit
fi

if [[ $CORRECTION ]]
then
GMEM=$((${MEM} * 9 / 10))
sed -i "s/%mem=.*/%mem=${GMEM}MB/" ${1}
sed -i "s/%nprocshared=.*/%nprocshared=${CORE}/" ${1}
sed -i "s/%chk=.*chk/%chk=${1%com}chk/" ${1}
fi

if [[ !$QUIET ]]
then
echo -e "${RED}------------------------------------------------ \n\n${NC}"
more ${1}
echo -e "${RED}------------------------------------------------ \n\n${NC}"
echo qsub -N${NMFL:0:15} -v in=${1} ~/bin/.rng
echo "Cores : $CORE; Memory : $MEM; Cue : $CUE"
echo -e "${RED}--------------Are you sure? [y/N]--------------- ${NC}"
read -r -p " " response
else
response="y"
fi

if [[ $response =~ ^([yY][eE][sS]|[yY])$ ]]
then
qsub -N${NMFL:0:15} -v in=${1%.com} ~/bin/.rng
echo -e "${YELLOW}\n $(date -u +'%H:%M') - Work sent \n${NC}"
else
echo -e "${YELLOW}\n Work aborted \n${NC}"
fi

shift
done
</pre>

I've reduced the function name to gf, more similar to gv and shorter.
A complete guide to the function is printed writing '''gf''' or '''gf ?''' or '''gf help''' in the terminal.
The old rng file are no more need.

I also suggest you to add this other 2 functions/alias if you want. I found really useful when modding your .bashrc as convulsively as I do.

<pre>
alias bhrc="cd ~; cp .bashrc .bashrc.old;vi .bashrc; loadbh; cd ~-"
alias bhrc.old="cd ~;cp .bashrc.old .bashrc; loadbh; cd ~-"
alias loadbh="source ~/.bashrc"
</pre>

'''bhrc''' and '''gfunc''' have become my favorite commands quite soon!! And '''bhrc.old''' is my panic button, a perfect backup plan if you mess up something in the bashrc file.