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added all the functions, but with warnings, saying input tests correc…
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…tness is not checked.
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@bc118
bc118 committed Aug 23, 2024
1 parent c55002e commit e669c16
Showing 1 changed file with 59 additions and 58 deletions.
117 changes: 59 additions & 58 deletions mosdef_dihedral_fit/utils/file_read_and_write.py
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Original file line number Diff line number Diff line change
Expand Up @@ -479,35 +479,35 @@ def get_final_gaussian_output_file_data(
Returns
-------
| list of:
| all_dihedral_angle_degrees_list: list (nested list)
| This is the list of the optimized Gaussian dihedral angles (degrees) with the
| specific angles removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| all_energy_hartree_list: list (nested list)
| This is the list of the optimized Gaussian energies with the specific energies
| (hartree) removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| all_coordinates_ang_list: list (nested list)
| This is the list of the optimized Gaussian energies with the specific energies
| (hartree) removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| element_names_list: list
| This is the list of the Gaussian element names per the
| 'qm_log_file_dict' list (value) input.
| The list length is dependant on the number of elements in the Gaussian log file
| These values are confirmed to be the same for all entered Gaussian log files.
| number_of_atoms: int
| This is the number of atoms in the Gaussian
| 'qm_log_file_dict' list (value) input.
| These values are confirmed to be the same for all entered Gaussian log files.
| manual_dihedral_atom_numbers_list: list, list of four (4) int (example: [3,2,1,5])
| This is a list of the dihedral atom numbers in order that were used for the dihedral
| fit. This information needs to be correct and in order to produce correct results.
| The values must be the same in all the combined files.
list of:
| all_dihedral_angle_degrees_list: list (nested list)
| This is the list of the optimized Gaussian dihedral angles (degrees) with the
| specific angles removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| all_energy_hartree_list: list (nested list)
| This is the list of the optimized Gaussian energies with the specific energies
| (hartree) removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| all_coordinates_ang_list: list (nested list)
| This is the list of the optimized Gaussian energies with the specific energies
| (hartree) removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| element_names_list: list
| This is the list of the Gaussian element names per the
| 'qm_log_file_dict' list (value) input.
| The list length is dependant on the number of elements in the Gaussian log file
| These values are confirmed to be the same for all entered Gaussian log files.
| number_of_atoms: int
| This is the number of atoms in the Gaussian
| 'qm_log_file_dict' list (value) input.
| These values are confirmed to be the same for all entered Gaussian log files.
| manual_dihedral_atom_numbers_list: list, list of four (4) int (example: [3,2,1,5])
| This is a list of the dihedral atom numbers in order that were used for the dihedral
| fit. This information needs to be correct and in order to produce correct results.
| The values must be the same in all the combined files.
"""
if not isinstance(qm_log_file_dict, dict):
raise TypeError(
Expand Down Expand Up @@ -763,35 +763,36 @@ def get_gaussian_log_file_data(
Returns
-------
all_dihedral_angle_degrees_list: list (nested list of str)
This is the list of the optimized Gaussian dihedral angles (degrees) with the
specific angles removed per the 'qm_log_file_dict' list
(value) input. This is a nested list, with an inner list for every
Gaussian log file or 'qm_log_file_dict' (key).
all_energy_hartree_list: list (nested list of str)
This is the list of the optimized Gaussian energies with the specific energies
(hartree) removed per the 'qm_log_file_dict' list
(value) input. This is a nested list, with an inner list for every
Gaussian log file or 'qm_log_file_dict' (key).
all_coordinates_ang_list: list (nested list of float)
This is the list of the optimized Gaussian energies with the specific energies
(hartree) removed per the 'qm_log_file_dict' list
(value) input. This is a nested list, with an inner list for every
Gaussian log file or 'qm_log_file_dict' (key).
element_names_list: list of str
This is the list of the Gaussian element names per the
'qm_log_file_dict' list (value) input.
The list length is dependant on the number of elements in the Gaussian log file
These values are confirmed to be the same for all entered Gaussian log files.
number_of_atoms: int
This is the number of atoms in the Gaussian
'qm_log_file_dict' list (value) input.
These values are confirmed to be the same for all entered Gaussian log files.
dihedral_atom_numbers_list: list of 4 int
This is the list of the dihedral atom numbers used in the Gaussian
dihedral scan, which are taken from the Gaussian
'qm_log_file_dict' list (value) input.
These values are confirmed to be the same for all entered Gaussian log files.
list of:
| all_dihedral_angle_degrees_list: list (nested list of str)
| This is the list of the optimized Gaussian dihedral angles (degrees) with the
| specific angles removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| all_energy_hartree_list: list (nested list of str)
| This is the list of the optimized Gaussian energies with the specific energies
| (hartree) removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| all_coordinates_ang_list: list (nested list of float)
| This is the list of the optimized Gaussian energies with the specific energies
| (hartree) removed per the 'qm_log_file_dict' list
| (value) input. This is a nested list, with an inner list for every
| Gaussian log file or 'qm_log_file_dict' (key).
| element_names_list: list of str
| This is the list of the Gaussian element names per the
| 'qm_log_file_dict' list (value) input.
| The list length is dependant on the number of elements in the Gaussian log file
| These values are confirmed to be the same for all entered Gaussian log files.
| number_of_atoms: int
| This is the number of atoms in the Gaussian
| 'qm_log_file_dict' list (value) input.
| These values are confirmed to be the same for all entered Gaussian log files.
| dihedral_atom_numbers_list: list of 4 int
| This is the list of the dihedral atom numbers used in the Gaussian
| dihedral scan, which are taken from the Gaussian
| 'qm_log_file_dict' list (value) input.
| These values are confirmed to be the same for all entered Gaussian log files.
"""
if not isinstance(qm_log_file_dict, dict):
raise TypeError(
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