Calculation Parameters and Submission Information Settings

The following provide information about the settings and other advice for the Gaussian/ORCA parameters and submission information dictionaries required for running this program.

Tags needed for the calculation_parameters dictionaries

The calculation_parameters_for_atomic_transition_charges, calculation_parameters_for_reorganisation_energy, calculation_parameters_for_electronic_energy_transfer, and calculation_parameters_for_intermolecular_charge_transfer dictionaries allow you to give the parameters needed for the Gaussian/ORCA input files. These include:

• 'calc_software' (str.): This is the program that you would like to use to perform your quantum calculations. This can be either 'Gaussian' or 'ORCA'.
• 'mem' (str.): This is the amount of memory that is used by Gaussian. Gaussian needs this variable. ORCA does not use this variable.
• 'method' (str.): The level of theory you want to use (i.e. the functional). Example: 'wB97XD' for Gaussian, or wB97X-D3 for ORCA. Note that the input names for the same functionals may be different for Gaussian and ORCA. Check the manuals before running the ECCP program to make sure you are calculating molecules and dimers with the desired functional.
• 'basis' (str.): The basis set you want to use. Example: '6-311G(d)'. Note that the input names for the same basis sets may be different for Gaussian and ORCA. Check the manuals before running the ECCP program to make sure you are calculating molecules and dimers with the desired basis set.
• 'td_settings' (str.): This allows you to provide the settings for performing TD-DFT calculations. For example, if you want to perform TD-DFT calculations with the Tamm-Dancoff approximation and solve for 3 states, you want to set this to 'tda(nstates=3)'. Default: 'TD'
• 'temp_folder_path' (str.): This is the scratch drive to place files into. This is useful if you want the Gaussian/ORCA temporary files to be saved onto a local disk rather than a NFS if running on a computer cluster. Set to None if you do not want to give this. Default: None.

Other parameters that can be given in the calculation_parameters_for_atomic_transition_charges, calculation_parameters_for_electronic_energy_transfer, and calculation_parameters_for_intermolecular_charge_transfer dictionaries are:

• 'extra' (str.): These are any extra tags that you need to add. For example in Gaussian: '# maxdisk=2TB scf=(xqc,maxcycle=512) scrf=(iefpcm,read)'
• 'addsec' (str.): These are the lines that you want to write to the .gjf file that come after the atomic positions. For example, if you added 'scrf=(iefpcm,read)' in your 'extra' entry, you will want to read in the relative electric permittivity after the atomic positions by setting calculation_parameters_for_atomic_transition_charges['addsec'] = 'Eps=4.0', where in this example we have set the relative electric permittivity to 4.0. This tag is only needed for Gaussian. This is because all the variable you would write in here for Gaussian you write in calculation_parameters['extra'] for ORCA.

You can also specify where you would like certain files to be placed, particularly if you want to place some of the temporary Gaussian/ORCA files into a SCRATCH directory. If you want all the temporary files to be placed in a general SCRATCH files, provide a entry for 'scratch_path' in calculation_parameters dictionary:

• 'temp_folder_path' (str.): This is the place that you want to store temporary Gaussian/ORCA files in (the scratch drive). The ECCP will write the script for that appropriate folders are made in your 'temp_folder_path' that temporary Gaussian/ORCA files will be saved to. Checkpoint files will be saved to the same place as the .gjf file to allow you to easily resubmit incomplete jobs.
• 'place_chk_in_temp' (bool.): If you have given a directory for 'temp_folder_path', you can choose to also place the checkpoint file in the 'temp_folder_path' directory as well if this is set to True. If you want the checkpoint file to be place in the same place as the .gjf (to allow you to easily continue the calculation if it does not finish in time), set this to False. Default: False

Examples of the calculation_parameters_for_atomic_transition_charges, calculation_parameters_for_reorganisation_energy, calculation_parameters_for_electronic_energy_transfer, and calculation_parameters_for_intermolecular_charge_transfer dictionaries are given below:

# The following dictionaries provide the Gaussian/ORCA parameters and Submission information required for performing 
# Atomic Transition Charge (ATC) calculations on your molecules.

# This dictionary will add tags to your Gaussian/ORCA input file.
calculation_parameters_for_atomic_transition_charges = {}
calculation_parameters_for_atomic_transition_charges['calc_software']                = 'Gaussian'
calculation_parameters_for_atomic_transition_charges['mem']                          = '64GB'
calculation_parameters_for_atomic_transition_charges['method']                       = 'wB97XD'
calculation_parameters_for_atomic_transition_charges['basis']                        = '6-31+G(d,p)'
calculation_parameters_for_atomic_transition_charges['td_settings']                  = 'tda(nstates=10)'

# The following dictionaries provide the Gaussian/ORCA parameters and Submission information required for performing 
# reorganisation energy (RE) calculations on your molecules.

# This dictionary will add tags to your Gaussian/ORCA input file.
calculation_parameters_for_reorganisation_energy = {}
calculation_parameters_for_reorganisation_energy['calc_software']    = 'Gaussian'
calculation_parameters_for_reorganisation_energy['mem']              = '256GB'
calculation_parameters_for_reorganisation_energy['method']           = calculation_parameters_for_atomic_transition_charges['method']
calculation_parameters_for_reorganisation_energy['basis']            = calculation_parameters_for_atomic_transition_charges['basis']

# The following dictionaries provide the Gaussian/ORCA parameters and Submission information required for performing 
# Electronic Energy Transfer (EET) calculations on your molecules.

# This dictionary will add tags to your Gaussian/ORCA .gjf file
calculation_parameters_for_electronic_energy_transfer = {}
calculation_parameters_for_electronic_energy_transfer['calc_software']                = 'Gaussian'
calculation_parameters_for_electronic_energy_transfer['mem']                          = '64GB'
calculation_parameters_for_electronic_energy_transfer['method']                       = calculation_parameters_for_atomic_transition_charges['method']
calculation_parameters_for_electronic_energy_transfer['basis']                        = calculation_parameters_for_atomic_transition_charges['basis']
calculation_parameters_for_electronic_energy_transfer['td_settings']                  = calculation_parameters_for_atomic_transition_charges['td_settings']

# The following dictionaries provide the Gaussian/ORCA parameters and Submission information required for obtaining 
# eigendata (such as overlap orbtials and molecular orbital energies and coefficients).

Tags needed for the calculation_parameters_for_franck_condon_factors dictionary

THIS WILL PROBABLY CHANGE: UPDATE THIS WHEN THIS PROCESS HAS BEEN SORTED.

The Franck-Condon calculation performed by the Gaussian/ORCA program is a bit different to other calculations, as all the calculations that need to be done are performed by the Reorganisation Energy component. Here, Gaussian will use the frequency checkpoint files created during the ground and excited state optimisation calculations (performed by the Reorganisation Energy component). For this reason, we don't need to specify all the inputs as in Calculation Parameter Settings. The inputs needed for submission_information_for_franck_condon_factors are:

• 'mem' (str.): This is the amount of memory that is used by Gaussian. Recommended to set this to '8GB'
• 'method' (str.): The level of theory you want to use (i.e. the functional). Example: 'wB97XD'
• 'basis' (str.): The basis set you want to use. Example: '6-311G(d)'

Note: Recommendations for submission_information_for_franck_condon_factors, submission_information_for_franck_condon_factors['cpus_per_task'] = 2 and submission_information_for_franck_condon_factors['mem'] = '16GB'.

An example of calculation_parameters_for_franck_condon_factors is given below

# Franck-Condon (FC) (and Huang-Rhys (HR)) calculations on your molecules. 
# NOTE: If you want to use this, you also need to set Gaussian/ORCA parameters and submission information for obtaining reorganisation energies. 

# This dictionary will add tags to your Gaussian/ORCA input file.
calculation_parameters_for_franck_condon_factors = {}
calculation_parameters_for_franck_condon_factors['calc_software'] = 'Gaussian'
calculation_parameters_for_franck_condon_factors['mem']           = '8GB'

Advice for settings for the calculation_parameters dictionaries

The Gaussian jobs that use the calculation_parameters_for_atomic_transition_charges, calculation_parameters_for_reorganisation_energy, calculation_parameters_for_electronic_energy_transfer, and calculation_parameters_for_intermolecular_charge_transfer dictionaries perform single point calculations, as well as other calculations for TD-DFT calculations. The Gaussian jobs that use the calculation_parameters_for_reorganisation_energy dictionary perform geometry optimisation calculations, which are far more computationally intensive to perform.

The amount of memory that you will need to use for calculation_parameters_for_reorganisation_energy should be double or more needed for calculation_parameters.

Recommendations for calculation_parameters_for_franck_condon_factors and submission_information_for_franck_condon_factors dictionaries:

• calculation_parameters_for_franck_condon_factors['mem'] = '14GB'
• submission_information_for_franck_condon_factors['mem'] = '16GB'
• submission_information_for_franck_condon_factors['cpus_per_task'] = 2

Tags needed for the submission_information dictionaries

The submission_information_for_atomic_transition_charges, submission_information_for_multiwfn, submission_information_for_reorganisation_energy, submission_information_for_franck_condon_factors, submission_information_for_electronic_energy_transfer, and dimer_eigendata_file_creation_information dictionaries allow you to place the parameters needed for the submit.sl , multiwfn_submit.sl, and the various reorganisation submit.sl files. These include:

• 'cpus_per_task': This the the number of CPU's you want to use. This information is also passed on to your Gaussian .gjf file. THIS VARIABLE IS ONLY USED FOR GAUSSIAN CALCULATIONS.
• 'ntasks': This the the number of CPU's you want to use. This information is also passed on to your ORCA .inp file. THIS VARIABLE IS ONLY USED FOR ORCA CALCULATIONS.
• 'mem': This is the total amount of RAM memory you want to use across all your CPUs.
• 'time': This is the amount of time you want to run this job for. Written HH:MM:SS
• 'partition': This is the name of the partition you want to run your job on.
• 'constraint': This assigns particular nodes to run Gaussian jobs. This is a variable that is needed at Victoria University of Wellington. See https://slurm.schedmd.com/sbatch.html for more information about this. This is set to 'AVX' on the Rāpoi computer cluster at Victoria University of Wellington.
• 'email': This is the email you want to use to notify you about this job
• 'gaussian_version': This is the version of gaussian you want to use. For example: 'g16'. This setting is required for submission_information and submission_information_for_reorganisation_energy, as these processes use Gaussian to perform ATC, RE, and EET calculations. This tag is not needed for the submission_information_for_multiwfn dictionary. THIS VARIABLE IS ONLY USED FOR GAUSSIAN CALCULATIONS.
• 'ORCA_version': This is the version of ORCA you want to use. For example: 'ORCA/5.0.3'. This setting is required for submission_information and submission_information_for_reorganisation_energy, as these processes use ORCA to perform ATC, RE, and EET calculations. This tag is not needed for the submission_information_for_multiwfn dictionary. THIS VARIABLE IS ONLY USED FOR GAUSSIAN CALCULATIONS.
• 'python_version': This is the version of python you want to use. For example: '3.8.1' for Python 3.8.1. This tag is only needed for the submission_information_for_reorganisation_energy dictionary, as python is only used here to create single point calculations from the results of the geometrically optimised Gaussian/ORCA calculations.

For the submission_information_for_multiwfn dictionary, you only need to provide the 'cpus_per_task'/'ntasks', 'mem', 'time', and 'partition' input parameters (and optionally the 'constraint' and 'email' input parameters).

Examples of the submission_information_for_atomic_transition_charges, submission_information_for_multiwfn, submission_information_for_reorganisation_energy, submission_information_for_franck_condon_factors, submission_information_for_electronic_energy_transfer, and dimer_eigendata_file_creation_information dictionaries are given below:

calculation_parameters_for_atomic_transition_charges['temp_folder_path']             = '/tmp/wealge'
calculation_parameters_for_atomic_transition_charges['extra']                        = '# maxdisk=2TB scf=(xqc,maxcycle=512)'

# This dictionary will add tags to your submit.sl file for performing Gaussian/ORCA Calculations to get the initial ATC wfn files and to perofmr EET calculations
submission_information_for_atomic_transition_charges = {}
submission_information_for_atomic_transition_charges['cpus_per_task']    = 32
submission_information_for_atomic_transition_charges['mem']              = '68GB' # This has been set to calculation_parameters_for_atomic_transition_charges['mem'] + 12 GBs
submission_information_for_atomic_transition_charges['time']             = '10-00:00'
submission_information_for_atomic_transition_charges['partition']        = 'parallel'
submission_information_for_atomic_transition_charges['constraint']       = 'AVX'
submission_information_for_atomic_transition_charges['email']            = 'geoffreywealslurmnotifications@gmail.com'
submission_information_for_atomic_transition_charges['gaussian_version'] = 'gaussian/g16'
submission_information_for_atomic_transition_charges['python_version']   = 'python/3.8.1'

# This tag indicates if you want to obtain Gaussian/ORCA input files of molecules for performing ATC calculations. 
submission_information_for_multiwfn = {}
submission_information_for_multiwfn['cpus_per_task'] = 16
submission_information_for_multiwfn['mem']           = '32GB'
submission_information_for_multiwfn['time']          = '0-03:00'

#calculation_parameters_for_reorganisation_energy['temp_folder_path'] = calculation_parameters_for_atomic_transition_charges['temp_folder_path']
calculation_parameters_for_reorganisation_energy['extra']            = '# maxdisk=2TB scf=(xqc,maxcycle=512)'

# This tag indicates if you want to obtain Gaussian/ORCA input files of molecules for performing ATC calculations. 
submission_information_for_reorganisation_energy = {}
submission_information_for_reorganisation_energy['cpus_per_task']    = 128
submission_information_for_reorganisation_energy['mem']              = '264GB' # This has been set to calculation_parameters_for_reorganisation_energy['mem'] + 24 GBs
submission_information_for_reorganisation_energy['time']             = '10-00:00'
submission_information_for_reorganisation_energy['partition']        = 'parallel'
submission_information_for_reorganisation_energy['constraint']       = 'AVX'

calculation_parameters_for_franck_condon_factors['basis']         = calculation_parameters_for_atomic_transition_charges['basis']
calculation_parameters_for_franck_condon_factors['extra']         = '# maxdisk=2TB scf=(xqc,maxcycle=512)'

# This tag indicates if you want to obtain Gaussian/ORCA input files of molecules for performing FC calculations. 
submission_information_for_franck_condon_factors = {}
submission_information_for_franck_condon_factors['cpus_per_task']    = 2
submission_information_for_franck_condon_factors['mem']              = '16GB' # This has been set to calculation_parameters_for_reorganisation_energy['mem'] + 24 GBs
submission_information_for_franck_condon_factors['time']             = '00-02:00'
submission_information_for_franck_condon_factors['partition']        = 'quicktest'
submission_information_for_franck_condon_factors['constraint']       = 'AVX'

#calculation_parameters_for_electronic_energy_transfer['temp_folder_path']             = calculation_parameters_for_atomic_transition_charges['temp_folder_path']
calculation_parameters_for_electronic_energy_transfer['extra']                        = '# maxdisk=2TB scf=(xqc,maxcycle=512)'

# This dictionary will add tags to your submit.sl file for performing Gaussian/ORCA Calculations to get the initial ATC wfn files and to perform EET calculations
submission_information_for_electronic_energy_transfer = {}
submission_information_for_electronic_energy_transfer['cpus_per_task']    = 32
submission_information_for_electronic_energy_transfer['mem']              = '68GB' # This has been set to calculation_parameters_for_electronic_energy_transfer['mem'] + 12 GBs
submission_information_for_electronic_energy_transfer['time']             = '10-00:00'
submission_information_for_electronic_energy_transfer['partition']        = 'parallel'
submission_information_for_electronic_energy_transfer['constraint']       = 'AVX'

# This dictionary will add tags to your Gaussian/ORCA input file
calculation_parameters_for_eigendata = dict(calculation_parameters_for_electronic_energy_transfer)

Advice for settings for the submission_information dictionaries

The Gaussian/ORCA calculations that use the submission_information_for_atomic_transition_charges, submission_information_for_electronic_energy_transfer, and dimer_eigendata_file_creation_information dictionaries perform single point calculations, as well as other calculations for TD-DFT calculations. The Gaussian/ORCA jobs that use the submission_information_for_reorganisation_energy dictionary perform geometry optimisation calculations, which are far more computationally intensive to perform.

The amount of cpus, memory and computational time that you should need to use for submission_information_for_reorganisation_energy should be double or more needed for submission_information_for_atomic_transition_charges and submission_information_for_electronic_energy_transfer dictionaries.

The Multiwfn program to perform the ATC calculations is not as computationally expensive as Gaussian, and likely will finish within a fraction of time needed for the Gaussian calculation. For this reason, the amount of cpus, memory and computational time submission_information_for_multiwfn can be the same or less than for `submission_information_for_atomic_transition_charges, and submission_information_for_electronic_energy_transfer dictionaries.

Recommendations for calculation_parameters_for_franck_condon_factors and submission_information_for_franck_condon_factors dictionaries:

• calculation_parameters_for_franck_condon_factors['mem'] = '14GB'
• submission_information_for_franck_condon_factors['mem'] = '16GB'
• submission_information_for_franck_condon_factors['cpus_per_task'] = 2