ChemWiki - User contributions [en]

Mod:ts tutorial

2019-10-17T11:31:07Z

Lhf216: /* Introduction */

== Introduction ==

Within this lab, you will be modelling several chemical reactions and analysing them by calculating '''Transition State (TS)''' structures. Locating transition states is an important step in confirming the mechanism of a reaction - for example, is a particular reaction stepwise or concerted? Will certain reaction pathways be favoured? In the lab, you will be analysing the geometry and the MOs of the TS structure and calculating reaction barriers to gain chemical insight into reaction mechanisms.

A simple energy profile (below, left) for a reaction is plotted using the reaction coordinate. Along the reaction coordinate, the TS '''(2)''' is the point of maximum energy, linking a set of reactants '''(1)''' and products '''(3)'''. The TS is, therefore, a stationary point (i.e. a gradient of zero) with a negative second derivative along the reaction coordinate.

[[File:TSTutorial1.png|centre|800px|alt=Alt|Fig 1 (left): A 1D Energy profile for a reaction. Fig 2 (right): A PES for 2 coordinates.]]

The energy profile is a 1-dimensional simplification of the full Potential Energy Surface (PES) of the system, where the energy is a function of only one degree of freedom - the reaction coordinate. The system has been set in equilibrium in all other degrees of freedom (minimising) and the degree of freedom relating to the reaction coordinate has been varied. In reality, a chemical system undergoing a reaction will explore more than the reaction coordinate - it can be displaced away from its equilibrium position in any degree of freedom. The potential energy can be plotted against any one or a combination of these degrees of freedom or coordinates. A 2D PES is shown on the right, resulting from varying 2 coordinates. It is an example of the dimerisation of cyclopentadiene. In Coordinate 1 (left to right), the bonding atoms are brought closer together and sp3 hybridised. In Coordinate 2 (bottom to top), the cyclopentadiene molecules are rotated about the reaction centre (twisted). This PES shows some twisting is required to prevent the atoms from getting too close to the highlighted methylene.
<jmol>
<jmolApplet>
<title></title><color>white</color><size>400</size>
<uploadedFileContents>Ts_tutorial_CPD_dimer_TS.log</uploadedFileContents>
<script>vibrating=0; spinning=0; frame 21; frank off; vector on; vector scale -4; vector 0.04; color vectors red</script>
<name>CPD_Dimer_TS</name>
</jmolApplet>
<jmolbutton>
<script>if(vibrating==0) vibrating=1; vibration 2; else; vibrating=0; vibration off; endif</script>
<text>Toggle vibrate</text>
<target>CPD_Dimer_TS</target>
</jmolbutton>
</jmol>
 
<jmol>
<jmolmenu>
<item>
<script>frame 21; if(vibrating==0) vibration off; else; vibration 2; endif</script>
<text>Coordinate 1</text>
<target>CPD_Dimer_TS</target>
</item>
<item>
<script>frame 22; if(vibrating==0) vibration off; else; vibration 2; endif</script>
<text>Coordinate 2</text>
<target>CPD_Dimer_TS</target>
</item>
</jmolmenu>
</jmol>

 
These coordinates are in fact the first two '''normal modes''' of the system. Recalling the number of normal modes of vibration = 3N - 6, this system with 22 atoms has 60 normal modes. You can have a look at some of the other vibrations in the example above by right-clicking and selecting a model. Models 1-20 are steps of an optimisation calculation, and models 21-80 are the 60 normal modes. You should notice that the first normal mode has a 'negative' frequency. This negative is meant to depict an imaginary number, the result of calculating the frequency of a harmonic oscillator with a negative force constant (square of a negative). '''At every TS there must be only one imaginary frequency''' as all other coordinates are minimised.

==Gaussian Calculations==

To explore the reactions you will need to calculate the reactants, products and TS structures of the system using GaussView and Gaussian.

From previous labs you should already be familiar with:
::* Using GaussView to construct molecules (Make sure you are familiar with the table of controls in the '''[[Mod:gv_basic|Basic GaussView Tutorial]]''' before beginning this tutorial)
::* Setting up calculations using GaussView to run with Gaussian
::* Running and analysing Optimisation and Frequency calculations for stable minima
::* Constructing MO diagrams using ChemDraw
::* Viewing and analysing MOs using GaussView

To calculate reactants and products, a suitable starting structure can be drawn in GaussView and then optimised to a minimum using Gaussian. When you are optimising to a minimum all degrees of freedom are altered to try to minimise the energy. The resulting minima will be your stable reactants/products. You can use a frequency calculation to confirm that you are at a minimum energy structure by checking that all of the normal modes are real (positive in Gaussian).

===Transition State (TS Opt) Calculation===

The calculation of TS structures is less straightforward. The TS is a maximum in one degree of freedom (the reaction coordinate) meaning that a conventional optimisation (where all degrees of freedom are minimised) doesn’t work. Instead, a different method - a '''TS Optimisation''' - is used in Gaussian. This method requires at least one imaginary (negative in Gaussian) frequency which the TS optimisation can follow.

When starting a TS Optimisation, it is important to begin from a guess structure which is close to the first-order saddle point structure that you wish to locate. The worse the starting guess structure is, the more likely that the calculation will fail to find the correct TS. For example, in the image below, the guess TS 1 structure is too far away from the actual saddle point. The calculation would struggle to find the correct TS structure and will most likely fail. In most cases, the wrong TS will be found (check the negative vibrational mode - does it look like the motion you would expect to see?) or there will be multiple imaginary frequencies. A converged structure with multiple imaginary frequencies is indicative of a higher-order saddle point. In comparison, guess TS 2 is much closer to the structure it is aiming to find and will be more likely to locate the TS successfully.

[[File:TSTutorial2.png|centre|700px]]

Chemical intuition plays a large part in starting from a suitable guess TS structure. Below is the general procedure for setting up and submitting Gaussian TS Optimisations. The tutorial exercises will take you through approaches for generating the TS structure to use in step 1.

 

{| style="background-color:#eeffee;padding:0.5em;border:1px solid #b0e0b0;"
|
{| style="background-color:#ddfcee;padding:0.1em;width:100%;"
| '''''TS Opt Procedure'''''
|}

'''1. Generate a guess TS structure'''

Use one of the approaches described in the [[mod:ts_tutorial#Tutorial_Exercises:_Generating_a_guess_TS|tutorial exercises]] to generate your guess TS structure.

'''2. Calculation set up'''

In the Job Type tab:
::*Choose: ‘Opt+Freq’.
::*Select to optimise to 'TS (Berny)'.
::*Set 'Calculate force constants' to 'once' - Force constants are required for TS calculations. The algorithm must have the local curvature as an input to 'know' which direction the reaction path is.

In the Method tab select the method to use:

::*''For PM6:'' Set the method (second dropdown box) to ‘Semi-Empirical' and choose PM6 as the method.
::*''For B3LYP/6-31G(d)'': Set the method (second dropdown box) to DFT and choose ‘B3LYP’. For the basis set choose 6-31 and (d) for the polarisation function.

Press 'Submit'. Note that using the Windows computers you can run into serious errors by running multiple jobs simultaneously.

'''3. Analysing the calculation'''

If the job succeeds, open the log file. If it doesn't, then try adding in the keyword '''opt=noeigen''' and resubmitting the calculation. If this also fails then go to the '''[[Mod:ts_troubleshooting|Troubleshooting]]''' page.

Hopefully, it should look like the TS you were expecting. To analyse the structure:
::*Check that it is converged, (see the [[Mod:ts_tutorial#Analysing_Calculations|Analysis section]] of the Appendix for a reminder).
::*Check the vibrations. Right-click on the window and select 'Results' then 'Vibrations'. If there is more than one negative frequency, go to the '''[[Mod:ts_troubleshooting|Troubleshooting]]''' page. If there is one, check that it is correct by choosing it and pressing 'Start Animation'. The vibration should correspond to the reaction coordinate (i.e. it should look like it's going between the reactants and products).
::*[[Mod:ts_tutorial#Intrinsic Reaction Coordinate (IRC) Calculation|IRC]] calculations can also be run to confirm that it is the correct TS.

'''4. Reoptimise with a more accurate method'''

If the results are fine and you used PM6 then you can now reoptimise with a more accurate method if necessary. Copy the structure to a new window (Shortcut: ctrl + (C, N, V) ). Changing the method, repeat step 2 and 3.
|}

==Tutorial Exercises: Generating a guess TS==
 

===Approach 1: Straight Guess===

The first way to locate a TS is to just draw a guess structure and run a straight TS Optimisation on this. This usually fails and is not recommended unless you are very sure that you are close to the TS and have a very small system.

'''Advantages:''' Fastest method

'''Disadvantages:''' Very unreliable. Requires knowledge of the TS

{| style="background-color:#eeffee;padding:0.5em;border:1px solid #b0e0b0;"
|
{| style="background-color:#ddfcee;padding:0.1em;width:100%;"
| '''''General Procedure'''''
|}

'''1.''' Draw a guess TS structure using GaussView. This can be from previously optimised fragments (with copy-and-paste). In bond-forming reactions, the distances between the reacting atoms will be somewhere in between the reactant and product distances. For example, the C-C distance in the TS of a C-C forming reaction will be somewhere in between their combined Van der Waals radii and a C-C bond length. The value of '''2.2''' is often used for C-C bond forming reactions.

'''2.''' Set up and run the TS Opt calculation by the procedure [[Mod:ts_tutorial#Transition_State_Optimisation|above]]

|}

==== Practice: Cope Rearrangement ====



[[Image:pic1.jpg|right|thumb|Cope rearrangement]]

The classic example of a Cope rearrangement is the [3,3]-sigmatropic rearrangement of 1,5-hexadiene. Its mechanism has been debated for a long time (stepwise/dissociative/concerted) but it is now accepted that it rearranges in a concerted, pericyclic fashion via a diradical transition state. This TS bears similarity to either the cyclohexane boat or chair conformation:

 

{| align="center"
|- align="center"
| [[Image:pic2a.jpg]]
| style="width: 50px;" |
| [[Image:pic2b.jpg]]
|- align = "center"
| [[Image:appendix2a.jpg|300px]]
|
| [[Image:appendix2b.jpg|300px]]
|- align="center"
| align="center" | ''Chair Transition State''
|
| align="center" | ''Boat Transition State''
|}

 

 

{| style="background-color:#ffeeee;padding:0.5em;border:1px solid #e0b0b0;"
|
{| style="background-color:#fcdddd;padding:0.1em;width:100%;"
| '''''Procedure'''''
|}

* First, the allyl radical fragments (CH2CHCH2) are drawn and optimised. Open a new window and in the builder window, select '''Element Fragment'''. Select '''Carbon Trivalent (S-A-A)''' for the central atom. For the neighbouring carbons choose '''Carbon Trivalent (S-S-D)'''. As a reminder, clicking on the window will place the fragment where you click, replacing dangling bonds or atoms if you click on them. The fragment can be seen in the GaussView window, with the highlighted blue atom indicating which atom will be centred (this can be changed by clicking different atoms in this window).

* You should now have a fragment that resembles half of a TS. In addition, at the bottom of the molecular editor window it should read '''8 atoms, 23 electrons, neutral, doublet'''. This indicates that the fragment is a radical. Now you need to optimise this fragment. Set up the job as an optimisation job (optimise to a minimum), with the PM6 method. This should complete in seconds.

* We will now set up the boat TS. Copy the fragment you have generated from the log file. You should see the copied fragment in the GaussView window. Open a new window and click once to place the fragment. Place the second fragment somewhere below it. Make sure your next click doesn't add a third fragment by changing the mode to '''Inquire''' in the GaussView window (question mark icon).

* Translations occur in the plane of the window, so to move the fragment into place, rotate the view by 90º around the Y axis ('''View''', '''Positioning Tools''') and move one fragment to be roughly 2.2 Å away from the other, such that the terminal carbons line up. Try to maintain the correct symmetry.

* Run a TS Optimisation on the structure following the calculation procedure [[Mod:ts_tutorial#Transition_State_Optimisation|above]]. There's a good chance the job will fail with an error in link 9999. This is because it's very difficult to land close enough to the TS with this method. Most of the time, this can be corrected by adding '''Opt=NoEigen''' and resubmitting. Check that you have the correct TS, with one imaginary frequency at about 900i cm-1.

* Reoptimise this at the B3LYP/6-31G(d) level. There should be an imaginary frequency around 530i cm -1

* Now, repeat for the chair conformer. To do this with the allyl fragments, rotate one of them by 180º.

* You should now have two transition states, but which conformers of 1,5-hexadiene do they link? Open the PM6 optimised TS structures and run '''[[Mod:ts_tutorial#Intrinsic_Reaction_Coordinate_.28IRC.29_Calculation|IRC]]''' calculations on them. Use '''Always''' when calculating force constants and make sure you're using PM6 as the method. For each IRC calculation, take the first and last geometry and optimise them (a minimum, not a TS of course) with HF/3-21G. Now compare geometries and energies with those on '''[[Mod:phys3_appendix1|this page]]'''.

|}

 
===Approach 2: Freezing Atoms===

This method requires drawing a guess TS structure and freezing the atoms directly involved in the reaction. Optimising the structure to a minimum allows the rest of the degrees of freedom, which are not involved in the reaction mechanism, to equilibrate while the frozen atoms are prevented from moving. This ensures the system is as close as possible to the TS before the actual TS optimisation.

'''Advantages:''' Fastest reliable method

'''Disadvantages:''' Requires knowledge of the TS

{| style="background-color:#eeffee;padding:0.5em;border:1px solid #b0e0b0;"
|
{| style="background-color:#ddfcee;padding:0.1em;width:100%;"
| '''''General Procedure'''''
|}

'''1.''' Follow approach 1 by drawing a guess TS structure. Make sure the distances between the atoms that you will freeze are reasonable.

'''2.''' Freeze the distances between the atoms involved in the reaction (note that GaussView and Gaussian refer to these distances as 'bonds' even though they might not be 'bonded'). To do this, click on 'Edit' then '''Redundant Coordinate Editor'''. On the molecular editor window, select the atoms of a bond to freeze. Go back to the Redundant Coordinate Editor and change 'Unidentified' to 'Bond', 'Add' to 'Freeze'. For each atom pair, you need to add a coordinate. Before closing the window, make sure there are no errors (shown at the bottom of the window) and that the correct pairs are frozen.

'''3.''' Set up the calculation. You should notice that the keywords line now contains '''opt=modredundant'''.

'''4.''' When the job has terminated successfully, open the log file in GaussView. Check that the frozen 'bonds' have remained the same length. Now copy this geometry into a new window and run a TS optimisation on the structure. Ensure that frozen bonds are removed in the TS calculation. Gaussian will behave unpredictably if you attempt to search for a TS with bonds still frozen.

|}

==== Practice: Cyclopentadiene Dimerisation ====

 

[[File:Ts_tutorial_cpd_dimer_scheme.png|600px]]

 

If you've used cyclopentadiene in the lab, chances are you've needed to 'crack' it. The reason for this is that cyclopentadiene dimerises with a half-life of hours at room temperature, or more slowly at lower temperatures. This dimerisation is an example of a Diels Alder reaction. Cracking is the process of heating it to reverse the reaction back to the reactive monomer. This is due to the negative entropy of the reaction that disfavours dissociation, which becomes more significant at higher temperatures.

 
{| style="background-color:#ffeeee;padding:0.5em;border:1px solid #e0b0b0;"
|
{| style="background-color:#fcdddd;padding:0.1em;width:100%;"
| '''''Procedure'''''
|}

* GaussView includes some ring fragments such as cyclopentadiene. Locate it beside the '''Element Fragment''' icon and draw two rings close together. Now, rotate them into the endo position (seen in the '''[[Mod:ts_tutorial#Beyond_1D_-_The_Potential_Energy_Surface|intro section]]''').

* Freeze the appropriate reacting termini and optimise to a minimum with PM6.

* Now run the TS optimisation and check that you have the correct imaginary frequency (about 850i cm-1).

* Run an IRC to confirm that this is the dimerisation reaction. You will need to set '''Calculate Force Constants''' to '''Always'''.

{| style="background-color:#fcdddd;padding:0.1em;width:100%;"
| '''''Extra'''''
|}

Repeat the above for the exo TS. Minimise the reactants for both the endo and exo and compare the '''[[Mod:ts_tutorial#Reaction_Barriers_and_Reaction_Energies|reaction barriers]]'''. Which is more kinetically favourable? Now minimise the products and compare the reaction energies. Which is the more thermodynamically favourable?

|}
 

===Approach 3: Starting from Reactants/Products===

Sometimes we will not know enough about the form of the TS to draw a guess structure straight away. In this case, we can start from either the reactants and products, changing bond lengths to resemble the TS.

'''Advantages:''' More reliable than previous methods. Doesn't require much knowledge of the TS.

'''Disadvantages:''' Requires additional steps. Difficult if minima are far away in geometry from TS. There can be problems if you start from the products but your TS resembles the minima.

{| style="background-color:#eeffee;padding:0.5em;border:1px solid #b0e0b0;"
|
{| style="background-color:#ddfcee;padding:0.1em;width:100%;"
| '''''General Procedure'''''
|}

'''1.''' At this point, you'll need to decide whether to use the reactants or the products. As a general rule, choose whichever has the fewest molecules, so for a dimerisation reaction choose the dimer. Draw and optimise this structure. Open the resulting log file and check it's the correct structure. Copy this structure into a new window.

'''2.''' Decide which lengths and/or angles will change during the reaction. Modify them using the appropriate editing tools. Often it's enough to just change the atoms directly involved in the reaction, but if this doesn't work, try altering neighbouring atoms to reflect the change in hybridisation they might undergo. In a classic Diels Alder reaction, for example, 3 double bonds become single bonds and one single bond becomes a double bond, so it might be worth changing these values to somewhere in between. The dienophile carbon atoms become sp3 hybridised, so the neighbouring atoms might need to be distorted a little to reflect this.

'''3.''' Follow approach 2: freeze the degrees of freedom you think are involved in the reaction coordinate and optimise, then run a TS optimisation on the resulting (unfrozen!) structure.

|}

==== Practice: Xylylene-SO2 Diels Alder Cycloaddition ====

 

[[File:Ts_tutorial_xylylene_so2_scheme.png|600px]]

 

This is an example of a hetero-Diels Alder reaction, where SO2 is used as a dienophile. Without knowing the direction of approach of the SO2 or whether the barrier is early or late, it can be difficult to use draw a guess TS directly. Therefore, we'll start from the product.

 
{| style="background-color:#ffeeee;padding:0.5em;border:1px solid #e0b0b0;"
|
{| style="background-color:#fcdddd;padding:0.1em;width:100%;"
| '''''Procedure'''''
|}

* Select naphthalene from the '''Ring Fragments'''. Two carbons at the end will be replaced to form the SO2 part.

* Replace the atoms with appropriate O and S fragments, and don't forget to add the additional hydrogen atoms with '''Add Valence''' to form xylylene.

* Now use opt+freq to optimise to a minimum. You'll probably notice some negative frequencies due to symmetry. In the '''Vibrations''' window, use manual displacement to break symmetry and reoptimise. In future, if you expect issues with symmetry you can try to break it before the initial optimisation to save time.

* Delete the bonds between xylylene and SO2 and separate them by about 2.0 Å for the C-O pair and 2.4 Å for the C-S pair. Now use the '''Redundant Coordinate Editor''' to freeze the pairs and optimise to a minimum followed by a TS calculation with '''opt=noeigen'''.

* Analyse the results as normal.

{| style="background-color:#fcdddd;padding:0.1em;width:100%;"
| '''''Extra'''''
|}

Aside from endo/exo conformers, there is an entirely different way for SO2 and xylylene to react known a ''cheletropic'' or ''chelotropic'' reaction. Try using the above to find the TS for a cheletropic reaction between the sulfur of SO2 and xylylene. This time, start with an iso-indene fragment. Compare the reaction barriers and enthalpies of reaction between the two reactions.

|}

== Appendix ==

=== Analysing Calculations ===

==== Convergence ====

Check that the job has properly converged. For each step in optimisation, the gradient will be calculated to determine if the system is at a stationary point. To prove that a stationary point has been found, open the log file and scroll from the bottom to find a section that looks like this:

<pre> Item Value Threshold Converged?
Maximum Force 0.000098 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.001379 0.001800 YES
RMS Displacement 0.000379 0.001200 YES
Predicted change in Energy=-4.942954D-08
Optimization completed.
-- Stationary point found.</pre>

This job has landed on a stationary point. Compare to the following, which did not converge properly:

<pre> Item Value Threshold Converged?
Maximum Force 0.000155 0.000450 YES
RMS Force 0.000021 0.000300 YES
Maximum Displacement 0.002340 0.001800 NO
RMS Displacement 0.000561 0.001200 YES
Predicted change in Energy=-2.681147D-07</pre>

==== Frequency Calculation ====

If you haven't already done so, run a frequency calculation on the job (remember to hold parameters the same - method, basis set, solvation etc).

For a reactant or product then check that all of the vibrations are positive. For a TS, check that you have one negative vibration and that it corresponds to the reaction by visualising the vibration ('''Results''', '''Display Vibrations'''). This is a very good indication that you have the correct TS structure.

====Intrinsic Reaction Coordinate (IRC) Calculation====

Once you have your TS, you can run an IRC to confirm that it is the correct structure. An IRC follows the minimum energy pathway to reactants and/or products on the PES. By checking the end structures given by the IRC to the products/reactants that you expect to form then you can confirm that the TS links the correct two minima.

 

{| style="background-color:#eeffee;padding:0.5em;border:1px solid #b0e0b0;"
|
{| style="background-color:#ddfcee;padding:0.1em;width:100%;"
| '''''IRC Calculation Procedure'''''
|}

'''1. Calculation set up'''

Using your optimised TS structure set up a Gaussian calculation. (Note: Your starting structure '''must have only one imaginary frequency''' to run an IRC)

In the Job Type tab:
::*Choose: ‘IRC’.
::*Keep Follow IRC in 'Both directions' unless it is a symmetric TS, then it's a wasted effort to perform the calculation in both directions, so this option can be changed to 'Forward only'.
::*Change Calculate Force constants to 'Always'. Force constants are required as you'll be starting on a stationary point and the gradient alone isn't enough. Choosing Always (instead of once) isn't necessary but helps for difficult PESs.
::*By default, Gaussian will take 10 steps down the PES, but this often isn't enough. Check the box 'Compute more points' and choose a higher number such as 200 (note that Gaussian will stop once converged, so if you're seeking convergence, any number larger than the number of steps it takes to converge is fine).

In the Method tab make sure that you use the same method at which the TS has been optimised. This is because the IRC calculation (and similarly for a frequency calculation) operates on the PES and so must be calculated at the same level of theory as the underlying PES. E.g. if you want an IRC for PM6, use the PM6 TS.
It is advised that any IRC is run using PM6. This is because IRCs take a long time if you use an expensive method and basis set (e.g. B3LYP/6-31G(d)) while calculating force constants. If you only have your TS structure optimised at the B3LYP/6-31G(d) level then running a TS optimisation on this structure using PM6 and then an IRC on this may be faster.

'''2. Check calculation'''

IRCs can be problematic, especially for reactions where the PES is not well defined. Some common problems with IRCs are shown below and if you are having trouble getting them to run successfully ask a demonstrator. Otherwise, if the IRC has run until a stationary point has been found in both the reverse and forward direction then you can analyse the endpoints to confirm the TS.

'''3. Confirming the TS'''

Take the first and the last step of the IRC. (I.e. the endpoints of both the reverse and the forward pathways).

Optimise the structures to a minimum.

Once complete open the log file in GaussView - do the optimised structures look like the products/reactants you expect? Compare them to your optimised reactants and products - are they the same? If so then your TS links the correct two minima on the PES.

For a unimolecular reaction then optimising the endpoint structures will work well. When there are two or more reactants, an optimisation becomes very difficult as the PES is bumpy and the gradients are small. This can yield reactants/products in the IRC that are irrelevant to the reaction - don't use these for your reaction profiles.
|}

==== Reaction Barriers and Reaction Energies ====

Barriers and reaction energies can be calculated at room temperature and 0K using information from the log file of a frequency calculation. You will need to run a frequency calculation for each of the '''optimised''' reactants, TS and products. Using Notepad or Notepad++, open each log file and search for a section named "'''Thermochemistry'''".

For 0K, the value to use is the "'''Sum of electronic and zero-point Energies'''".

For room temperature, the value to use is the "'''Sum of electronic and thermal Free Energies'''".

If there are multiple reactants/products then make sure that you use the optimised isolated structures (the assumption that they react from infinite separation) to calculate the correct energy barrier from.

=== Useful Tips and information ===

==== Comparing results of jobs ====

When comparing energies between structures, it's important to ensure that the energies are calculated in the same way. In every case, make sure the computational method, basis set, solvation method, convergence criteria and grid are the same. This means if you are using "int=grid=ultrafine" or "opt=tight" in one calculation, it must be used in all calculations for structures that are being compared.

==== Bond types are ignored by Gaussian ====

In a quantum mechanical calculation, all Gaussian uses from the geometry is the distances between the atoms. This means specifying a bond type is meaningless and mostly aesthetic - it won't remove two hydrogens if you change a single bond to a double bond. However, they are very important in a molecular mechanical calculation! Check that the number of atoms is correct in all calculations.

==== Job Monitoring ====

For jobs that are expected to take a long time or are taking longer than expected, it's worth opening them in GaussView to see how they are doing. In GaussView, choose '''File''' then '''Open'''. Locate the log file of the job you want to monitor and make sure ''''Read Intermediate Geometries''' is selected and open the file. Now you can periodically refresh the job with '''File''', '''Refresh'''. Check that the job looks like it's converging to the correct geometry.

==== Creating a follow-up job manually ====

If a checkpoint file (.chk) exists for a file, Gaussian can read the output of it as the input of a new calculation. This has numerous advantages:

* A step in generating the guess wavefunction can be skipped (it's taken from the previous job)
* Force constants can be read into calculations such as IRCs
* Easier to be consistent between calculations
* Additional features, such as restarting previously failed calculations

The drawback is that it's much harder to get used to than GaussView. The general structure of a follow-up input file is:

<pre>%mem=<memory>
%nprocshared=<processors>
%oldchk=<old checkpoint path>
%chk=<new checkpoint path>
# <keywords> guess=read geom=allcheck
<NEWLINE></pre>

Note that all Gaussian inputs must finish with a new line - the parser will read sections until it encounters a newline character, and finish if it reaches the end of a file.

Create the file using Notepad ++. For the '''memory''', choose 1GB to begin with. You might need more if the program runs out of memory. For '''processors''', choose the number of physical processors that you want to run on, which will be up to 4 for the Windows computers. Direct %oldchk to the path of the checkpoint file you want to read from. Note that it should be an absolute path. Input the '''keywords''' as required. Save the file with the extension '.gjf'. In an Explorer window, drag the file into an instance of G09 and click Run.

==== Restarting failed jobs ====

Sometimes optimisations or IRC calculations fail for a variety of reasons. Create a '''[[Mod:ts_tutorial#Creating_a_follow-up_job_manually|follow-up input file]]'''. If you need to restart an optimisation, add into the keywords '''opt=restart''', or for an IRC, add '''IRC=restart'''. Note that if the keywords '''opt''' or '''IRC''' already exist, you'll need to add '''restart''' into the existing keywords.

=== Troubleshooting ===

If you encounter errors or problems with any part of this lab, feel free to discuss them with any of the demonstrators. If a demonstrator isn't around, see '''[[Mod:ts_troubleshooting|this link]]''' for Gaussian troubleshooting.

==== IRC Troubleshooting====
Gaussian will often produce an IRC that seems reversed. This is normal and is the result of not providing information as to what the reactants and products are. It can be corrected by identifying a bond that will lengthen over the course of the reaction, for example a bond breaking, or a double bond becoming a single bond. Once the two atoms ('''N1''' and '''N2''') are identified, include this line in the IRC calculation replacing N1 and N2 with the atom numbers:

<pre>irc=(phase=(N1,N2))</pre>

{|class=wikitable
|-
!Example IRC
!Notes/Solutions for errors
|-
|[[File:Ts_tutorial_IRC_success.png|400px]]
|A successful, asymmetric IRC.

Note that the gradient must be 0 at the TS, reactants and products (minima).
|-
|[[File:Ts_tutorial_IRC_fail_1.png|400px]]
|Failed IRC as the initial geometry is not a TS.

This can happen when the method and/or basis sets are not consistent between the TS and IRC calculation.
|-
|[[File:Ts_tutorial_IRC_fail_2.png|400px]]
|Failed IRC as the PES is too flat at the TS and the algorithm cannot decide which direction to move down.

See '''[[Mod:ts_troubleshooting#IRC_finishes_on_the_first_step|this page]]''' for a fix.
|-
|[[File:Ts_tutorial_IRC_fail_3.png|400px]]
|Failed IRC at the first or last point on the IRC. The gradient is 0 here, but it fails as it is not a minimum.

See '''[[Mod:ts_troubleshooting#.22Maximum_number_of_corrector_steps_exceeded.22|this page]]''' for a fix.
|}

Mod:ts troubleshooting

2019-10-15T10:22:35Z

Lhf216: /* Common Issues Encountered using Gaussian */

== Common Issues Encountered using Gaussian ==

==== '"Guess=TCheck" .... were specified ... Continue anyway' appears and the job fails ====

This is the what happens when you set up a job from a log file or chk file. The default behaviour of GaussView is to create follow-on jobs (using the geometry, wavefunction and some other parameters from the previous job). This can be useful, but it's beyond the scope of this course. To correct this error, delete '''genchk geom=allcheck''' from the additional input line, in the '''Guess''' tab change the '''Guess method''' to '''Default''' and in the '''Solvation''' tab change the Model to '''None''' (or whatever model you were using). To ''prevent'' this error, copy the geometry to a new window and set up the job from there.

==== NtrErr Called from FileIO ====

This means Gaussian can't open a file or write to it (usually because it doesn't exist). Check the inputs in the job setup window, or see [[Mod:ts_tutorial#.27.22Guess.3DTCheck.22_...._were_specified_..._Continue_anyway.27_appears_and_the_job_fails|above]].

==== Job fails: Error termination request processed by link 9999 ====

This can mean one of many things unfortunately, as link 9999 is the job cleanup program of Gaussian. This often indicates a problem with the starting geometry. Open the log file in GaussView and see what the last step looks like. This often gives a clue as to what is wrong with the starting geometry. Some things to check are the geometry itself, that there are no extra or missing atoms, that the charge is correct etc.

If you keep getting this for a TS calculation, it indicates that in the initial force constant calculation, multiple negative eigenvalues were found. This will cause the TS calculation to fail by default (which direction should the TS calculation go?). To suppress the failure and force a search for the most significant eigenvalue specify '''opt=noeigen'''. Note that for a bad starting geometry this can land you on the wrong TS or with multiple imaginary frequencies, so monitor the job to check it's going in the right direction.

==== Opt=TS requires force constants or ModRedundant ====

This means you have requested a TS calculation but have not specified the prior calculation of force constants. To correct this, go to the job setup window and for '''Calculate Force Constants''' change 'Never' to '''Once'''.

==== More than one imaginary frequency ====

This indicates an inadequate starting geometry. Visualise each imaginary frequency (shown as a negative number in Gaussian/GaussView). Often the additional imaginary frequencies are symmetry-breaking where the optimisation algorithm gets 'stuck' on the top of a hill (stationary point). To resolve the problem, you can break the symmetry manually. At the bottom of the '''Display Vibrations''' window select '''Manual Displacement''' and choose a non-zero value, save the structure and run another TS optimisation. You might need to try different values for the manual displacement.

You should also check that all parameters are held constant between an optimisation and frequency calculation. This includes method, basis set, solvation or anything else that would change the energy or geometry in a calculation.

==== Edited Redundant Coordinates were ignored ====

This can indicate a bug with Gaussian. First check the job setup window that opt=modredundant is specified. The best way to fix this problem is to open the input file ('.com' or '.gjf'), scroll to the bottom where the redundant coordinates are specified and check they read something like:

B <atom number 1> <atom number 2> F

instead of

B <atom number 1> <atom number 2> <length> F

==== Molecule flying apart in TS calculation ====

If your system looks like it's breaking apart at the bond-forming centre, it suggests that TS calculation is moving in the wrong direction and minimising the reaction coordinate to reactants/products. In other words, the rest of the structure isn't properly minimised. Repeat [[Mod:ts_tutorial#Method_2|Method 2]] but make sure the atoms in the reaction centre are close enough together.

==== IRC finishes on the first step ====

An IRC will terminate when it encounters a shallow enough gradient. Sometimes the TS is too flat and the calculation terminates instantly. There are a couple strategies to deal with this: First, add in the '''Additional Keywords''' line '''IRC=stepsize=''n''''', where n is an integer greater than 10 (default) Try 20 to begin with, then 30. This will cause the IRC calculation to take larger steps, hopefully to a region where the gradient is steeper.

A second, more thorough strategy is to tighten the convergence threshold. However, this requires reoptimising the TS with '''opt=tight int=grid=ultrafine'''. Rerun a frequency calculation also with '''int=grid=ultrafine'''. Now, for the IRC, specify '''IRC=tight int=grid=ultrafine''' or '''IRC=VTight int=grid=ultrafine'''. Note that with this strategy, it's not valid to compare energies or even differences in energy between other jobs that aren't optimised with '''opt=tight int=grid=ultrafine'''.

==== "Maximum number of corrector steps exceeded" ====

A quick fix is to simply increase the number of corrector steps and rerun, but this can often fail too. Specify '''IRC=MaxCycle=n''' where n is an integer greater than 20 (default). Try 50. In the case of failure, follow the [[Mod:ts_tutorial#IRC_finishes_on_the_first_step|above]].

If this fails again, it might be that the calculation has landed on a bifurcation point/transition state linking two chiral minima. The IRC calculation has followed the PES down until the gradient has reached 0, so under normal circumstances it will terminate. However, the calculation breaks when it checks whether it can go further down in energy and which direction to go. This behaviour is normal and serves as a warning to tell the user that a minimum hasn't been found. This warning can be suppressed by setting '''Recorrect Steps''' to '''Never'''. Note that this geometry of the IRC is '''not''' a minimum now. You must reoptimise the geometry to a minimum by breaking symmetry and checking vibrations.

==== "Missing or bad data: RBond" when opening a Checkpoint file ====

This is a Gaussian bug. The easiest way to fix it is to open the log file, copy the geometry and run a single point energy calculation ('''Energy''' under '''Job Type'''). In addition, under '''General''', uncheck '''Write Connectivity'''. Make sure the method, basis set and all other parameters are the same.

==== Input conversion error in IntKMC ====
Gaussian may instantly terminate your calculation with the above error message if the pathway to the submitted .gjf includes signs which cannot be interpreted correctly by Gaussian like spaces.

e.g. if folders in your pathway include spaces in their naming like "PC/usr123/TS Lab/exr 2/file.gjf", make sure to find the spaces and delete or replace them. to attain:

"PC/usr123/TS_Lab/exr_2/file.gjf" or "PC/usr123/TSLab/exr2/file.gjf" and your calculation should run fine.

Mod:Hunt Research Group

2019-05-09T14:31:36Z

Lhf216:

==Hunt Group Wiki==

Back to the main [http://www.ch.ic.ac.uk/hunt web-page]
===Report and Paper Writing===
#procedures [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_procedures link]
#advice [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_writing link]
#report components [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/report_components link]
#files to provide when writing a paper [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/paper link]

===Group Admin===
#Which files to store on the database and database template [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/database link]
#How to access DROBO [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/drobo link]

===HPC Resources===
#'''Hunt group HPC servers and run scripts''' [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/hpc 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 run jobs interactively [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/run_interactive link]
#Computing resources available in the chemistry department [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/computing_resources link]
#New gf script (more convenient job submitting) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/new_gf_script link]
#Retired: How to make qsub more comfortable (gfunc) [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpQSUB link]
#Tired of entering your password all the time: set up a SSH keypair [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/SSHkeyfile link]
#How to make ssh more comfortable [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/pimpSSH link]
#How to comfortably search through old BASH commands [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/searchbash link]
#Using VPN from home, for Sierra follow the college instructions [[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 remote desktop [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/mac_remote link]
#How to use a slimmed down terminal on your IPhone [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/termius]

===Using evil Windows and PCs===
#Use Imperial Software Hub to access gaussview and gaussian [http://www.imperial.ac.uk/admin-services/ict/store/software/software-hub/ link]
#Using windows and setting up a connection to HPC [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]

===Key Papers, References and Resources===
*'''Papers'''
#Meta study on DFT functionals [https://pubs.acs.org/doi/abs/10.1021/ct401111c doi]
#M06 suite of DFT functionals [https://link.springer.com/article/10.1007/s00214-007-0310-x doi]
#SMD for ILs [https://pubs.acs.org/doi/abs/10.1021/jp304365v doi]
*'''Notes'''
#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)
#DFT Workshop Notes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/DFT_Workshop]
#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]

===Gaussian General===
#We are starting 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]
# Here is an already existing database of common errors [https://docs.computecanada.ca/wiki/Gaussian_error_messages link]
# [http://www.ch.ic.ac.uk/hunt/g03_man/index.htm G03 Manual]
#partial optimisations and scans [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/z-matrix link]
#General procedure for locating transition state structures [[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]
#IL ONIOM clusters [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/oniomclusers link]
#problems with scf convergence [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/scf_convergence link]
#manipulating checkpoint files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:usingchkfiles link]
#for NMR calculations look here: [http://cheshirenmr.info/index.htm Chemical Shift Repository]

===Gaussian Advanced===
#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]
#How to run NBO5.9 on the HPC [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/NBO5.9 link]
#generating natural transition orbitals [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/nto link]
#computing excited state polarisabilities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_ES_alpha link]
#computing deuterated and/or anharmonic spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Danharm link]
#How to run at a higher temperature [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:high_temp link]
#Correcting the entropy due to low modes [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:low_modes_entropy link]
#Optimisation of charged molecules in an electric field [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Optimising_charged_molecules_in_electric_fields link]

===Solvation===
#Using solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent link]
#Using SMD on ILs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:_Using_SMD_on_ILs link]
#Troublesome optimisations in SMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:troublesome_smd link]
#Atomic radii and solvent models [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/atomic_radii link]
#Molecular volume calculations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/molecular_volume link]
#The cavity [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/solvent_cavity link]
#How to download and use GeomView to visualise solvation cavities [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/geomview link]
#Surfaces (Solvent-Accessible and Connolly) in Jmol [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/jmolsurfaces link]

===Codes to Help Gaussian Analysis===
# Extract last Standard Orientation structure of gaussian log file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_single_geom link]
# Extract geometry and charges (ESP) into a .pdb file for visualising in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ESP_charges_for_VMD link]
# Codes to extract CHELPG and NBO charge values to excel [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/chelpg_extract link]
# Extract ESP and NBO charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/extract_ESP_charges link]
# Extract E2 Values (From NBO Calculations) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/NBO_Matlab_Code link]
# Calculate pDoS/XP spectra code (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Calc_XPS_Code link]
#Simple script to simply pull thermodynamic data and low frequencies from log files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:simple_freq_script link]
#Script to pull thermodynamic data and low frequencies from log files AND evaluate to a reference [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:freq_script link]
# Codes to extract frequency data from gaussian .log files and generate vibrational spectra [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:frequency_spectrum_script link]
# Optimally Tuned Range Seperated Hybrid Functionals [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/OTRSH_Funct link]
# Some G09 Parsers [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Some_G09_Parsers link]
# Codes to visualise data matrices (correlation matrices/heatmaps)[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/heatmap link]
#Python API for analysis of Gaussian compuations [https://pygauss.readthedocs.org - Documentation]
# Charge arm [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/charge_arm link]

===QC Visualisation===
*'''Using AIMALL: density based visualisation'''
#download [http://aim.tkgristmill.com AIMALL]
#basic instructions [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_basics link]
#AimAll with pseudo potentials [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group:aim_pseudopotentials link]

*'''ESPs and manipulating gaussian cube files'''
#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]
#Manipulating cube files [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/cube_files link]
#Format of cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/cube_format link]
#Using A. Stone's distributed multipole analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/GDMA link]

*'''NCI plots'''
#get the program here: [http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html link]
#How to install NCIPlot on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallNCIPlot link]
#Using NCIPlot [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/UseNCIPlot link]

*'''MOs'''
#Visualising MOs using Jmol [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:basic_jmol_instructions link]

===Setup and Running Classical MD Simulations===
#DL_POLY Installing DL_POLY_4.09 on MacOS Mojave 10.14.4 [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Installing_DL_POLY_4.09_on_MacOS_Mojave link]
#DLPOLY old Installation for an IMac [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.
#GROMACS installing and getting started with gromacs [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/gromacs_1 link]
#using Agilio Padua force fields for ionic liquids [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ilff link]
#Packmol installing and running to generate a starting box [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/packmol_1 link]
#initial rough relaxation [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/Starting_MD link]
#GROMACS general run [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_run link]
#GROMACS viewing data [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_viewing_MD link]
#GROMACS control file [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/gromacs_control_MD link]
#Equilibration and production simulations [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/EquilibrationandProduction link]
#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]
#Molten Salt Simulations [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/MoltenSaltSimulation link]
#Common Errors [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/CommonErrors link]
#Voids in ILs[https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/voids 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]

===MD Visualisation===
*'''VMD: a molecular dynamics visualisation package'''
#VMD can be installed from the [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD VMD downloads page]
#Quick reminder [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDReminder link]
#Colour in VMD [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDColor link]
#Changing the graphical representation of your structures [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/vmd link]
#VMD indexing [https://www.ch.ic.ac.uk/wiki/index.php/Talk:Mod:Hunt_Research_Group/VMDindexing link]
#Using scripts in VMD [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScripts link]
#Dealing with periodic boundaries and bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdScriptsPeriodic link]
#Dealing with bonding (under construction) [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdBonding 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]
#Overlapping two structures [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/VmdVisual link]
*'''Ovito: a molecular dynamics visualisation package'''
#Download Ovito [http://www.ovito.org/index.php/download]
#Using Ovito basics [//wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Ovito_basics link]
*'''SDFs'''
#How to generate SDFs [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/sdfs_generate link]

===MD Post processing===
#Python script to convert a HISTORY file into a xyz file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/hist_to_xyz link]
#Python script to reduce the number of steps in a lammps traj file [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_to_xyz link]
#Python script to convert a lammps traj file to xyz coordinates and at the same time fold all atoms into a cell and center at the origin [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/lam_fold_xyz link]
#Center the trajectory at a particular atom ('''needs fixing''') [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Recenter link]
#How to generate SDFs with TRAVIS [[Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS|link]]
#Tcl script to follow a particular atom [[Talk:Mod:Hunt Research Group/Traj_atom_following|link]]

===Coding===
*'''installing Xcode and other programming environments'''
#to use many programs you will need a compiler, this is not installed by default on your mac
#How to install Xcode on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/InstallXcode link]
#using MacPorts as code for managing other codes on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/MacPorts link]
#HomeBrew and Fink are other options (HomeBrew is not advised for us)
#gfortran on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Gfortran link]
#using python on your mac [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/python 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]

*'''Jan's charge based analysis Code'''
#charge analysis [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/Jan_charges link]
#Obtaining NBO, ESP, and RESP charges [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Charges link]

*'''Oxana's visualisation of ESPs Code'''
#Scripts for reading, saving, manipulating and visualising data from cube files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/Python_scripts_for_cube_files link]

===Other Codes===
#ADF Submission script [http://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/ADF_sricpt link]
#How to install POLYRATE [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group/polyrate link]
#XMGRACE, gfortran, c compilers for Lion [http://hpc.sourceforge.net/]

===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]

===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]
#Using MolCluster [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/MolCluster link]
#Running ChemShell [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell link]
#Explaining ChemShell files [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/ChemShell_files link]
#Step By Step [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Talk:Mod:Hunt_Research_Group/Chemshell_Step_By_Step link]

===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 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/termius

2019-05-09T14:28:19Z

Lhf216:

[[File:Term4.png|thumb|Termius Terminal Interface]]

==Terminal on your Iphone==
have you ever wanted to submit some jobs at the pub? Well, look no further!

To use this App effectively outside of the university wifi you will need to be connected to the imperial network via VPN. To connect to the imperial network via VPN from your iPhone follow the instructions in the following link:

https://www.imperial.ac.uk/admin-services/ict/self-service/connect-communicate/remote-access/method/set-up-vpn/ios/

following the download of Open VPN download the '''Termius''' App

- open the Termius app and create an account

- In the main terminus Interface select '''Hosts'''
[[File:Term3.png|none|thumb|550x550px|Terminus Main Interface]]
- Create a new host by tapping the little <nowiki>'''+'''</nowiki>
[[File:Term2.png|none|thumb|Terminus host selection interface]]
- Fill in the relevant fields (most importantly the Hostname: login.cx1.hpc.imperial.ac.uk, your username [lhf216 for me on the image] and your password [********* for me on the image])
[[File:Term1.png|none|thumb]]
- Start Using Terminal on your iPhone

I find this really useful for submitting jobs and checking progress while on the road. However, If you want to carry out more thorough evaluations on your files I would still recommend using a PC/MAC as vi is rather tedious to use. Enjoy!

File:Term4.png

2019-05-09T14:20:01Z

Lhf216:

Mod:Hunt Research Group/termius

2019-05-09T14:19:18Z

Lhf216:

==Terminal on your Iphone==
have you ever wanted to submit some jobs at the pub? Well, look no further!

To use this App effectively outside of the university wifi you will need to be connected to the imperial network via VPN. To connect to the imperial network via VPN from your iPhone follow the instructions in the following link:

https://www.imperial.ac.uk/admin-services/ict/self-service/connect-communicate/remote-access/method/set-up-vpn/ios/

following the download of Open VPN download the '''Termius''' App

- open the Termius app and create an account

- In the main terminus Interface select '''Hosts'''
[[File:Term3.png|none|thumb|550x550px|Terminus Main Interface]]
- Create a new host by tapping the little <nowiki>'''+'''</nowiki>
[[File:Term2.png|none|thumb|Terminus host selection interface]]
- Fill in the relevant fields (most importantly the Hostname: login.cx1.hpc.imperial.ac.uk, your username [lhf216 for me on the image] and your password [********* for me on the image])
[[File:Term1.png|none|thumb]]
-

Mod:Hunt Research Group/termius

2019-05-09T13:58:30Z

Lhf216:

Mod:Hunt Research Group/termius

2019-05-09T13:55:55Z

Lhf216: /* Terminal on your Iphone */

File:Term3.png

2019-05-09T13:48:01Z

Lhf216: Terminus Interface 3

Terminus Interface 3

File:Term2.png

2019-05-09T13:45:46Z

Lhf216: Terminus Interface 2

Terminus Interface 2

File:Term1.png

2019-05-09T13:40:30Z

Lhf216: Terminus interface 1

Terminus interface 1

Mod:Hunt Research Group/termius

2019-05-09T13:32:55Z

Lhf216: Created page with "==Terminal on your Iphone== have you ever wanted to submit some jobs at the pub? Well, look no further! To use this App effectively outside of the university wifi you will n..."

Mod:Hunt Research Group/hpc

2019-02-08T17:54:51Z

Lhf216: /* Runscript */

=Running jobs on the Imperial HPC=
Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

The aim of this wiki is to get new users set up on the Imperial HPC and to take you through:
*Introduce the Imperial HPC
*Logging in to the HPC
*Setting up your HPC environment (.bashrc)
*Job submission
*Managing your jobs

Before going through this wiki make sure that you have a:
*HPC account
*Are on the HPC Gaussian users list

== Introduction ==

HPC systems are usually composed of a cluster of nodes (computers). Just like your laptop/desktop, each node has CPUs (cores/processors), disk space and memory (RAM).
The imperial HPC has several clusters: CX1 (general), CX2 (high-end parallel jobs) and AX4 (big data). You will be using CX1 for your work.

Upon logging in you will find yourself on one of the login nodes. These nodes act as a gateway to the actual compute nodes (where your jobs will be run) and are good for file transfers, small job testing and setting up software. Don't use the login node as the place to run your job (it slows it down for everyone!)

From the login node, you will submit your jobs to the compute nodes on CX1. The job submission is handled by something called a '''scheduler'''. Imperial use PBS as the scheduler but others exist and all operate in a similar way with similar syntax.
The job of the scheduler is to submit (non-interactively) the job to run on the compute node appropriately to ensure the resources available are being used efficiently.
When you queue a job to run, you have to tell it which queue to send it to and the resources you want (number of processors, memory and walltime), the scheduler will do the rest.

== Logging on ==
To login to the Imperial HPC from a Linux/Unix (mac) system a secure shell client can be used (ssh):

# Open a terminal window
# Type the line: 
<code> ssh -XY username@login.cx1.hpc.imperial.ac.uk </code> 
Replacing username with your username e.g. th194
# If it is your first time logging in then you will be asked to accept the host, type yes to do so.
# Enter password when prompted

You are now on one of the HPC login nodes!

Notes:
* The -XY flags in the ssh command enable X11 forwarding

==Setting up your .bashrc==

Similarly to when setting up your local mac environment, you can use a .bashrc to set variables for your HPC bash environment.
Below are the steps to do so and an example .bashrc with some useful alias' on. As you progress you can edit your .bashrc (always remember to source it to activate any updates) and if you think of any particularly useful lines then let the group know!

#Using your favourite text editor create the file ''.bashrc''
#Copy and paste the script below into the new file
# Initialise your .bashrc by executing the command: <code>source ~/.bashrc</code>

Initial .bashrc to copy:
<pre>#!/bin/bash

# Change the prompt
export PS1="[\$USER@\h]\$PWD \$ "

# Bash history commands
HISTSIZE=100
PATH=$PATH:~/bin
EDITOR=vi
export EDITOR

# alias definitions
alias force="grep -i 'Maximum Force'"
alias dist="grep -i 'Maximum Disp'"
alias energy="grep -i 'SCF Done:'"

alias q='qstat'
alias qs="qstat -q pqph; qstat -q pqcdt; qstat -q pqchem"
alias qq="qstat -q"
alias gv="module load gaussian gaussview; gaussview"</pre>

The script mainly contains alias definitions. The most important ones for the HPC are probably the gv alias to allow easy loading of GuassView and the qstat aliases. Once you are more familiar with bash and your HPC use you should feel free to edit your .bashrc to suit you.

You should now see that your command line prompt has changed. If it hasn't then the above hasn't worked. If it has then you can now see that you are logged on to one of the login nodes on the HPC (`user@login-#-internal` where # is the number of the login node).

==Job Submission==

To introduce you to the HPC we are going to run a test Gaussian calculation. To do this we need the necessary input files for the calculation (.com and .chk file) and a way to submit out Gaussian job to cx1 to run. Remember, the PBS scheduler manages running the job on the compute nodes. To run our job successfully PBS needs to know the resources and programs that our job requires. We use a runscript (or jobscript) to contain this information. The runscript is essentially a set of instructions on how to run the job.

Therefore, to run our job we need:
* Input files (.com/.chk)
* A runscript to tell PBS how to run our job

===Input Files===

# In your home directory set up a folder for the test job and cd into this folder. If you have a job you want to run on the HPC then we will use that file. This file is likely to be located on your local machine somewhere, in which case:
# Open a new terminal window and cd to the directory where your .com file is located
# We want to copy this to your new directory on the hpc, which can be done with the command: <code>scp test.com username@login.cx1.hpc.ic.ac.uk:/rds/general/user/username/home</code> This command is a secure copy and should be familiar from the unix cp command. '''Make sure you edit the destination to be the directory for your test job, put your shortcode instead of username and change the name of the file from test.com if it is different.'''
# Enter your password at the prompt
# If the copy was successful then your test .com file should now be located in your directory on the HPC.
# If the job requires a .chk file then repeat the process for this file
# A file created on your mac will not run on the hpc, it needs some additional information
# you need to add a %mem= for how much memory is required and a %nprocs= for how many processors are required commands, the following is the first part of a test.com file setup for the hpc
<pre>
%mem=45000MB
%nprocs=12
%chk=test.chk
# hf/3-21g geom=connectivity

Title Card Required

0 1
C
</pre>

'''Checking the .com file'''

We now have a runscript and our input files within the directory. The resources requested in the run script above must match those entered at the top of your .com file.
#Open your .com file
#'''%chk''' should have the name of the checkpoint file which must be the same as the .com file
#'''%NProcShared''' is the number of processors requested and must match the number requested in the runscript. Edit it to 12.
#'''%mem''' should be slightly less than the memory requested in the runscript. Edit it to 46000MB

NB: There is an easier way to access your files on the HPC which is to mount it locally, this is almost like creating a tunnel between the two so that they can see each other directly. See the bottom of the page for information on how to do this later.

===Runscript===

As mentioned before the runscript contains all of the instructions to successfully run our job. The runscript usually contains PBS directives, which tell PBS the resources our job needs, and then a list of commands executing the job.

'''Modules'''

To run our job we will be using Gaussian. Firstly, check that you are registered as a user for the Gaussian group. If you are not then the job will fail to run as you will not be able to execute Gaussian. If you are not on the list then email Tricia to get added.

Gaussian and other programmes, such as GaussView, are available on the HPC as '''modules'''. To use a module you have to load it first, an example of module load commands were in the .bashrc file before.

Useful commands:

: <code>module avail</code>: This lists the modules available on the HPC. The names of the modules are usually the programme name and the version (e.g. gaussian/g09-d01)
: <code>module load</code>: Used to load a required module. Only once loaded can the program be used. (e.g. <code>module load gaussian/g09-d01</code> loads guassian to your local environment)

We will be loading gaussian for use in our runscript.

'''Computational Resources'''

To tell PBS the resources our job needs we use special PBS directives. These are lines in the script which start with <code>#PBS</code>. Resource requests are denoted by the flag <code>-l</code> and then the resource itself. These can be:

: <code>walltime=[hhh:mm:ss]</code>: The amount of real time the job requires to run. (There is usually a limit to the walltime available and this will change for each queue).
: <code>select=[integer]</code>: The number of nodes our job needs to run on.
: <code>nprocs=[integer]</code>: The number of processors on each node.
: <code>mem=[integer|GB/MB</code>]: The amount of memory required.

'''Queues'''

We also need to tell PBS where to submit our job, this is the queue. The PBS directive to set the queue is:
: <code>-q [queue name]</code>

There are several queues which you may have access too. A queue will have a set number of resources assigned to it and different limits (e.g. to walltime). The number of people who are using a queue defines how busy it will be and therefore, how long it may take waiting for your job to run. Specifying resources efficiently will help jobs run faster on the queue.
Queues include:

:'''pqph''' (various, see below) this is the hunt group queue, runs on the servers listed below
:: Each user has can have a '''maximum of 12 running jobs'''
:: To help balance usage please have a '''maximum of 20 jobs running or qued'''
:'''pqchem''' (42 nodes) this is the chemistry department queue,
:'''chemlab1''' (2 chassis) this is for the computational chemistry lab but can be used out of term time
: which can be accessed from https://scanweb.cc.ic.ac.uk/

'''Script'''

The below script it an example run script.
*The script starts with "#!/bin/sh", without this the job will always go to the queue "short" instead of the queue asked for.
*The next part of the script is the PBS directives discussed above which set the resources and variables needed.
*The module for gaussian is then loaded
*The script then checks to see if a .chk file exists and if so, copies it over to the temporary working directory on the compute node.
*Gaussian is run using the pbsexec command
*The final section executes when the job has complete and searches for the output files (e.g. .log file) to copy back over to your hom directory.

The script needs to be placed in the directory you are running the job from:
#Open a new file 'rs12' and copy the below into it:

<pre>#!/bin/sh

# submit jobs to the queue with this script using the following command:
# qsub -N jobname -v in=name rs12
# rs12 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}

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -l select=1:ncpus=12:mem=47000MB
#PBS -j oe
#PBS -q pqph

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directory from which the job was submitted.
test -r $PBS_O_WORKDIR/${in}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in}.chk"
cp $PBS_O_WORKDIR/${in}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in}.chk"
fi
#
# run gaussian
#
pbsexec g09 $PBS_O_WORKDIR/${in}.com
#
# job has ended copy back the checkpoint file
# check to see if there are other external files like .wfn or .mos and copy these as well
#
cp $TMPDIR/${in}.chk /$PBS_O_WORKDIR/.
# exit
</pre>

*Everyone should START by using this script, and not the automated submission script (see later)

We now have compatiable input files and a runscript. We are ready to submit our job!

'''Job Submission'''

The instructions to submit a job are the same as those at the top of the runscript. We run the command:
<code> qsub -N jobname -v in=name rs12</code>

* <code>qsub</code> is the PBS command to submit the job.
* jobname is the name you will see for your job in the qstat command
* name is the actual file minus .com etc it is passed into this script as ${in}
* rs12 is the name of the runscript

'''the run script must be in the same directory as your job!'''

# Run the command with the appropriate substitutions
If successful, a job number (XXXXXXX.cx1) should be printed out to the terminal, this is your jobID which PBS assigns to a submitted job.

== Monitoring your Job ==

Now that your job has been submitted you can monitor by using the command <code>qstat</code>. This gives you the status of your jobs in the queues. Useful commands may be:
:<code>qstat</code> to get your jobs that are running
:<code>qstat -q</code> to get a list of all queues
:<code>qstat -f</code> to get a full printout of all your queued jobs information

To delete a job from the queue you can use the command:

:<code>qdel [jobID]</code> to remove a job from the queue

A short script to list all the queues in one command:
::type qstatme and it will list the info for the three queues pqph, chemlab1 and pqchem
<pre>
#!/bin/bash
#
qstat -q | grep 'pqph '
qstat -q | grep 'chemlab1 '
qstat -q | grep 'pqchem '
</pre>

In your bashrc there was an alias set for some of these options. Typing 'q' in the terminal should produce the same result as 'qstat'.
The status of your job in the queue will either be Q (waiting to run), or R (running) and the run time so far.

Keep checking your job until it has run. If successful then you the .log file should be copied back to your working directory, check this to see if your job was successful.
You will also find a file which has the extension: .o[jobID], this is the merged output and error files for your job. If there has been an error it will be detailed with this file along with the resources requested and used by your job.

==ONLY once you have used the queuing script for some time==
*use the gf script created by Giacommo made which makes it easier to submit jobs to the hpc.
*The link below contains the script and instructions for using it.
::https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/pimpQSUB

== Memory needed to run ==

*Gaussian is greedy and will exceed the allocated memory
:: each proc needs a gaussian executable, which takes about 8MW (or 12 for MP2 frequencies)
::MW is megaword which is the unit gaussian allocates memory
::1MW is about 8.4MB
:::so each proc needs 1*8*8.4 approximately 68MB just to run
:::so 12 proc jobs require 12*68=816MB just to run
:::so 16 proc jobs require 16*68=1088MB just to run
:::so 20 proc jobs require 20*68=1360MB just to run
:::so 24 proc jobs require 24*68=1632MB just to run
:::so 40 proc jobs require 40*68=2720MB just to run
:::so 48 proc jobs require 48*68=3264MB just to run
::so when allocating memory inside the gaussian job you must reduce the memory by at least this amount
*thus best to reduce the memory by about 100MB*no.processors inside the gaussian script
*you also need some overhead within the PBS script

*the memory can be given in binary such as 251 GB (binary) is really 251 GB =251000*1,048,576 Bytes =264GB (decimal)

== Recommended specifications ==

in the following
: the first line gives the processor and memory
: the second line the amount to allocate in the PBS script
: the third and fourth lines the amount to allocated in the gaussian com file

:'''Small jobs''' use half a 24proc node: 12 cpu 47 GB
::\#PBS -lselect=1:ncpus=12:mem=46000MB
::%nprocs=12
::%mem=45000MB

:'''Medium jobs''' 7 nodes: 32 cpu 62 GB
::\#PBS -lselect=1:ncpus=32:mem=61000MB
::%nprocs=32
::%mem=58000MB

:'''Medium jobs''' 12 nodes: 24 cpu 92 GB
::\#PBS -lselect=1:ncpus=24:mem=91000MB
::%nprocs=24
::%mem=88000MB

:'''Large jobs''' 7 nodes: 40 cpu 125 GB
::\#PBS -lselect=1:ncpus=40:mem=124000MB
::%nprocs=40
::%mem=120000MB

:'''Largest jobs''' 4 nodes: 48 cpu 256 GB
::\#PBS -lselect=1:ncpus=48:mem=255000MB
::%nprocs=48
::%mem=250000MB

*add tmpspace=400 only for large disk jobs to ensure you are put on a node with enough disk!!
*Note that this requires you to include maxdisk=400gb in your gaussian input.
:NOTE the queing system does not check disk allocations. When requesting large disk jobs remember to request all of the processors on a node even if you are not using all of the processors. For large jobs the maximum disk space you can request is '''800GB''' on the 12 processor nodes.

==more details for if you seem to be having memory or disk issues==
*normal jobs
::will need 2*N^2 W *8.4 to get B (1,048,576B =1MB)
:: so 300 basis functions will need 180000W =0.18MW =1.5MB in addition to the above requirements
::require 2ON^2 W of disk to run where O=number of occupied orbitals, N=number of basis functions

*MP2 jobs
:: work best with %mem and maxdisk defined
:: in-core requires N^4/4 divided by 1,000,000 MW memory
:: so 400 basis functions will need 6400MW=53760MB=54GB memory per node, which is unlikely!
:: semi-direct requires 2*O(N^2) memory and N^3 disk
:: so N=476 basis functions O=56 occupied orbitals will need
::25.4MW=214MB of memory
::and 108MW=906MB disk (this is not actually true it will need much more probably around 1800MB disk per processor!)
::so total memory for MP2 freq 8proc will be
::12*8*8.4=807MB to run and 8*214=1712MB for calcs and some extra 400MB=3019MB=3.3GB
::gaussian does not like GB directive so give %mem in MB

== checkpoint and other files ==
: checkpoint files should be exactly the same name as the input file name
: for jobs that may exceed the wall time specify the full path of the checkpoint file, for example
::%chk=/work/phunt/tmp/filename.chk
:this means the checkpoint file will be written into your personal work directory, it may slow the job down
:this is also the reason /work is sometimes very slow on CX1 so only do this as an exception!

== Resources ==

The Imperial Research Computing service have a hpc wiki which has useful information including an intro to shell scripting, modules and job management information:
::https://wiki.imperial.ac.uk/display/HPC/High+Performance+Computing

The RCS also run several courses throughout the year, including intro to Linux, HPC, python and more advanced topics. Upcoming courses can be viewed from:
::https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/training/

===Next steps===
Mount
Alias shortcut for logging in
Keypair page
Once you are comfortable and understand the job submission process then the automatic job script which ... can be used

== Other information (may be out of date) ==
:3.1 CPMD:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Runcpmd_md.sh
:3.2 DL-POLY:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Mpirun.sh
::Note: You´ll not be able to see the output until the job finishes : the directory /tmp/pb.XXX isn´t accessible to you because it is on the private disk of the node running the job.
::To get DLPOLY to terminate before the job hits the walltime limit and killed, you need to run it through a program called pbsexec, for example:
::pbsexec mpiexec DLPOLY.X
::This will kill DLPOLY 15 minutes before the walltime limit, giving your script time to transfer files back to $work.

Mod:Hunt Research Group/mac setup

2018-10-04T07:45:36Z

Lhf216:

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

==== For NEW computers: make a group ====
::if you are a new user on an existing computer, the groups will already be set up!
::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 "gaussian"
::exit

==== set-up the terminal ====
::you will find the terminal app in the Utilities folder in your Applications directory
::drag this app onto your Dock, you will be using it a lot!
::open a terminal
::check you are in your home directory type "ls" to list the files/folders

==== set-up your .bashrc_profile ====
::create the file ".bash_profile"
::copy and paste the following into it
<pre>
#echo "bash_profile"
. ~/.bashrc
</pre>

==== set-up your .bashrc ====
::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 g16root="/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 $g16root/g16/bsd/g16.profile
#
# gaussview
#
# where to find gaussview
export GV_DIR="/Applications/gv"
# libraries
export LD_LIBRARY_PATH=$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>

::edit key lines for the version of gaussian and gaussview that you have
::make sure you have a ~/Work/Jobs/tmp" directory
::type "source ~/.bashrc" into your terminal to active all the alias commands.
::if you are using visualisation tools you may want to add some of the following into your .bashrc
<pre>
#
# image magic
#
export PATH="$PATH:/Applications/ImageMagick-7.0.3/bin"
export MAGICK_HOME="/Applications/ImageMagick-7.0.3"
# export DYLD_LIBRARY_PATH="$MAGICK_HOME/lib/"
#
# multiwfn
#
export KMP_STACKSIZE=64000000
export Multiwfnpath="/Applications/Multiwfn_3.4_bin_Mac"
export DYLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/Applications/Multiwfn
#
# nciplot
#
export NCIPLOT_HOME=/Applications/nciplot-3.0/src/nciplot
export OMP_NUM_THREADS=2
alias nciplot="/Applications/nciplot-3.0/src/nciplot"
#
# vmd
#
alias vmd="open /Applications/VMD_1.9.3.app"
#
</pre>
::again edit key lines for the version of gaussian and gaussview that you have

==== set-up your .login ====
::create the file ".login"
::this is needed because gaussview looks for csh stuff
::copy and paste the following into it
<pre>
setenv g16root /Applications
source $g16root/g16/bsd/g16.login
setenv GAUSS_SCRDIR /Users/$USER/Work/Jobs/tmp
setenv GV_DIR /Applications/gv
setenv GAUSS_EXEDIR /Applications/g16
</pre>
::of course you may need to change version specific information (or directory structure)
::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
::inside work make a directory called tmp (this is where you should direct gaussview to put temporary files)

==== run a test job ====
::cd into your testing directory
::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>

==== For NEW computers: install gaussian ====
::if you are a new user on an existing computer, the groups will already be set up!
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Work/Gaussian_Images/G16_A03_mac
</pre>
::read the "readme" file
::change to the cshell
<pre>
csh
</pre>
::tell the script where gaussian (G16) is to be installed
<pre>
setenv g16root "/Applications"
</pre>
::now goto the g16root directory
<pre>
cd $g16root
</pre>
::read and extract the files
<pre>
bzip2 -d -c /Users/tricia/Work/Gaussian_Images/G16_A03_mac/tar/*.tbz | tar xvf -
</pre>
::this will unpack and copy the contents of the tar file 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 g16
</pre>
::check this has worked, type "ls -al"
::you should see a list with something like the following
<pre>
drwxr-x--- 195 tricia gaussian 6630 30 Dec 2016 g16
</pre>
::goto the gaussian directory and run the install script
<pre>
cd g16
./bsd/install
</pre>
::you are not quite ready to run as the variables g16root, GAUSS_SCRDIR and the g16.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 $g16root/g16/bsd/g16.profile" in your .bashrc
:::goto the direcotry g16/bsd
:::edit the file g16.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

====For NEW computers: install gaussview ====
::assuming you are still in shell and that g16root is set
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Work/Gaussian_Images/G16_A03_mac
</pre>
::read the "readme" file
::unpack the file
<pre>
bzip2 -d -c /Users/tricia/Work/Gaussian_Images/GV6_17_mac/tar/*.tbz | tar xvf -
</pre>
::change the group premisions to the same as those for g09
<pre>
chgrp -R gaussian gv
</pre>

::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>

=====For OLD computers: setup for gaussian and gaussview=====
::you will need to be added to the gaussian group on your computer before you have access to gaussview and gaussian
::goto System Preferences
::click on Users and Groups
::unlock this pane by entering an administrators name and password, if you are not an administrator come and see me
::click on Groups (appears after all the users)
::click on the group gaussian and then tick the box next to your name on the right hand panel
::lock and leave this panel
::reboot your computer (this step is required!)
::check to see that you have access to the gaussian and gaussview directories

=====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 gaussian 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 a terminal
::type "gv" in the window (and press return)
::or start gaussview view by clicking on the icon in the Dock
::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

Rep:Mod:01342206

2018-03-01T09:16:17Z

Lhf216:

=NH3=
 

{| class="wikitable"
!Name
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-56.55776873</nowiki>
|-
!RMS Gradient (au)
|0.00000485
|-
!Point Group
|C3V
|}
Optimised N-H bond length in NH3 : 1.0179Å

Optimised H-N-H bond angle : 105.74115°

<pre> Item Value Threshold Converged?

Maximum Force 0.000004 0.000450 YES

RMS Force 0.000004 0.000300 YES

Maximum Displacement 0.000072 0.001800 YES

RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>HYUN NH3 OPT POP 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[media:HYUN NH3 OPT POP 1.LOG| here]]

[[File:Display vibrations.PNG]]

* Modes 5 and 6, as well as 2 and 3 are degenerate.
* Using the 3N-6 rule, it can be expected that there will be 6 vibrations as the value of N will be 4.
* Modes 1,2 and 3 are bending vibrations while 4,5, and 6 are bond stretches.
* Mode 1 is the umbrella vibrational mode.
* Mode 4 is highly symmetric
* 4 should be seen as there are 2 degenerate modes and 2 other peaks. However 4,5 and 6 may be too small to be seen and differentiated.
 
[[File:Chargenh3.PNG]]

* The charge on N is -1.125 and the charge on the H is 0.375.
* As expected there is a partially negative charge on N as it is more electronegative than H.Therefore it will attract more electron density.

 

==N2==
{| class="wikitable"
!Name
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-109.52412868</nowiki>
|-
!RMS Gradient (au)
|0.00000060
|-
!Point Group
|D*H
|}

<pre> Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH N2 OPT POP 1.LOG| here]]

1 Vibrational mode is present for N2 at 2457.

 

==H2==
{| class="wikitable"
!Name
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-1.17853936</nowiki>
|-
!RMS Gradient (au)
|0.00000017
|-
!Point Group
|D*H
|}

<pre> Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH H2.LOG| here]]

1 Vibrational mode is present for H2 at 4466.

==Energy Calculations==

*E(NH3)=-148492.421801kJmol-1
*2*E(NH3)=-296984.843602kJmol-1
*E(N2)=-287555.599849kJmol-1
*E(H2)=-3094.25508968kJmol-1
*3*E(H2)=-9282.76526904kJmol-1
*ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-146.478602kJmol-1

===Literature value comparisons===

The reactants are more stable. The literature value is -46kJmol-1. Literature values are taken from experimental observation. There is a difference between the literature value and the quantum mechanical estimation due to several reasons. One of them being that quantum mechanical estimations do not take real world imperfections into considerations. Also when calculating literature values, there is more than one molecule present, therefore there will be collisions and interactions between the molecules, and not just an energy value for a single molecule in space.

 

=ClF3=

{| class="wikitable"
!Name
|ClF3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-759.38175725</nowiki>
|-
!RMS Gradient (au)
|0.06637914
|-
!Point Group
|D3H
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000049 0.001800 YES
RMS Displacement 0.000032 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH CLF3.LOG| here]]

[[File:Vibclf3.PNG]]

<jmol><jmolApplet>
<title>ClF3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MWH CLF3.LOG</uploadedFileContents>
</jmolApplet></jmol>

Charge on Cl is 1.188, charge on F is -0.395.
F is more electronegative than Cl and attracts electron density towards itself.
 
==Molecular Orbitals of ClF3==
[[File:9 mo clf3.PNG|200px]]
4 in-phase s orbitals forming a bonding orbital

[[File:13 mo clf3.PNG|200px]]
2 in-phase p orbitals can be seen on the top of the image also with the p orbital of the Cl that is perpendicular to it. The p orbital of the Cl is also in-phase with the p orbital of the F atom on the bottom. They are all sigma bonds.

[[File:15 mo clf3.PNG|200px]]
4 in-phase p orbitals creating a pi bond.

[[File:22 mo clf3.PNG|200px]]
All 3 p orbitals are out-of-phase with the p orbital of the Cl, creating an anti-bonding orbital. This is also the HOMO of this molecule.

[[File:23 mo clf3.PNG|200px]]
This is the LUMO of this molecule. It seems as if there is a sp2 hybridiesd orbital that can be seen as one of the phases is larger in size than the other.

==Cl2==

{| class="wikitable"
!Name
|Cl2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-920.34987886</nowiki>
|-
!RMS Gradient (au)
|0.00002511
|-
!Point Group
|D*H
|}

<pre> Item Value Threshold Converged?
Maximum Force 0.000043 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000121 0.001800 YES
RMS Displacement 0.000172 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH CL2.LOG| here]]

==F2==

{| class="wikitable"
!Name
|F2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-199.49825218</nowiki>
|-
!RMS Gradient (au)
|0.00007365
|-
!Point Group
|D*H
|}

<pre> Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000128 0.000300 YES
Maximum Displacement 0.000156 0.001800 YES
RMS Displacement 0.000221 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH F2.LOG| here]]

==Energy Calculations==

* E(ClF3)= -759.38175725
* 2*E(ClF3)= -1518.76351 au
* E(Cl2)= -920.34987886 au
* E(F2)=-199.49825218 au
* 3*E(F2)= -598.494757 au
* ΔE=2*E(ClF3)-[E(Cl2)+3*E(F2)]=0.08113 au = +213.006815kJmol-1

Rep:Mod:01342206

2018-03-01T09:13:18Z

Lhf216:

=NH3=
 

{| class="wikitable"
!Name
|NH3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-56.55776873</nowiki>
|-
!RMS Gradient (au)
|0.00000485
|-
!Point Group
|C3V
|}
Optimised N-H bond length in NH3 : 1.0179Å

Optimised H-N-H bond angle : 105.74115°

<pre> Item Value Threshold Converged?

Maximum Force 0.000004 0.000450 YES

RMS Force 0.000004 0.000300 YES

Maximum Displacement 0.000072 0.001800 YES

RMS Displacement 0.000035 0.001200 YES </pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>HYUN NH3 OPT POP 1.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimisation file is liked to [[file:HYUN NH3 OPT POP 1.LOG| here]]

[[File:Display vibrations.PNG]]

* Modes 5 and 6, as well as 2 and 3 are degenerate.
* Using the 3N-6 rule, it can be expected that there will be 6 vibrations as the value of N will be 4.
* Modes 1,2 and 3 are bending vibrations while 4,5, and 6 are bond stretches.
* Mode 1 is the umbrella vibrational mode.
* Mode 4 is highly symmetric
* 4 should be seen as there are 2 degenerate modes and 2 other peaks. However 4,5 and 6 may be too small to be seen and differentiated.
 
[[File:Chargenh3.PNG]]

* The charge on N is -1.125 and the charge on the H is 0.375.
* As expected there is a partially negative charge on N as it is more electronegative than H.Therefore it will attract more electron density.

 

==N2==
{| class="wikitable"
!Name
|N2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-109.52412868</nowiki>
|-
!RMS Gradient (au)
|0.00000060
|-
!Point Group
|D*H
|}

<pre> Item Value Threshold Converged?
Maximum Force 0.000001 0.000450 YES
RMS Force 0.000001 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000000 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH N2 OPT POP 1.LOG| here]]

1 Vibrational mode is present for N2 at 2457.

 

==H2==
{| class="wikitable"
!Name
|H2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-1.17853936</nowiki>
|-
!RMS Gradient (au)
|0.00000017
|-
!Point Group
|D*H
|}

<pre> Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000000 0.001800 YES
RMS Displacement 0.000001 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH H2.LOG| here]]

1 Vibrational mode is present for H2 at 4466.

==Energy Calculations==

*E(NH3)=-148492.421801kJmol-1
*2*E(NH3)=-296984.843602kJmol-1
*E(N2)=-287555.599849kJmol-1
*E(H2)=-3094.25508968kJmol-1
*3*E(H2)=-9282.76526904kJmol-1
*ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-146.478602kJmol-1

===Literature value comparisons===

The reactants are more stable. The literature value is -46kJmol-1. Literature values are taken from experimental observation. There is a difference between the literature value and the quantum mechanical estimation due to several reasons. One of them being that quantum mechanical estimations do not take real world imperfections into considerations. Also when calculating literature values, there is more than one molecule present, therefore there will be collisions and interactions between the molecules, and not just an energy value for a single molecule in space.

 

=ClF3=

{| class="wikitable"
!Name
|ClF3
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-759.38175725</nowiki>
|-
!RMS Gradient (au)
|0.06637914
|-
!Point Group
|D3H
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000049 0.001800 YES
RMS Displacement 0.000032 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH CLF3.LOG| here]]

[[File:Vibclf3.PNG]]

<jmol><jmolApplet>
<title>ClF3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>MWH CLF3.LOG</uploadedFileContents>
</jmolApplet></jmol>

Charge on Cl is 1.188, charge on F is -0.395.
F is more electronegative than Cl and attracts electron density towards itself.
 
==Molecular Orbitals of ClF3==
[[File:9 mo clf3.PNG|200px]]
4 in-phase s orbitals forming a bonding orbital

[[File:13 mo clf3.PNG|200px]]
2 in-phase p orbitals can be seen on the top of the image also with the p orbital of the Cl that is perpendicular to it. The p orbital of the Cl is also in-phase with the p orbital of the F atom on the bottom. They are all sigma bonds.

[[File:15 mo clf3.PNG|200px]]
4 in-phase p orbitals creating a pi bond.

[[File:22 mo clf3.PNG|200px]]
All 3 p orbitals are out-of-phase with the p orbital of the Cl, creating an anti-bonding orbital. This is also the HOMO of this molecule.

[[File:23 mo clf3.PNG|200px]]
This is the LUMO of this molecule. It seems as if there is a sp2 hybridiesd orbital that can be seen as one of the phases is larger in size than the other.

==Cl2==

{| class="wikitable"
!Name
|Cl2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-920.34987886</nowiki>
|-
!RMS Gradient (au)
|0.00002511
|-
!Point Group
|D*H
|}

<pre> Item Value Threshold Converged?
Maximum Force 0.000043 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000121 0.001800 YES
RMS Displacement 0.000172 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH CL2.LOG| here]]

==F2==

{| class="wikitable"
!Name
|F2
|-
!Calculation Method
|RB3LYP
|-
!Basis Set
|6-31G(d,p)
|-
!Final Energy (au)
|<nowiki>-199.49825218</nowiki>
|-
!RMS Gradient (au)
|0.00007365
|-
!Point Group
|D*H
|}

<pre> Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000128 0.000300 YES
Maximum Displacement 0.000156 0.001800 YES
RMS Displacement 0.000221 0.001200 YES</pre>

The optimisation file is liked to [[Media:MWH F2.LOG| here]]

==Energy Calculations==

* E(ClF3)= -759.38175725
* 2*E(ClF3)= -1518.76351 au
* E(Cl2)= -920.34987886 au
* E(F2)=-199.49825218 au
* 3*E(F2)= -598.494757 au
* ΔE=2*E(ClF3)-[E(Cl2)+3*E(F2)]=0.08113 au = +213.006815kJmol-1

Lennarts test

2018-02-28T19:41:09Z

Lhf216:

== Lennarts trial wiki to test techniques ==
[[File:IMG 0259.JPG|thumb|left|bossman]]

Lennarts test

2018-02-28T19:40:03Z

Lhf216:

== Lennarts trial wiki to test techniques ==
[[File:IMG 0259.JPG|thumb|bossman]]

File:IMG 0259.JPG

2018-02-28T19:33:56Z

Lhf216: hiking

hiking

Lennarts test

2018-02-28T19:07:25Z

Lhf216: Created page with "== Lennarts trial wiki to test techniques =="

== Lennarts trial wiki to test techniques ==

Lennart trial

2018-02-27T14:32:27Z

Lhf216: Created page with "== Lennys trial == computational magic"

== Lennys trial ==

computational magic

Mod:Hunt Research Group/calendar

2017-12-07T20:36:01Z

Lhf216: /* Calendar */

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

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia
| Ken (Not Done)
| Becky (Done)
|-
| Sophie
|Lennart
|
|-
|
|
|
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun
|-
|16th Oct
|17th
|18th
|19th
|20th
Ken Away
| style="background: grey;" |21st
| style="background: grey;" |22nd
|-
|23rd Tricia in Spain
|24th Tricia in Spain
|25th Tricia in Spain
|26th Tricia in Spain
|27th Tricia in Spain Oxana away
| style="background: grey;" |28th
| style="background: grey;" |29th
|-
|30th
|31st
| style="background: yellow;" |1st Nov
|2nd
|3rd
| style="background: grey;" |4th
| style="background: grey;" |5th
|-
|6th
|7th
|8th
|9th
|10th Tricia at Nottingham
| style="background: grey;" |11th
| style="background: grey;" |12th
|-
|13th
|14th
|15th
|16th
|17th
| style="background: grey;" |18th
| style="background: grey;" |19th
|-
|20th
Sophie Away
|21st
|22nd
|23rd
Inyoung in Iceland
|24th
Inyoung in Iceland

Lennart in Germany
| style="background: grey;" |25th
| style="background: grey;" |26th
|-
|27th
|28th
|29th
|30th
| style="background: yellow;" |1st Dec
| style="background: grey;" |2nd
| style="background: grey;" |3rd
|-
|4th Tricia in Germany
Lennart in Germany
|5th Tricia in Germany
|6th Tricia in Germany
|7th Tricia in Germany
|8th Tricia in Germany
Ken Away
| style="background: grey;" |9th
| style="background: grey;" |10th

|-
|11st
Ken Away
|12th
Ken Away
|13th
Ken Away
|14th
|15th
| style="background: grey;" |16th
| style="background: grey;" |17th
|-
|18th
Sophie Away

Lennart in South Africa
|19th
Sophie Away

Lennart in South Africa
|20th
Sophie Away

Lennart in South Africa
|21st
Sophie Away

Lennart in South Africa
|22nd
Sophie Away

Lennart in South Africa
| style="background: grey;" |23rd
| style="background: grey;" |24th
|-
|25th
College Closed
|26th
College Closed
|27th
College Closed
|28th
College Closed
|29th
College Closed
| style="background: grey;" |30th
| style="background: grey;" |31st
|-
| style="background: yellow;" |1st Jan
College Closed
|2nd
College Open

Tricia Away

Lennart in South Africa
|3rd
Tricia Away

Lennart in South Africa
|4th
Tricia Away

Lennart in South Africa
|5th
Tricia Away

Lennart in South Africa
| style="background: grey;" |6th
| style="background: grey;" |7th
|}

Mod:Hunt Research Group/calendar

2016-12-08T11:01:38Z

Lhf216:

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

{| class="wikitable"
|-
! 1
! 2
! 3
|-
| Tricia (Not done)
|
| Becky (Done)
|-
| Richard (Not done)
| Ken (Done)
| Aiswarya (Not Done)
|-
|
| Lennart Frankemoelle (not done)
|Nukorn (Not done)
|-
|Mikkaila (Done)
|Jin (not done)
|Shijia (Not done)
|-
|-)
|}
Everyone should be away during the college closure dates, so you don't need to add your name on those days

Tricia maybe: Tricia may or may-not be in college i.e. working from home
{| class="wikitable" style="width: 100%"
!Mon
!Tue
!Wed
!Thur
!Fri
!Sat
!Sun

|-
|5th
|6th
|7th
|8th
|9th
| style="background: grey;" |10th
| style="background: grey;" |11th

|-
|12th
|13th
|14th
|15th
| style="background: yellow;" |16th End of term
| style="background: grey;" |17th
| style="background: grey;" |18th

|-
|19th
Ken away

Nukorn away

Lennart away
|20th
Ken away

Nukorn away

Lennart away
|21st
Ken away

Mikkaila Away

Nukorn away

Lennart away
|22nd
Becky away

Ken away

Mikkaila Away

Nukorn away

Lennart away
|23rd
Becky away

Ken Away

Mikkaila Away

Nukorn away

Lennart away
| style="background: grey;" |24th
| style="background: grey;" |25th

|-
| style="background: red;" |26th College closure
| style="background: red;" |27th
| style="background: red;" |28th
| style="background: red;" |29th
| style="background: red;" |30th
| style="background: grey;"|31st
| style="background: yellow;" |1st January

|-
| style="background: red;"|2nd
| style="background: red;"|3rd
|4th
Becky away

Ken away
|5th
Becky away

Ken away
|6th
Becky away

Ken away
| style="background: grey;" |7th
| style="background: grey;" |8th

|-
| style="background: yellow;" |9th Term starts
|10th
|11th
|12th
|13th
| style="background: grey;" |14th
| style="background: grey;" |15th

|-
|16th
|17th
|18th
|19th
|20th
| style="background: grey;" |21st
| style="background: grey;" |22nd

|-
|23rd
|24th
|25th
|26th
|27th
| style="background: grey;" |28th
| style="background: grey;" |29th

|-
|30th
|31st
| style="background: yellow;" |1st February
|2nd
|3rd
| style="background: grey;" |4th
| style="background: grey;" |5th

|-
|6th
|7th
|8th
|9th
|10th
| style="background: grey;" |11th
| style="background: grey;" |12th

|-
|13th
|14th
|15th
|16th
|17th
| style="background: grey;" |18th
| style="background: grey;" |19th

|}