ChemWiki - User contributions [en]

Resgrp:comp-photo-dyn/mctdh90.31dv/run

2009-02-04T11:30:18Z

Mlaraujo: /* '''Current Known Bugs''' */

= '''Basic use of the MCTDH package''' =

(Need a general introduction about how the program works including: choice of number of gaussians; what the database is and how to create/maintain it; nos of processors that should be used; definition of final propagation time and propagation time step; use of initial momentum; and 'explain why we would ever need to start from the lower state. Or can we assume that the user should understand this already (and know, for example, how many gaussians is appropriate?))

=='''Symmetry Considerations'''==

The way the diabatisation is performed in mctdh90.31dv sometimes leads to complications involving symmetry. The diabatic states are defined using the conical intersection described in coin.log. If the molecule is highly symmetric, there will be more than one conical intersection (all identical by symmetry). If the wavepacket moves close to one of the other conical intersections that is not described in coin.log, the diabatic states may not be properly described in this area of the PES. This of course means that the behaviour of the wavepacket(s) is likely to be described poorly also.

If the conical intersection has lower symmetry than the starting material, the symmetry must necessarily be broken during the dynamics calculation before the conical intersection is reached. The breaking of each mode will occur either due to the accumulation of small numerical inaccuracies or if a momentum is given which forces particular modes to break symmetry.
Mctdh90.31dv uses frequency-mass-weighted normal coordinates to describe molecular geometries. Each frequency-mass-weighted coordinate corresponds to a vibration of the molecule (and there are therefore 3N-6 coordinates). Displacements of atoms are described by a (or a combination of) vibration(s). Each vibration can be displaced in one of two directions: positive or negative. The 3N-6 frequency-mass-weighted coordinates can be classified by symmetry. Whether a particular symmetry mode is broken in the positive or negative direction will be equally likely if no initial momentum is given. Thus for each mode that is broken during a simulation the symmetry may break in the positive direction or the negative direction. There will be 2x possible conical intersections corresponding to a particular starting geometry, where x is the number of modes that must be broken going from starting material to conical intersection.

Example: Butadiene

Cis-butadiene belongs to the C2h point group and its 3N-6 frequency-mass-weighted coordinates can be classified as Ag, Bg, Au or Bu (see the C2h character table and GAUSSIAN frequency output). The S1/S0 conical intersection has no symmetry. Thus there are four symmetry modes that must be broken going from starting material to conical intersection. There are sixteen (24) equivalent conical intersections that could be specified in coin.log, corresponding to all possible ways of distorting the starting geometry into the conical intersection geometry. The sixteen conical intersections correspond to: two structures resulting from disrotatory motion in one direction followed by out-of-plane twisting (and their enantiomers); two structures resulting from disrotatory motion in the other direction followed by out-of-plane twisting (and their enantiomers); two structures resulting from conrotatory motion in one direction followed by out-of-plane twisting (and their enantiomers); and two structures resulting from conrotatory motion in the other direction followed by out-of-plane twisting (and their enantiomers). Each of the sixteen conical intersections will have a different arrangement of atomic labels but all can be reached by distorting the starting geometry.

=='''Creating the Directories'''==

* First of all, create a folder in which to save the calculations in your $HOME and $WORK directories. Create a directory in $HOME, and an identical directory in $WORK that has the same path. Keep pathlengths as short as possible (if the total path becomes too long the dynamics code will not run). For simplicity, in this case, we are going to assume that this directory is named ''buta'' (for butadiene).

mkdir buta

* Create a subdirectory called '''dd_data''' in the new directory in $WORK. Thus you should start with:

/home/$USER/buta
/work/$USER/buta/dd_data

* Important Note: it is essential to have the same path in both directories, $HOME and $WORK. Do not change the path-names within the HOME/WORK directories. If you re-name or move any subdirectory in your, for example HOME directory, you have to be consistent and make the same changes in the $WORK directory.

=='''Gaussian Output to be Used as Input for the Dynamics Program'''==

* Populate the new directory /work/$USER/buta/dd_data with four files which must be named: '''coin.log'''; '''start.fchk'''; '''start.log'''; and '''template.dat'''.These files are required in order to run any dynamics simulation, they are the basis that the script dd_generator (see the following section) will use to create the necessary files for running MCTDH. You may also create a file named "'momentum.dat"' if you wish to give a momentum to the wavepacket(s) (this is optional and may be created later instead).

'''coin.log''' is the logfile resulting from the optimisation of the conical intersection. NB The MCTDH program will rotate the conical intersection before starting the dynamics. To do this it must be provided with three angles which describe the appropriate rotation. There is an Excel spreadsheet available to calculate these angles (see the section entitled "Rotating the Conical Intersection"). NB the final conical intersection log file must only contain one geometry (otherwise the dynamics program will not know which geometry to use). IS THIS STATEMENT TRUE FOR THIS VERSION??

[[Media:coin.log]]

(Insert a link here to section "Rotating the Conical Intersection")

'''start.fchk''' is the formatted checkpoint file from the high precision vibrational modes of the ground state with state averaged orbitals (Part A, 6)

[[Media:start.fchk]]

'''start.log''' is the log file from the high precision vibrational modes of the ground state with state averaged orbitals (Part A, 6)

[[Media:start.log]]

'''template.dat''' is a template for the creation of GAUSSIAN input files by the MCTDH program. It contains all the mutual keywords of the GAUSSIAN calculations which will be run on-the-fly by MCTDH. It also contains other information relating to the GAUSSIAN calculations such as memory requirements.

[[Media:template.dat]]

'''momentum.dat''' is a file containing a list of values to be used as vectors to indicate the momentum to be given to a particular (set of) wavepacket(s). The vectors must be listed in the order of the frequency-mass-weighted normal coordinates specified in the Excel spreadsheet. They give the magnitude of the momentum to be given along each of these frequency-mass-weighted normal coordinates. N.B. The signs of the values here are important!

[[Media:momentum.dat]]

=='''The Generator'''==

* The "generator" script uses the GAUSSIAN output files (above) along with other information supplied by the user to create input files for MCTDH.

* Navigate to /home/$USER/buta and run the generator by typing:

dd_generator

for the HPC Cluster, or

dd_generator_MAC

for a MAC OS X system

* Typing dd_generator will run the script automatically. After installing the MCTDH package this command has been added to your list of executable commands.

********************************************************************************
******************** ------- DD GENERATOR -------- *****************
********************************************************************************

* The generator will ask a series of questions and will use the answers provided to prepare the input files for the dynamics program. The questions it asks are listed below along with answers for a trial run on butadiene.

==== List of questions ====

<blockquote style="background: white; border: 1px solid black; padding: 1em;">
<table border="1">

<tr><td> '''Question''' </td> <td> '''Answer for this tutorial''' </td> <td> '''Explanation''' </td> </tr>
<tr><td> '''Which version of GAUSSIAN should we use? (gdv|g03)''' </td> <td> g03 </td> <td> </td></tr>
<tr><td> '''How many shared-memory processors should we use? (1|2|4|8)
N.B.: (ncpus=1) serial or (ncpus=2|4|8) parallel (omp) version of MCTDH launched as batch job
and launching monoprocessor GAUSSIAN interactive jobs (nprocshared=1 or no specification)
'''</td> <td> 1 </td> <td> </td></tr>
<tr><td> '''What is the name of the molecule?''' </td> <td> butadiene </td> <td> The first four letters will be used to name the new files that the generator is creating </td></tr>
<tr><td> '''What is the number of atoms?''' </td> <td> 10 </td> <td> </td></tr>
<tr><td> '''The number of nuclear degrees of freedom is 24.
Do you want to reduce the dimensionality? (y|n)
(N.B.: this can be used also for re-ordering the coordinates)
''' </td> <td> n </td> <td> </td></tr>
<tr><td> '''What is the number of nuclear Gaussian functions?''' </td> <td> 1 </td><td> 1 means 1 gaussian on state 1 and 1 gaussian on state 2. This is the "single-set" implementation of MCTDH therefore the gaussian wavepacket on state 1 is the same as the gaussian wavepacket on state 2.</td> </tr>
<tr><td> ''''What is the final propagation time (in fs)?'''</td> <td> 200 </td> <td> </td></tr>
<tr><td> '''What is the propagation time step (in fs)?'''</td> <td> 0.1 </td><td> </td> </tr>
<tr><td> '''What is the number of electronic states? (1|2)''''</td> <td> 2 </td> <td> </td></tr>
<tr><td> '''What is the highest electronic root?''''</td> <td> 2 </td> <td> </td></tr>
<tr><td> '''From which electronic state should the wavepacket start? (2|1)''''</td> <td> 2 </td> <td> </td></tr>
<tr><td> '''Will there be an initial momentum given to the wavepacket? (y|n)'''</td> <td> y </td> <td> </td></tr>
<tr><td> '''Do you want to add a reference label to the name of the case? (y|n)'''</td> <td> y </td> <td> </td></tr>
<tr><td> '''Please type your text:'''</td> <td> trial </td> <td>This question is only asked if the answer to the previous question was yes. </td></tr>
<tr><td> '''What will be the status of the database? (rdwr|rd|wr|none)'''</td> <td> none </td> <td> Choose rd for read, wr for write etc. In this case we are not going to use the database, but if it was used (rd or rdwr is specified) the script would ask the user to specify the threshold below which the database values will be used (%). In this case the value none is chosen so this question is not asked.</td></tr>
<tr><td> '''Please type the value of the maximum-difference criterion (in %):'''</td> <td> 1 </td> <td>If 1 is specified, the database value will be used if the geometry is within 1% of the new geometry being calculated</td></tr>
<tr><td> '''>> Manual rotation (using Excel spreadsheet) <<
Please type the values of the three Euler angles (in deg)</td> <td> 176.543006
185.772905
4.538147 </td><td>From the spreadsheet [[Media:spreadsheet.xls]]</td></tr>

<tr><td>The generator will now tell you that it has read the files start.fchk from the folder /work/dm107/dyn/dd_data/ and written the file start.chk.

<pre>
Read formatted file /work/$USER/buta/dd_data/start.fchk
Write checkpoint file /work/$USER/buta/dd_data/start.chk
using /apps/gaussian/g03_e01/g03/unfchk

</pre></td></tr>
<tr><td> '''Do you want to read the direction of the initial momentum from the existing file in /work/$USER/buta/dd_data? (y|n)
(you still have time to change it now, before answering)
'''</td> <td> y </td> <td>This question is only asked if the answer to the question "Will there be an initial momentum given to the wavepacket?" was yes. </td></tr>
<tr><td> '''Please type the value of the excess kinetic energy (in eV) for calculating the magnitude:''' </td> <td> 1 </td> <td> </td></tr>
</table>
</blockquote>

=='''Files created by the generator.'''==

* The generator will now tell you that it has read the files start.log, coin.log and momentum.dat (if a momentum has been specified) from the folder /work/dm107/dyn/dd_data/:

<pre>
about to read parameters...
... parameters just read
about to read file /work/dm107/dyn_90dev/dd_data/start.log
...
... file /work/dm107/dyn_90dev/dd_data/start.log
read successfully
about to read file /work/dm107/dyn_90dev/dd_data/coin.log
...
*********************************************************
Mass-weighted displacement from start to coin:
old total norm: 22.070387
new total norm: 4.669035
vibrational part: 4.669035
rotational part: 0.000000
*********************************************************
... file /work/dm107/dyn_90dev/dd_data/coin.log
read successfully
about to read file /work/dm107/dyn_90dev/dd_data/momentum.dat
...
*********************************************************
Using the momentum given in momentum.dat would have given
an excess kinetic energy (in eV) of: 15.269
For your information, the momentum has been multiplied
by a factor of: 0.572
*********************************************************

... file /work/dm107/dyn_90dev/dd_data/momentum.dat
read successfully
</pre>

and that the extraction of data and the creation of a summary file were done successfully

<pre>
Data extracted successfully
The summary of this file generation is in:
-rw-r--r-- 1 dm107 hpc-users 3070 Dec 2 17:06 /home/dm107/dyn_90dev/but1dd1o.txt

Do not forget you still can add a momentum, change the integrator, change convergence criteria for GAUSSIAN and MCTDH...

Do not forget to check the order of the atoms of the conical intersection geometry in /work/dm107/dyn_90dev/dd_data/coin.log

Now go to your jobscript file and give values to the memory and walltime.

Good luck!
</pre>

* The dd_generator script has generated four files in the same directory (/home/$USER/buta):

# but1dd1p_trial.inp
# but1dd1p_trial.job
# but1dd1p_trial.txt
# but1dd_none.op

(Link to a more detailed explanation of this files)

* The script has also created some files and directories in /work/$USER/buta where the MCTDH and GAUSSIAN calculations will be stored:

1) Directories:

* butadd1p_trial
* butadd1p_trial/dd_data

2) Files (in butadd1o_trial/dd_data):

# refdb.dat
# start.chk
# template.dat
# forward.dat
# backward.dat

=='''Modifications to be made to the files before running the dynamics.'''==

* In the .job file in /home/$USER/buta specify the memory and walltime if you are in the HPC Cluster.

* When running a development version of GAUSSIAN (gdvg03 or gdvg01), copy the start.chk file into the folder /work/$USER/dyn_90dev/but1dd1p_trial/dd_data. The unformatted checkpoint file form start.fchk that dd_generator has created is corrupted. IS THIS STATEMENT TRUE FOR THIS VERSION??

=='''Running the dynamics.'''==

* Navigate to /home/$USER/buta. Queue the job file. In this case, type:

qsub butadd1p_trial.job

for MAC OS X users the shell command is already written in butadd1p_trial.job

='''Analysis of the results'''=

The most important files are the output and .res files.

=== Detailed information about files and directories ===

* The log file (log)

This file contains information such as the source code version, type of calculation performed, integrator used, numerical parameters, which data files are opened, any error messages, and much more. The information provided by the log file can be very helpful, in particular when searching for errors. One should always carefully inspect the log file.

* The output file (output)

The output contains some standard results:

'''Time''': time in fs.

'''CPU''': CPU time in s.

'''Norm''':

'''E-tot''': the total energy in eV. This value should be conserved (i.e by the end of the run the E-tot value should not be too different from what it was a time=0).

'''E-corr''': correlated Hamiltonian energy

'''Delta-E''': diference between E-tot at time t=0 and the current time t

Note: In a multi-packet run, i.e. when npacket > 1, the total energy and the norm of the wavefunction, as given in the "total" part, are averaged over the packets.

'''population''' : diabatic populations of state 1 and state 2 (in that order) at the current time t

For every mode:

'''< q >''': position expectation value

'''<dq>''': standard deviation Sqrt[< q2 > - < q >2]

'''''' : momentum expectation value

'''<dq>''': standard deviation Sqrt[< p2 > - 2]

* dvr

* oper

*ddpeserr

*input

*op.log

*psi

*check

*auto

*ddpes

*restart

*stop

*speed

*timing

*update

= '''Current Known Bugs''' =

Parallelisation:
It is not possible to run calculations in parallel with version 90.31dv (reading the same template.dat file simultaneously by each processor is causing problems).

Total energy:

1) The total energy can be "artificially" increased by much. If so, try a different integrator.

2) If Delta-E suddenly becomes too large, you can get the following message:
"ERROR in subroutine WRGAUSSIAN :
Do not use $Swap:...$ metastring in file /.../template.dat"
Often, when getting this message, no more steps are added to the simulation, although the calculation seems to keep running (the integrator keeps trying and failing).

Using the database:

1) Every record generated with mctdh90.31dev and several GWPs is corrupted, so, for now, when launching calculations with more that one wavepacket, use "formdd_none.op" (i.e. do not read nor write the database).
[For instance, when using dbrdwr and starting from a clean db, all newly generated records are added to the existing database, even if they are identical to records that were already written in the db.]

2) Records obtained in calculations with one GWP should be OK, but this is still to be confirmed.

"Impossible case":
Error message that forces the calculation to stop. It seems to be associated with moving towards an "unexpected" geometry (e.g. a radical).

Resgrp:comp-photo-dyn/mctdh90.31dv/run

2009-02-04T11:29:56Z

Mlaraujo: /* '''Current Known Bugs''' */

= '''Basic use of the MCTDH package''' =

(Need a general introduction about how the program works including: choice of number of gaussians; what the database is and how to create/maintain it; nos of processors that should be used; definition of final propagation time and propagation time step; use of initial momentum; and 'explain why we would ever need to start from the lower state. Or can we assume that the user should understand this already (and know, for example, how many gaussians is appropriate?))

=='''Symmetry Considerations'''==

The way the diabatisation is performed in mctdh90.31dv sometimes leads to complications involving symmetry. The diabatic states are defined using the conical intersection described in coin.log. If the molecule is highly symmetric, there will be more than one conical intersection (all identical by symmetry). If the wavepacket moves close to one of the other conical intersections that is not described in coin.log, the diabatic states may not be properly described in this area of the PES. This of course means that the behaviour of the wavepacket(s) is likely to be described poorly also.

If the conical intersection has lower symmetry than the starting material, the symmetry must necessarily be broken during the dynamics calculation before the conical intersection is reached. The breaking of each mode will occur either due to the accumulation of small numerical inaccuracies or if a momentum is given which forces particular modes to break symmetry.
Mctdh90.31dv uses frequency-mass-weighted normal coordinates to describe molecular geometries. Each frequency-mass-weighted coordinate corresponds to a vibration of the molecule (and there are therefore 3N-6 coordinates). Displacements of atoms are described by a (or a combination of) vibration(s). Each vibration can be displaced in one of two directions: positive or negative. The 3N-6 frequency-mass-weighted coordinates can be classified by symmetry. Whether a particular symmetry mode is broken in the positive or negative direction will be equally likely if no initial momentum is given. Thus for each mode that is broken during a simulation the symmetry may break in the positive direction or the negative direction. There will be 2x possible conical intersections corresponding to a particular starting geometry, where x is the number of modes that must be broken going from starting material to conical intersection.

Example: Butadiene

Cis-butadiene belongs to the C2h point group and its 3N-6 frequency-mass-weighted coordinates can be classified as Ag, Bg, Au or Bu (see the C2h character table and GAUSSIAN frequency output). The S1/S0 conical intersection has no symmetry. Thus there are four symmetry modes that must be broken going from starting material to conical intersection. There are sixteen (24) equivalent conical intersections that could be specified in coin.log, corresponding to all possible ways of distorting the starting geometry into the conical intersection geometry. The sixteen conical intersections correspond to: two structures resulting from disrotatory motion in one direction followed by out-of-plane twisting (and their enantiomers); two structures resulting from disrotatory motion in the other direction followed by out-of-plane twisting (and their enantiomers); two structures resulting from conrotatory motion in one direction followed by out-of-plane twisting (and their enantiomers); and two structures resulting from conrotatory motion in the other direction followed by out-of-plane twisting (and their enantiomers). Each of the sixteen conical intersections will have a different arrangement of atomic labels but all can be reached by distorting the starting geometry.

=='''Creating the Directories'''==

* First of all, create a folder in which to save the calculations in your $HOME and $WORK directories. Create a directory in $HOME, and an identical directory in $WORK that has the same path. Keep pathlengths as short as possible (if the total path becomes too long the dynamics code will not run). For simplicity, in this case, we are going to assume that this directory is named ''buta'' (for butadiene).

mkdir buta

* Create a subdirectory called '''dd_data''' in the new directory in $WORK. Thus you should start with:

/home/$USER/buta
/work/$USER/buta/dd_data

* Important Note: it is essential to have the same path in both directories, $HOME and $WORK. Do not change the path-names within the HOME/WORK directories. If you re-name or move any subdirectory in your, for example HOME directory, you have to be consistent and make the same changes in the $WORK directory.

=='''Gaussian Output to be Used as Input for the Dynamics Program'''==

* Populate the new directory /work/$USER/buta/dd_data with four files which must be named: '''coin.log'''; '''start.fchk'''; '''start.log'''; and '''template.dat'''.These files are required in order to run any dynamics simulation, they are the basis that the script dd_generator (see the following section) will use to create the necessary files for running MCTDH. You may also create a file named "'momentum.dat"' if you wish to give a momentum to the wavepacket(s) (this is optional and may be created later instead).

'''coin.log''' is the logfile resulting from the optimisation of the conical intersection. NB The MCTDH program will rotate the conical intersection before starting the dynamics. To do this it must be provided with three angles which describe the appropriate rotation. There is an Excel spreadsheet available to calculate these angles (see the section entitled "Rotating the Conical Intersection"). NB the final conical intersection log file must only contain one geometry (otherwise the dynamics program will not know which geometry to use). IS THIS STATEMENT TRUE FOR THIS VERSION??

[[Media:coin.log]]

(Insert a link here to section "Rotating the Conical Intersection")

'''start.fchk''' is the formatted checkpoint file from the high precision vibrational modes of the ground state with state averaged orbitals (Part A, 6)

[[Media:start.fchk]]

'''start.log''' is the log file from the high precision vibrational modes of the ground state with state averaged orbitals (Part A, 6)

[[Media:start.log]]

'''template.dat''' is a template for the creation of GAUSSIAN input files by the MCTDH program. It contains all the mutual keywords of the GAUSSIAN calculations which will be run on-the-fly by MCTDH. It also contains other information relating to the GAUSSIAN calculations such as memory requirements.

[[Media:template.dat]]

'''momentum.dat''' is a file containing a list of values to be used as vectors to indicate the momentum to be given to a particular (set of) wavepacket(s). The vectors must be listed in the order of the frequency-mass-weighted normal coordinates specified in the Excel spreadsheet. They give the magnitude of the momentum to be given along each of these frequency-mass-weighted normal coordinates. N.B. The signs of the values here are important!

[[Media:momentum.dat]]

=='''The Generator'''==

* The "generator" script uses the GAUSSIAN output files (above) along with other information supplied by the user to create input files for MCTDH.

* Navigate to /home/$USER/buta and run the generator by typing:

dd_generator

for the HPC Cluster, or

dd_generator_MAC

for a MAC OS X system

* Typing dd_generator will run the script automatically. After installing the MCTDH package this command has been added to your list of executable commands.

********************************************************************************
******************** ------- DD GENERATOR -------- *****************
********************************************************************************

* The generator will ask a series of questions and will use the answers provided to prepare the input files for the dynamics program. The questions it asks are listed below along with answers for a trial run on butadiene.

==== List of questions ====

<blockquote style="background: white; border: 1px solid black; padding: 1em;">
<table border="1">

<tr><td> '''Question''' </td> <td> '''Answer for this tutorial''' </td> <td> '''Explanation''' </td> </tr>
<tr><td> '''Which version of GAUSSIAN should we use? (gdv|g03)''' </td> <td> g03 </td> <td> </td></tr>
<tr><td> '''How many shared-memory processors should we use? (1|2|4|8)
N.B.: (ncpus=1) serial or (ncpus=2|4|8) parallel (omp) version of MCTDH launched as batch job
and launching monoprocessor GAUSSIAN interactive jobs (nprocshared=1 or no specification)
'''</td> <td> 1 </td> <td> </td></tr>
<tr><td> '''What is the name of the molecule?''' </td> <td> butadiene </td> <td> The first four letters will be used to name the new files that the generator is creating </td></tr>
<tr><td> '''What is the number of atoms?''' </td> <td> 10 </td> <td> </td></tr>
<tr><td> '''The number of nuclear degrees of freedom is 24.
Do you want to reduce the dimensionality? (y|n)
(N.B.: this can be used also for re-ordering the coordinates)
''' </td> <td> n </td> <td> </td></tr>
<tr><td> '''What is the number of nuclear Gaussian functions?''' </td> <td> 1 </td><td> 1 means 1 gaussian on state 1 and 1 gaussian on state 2. This is the "single-set" implementation of MCTDH therefore the gaussian wavepacket on state 1 is the same as the gaussian wavepacket on state 2.</td> </tr>
<tr><td> ''''What is the final propagation time (in fs)?'''</td> <td> 200 </td> <td> </td></tr>
<tr><td> '''What is the propagation time step (in fs)?'''</td> <td> 0.1 </td><td> </td> </tr>
<tr><td> '''What is the number of electronic states? (1|2)''''</td> <td> 2 </td> <td> </td></tr>
<tr><td> '''What is the highest electronic root?''''</td> <td> 2 </td> <td> </td></tr>
<tr><td> '''From which electronic state should the wavepacket start? (2|1)''''</td> <td> 2 </td> <td> </td></tr>
<tr><td> '''Will there be an initial momentum given to the wavepacket? (y|n)'''</td> <td> y </td> <td> </td></tr>
<tr><td> '''Do you want to add a reference label to the name of the case? (y|n)'''</td> <td> y </td> <td> </td></tr>
<tr><td> '''Please type your text:'''</td> <td> trial </td> <td>This question is only asked if the answer to the previous question was yes. </td></tr>
<tr><td> '''What will be the status of the database? (rdwr|rd|wr|none)'''</td> <td> none </td> <td> Choose rd for read, wr for write etc. In this case we are not going to use the database, but if it was used (rd or rdwr is specified) the script would ask the user to specify the threshold below which the database values will be used (%). In this case the value none is chosen so this question is not asked.</td></tr>
<tr><td> '''Please type the value of the maximum-difference criterion (in %):'''</td> <td> 1 </td> <td>If 1 is specified, the database value will be used if the geometry is within 1% of the new geometry being calculated</td></tr>
<tr><td> '''>> Manual rotation (using Excel spreadsheet) <<
Please type the values of the three Euler angles (in deg)</td> <td> 176.543006
185.772905
4.538147 </td><td>From the spreadsheet [[Media:spreadsheet.xls]]</td></tr>

<tr><td>The generator will now tell you that it has read the files start.fchk from the folder /work/dm107/dyn/dd_data/ and written the file start.chk.

<pre>
Read formatted file /work/$USER/buta/dd_data/start.fchk
Write checkpoint file /work/$USER/buta/dd_data/start.chk
using /apps/gaussian/g03_e01/g03/unfchk

</pre></td></tr>
<tr><td> '''Do you want to read the direction of the initial momentum from the existing file in /work/$USER/buta/dd_data? (y|n)
(you still have time to change it now, before answering)
'''</td> <td> y </td> <td>This question is only asked if the answer to the question "Will there be an initial momentum given to the wavepacket?" was yes. </td></tr>
<tr><td> '''Please type the value of the excess kinetic energy (in eV) for calculating the magnitude:''' </td> <td> 1 </td> <td> </td></tr>
</table>
</blockquote>

=='''Files created by the generator.'''==

* The generator will now tell you that it has read the files start.log, coin.log and momentum.dat (if a momentum has been specified) from the folder /work/dm107/dyn/dd_data/:

<pre>
about to read parameters...
... parameters just read
about to read file /work/dm107/dyn_90dev/dd_data/start.log
...
... file /work/dm107/dyn_90dev/dd_data/start.log
read successfully
about to read file /work/dm107/dyn_90dev/dd_data/coin.log
...
*********************************************************
Mass-weighted displacement from start to coin:
old total norm: 22.070387
new total norm: 4.669035
vibrational part: 4.669035
rotational part: 0.000000
*********************************************************
... file /work/dm107/dyn_90dev/dd_data/coin.log
read successfully
about to read file /work/dm107/dyn_90dev/dd_data/momentum.dat
...
*********************************************************
Using the momentum given in momentum.dat would have given
an excess kinetic energy (in eV) of: 15.269
For your information, the momentum has been multiplied
by a factor of: 0.572
*********************************************************

... file /work/dm107/dyn_90dev/dd_data/momentum.dat
read successfully
</pre>

and that the extraction of data and the creation of a summary file were done successfully

<pre>
Data extracted successfully
The summary of this file generation is in:
-rw-r--r-- 1 dm107 hpc-users 3070 Dec 2 17:06 /home/dm107/dyn_90dev/but1dd1o.txt

Do not forget you still can add a momentum, change the integrator, change convergence criteria for GAUSSIAN and MCTDH...

Do not forget to check the order of the atoms of the conical intersection geometry in /work/dm107/dyn_90dev/dd_data/coin.log

Now go to your jobscript file and give values to the memory and walltime.

Good luck!
</pre>

* The dd_generator script has generated four files in the same directory (/home/$USER/buta):

# but1dd1p_trial.inp
# but1dd1p_trial.job
# but1dd1p_trial.txt
# but1dd_none.op

(Link to a more detailed explanation of this files)

* The script has also created some files and directories in /work/$USER/buta where the MCTDH and GAUSSIAN calculations will be stored:

1) Directories:

* butadd1p_trial
* butadd1p_trial/dd_data

2) Files (in butadd1o_trial/dd_data):

# refdb.dat
# start.chk
# template.dat
# forward.dat
# backward.dat

=='''Modifications to be made to the files before running the dynamics.'''==

* In the .job file in /home/$USER/buta specify the memory and walltime if you are in the HPC Cluster.

* When running a development version of GAUSSIAN (gdvg03 or gdvg01), copy the start.chk file into the folder /work/$USER/dyn_90dev/but1dd1p_trial/dd_data. The unformatted checkpoint file form start.fchk that dd_generator has created is corrupted. IS THIS STATEMENT TRUE FOR THIS VERSION??

=='''Running the dynamics.'''==

* Navigate to /home/$USER/buta. Queue the job file. In this case, type:

qsub butadd1p_trial.job

for MAC OS X users the shell command is already written in butadd1p_trial.job

='''Analysis of the results'''=

The most important files are the output and .res files.

=== Detailed information about files and directories ===

* The log file (log)

This file contains information such as the source code version, type of calculation performed, integrator used, numerical parameters, which data files are opened, any error messages, and much more. The information provided by the log file can be very helpful, in particular when searching for errors. One should always carefully inspect the log file.

* The output file (output)

The output contains some standard results:

'''Time''': time in fs.

'''CPU''': CPU time in s.

'''Norm''':

'''E-tot''': the total energy in eV. This value should be conserved (i.e by the end of the run the E-tot value should not be too different from what it was a time=0).

'''E-corr''': correlated Hamiltonian energy

'''Delta-E''': diference between E-tot at time t=0 and the current time t

Note: In a multi-packet run, i.e. when npacket > 1, the total energy and the norm of the wavefunction, as given in the "total" part, are averaged over the packets.

'''population''' : diabatic populations of state 1 and state 2 (in that order) at the current time t

For every mode:

'''< q >''': position expectation value

'''<dq>''': standard deviation Sqrt[< q2 > - < q >2]

'''''' : momentum expectation value

'''<dq>''': standard deviation Sqrt[< p2 > - 2]

* dvr

* oper

*ddpeserr

*input

*op.log

*psi

*check

*auto

*ddpes

*restart

*stop

*speed

*timing

*update

= '''Current Known Bugs''' =

Parallelisation:
It is not possible to run calculations in parallel with version 90.31dv (reading the same template.dat file simultaneously by each processor is causing problems).

Total energy:
1) The total energy can be "artificially" increased by much. If so, try a different integrator.

2) If Delta-E suddenly becomes too large, you can get the following message:
"ERROR in subroutine WRGAUSSIAN :
Do not use $Swap:...$ metastring in file /.../template.dat"
Often, when getting this message, no more steps are added to the simulation, although the calculation seems to keep running (the integrator keeps trying and failing).

Using the database:
1) Every record generated with mctdh90.31dev and several GWPs is corrupted, so, for now, when launching calculations with more that one wavepacket, use "formdd_none.op" (i.e. do not read nor write the database).
[For instance, when using dbrdwr and starting from a clean db, all newly generated records are added to the existing database, even if they are identical to records that were already written in the db.]

2) Records obtained in calculations with one GWP should be OK, but this is still to be confirmed.

"Impossible case":
Error message that forces the calculation to stop. It seems to be associated with moving towards an "unexpected" geometry (e.g. a radical).