Gaussian_methods¶
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libra_py.Gaussian_methods.
cube_generator_gaussian
(project_name, time_step, min_band, max_band, nprocs, sample_cube_file, isUKS)[source]¶ This function generates the cube files by first forming the ‘fchk’ file from ‘chk’ file. Then it will generate the cube files from min_band to max_band the same as CP2K naming. This will helps us to use the read_cube and integrate_cube functions easier.
- Parameters
project_name (string) – The project_name.
time_step (integer) – The time step.
min_band (integer) – The minimum state number.
max_band (integer) – The maximum state number.
nprocs (integer) – The number of processors used to generate the cubes using ‘cubegen’.
sample_cube_file (str) – The path to a sample cube file. This file is used to generate the cube files according the mesh of this file. Therefore the integration will be plausible.
isUKS (integer) – The unrestricted spin calculation flag. 1 is for spin unrestricted calculations. Other numbers are for spin restricted calculations
- Returns
None
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libra_py.Gaussian_methods.
gaussian_distribute
(istep, fstep, nsteps_this_job, trajectory_xyz_file, gaussian_input, curr_job_number)[source]¶ Distributes Gaussian jobs for trivial parallelization
- Make sure that your Gaussian input file has absolute paths to the following input parameters:
This parameters should be set in the input template chk file —> e.g. %chk=/home/username/gaussian_calculations/check_file.chk rwf file —> e.g. %rwf=/home/username/gaussian_calculations/check_file.rwf
- Parameters
istep (integer) – The initial time step in the trajectory xyz file.
fstep (integer) – The final time step in the trajectory xyz file.
nsteps_this_job (integer) – The number of steps for this job.
trajectory_xyz_file (string) – The full path to trajectory xyz file.
gaussian_input (string) – The sample Gaussian input template.
curr_job_number (integer) – The current job number.
- Returns
None
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libra_py.Gaussian_methods.
gaussian_input
(project_name, time_step, sample_input, trajectory_xyz_file_name)[source]¶ This function creates a Gaussian input file for the time_step geometry using an input template.
- Parameters
project_name (string) – The project name.
time_step (integer) – The time step.
sample_input (string) – The Gaussian sample input.
trajectory_xyz_file_name (string) – The trajectory xyz file name.
- Returns
None
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libra_py.Gaussian_methods.
read_energies_from_gaussian_log_file
(params)[source]¶ This function read the energies from Gaussian log file and returns the Kohn-Sham and total_energies.
- Parameters
params (dictionary) –
The dictionary containing the input parameters.
logfile_name (string): The log file name.
min_band (integer): The minimum state number.
max_band (integer): The maximum state number.
spin (integer): The spin component. 1 is for alpha and 2 is for beta spin.
- Returns
The Kohn-Sham energies.
total_energy (float): The total energy of the system.
- Return type
ks_energies (1D numpy array)
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libra_py.Gaussian_methods.
read_gaussian_tddft_log_file
(params)[source]¶ This function read Gaussian output file and extracts the excitation analysis results.
- Parameters
params (dictionary) –
The dictionary containing the input parameters.
logfile_name (string): The log file name.
tolerance (float): The tolerance factor for choosing the excited states of the excitation analysis.
number_of_states (integer): The number of excited states to be considered in the excitation analysis.
- isUKS (integer): This parameter is the flag for restricted or unrestricted spin calculations. If it is
set to 1 the unrestricted spin calculations will be considered.
- Returns
The excitation energies.
ci_basis (list): The list containnig the CI basis of the excitation analysis.
ci_coefficients (list): The list containing the ci_coefficients for each excitation.
spin_components (list): The list containing the spin components for each excitation.
- Return type
excitation_energies (1D numpy arra)
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libra_py.Gaussian_methods.
read_trajectory_xyz_file_gaussian
(trajectory_xyz_file_name: str, time_step: int)[source]¶ This function reads the trajectory of a molecular dynamics .xyz file and extract the ‘time_step’ th step then returns it in form of a numpy array.
- Parameters
trajectory_xyz_file_name (string) – The trajectory .xyz file name.
time_step (integer) – The desired time to extract its .xyz coordinates which starts from zero.
- Returns
The numpy array containing the coordinates of the time_step.
- Return type
coordinates (2D numpy array)