ChemWiki - User contributions [en]

Resgrp:comp-photo-dyn/mctdh90dev/input

2008-12-11T09:25:57Z

Marobb: /* 7a. The Frank-Condon Point */

= Creating Input for Dynamics Calculations =

== MCTDH versions ==

* Current version (mctdh90dev): The input required for the dynamics calculation is an optimised ground state structure and an optimised conical intersection in the appropriate orientation . The ground state structure must have been optimised with state averaged orbitals. These orbitals must be "cleaned" and the high precision frequencies must have been calculated.

* Development version (mctdh90.31dev): The only input required for the dynamics calculation is an optimised ground state structure and an optimised conical intersection (the rotation will be "automatic"). Again, the ground state structure must have been optimised with state averaged orbitals. These orbitals must be "cleaned" and finally high precision frequencies must be calculated.

* The main objective of this tutorial is learn how to run dynamics calculations, thus we will give you the optimised geometries in the appropiate rotation. (A description of how to rotate a structure will follow in due course)

== State Averaged Orbitals==

Discussion on the necessity of using state averaged orbitals to go here. NEED TO REPRESENT BOTH GROUND AND EXCITED STATES AT THE SAME TIME. I AM NOT CLEAR WHY YOU ARE USING STATE AVERAGING AT EQUILIBRIUM GEOMETRY. NORMALLY THIS WOULD NOT BE A SENSIBLE THING TO DO.

= Gaussian Calculations - CASSCF =

== '''1. Generate a starting geometry.''' ==

First of all, we need a set of initial orbitals for the CASSCF calculation, which can be obtained from a simple restricted Hartree-Fock (RHF/STO-3G) optimization. It is useful in systems with high symmetry to start with the molecule in the standard orientation and from a symmetrised geometry. This can be achieved by running a Gaussian calculation without the nosymm keyword and using the geometry returned by this calculation.

* NB You should use the structures given in this tutorial because they are oriented appropriately.

[[Media:buta-s-orient.gjf]]

[[Media:buta-s-orient.log]]

== '''2. Identify the Orbitals Required for the CASSCF Calculation''' ==

Use the geometry from 1. Calculate the HF orbitals with a tight basis set e.g. STO-3G (so that it is easier to identify the relevant orbitals for CASSCF).

Keywords: '''HF/STO-3G pop=full nosymm geom=check'''

* Nosymm is required because every time a calculation is run on the molecule with a different symmetry Gaussian reorients the molecule for that particular point group and will destroy the active space. Nosymm disables this feature.
* Pop=full prints out the orbitals.
* Inspect the orbitals. Select those required for the CASSCF.

[[Media:buta-hf.gjf]]

[[Media:buta-hf.log]]

[[Media:buta-hf.fchk]]

== '''3. Identify the State Averaged Orbitals for the Ground State''' ==

An orbital inspection using any visualization software before performing any CASSCF calculation is essential to identify which orbitals make up the chosen active space. In some cases it may be necessary to use '''guess=alter''' to change the order of the orbitals to make sure the optimisation (see step 4) proceeds with the correct orbitals. Gaussian assumes that the electrons specified in a CASSCF calculation come from the highest occupied orbitals in the initial guess and then takes the remaining orbitals as the lowest virtuals of this guess.

* In this example, the relevant orbitals are the four pi orbitals, which contain four electrons (so the calculation is 4,4). The four orbitals that form the pi molecular orbitals are 14, 15, 16 and 17, thus we do not have to worry about swapping orbitals with the keword ''alter''.

Use the orbitals chosen in 2. (i.e. use the .chk from 2.) Use the final geometry from 2.

Keywords: '''CAS(4,4,nroot=2,stateaverage) STO-3G nosymm IOP(5/97=100,10/97=100) guess=read'''

Here, the weights of each state must be listed explicitly. The weights are 0.5 and 0.5. These must be specified by typing 0.5 followed by 7 spaces then 0.5 (on the same line) (The Gaussian program reads 10 characters (inc spaces) for the first weight and another 10 characters for the second weight. Thus the 7 spaces plus the three characters "0", "." and "5" make up the first 10 characters before the second weight is read.) This line must be repeated as many times as there are to be SCF cycles. Since this quantity is unknown, simply repeat the line many times (it may be repeated more than the number of SCF cycles).

* The IOp (5/97=100,10/97=100) tells the program to switch the order of the two states. This is so that we calculate the ground state rather than the excited state. (Gaussian CASSCF calculations always perform optimisations on the highest state listed, so by switching the order we force optimisation of what is actually the lower state.)
* Nroot=2 specifies the ''first'' excited state so the orbitals will averaged over the ground state and the first excited state.

* Inspect the orbitals. Select those required for the CASSCF optimisation. The relevant orbitals are still 14, 15, 16 and 17.

[[Media:buta-orbs-sa.gjf]]

[[Media:buta-orbs-sa.log]]

[[Media:buta-orbs-sa.fchk]]

== '''4. Perform a CASSCF Optimisation on the Ground State with the State Averaged Orbitals''' ==

Use the orbitals chosen in 3. Use the .chk from 3.

Keywords: '''opt=conical pop=full CAS(4,4,nroot=2,stateaverage) STO-3G nosymm IOP(10/10=700005) IOP(5/97=100,10/97=100) geom=checkpoint guess=read'''

N.B. This is not a conical intersection optimisation! However, the keyword opt=conical specifies automatically that the populations of the two states will each be 0.5. Thus there is no need to specify the populations manually (which can be tedious). The initial '7' in IOp (10/10=700005) specifies that the calculation should be an optimisation to a minimum (rather than a conical intersection). The final '5' ensures that the orbital rotation derivative contributions from the CP-MC-SCF equations are included. (This is necessary and is usually the default. However, in the current version of Gaussian, the combination of '''opt''' and '''stateaverage''' excludes this).
Stateaverage is the default for opt=conical.
Nroot=2 is the default for opt=conical.
Do not include the keyword '''freq''' in the optimisation. (This combination of IOps does not allow '''opt''' and '''freq''' to be keywords in the same job.)

[[Media:buta-cas.gjf]]

[[Media:buta-cas.log]]

== '''5. "Clean" the Orbitals''' ==

In this case, all the orbitals in the active space are pure pi orbitals. Due to small numerical inaccuracies, the final orbitals may include small contributions from other (non-pi) orbitals. The aim of this step is to remove these contributions so that the active space consists (in this example) only of contributions from the C 2PY atomic orbitals. The four relevant orbitals are occupied orbitals 14 and 15 and virtual orbitals 16 and 17. In fact, they are already clean in this example. Verify this by inspection of the "Molecular Orbital Coefficients" in the population analysis.

In other cases, multiple optimisations may be necessary to clean the orbitals:

Open the file in GaussView, and Edit/Symmetrize. Use this symmetrised geometry as a starting geometry for another optimsation as in 4 (including the keyword '''nosymm''').
Use the .chk from 4.
Re-run the optimisation exactly as in 4.

''Ideally here we include the keyword '''opt=(maxstep=1)'''. This should ensure that the optimisation takes the smallest possible step: we already know that the geometry is very close to the minimum and we need to prevent any significant re-orientation that might occur if large steps are taken. However, this does not seem to work (at least with g03).''

Repeat until the orbitals are clean.

== '''6. Calculate the (High Precision) Vibrational Modes for the Ground State ''with State Averaged Orbitals''''' ==

Use the .chk and the geometry from 5. The geometry must be specified explicitly. (With this combination of IOPs, Gaussian extracts the wrong geometry from the .chk file if '''geom=checkpoint''' is specified.)

Keywords: '''CAS(4,4,nroot=2) STO-3G freq=hpmodes guess=read IOP(5/17=41000200,10/10=700007) IOP(5/97=100,10/97=100)'''

The IOp (5/17=41000200,10/10=700007): includes the CP-MC-SCF correction (as above) (for a frequency calculation); and specifies state averaged orbitals. Do not include the keyword '''stateaverage''' with '''freq''' (the current version of Gaussian does not support this). Freq=hpmodes tells Gaussian to print the vibrational modes to 5 decimal places. As before, the IOp (5/97=100,10/97=100) forces calculation of the ground state. Do not use the keyword nosymm here. (Nosymm may prevent Gaussian from identifying the symmetries of the orbitals.)

[[Media:buta-hpfreq.gjf]]

[[Media:buta-hpfreq.log]]

== '''7. The Conical Intersection''' ==

One strategy for locating the conical intersection is to calculate the Frank-Condon point and run an optimisation from there, following (one of) the negative frequency(ies).

=== 7a. The Frank-Condon Point ===

Use the .chk from 4. Using the same orbitals perform a single point energy calculation for the first excited state.

Keywords: '''CAS(4,4,nroot=2,stateaverage) STO-3G pop=full nosymm guess=read geom=checkpoint'''

As in 3, the weights of each state must be listed explicitly. The weights are 0.5 and 0.5. These must be specified by typing 0.5 followed by 7 spaces then 0.5 (on the same line) ''(The Gaussian program reads 10 characters (inc spaces) for the first weight and another 10 characters for the second weight. Thus the 7 spaces plus the three characters "0", "." and "5" make up the first 10 characters before the second weight is read.)'' This line must be repeated as many times as there are to be SCF cycles. NO ONLY READ ONCE! Since this quantity is unknown, simply repeat the line many times (it may be repeated more than the number of SCF cycles).

[[Media:buta-fc.gjf]]

[[Media:buta-fc.log]]

=== 7b. Calculate the frequencies ===

Use the .chk and the geometry from 7a. The geometry must be specified explicitly. (With this combination of IOPs, Gaussian extracts the wrong geometry from the .chk file if '''geom=checkpoint''' is specified.)

Keywords: '''CAS(4,4,nroot=2) STO-3G nosymm freq guess=read IOP(5/17=41000200,10/10=700007)'''

The IOp (5/17=41000200,10/10=700007): includes the CP-MC-SCF correction (as above) (for a frequency calculation); and specifies state averaged orbitals. Do not include the keyword '''stateaverage''' with '''freq''' (the current version of Gaussian does not support this).

Identify the negative vibration leading to the conical intersection. Distort the geometry along this mode (Gaussview 4 will let you save the geometry) to get a starting geometry for a conical intersection optimsation.

[[Media:butafcfreq.gjf]]

[[Media:butafcfreq.log]]

=== 7c. Optimising the Conical Intersection ===

Use the .chk and the starting geometry obtained from 7b.

Keywords: '''CAS(4,4,nroot=2,stateaverage) STO-3G opt=conical pop=full nosymm guess=read'''

Stateaverage is the default for opt=conical.
Nroot=2 is the default for opt=conical.

Resgrp:comp-photo-dyn/mctdh90dev/install/cluster

2008-12-04T11:03:49Z

Marobb: /* Installing the program as an user */

= Installing the program as an user =

*First of all, to install the MCTDH package you have to go login to your cluster account.

ssh USERNAME@login.cx1.hpc.ic.ac.uk

* You should now be logged into your $HOME directory (/home/$USER). Make a backup of your bash profile. During the installation of the MCTDH package your bash profile will be changed, thus saving it is a good preventive measure:

cp .bachrc .bashrc_{{CURRENTDAY}}_{{CURRENTMONTH}}_{{CURRENTYEAR}}

* We are going to install the MCTDH package version 90dev. The installation script is in the following folder: /home/gaussian-devel/mctdh/mctdh90dev, this directory will be termed the MCTDH directory during this tutorial.

* Go to this folder:

cd /home/gaussian-devel/mctdh/mctdh90dev

* Inside the install folder type:

./install_mctdh -u

The option "-u" is in order to add you as a new user to the already installed package.
This install script can be stopped any time with "Ctrl C", thus if you think you have made a wrong choice, just run it again!

* The install script asks a few simple questions, and automatically generates the executables and documentation:

1) The script requests your permission to modify your .bashrc profile.

For your convenience I will write some statements to your
configuration files
(i.e. to ~/.profile or ~/.bashrc or ~/.cshrc or ~/.kshrc).
"Your old ~/.XXX configuration file will be saved to ~/.save-XXX-$$."

Choose: b) write the commands to my ~/.bashrc file
(for bash users).
Or : c) rather write them to my ~/.cshrc file
(for csh and tcsh users).'
Or : k) rather write them to my ~/.kshrc file
(kcsh users).
Or : p) please, rather write them to my ~/.profile file.
(alternative for ksh and bash users (not recommended)).
Or : y) yes, write the commands to my ~/.bashrc file.
(same as b))
Or : n) no, do not touch my configuration files.

(b|c|k|p|y|n) ? :

Please answer "b", "c", "k", "p", or "y" or "n"'

* Answer "yes"

2) The script requests your permission to copy the file .mctdhrc to your $HOME directory.

The file mctdhrc may be copied to $HOME/.mctdhrc.
The .bashrc will then source .mctdhrc.
Doing so, the bash-functions cdm and minstall will be available
and a link $HOME/mctdh -> $MCTDH_DIR will be installed.

Shall I copy mctdhrc to $HOME/.mctdhrc (y/n) ? :

* Answer "yes"

* If the installation has been successful, you should see the message:

--------------------------------------------------------------------------------

***** END OF NEW USER INSTALLATION *****
--------------------------------------------------------------------------------

* At the end of the installation process, don't forget to source your .bashrc in order to set some environment variables. In your $HOME directory type:

source .bashrc

When the .bashrc is sourced, the the hidden file .mctdhrc will then be sourced as well. The .mctdhrc script sets the link mctdh -> /home/gaussian-devel/mctdh/mctdh90dev, and defines the bash-function cdm and menv.

* Now you should notice that:

# A link to the folder /home/gaussian-devel/mctdh has been created in your HOME directory.
# Now you have two new commands:

cdm: the command cdm cd-es to /home/gaussian-devel/mctdh/mctdh90dev and any subdirectory

menv: the MCTDH environment variables are listed

dd_generator: script which allows to create the required files to run dynamics calculation. The script asks a few simple questions, and automatically generates all the necessary files.

Resgrp:comp-photo-dyn/mctdh90dev/run/cluster

2008-12-04T10:49:46Z

Marobb: /* '''Gaussian Output to be Used as Input for the Dynamics Program''' */

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

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

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

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

mkdir buta

* Therefore, you should have:

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

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

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

and

/work/$USER/buta/dd_data

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

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

* Populate the new directory in /work/$USER/but/dd_data with four files which must be named: '''coin.log'''; '''start.fchk'''; '''start.log'''; and '''template''' (no extension). These files are requested in order to run any dynamics simulation, they are the basis that the script dd_generator will use to create the necessary files for running MCTDH.

'''coin.log''' is the logfile resulting from the optimisation of the conical intersection (Part A, 7). NB The optimised conical intersection must be rotated prior to running the dynamics. There is an Excel spreadsheet available to effect this transformation. After the rotation the structure should be re-optimised (in most cases it will not move but it is sensible to check the Gaussian output to verify that it has not been re-rotated during the final optimisation (otherwise repeat the rotation and optimisation until there is no further rotation during the optimisation). I SEE PROBLEMS HERE. IF YOU ROTATE THEN PREVIOUS GUESS IS RUBBISH.

[[Media:coin.log]]

(Here will be a link to how make the rotation)

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

[[Media:start.fchk]]

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

[[Media:start.log]]

'''template''' is a template gaussian input file to be used by the dynamics program (For example, use the input file from the high precision vibrational modes of the ground state with state averaged orbitals (Part A, 6)). The file '''template''' will be the template for the creation of GAUSSIAN inputs, it must contain all the mutual keywords of the GAUSSIAN calculations which will be run on the fly by MCTDH.

[[Media:template.noext]]

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

* The "generator" script uses the Gaussian output files from 2 along with other information supplied by the user to create input files for the dynamics program.

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

dd_generator

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

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

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

==== List of questions ====

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

<tr><td> '''Question''' </td> <td> '''Recommended answer''' </td> </tr>
<tr><td> '''Which version of GAUSSIAN should we use? (gdv|g03)''' </td> <td> * g03 </td> </tr>
<tr><td> '''How many processors should we use? (1|2|4)'''' </td> <td> * 1 </td> </tr>
<tr><td> '''What is the name of the molecule?''' </td> <td> * butadiene ''(the first four letters will be used to name the new files that the generator is creating)'' </td> </tr>
<tr><td> '''What is the number of atoms?''' </td> <td> * 10 </td> </tr>
<tr><td> '''What is the number of nuclear Gaussian functions?''' </td> <td> * 1 </td> </tr>
<tr><td> ''''What is the final propagation time (in fs)?'''</td> <td> * 100 </td> </tr>
<tr><td> '''What is the propagation time step (in fs)?'''</td> <td> * 0.1 </td> </tr>
<tr><td> '''From which electronic state should the wavepacket start? (2|1)''''</td> <td> * 2 </td> </tr>
<tr><td> '''Will there be an initial momentum given to the wavepacket? (y|n)'''</td> <td> * n </td> </tr>
<tr><td> '''Do you want to add a reference label to the name of the case? (y|n)'''</td> <td> * y </td> </tr>
<tr><td> '''Please type your text:'''</td> <td> * trial ''(NB remember to keep this short to prevent the total path becoming too long))'' </td> </tr>
<tr><td> '''What will be the status of the database? (rdwr|rd|wr|none)'''</td> <td> * none </td> </tr>

</table>
</blockquote>

* Choose rd for read, wr for write etc.
* In this case we are not going to use the data base, but if it was used (rd or rdwr is specified) the script would ask the user to specify the threshold below which the database values will be used (% criterion). In this case the value none is chosen so this question is not asked.

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

<tr><td> '''Please type the value of the maximum-difference criterion (in %):'''</td> <td> * 1 (if 1 is specified, the database value will be used if the geometry is within 1% of the new geometry being calculated) </td> </tr>

</table>
</blockquote>

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

* At the end the script dd_generator tells you that has read the files start.fchk, start.log, and coin.log from the folder /work/dm107/dyn/dd_data/ and written the file start.chk.

<pre>
Read formatted file /work/dm107/dyn_90dev/dd_data/start.fchk
Write checkpoint file /work/dm107/dyn_90dev/dd_data/start.chk
about to read parameters...
... parameters just read
about to read file /work/dm107/dyn_90dev/dd_data/start.log
...
... file /work/dm107/dyn_90dev/dd_data/start.log
read successfully
about to read file /work/dm107/dyn_90dev/dd_data/coin.log
...
... file /work/dm107/dyn_90dev/dd_data/coin.log
read successfully
</pre>

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

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

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

Do not forget to use a re-orientated conical intersection in /work/dm107/dyn_90dev/dd_data/coin.log

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

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

Good luck!
</pre>

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

# but1dd1o.inp
# but1dd1o.job
# but1dd1o.txt
# but1dd_wr.op

(Link to a more detailed explanation of this files)

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

1) Directories:

* butadd1o_trial
* butadd1o_trial/dd_data

2) Files (Inside butadd1o_trial/dd_data):

# refdb.dat
# start.chk
# template

3) Files inside /work/$USER/but/dd_data

backward.dat
forward.dat

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

* The log file

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

* The output file

The output contains some standard results:

Time: time in fs.
CPU: CPU time in fs.
Norm:
E-tot: the total energy. This value should be relatively conserved.
E-corr: correlated Hamiltonian energy
Delta-E: diference between E-tot at time t=0 and the current time t

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

For each state:

pop.: state population
E-corr:
E-tot

For every mode:

Position expectation value <q>
standard deviation Sqrt[<q**2>-<q>**2]
Momentum expectation value <p>
standard deviation Sqrt[<p**2>-<p>**2]

At the end of the propagation, the total CPU-time, host, date and time, path of the name-directory and (if specified in the input) the title of the run are printed.

=='''Some modifications must be made to the files before running the dynamics.'''==

* In the .job file in /home/$USER/but specify the memory and walltime.

* In the file named ''template'' in /work/$USER/but/butadd1o_trial/dd_data, complete the pathname to match its location. In this case the path should be /work/$USER/but/butadd1o_trial/dd_data.

* Only in the case of running gdv, copy the start.chk file into the folder /work/$USER/dyn_90dev/but1dd1o/dd_data

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

* Navigate to $HOME/but. Queue the job file. In this case, type:

qsub butadd1o_trial.job

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

()

Resgrp:comp-photo-dyn/mctdh90dev/run/cluster

2008-11-25T13:34:00Z

Marobb: /* Inside your $HOME */

= Basic use of the MCTDH package=

* First of all, you have to create a folder where to save the calculations in your $HOME and $WORK directories.

mkdir dynamycs

You have to do it in $HOME and $WORK directories. Therefore, you should have:

/home/$USER/dynamics
/work/$USER/dynamics

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

== Inside your $WORK ==

* Create a folder called dd_data in the dynamics ($WORK) directory

mkdir dd_data

* Copy the following file named template.dat NO IDEA WHAT THIS MEANS?

* Copy the GAUSSIAN output and checkpoint file of the initial structure as start.log, start.chk, respectively.

* Format the start.chk file. WHERE HAS THIS COME FROM? WHAT COMPUTATION DOES IT CORRESPOND TO?

formchk start.chk start.fchk

* Copy the log file of the conial intersection in the same directory with the name coin.log NOT CLEAR AT ALL
DO YOU MEAN SINGLE POINT, OPTIMIZATION OR WHAT

== Inside your $HOME ==

* Copy the script dd_generator, dd_filegen.f and dd_filegen.out to the bin folder in your $HOME directory.

* Inside the dynamics folder ($HOME). Type dd_generator to run the script. NEED TO EXPLAIN WHAT THIS IS. COPY FROM WHERE?

dd_generator

* The script generator will run. This scipt generates all the necessary files to run the dynamics simulation. It will ask you several questions:

# Version
# processors
# name
# atoms
# gauss func
# max time
Tells version
# step
# state
# high root
# start
# momentum
# label
# base

* The dd_generator script has generated four files in the same directory

# name.inp
# name.job
# name. txt
# name.op

* Now before launching the job to the qsub, you need to define the memory and time.

* Send the job to the qsub system.

qsub name.job

Resgrp:comp-photo-dyn/mctdh90dev/run/cluster

2008-11-25T13:32:48Z

Marobb: /* Inside your $WORK */

= Basic use of the MCTDH package=

* First of all, you have to create a folder where to save the calculations in your $HOME and $WORK directories.

mkdir dynamycs

You have to do it in $HOME and $WORK directories. Therefore, you should have:

/home/$USER/dynamics
/work/$USER/dynamics

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

== Inside your $WORK ==

* Create a folder called dd_data in the dynamics ($WORK) directory

mkdir dd_data

* Copy the following file named template.dat NO IDEA WHAT THIS MEANS?

* Copy the GAUSSIAN output and checkpoint file of the initial structure as start.log, start.chk, respectively.

* Format the start.chk file. WHERE HAS THIS COME FROM? WHAT COMPUTATION DOES IT CORRESPOND TO?

formchk start.chk start.fchk

* Copy the log file of the conial intersection in the same directory with the name coin.log NOT CLEAR AT ALL
DO YOU MEAN SINGLE POINT, OPTIMIZATION OR WHAT

== Inside your $HOME ==

* Copy the script dd_generator, dd_filegen.f and dd_filegen.out to the bin folder at your $HOME directory.

* Inside the dynamics folder ($HOME). Type dd_generator to run the script.

dd_generator

* The script generator will run. This scipt generates all the necessary files to run the dynamics simulation. It will ask you several questions:

# Version
# processors
# name
# atoms
# gauss func
# max time
Tells version
# step
# state
# high root
# start
# momentum
# label
# base

* The dd_generator script has generated four files in the same directory

# name.inp
# name.job
# name. txt
# name.op

* Now before launching the job to the qsub, you need to define the memory and time.

* Send the job to the qsub system.

qsub name.job

Resgrp:comp-photo-dyn/mctdh90dev/input

2008-11-25T09:38:18Z

Marobb: /* Part b: The Conical Intersection */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...

== Creating Input for Dynamics Calculations. Example: Butadiene.==

The only input required for the dynamics calculation is an optimised ground state structure. This structure must have been optimised with state averaged orbitals. These orbitals must be "cleaned" and finally high precision frequencies must be calculated. NOT TRUE YOU NEED OPTIMIZED CI IN ORDER TO GET DIAMATIZATION!

== Part a: The Ground State ==

MY COMMENTS IN UPPER CASE MAR

JUST A GENERAL COMMENT THAT I WILL ELABORATE ON BELOW. I THINK THE BEST STRATEGY IS ALWAYS TO DETERMINE THE STARTING SET OF ORBITALS IN ONE JOB STEP. AND THEN WHEN ONE IS CERTAIN THAT THIS IS CORRECT THEN THE OPTIMISATION CAN BEGIN. ALSO SOME DISCUSSION ABOUT STATE AVERAGING IS ESSENTIAL SINCE DOING A CALCULATION OF A MINIMUM GEOMETRY WITH THE ENERGY GAP MAY BE LARGE, ONE WOULD NOT NORMALLY USE STATE AVERAGE ORBITALS. YOU ARE USING A SPECIAL STRATEGY HERE FOR DYNAMICS BECAUSE YOU NEED TO REPRESENT BOTH GROUND AND EXCITED STATES AT THE SAME TIME.

'''1. Optimise the Ground State Structure (at a low level) to Identify the Orbitals Required for the CASSCF Calculation (see step 2)'''

Keywords: '''opt HF/STO-3G pop=full nosymm'''

Nosymm is required to ensure that the molecule is not re-orientated during the optimisation (this would destroy the active space).
Pop=full prints out the orbitals.
THIS IS A LITTLE BIT CONFUSING. THE TITLE IMPLIES SOMETHING TO DO WITH THE ORBITALS. AND I AGREE THAT ONE SHOULD DO THE INITIAL SELECTION OF THE CASSCF WINDOW USING A MINIMAL BASIS. BUT SURELY YOU WANT TO START THE DYNAMICS FROM A GOOD GROUND STATE OPTIMISED GEOMETRY AND THIS IS INDEPENDENT OF THE SELECTION OF THE ORBITALS. SO IT SEEMS TO ME THERE ARE TWO TASKS: ONE TO GET ESSENTIAL STARTING GEOMETRY AND THAT HAS NOTHING TO DO WITH CASSCF AND THEN THERE IS THE ISSUE OF CHOOSING THE STARTING ORBITALS AND THIS CAN BE DONE WITH THE MINIMUM BASIS. BUT YOU HAVE REALLY SAID ALMOST NOTHING ABOUT THIS.

'''2a. Perform a CASSCF Optimisation on the Ground State ''with State Averaged Orbitals'''''

Use the .chk from 1. Verify that the required orbitals are the two HOMOs and the two LUMOs. I'M QUITE NERVOUS ABOUT THIS STATEMENT. EVEN IN A MINIMUM BASIS THE ORBITALS MAY REQUIRE SOME THOUGHT. THE POINT REALLY IS THAT YOU NEED TO LOOK AT THE ORBITALS THAT HAVE COME FROM WHATEVER GUESS YOU ARE USING. AND YOU HAVE NOT SAID ANYTHING ABOUT INSPECTING THE GUESTS. (IN OTHER WORDS YOU NEED TO STOP THE CALCULATION AFTER THE GUESS, MAKE SURE THE ORBITALS ARE SAVED TO THE CHECKPOINT FILE ETC)It may be necessary in some cases to use guess=alter to change the order of the orbitals to make sure the desired orbitals are listed as the two HOMOs and two LUMOs. (Gaussian will use the two HOMOs and the two LUMOs in the CASSCF calculation.) In this case the orbitals are in the correct order. The relevant orbitals are the four pi orbitals, which contain four electrons (so the calculation is 4,4). Nroot=2 specifies the ''first'' excited state so the state averaged orbitals will be constructed for this state and the ground state.I GUESS THIS TYPE OF DISCUSSION AT THE END NEEDS TO GO AT THE BEGINNING.

Keywords: '''opt=conical CAS(4,4,nroot=2,stateaverage) STO-3G nosymm IOP(10/10=700005) IOP(5/97=100,10/97=100) geom=checkpoint guess=read'''

N.B. This is not a conical intersection optimisation! However, the keyword opt=conical specifies that the populations of the two states will each be 0.5, automatically. Thus there is no need to specify the populations manually (which can be tedious). The IOp (5/97=100,10/97=100) tells the program to switch the order of the two states. This is so that we optimise the ground state (rather than the excited state). Gaussian CASSCF calculations always perform optimisations on the highest state listed so by switching the order we force optimisation of what is actually the lower state. The initial '7' in IOp (10/10=700005) specifies that the calculation should be an optimisation to a minimum (rather than a conical intersection). The final '5' ensures that the orbital rotation derivative contributions from the CP-MC-SCF equations are included. (This is necessary and is usually the default. However, in the current version of Gaussian, the combination of '''opt''' and '''stateaverage''' excludes this).
Stateaverage is the default for opt=conical.
Nroot=2 is the default for opt=conical.
Do not include the keyword freq in the optimisation: perform a separate freq calculation (This combination of IOps does not allow '''opt''' and '''freq''' to be keywords in the same job.)

I AM NOT CLEAR WHY YOU ARE USING STATE AVERAGING AT EQUILIBRIUM GEOMETRY. NORMALLY THIS WOULD NOT BE A SENSIBLE THING TO DO.

BUT AGAIN I WOULD ALWAYS THINK OF THE BEST STRATEGY WOULD BE TO PERFORM A CALCULATION AT SOME GEOMETRY AND VERIFY THAT THE ACTIVE ORBITAL SET WAS CORRECT BEFORE BEGINNING A GEOMETRY OPTIMISATION. SO PROBABLY THIS LITTLE SECTION MIGHT BE DIVIDED INTO TWO.

'''3a. "Clean" the Orbitals'''

Use the .chk from 2a.

Keywords: '''opt=(conical,stepsize=1) CAS(4,4,nroot=2,stateaverage) STO-3G nosymm IOP(10/10=700005) IOP(5/97=100,10/97=100) geom=checkpoint guess=read'''

Open the file in GaussView, and Edit/Symmetrize. Use this symmetrised geometry as a starting geometry for another optimsation as in 2a (including the keyword '''nosymm'''). The only difference is that here we include the keyword '''opt=(stepsize=1)'''. This ensures that the optimisation takes the smallest possible step: we already know that the geometry is very close to the minimum and we need to prevent any significant re-orienting that might occur if large steps are taken. Repeat until the orbitals are clean (check by verifying the relevant orbitals in the population analysis). In this case the 4 relevant orbitals are occupied orbitals 14 and 15 and virtual orbitals 16 and 17. By the final optimisation they should consist only of contributions from the C 2PZ atomic orbitals.

'''4a. Calculate the (High Precision) Vibrational Modes for the Ground State ''with State Averaged Orbitals'''''

Use the .chk from 3a.

Keywords: '''CAS(4,4,nroot=2) STO-3G nosymm freq=hpmodes guess=read geom=checkpoint IOP(5/17=41000200,10/10=700007) IOP(5/97=100,10/97=100)'''

The IOp (5/17=41000200,10/10=700007): includes the CP-MC-SCF correction (as above); and specifies state averaged orbitals. Do not include the keyword '''stateaverage''' with '''freq''' (the current version of Gaussian does not support this). Freq=hpmodes tells Gaussian to print the vibrational modes to 5 decimal places. As before, the IOp (5/97=100,10/97=100) forces calculation of the ground state.

== Part b: The Conical Intersection ==

IN THIS MOLECULE YOU MIGHT ALSO TRY TO RUN AN IRC FROM THE FRANCK CONDON GEOMETRY. IT SHOULD TERMINATE ON THE COMICAL INTERSECTION

'''2b. Perform a CASSCF Optimisation on the Ground State'''

Use the .chk from 1. Verify that the required orbitals are the two HOMOs and the two LUMOs. It may be necessary in some cases to use guess=alter to change the order of the orbitals to make sure the desired orbitals are listed as the two HOMOs and two LUMOs. (Gaussian will use the two HOMOs and the two LUMOs in the CASSCF calculation.)

AGAIN THE TERMINOLOGY IS NOT VERY PRECISE. THE TERMS HOMO AND LUMO NORMALLY RELATED TO ENERGIES COMPUTED BY SCF. YOU MEAN SOMETHING DIFFERENT. YOU ARE USING THE TERM TO RELATE TO THE POSITION OF THE ORBITALS AFTER THEY HAVE BEEN REORDERED POSSIBLY.

Keywords: '''CAS(4,4,nroot=1) STO-3G pop=full nosymm opt guess=read geom=checkpoint'''

I WOULD SAY THAT STARTING FROM A GROUND STATE CASSCF IS NORMALLY A VERY BAD STRATEGY. BUT MORE IMPORTANT YOU ARE MIXING UP TO STRATEGIC ISSUES: CHOOSING THE ACTIVE SPACE, AND DOING THE OPTIMISATION. SO I SUGGEST THAT IN THE PREVIOUS SECTION YOU WRITE SOMETHING GENERALLY ABOUT CHOOSING THE ACTIVE SPACE AND THAT STRATEGY IS THE SAME EVERYWHERE. AND IN THIS SECTION YOU CONCENTRATE ON THE CONICAL INTERSECTION OPTIMISATION. HERE THE BIG ISSUE IS TO GET THE STARTING GEOMETRY. IN THIS CASE PROBABLY AN MEP IS THE BEST STRATEGY.

Nroot=1 is the default for opt.

'''3b.Perform a CASSCF Conical Intersection (CI) Optimisation'''

Use the .chk from 2b for the orbital guess. It may be necessary to use a starting geometry close to the desired CI geometry.

Keywords: '''CAS(4,4,nroot=2,stateaverage) STO-3G nosymm opt=conical guess=read'''

Stateaverage is the default for opt=conical.
Nroot=2 is the default for opt=conical.

Resgrp:comp-photo-dyn/mctdh90dev/input

2008-11-25T09:31:02Z

Marobb: /* Part a: The Ground State */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...

== Creating Input for Dynamics Calculations. Example: Butadiene.==

The only input required for the dynamics calculation is an optimised ground state structure. This structure must have been optimised with state averaged orbitals. These orbitals must be "cleaned" and finally high precision frequencies must be calculated. NOT TRUE YOU NEED OPTIMIZED CI IN ORDER TO GET DIAMATIZATION!

== Part a: The Ground State ==

MY COMMENTS IN UPPER CASE MAR

JUST A GENERAL COMMENT THAT I WILL ELABORATE ON BELOW. I THINK THE BEST STRATEGY IS ALWAYS TO DETERMINE THE STARTING SET OF ORBITALS IN ONE JOB STEP. AND THEN WHEN ONE IS CERTAIN THAT THIS IS CORRECT THEN THE OPTIMISATION CAN BEGIN. ALSO SOME DISCUSSION ABOUT STATE AVERAGING IS ESSENTIAL SINCE DOING A CALCULATION OF A MINIMUM GEOMETRY WITH THE ENERGY GAP MAY BE LARGE, ONE WOULD NOT NORMALLY USE STATE AVERAGE ORBITALS. YOU ARE USING A SPECIAL STRATEGY HERE FOR DYNAMICS BECAUSE YOU NEED TO REPRESENT BOTH GROUND AND EXCITED STATES AT THE SAME TIME.

'''1. Optimise the Ground State Structure (at a low level) to Identify the Orbitals Required for the CASSCF Calculation (see step 2)'''

Keywords: '''opt HF/STO-3G pop=full nosymm'''

Nosymm is required to ensure that the molecule is not re-orientated during the optimisation (this would destroy the active space).
Pop=full prints out the orbitals.
THIS IS A LITTLE BIT CONFUSING. THE TITLE IMPLIES SOMETHING TO DO WITH THE ORBITALS. AND I AGREE THAT ONE SHOULD DO THE INITIAL SELECTION OF THE CASSCF WINDOW USING A MINIMAL BASIS. BUT SURELY YOU WANT TO START THE DYNAMICS FROM A GOOD GROUND STATE OPTIMISED GEOMETRY AND THIS IS INDEPENDENT OF THE SELECTION OF THE ORBITALS. SO IT SEEMS TO ME THERE ARE TWO TASKS: ONE TO GET ESSENTIAL STARTING GEOMETRY AND THAT HAS NOTHING TO DO WITH CASSCF AND THEN THERE IS THE ISSUE OF CHOOSING THE STARTING ORBITALS AND THIS CAN BE DONE WITH THE MINIMUM BASIS. BUT YOU HAVE REALLY SAID ALMOST NOTHING ABOUT THIS.

'''2a. Perform a CASSCF Optimisation on the Ground State ''with State Averaged Orbitals'''''

Use the .chk from 1. Verify that the required orbitals are the two HOMOs and the two LUMOs. I'M QUITE NERVOUS ABOUT THIS STATEMENT. EVEN IN A MINIMUM BASIS THE ORBITALS MAY REQUIRE SOME THOUGHT. THE POINT REALLY IS THAT YOU NEED TO LOOK AT THE ORBITALS THAT HAVE COME FROM WHATEVER GUESS YOU ARE USING. AND YOU HAVE NOT SAID ANYTHING ABOUT INSPECTING THE GUESTS. (IN OTHER WORDS YOU NEED TO STOP THE CALCULATION AFTER THE GUESS, MAKE SURE THE ORBITALS ARE SAVED TO THE CHECKPOINT FILE ETC)It may be necessary in some cases to use guess=alter to change the order of the orbitals to make sure the desired orbitals are listed as the two HOMOs and two LUMOs. (Gaussian will use the two HOMOs and the two LUMOs in the CASSCF calculation.) In this case the orbitals are in the correct order. The relevant orbitals are the four pi orbitals, which contain four electrons (so the calculation is 4,4). Nroot=2 specifies the ''first'' excited state so the state averaged orbitals will be constructed for this state and the ground state.I GUESS THIS TYPE OF DISCUSSION AT THE END NEEDS TO GO AT THE BEGINNING.

Keywords: '''opt=conical CAS(4,4,nroot=2,stateaverage) STO-3G nosymm IOP(10/10=700005) IOP(5/97=100,10/97=100) geom=checkpoint guess=read'''

N.B. This is not a conical intersection optimisation! However, the keyword opt=conical specifies that the populations of the two states will each be 0.5, automatically. Thus there is no need to specify the populations manually (which can be tedious). The IOp (5/97=100,10/97=100) tells the program to switch the order of the two states. This is so that we optimise the ground state (rather than the excited state). Gaussian CASSCF calculations always perform optimisations on the highest state listed so by switching the order we force optimisation of what is actually the lower state. The initial '7' in IOp (10/10=700005) specifies that the calculation should be an optimisation to a minimum (rather than a conical intersection). The final '5' ensures that the orbital rotation derivative contributions from the CP-MC-SCF equations are included. (This is necessary and is usually the default. However, in the current version of Gaussian, the combination of '''opt''' and '''stateaverage''' excludes this).
Stateaverage is the default for opt=conical.
Nroot=2 is the default for opt=conical.
Do not include the keyword freq in the optimisation: perform a separate freq calculation (This combination of IOps does not allow '''opt''' and '''freq''' to be keywords in the same job.)

I AM NOT CLEAR WHY YOU ARE USING STATE AVERAGING AT EQUILIBRIUM GEOMETRY. NORMALLY THIS WOULD NOT BE A SENSIBLE THING TO DO.

BUT AGAIN I WOULD ALWAYS THINK OF THE BEST STRATEGY WOULD BE TO PERFORM A CALCULATION AT SOME GEOMETRY AND VERIFY THAT THE ACTIVE ORBITAL SET WAS CORRECT BEFORE BEGINNING A GEOMETRY OPTIMISATION. SO PROBABLY THIS LITTLE SECTION MIGHT BE DIVIDED INTO TWO.

'''3a. "Clean" the Orbitals'''

Use the .chk from 2a.

Keywords: '''opt=(conical,stepsize=1) CAS(4,4,nroot=2,stateaverage) STO-3G nosymm IOP(10/10=700005) IOP(5/97=100,10/97=100) geom=checkpoint guess=read'''

Open the file in GaussView, and Edit/Symmetrize. Use this symmetrised geometry as a starting geometry for another optimsation as in 2a (including the keyword '''nosymm'''). The only difference is that here we include the keyword '''opt=(stepsize=1)'''. This ensures that the optimisation takes the smallest possible step: we already know that the geometry is very close to the minimum and we need to prevent any significant re-orienting that might occur if large steps are taken. Repeat until the orbitals are clean (check by verifying the relevant orbitals in the population analysis). In this case the 4 relevant orbitals are occupied orbitals 14 and 15 and virtual orbitals 16 and 17. By the final optimisation they should consist only of contributions from the C 2PZ atomic orbitals.

'''4a. Calculate the (High Precision) Vibrational Modes for the Ground State ''with State Averaged Orbitals'''''

Use the .chk from 3a.

Keywords: '''CAS(4,4,nroot=2) STO-3G nosymm freq=hpmodes guess=read geom=checkpoint IOP(5/17=41000200,10/10=700007) IOP(5/97=100,10/97=100)'''

The IOp (5/17=41000200,10/10=700007): includes the CP-MC-SCF correction (as above); and specifies state averaged orbitals. Do not include the keyword '''stateaverage''' with '''freq''' (the current version of Gaussian does not support this). Freq=hpmodes tells Gaussian to print the vibrational modes to 5 decimal places. As before, the IOp (5/97=100,10/97=100) forces calculation of the ground state.

== Part b: The Conical Intersection ==

'''2b. Perform a CASSCF Optimisation on the Ground State'''

Use the .chk from 1. Verify that the required orbitals are the two HOMOs and the two LUMOs. It may be necessary in some cases to use guess=alter to change the order of the orbitals to make sure the desired orbitals are listed as the two HOMOs and two LUMOs. (Gaussian will use the two HOMOs and the two LUMOs in the CASSCF calculation.)

Keywords: '''CAS(4,4,nroot=1) STO-3G pop=full nosymm opt guess=read geom=checkpoint'''

Nroot=1 is the default for opt.

'''3b.Perform a CASSCF Conical Intersection (CI) Optimisation'''

Use the .chk from 2b for the orbital guess. It may be necessary to use a starting geometry close to the desired CI geometry.

Keywords: '''CAS(4,4,nroot=2,stateaverage) STO-3G nosymm opt=conical guess=read'''

Stateaverage is the default for opt=conical.
Nroot=2 is the default for opt=conical.

Resgrp:comp-photo-dyn/mctdh90dev/input

2008-11-25T09:19:45Z

Marobb: /* Part a: The Ground State */

Benjamin / Charlotte / David / Marta to create this please! Some Documentation and some tutorials...

== Creating Input for Dynamics Calculations. Example: Butadiene.==

The only input required for the dynamics calculation is an optimised ground state structure. This structure must have been optimised with state averaged orbitals. These orbitals must be "cleaned" and finally high precision frequencies must be calculated. NOT TRUE YOU NEED OPTIMIZED CI IN ORDER TO GET DIAMATIZATION!

== Part a: The Ground State ==

'''1. Optimise the Ground State Structure (at a low level) to Identify the Orbitals Required for the CASSCF Calculation (see step 2)'''

Keywords: '''opt HF/STO-3G pop=full nosymm'''

Nosymm is required to ensure that the molecule is not re-orientated during the optimisation (this would destroy the active space).
Pop=full prints out the orbitals.
THIS IS A LITTLE BIT CONFUSING. THE TITLE IMPLIES SOMETHING TO DO WITH THE ORBITALS. AND I AGREE THAT ONE SHOULD DO THE INITIAL SELECTION OF THE CASSCF WINDOW USING A MINIMAL BASIS. BUT SURELY YOU WANT TO START THE DYNAMICS FROM A GOOD GROUND STATE OPTIMISED GEOMETRY AND THIS IS INDEPENDENT OF THE SELECTION OF THE ORBITALS. SO IT SEEMS TO ME THERE ARE TWO TASKS: ONE TO GET ESSENTIAL STARTING GEOMETRY AND THAT HAS NOTHING TO DO WITH CASSCF AND THEN THERE IS THE ISSUE OF CHOOSING THE STARTING ORBITALS AND THIS CAN BE DONE WITH THE MINIMUM BASIS. BUT YOU HAVE REALLY SAID ALMOST NOTHING ABOUT THIS.

'''2a. Perform a CASSCF Optimisation on the Ground State ''with State Averaged Orbitals'''''

Use the .chk from 1. Verify that the required orbitals are the two HOMOs and the two LUMOs. It may be necessary in some cases to use guess=alter to change the order of the orbitals to make sure the desired orbitals are listed as the two HOMOs and two LUMOs. (Gaussian will use the two HOMOs and the two LUMOs in the CASSCF calculation.) In this case the orbitals are in the correct order. The relevant orbitals are the four pi orbitals, which contain four electrons (so the calculation is 4,4). Nroot=2 specifies the ''first'' excited state so the state averaged orbitals will be constructed for this state and the ground state.

Keywords: '''opt=conical CAS(4,4,nroot=2,stateaverage) STO-3G nosymm IOP(10/10=700005) IOP(5/97=100,10/97=100) geom=checkpoint guess=read'''

N.B. This is not a conical intersection optimisation! However, the keyword opt=conical specifies that the populations of the two states will each be 0.5, automatically. Thus there is no need to specify the populations manually (which can be tedious). The IOp (5/97=100,10/97=100) tells the program to switch the order of the two states. This is so that we optimise the ground state (rather than the excited state). Gaussian CASSCF calculations always perform optimisations on the highest state listed so by switching the order we force optimisation of what is actually the lower state. The initial '7' in IOp (10/10=700005) specifies that the calculation should be an optimisation to a minimum (rather than a conical intersection). The final '5' ensures that the orbital rotation derivative contributions from the CP-MC-SCF equations are included. (This is necessary and is usually the default. However, in the current version of Gaussian, the combination of '''opt''' and '''stateaverage''' excludes this).
Stateaverage is the default for opt=conical.
Nroot=2 is the default for opt=conical.
Do not include the keyword freq in the optimisation: perform a separate freq calculation (This combination of IOps does not allow '''opt''' and '''freq''' to be keywords in the same job.)

'''3a. "Clean" the Orbitals'''

Use the .chk from 2a.

Keywords: '''opt=(conical,stepsize=1) CAS(4,4,nroot=2,stateaverage) STO-3G nosymm IOP(10/10=700005) IOP(5/97=100,10/97=100) geom=checkpoint guess=read'''

Open the file in GaussView, and Edit/Symmetrize. Use this symmetrised geometry as a starting geometry for another optimsation as in 2a (including the keyword '''nosymm'''). The only difference is that here we include the keyword '''opt=(stepsize=1)'''. This ensures that the optimisation takes the smallest possible step: we already know that the geometry is very close to the minimum and we need to prevent any significant re-orienting that might occur if large steps are taken. Repeat until the orbitals are clean (check by verifying the relevant orbitals in the population analysis). In this case the 4 relevant orbitals are occupied orbitals 14 and 15 and virtual orbitals 16 and 17. By the final optimisation they should consist only of contributions from the C 2PZ atomic orbitals.

'''4a. Calculate the (High Precision) Vibrational Modes for the Ground State ''with State Averaged Orbitals'''''

Use the .chk from 3a.

Keywords: '''CAS(4,4,nroot=2) STO-3G nosymm freq=hpmodes guess=read geom=checkpoint IOP(5/17=41000200,10/10=700007) IOP(5/97=100,10/97=100)'''

The IOp (5/17=41000200,10/10=700007): includes the CP-MC-SCF correction (as above); and specifies state averaged orbitals. Do not include the keyword '''stateaverage''' with '''freq''' (the current version of Gaussian does not support this). Freq=hpmodes tells Gaussian to print the vibrational modes to 5 decimal places. As before, the IOp (5/97=100,10/97=100) forces calculation of the ground state.

== Part b: The Conical Intersection ==

'''2b. Perform a CASSCF Optimisation on the Ground State'''

Use the .chk from 1. Verify that the required orbitals are the two HOMOs and the two LUMOs. It may be necessary in some cases to use guess=alter to change the order of the orbitals to make sure the desired orbitals are listed as the two HOMOs and two LUMOs. (Gaussian will use the two HOMOs and the two LUMOs in the CASSCF calculation.)

Keywords: '''CAS(4,4,nroot=1) STO-3G pop=full nosymm opt guess=read geom=checkpoint'''

Nroot=1 is the default for opt.

'''3b.Perform a CASSCF Conical Intersection (CI) Optimisation'''

Use the .chk from 2b for the orbital guess. It may be necessary to use a starting geometry close to the desired CI geometry.

Keywords: '''CAS(4,4,nroot=2,stateaverage) STO-3G nosymm opt=conical guess=read'''

Stateaverage is the default for opt=conical.
Nroot=2 is the default for opt=conical.

Resgrp:comp-photo-dyn/mctdh90dev/input

2008-11-24T17:14:49Z

Marobb: /* Creating Input for Dynamics Calculations. Example: Butadiene. */