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Manually calculate the Raman Intensities #13

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4742e7c
Add the new code to manually calculate the Raman Intensities
lipelopesoliveira Apr 4, 2024
9d1aeae
Fix documentation and add tests for pol tensor
lipelopesoliveira Apr 24, 2024
05c831e
Correct the diff_cross_section function
lipelopesoliveira Apr 25, 2024
2a28880
Add phono3py on the environment file
lipelopesoliveira May 13, 2024
1bfe20e
Add Raman Cross Section on the output files
lipelopesoliveira May 15, 2024
2ae379e
Fix name of the pol. tensor file
lipelopesoliveira May 15, 2024
600c308
Fix possible error on readChemicalJSON function.
lipelopesoliveira Sep 3, 2024
6d3aebf
Add the modules to create the input and parse the results of the mole…
lipelopesoliveira Sep 3, 2024
d4377c9
Add other DispersionCorrection methods and improve the parsing of opt…
lipelopesoliveira Sep 3, 2024
1cd83bb
Improve the saving of the AXSF format
lipelopesoliveira Sep 3, 2024
2912862
Move some codes to the parse_cp2k module
lipelopesoliveira Sep 3, 2024
b4a8cde
Fix the molecular_dynamics module
lipelopesoliveira Sep 3, 2024
fb4f0c9
Fix error on get_forces of Raman
lipelopesoliveira Sep 9, 2024
d0437d6
Fix small errors
lipelopesoliveira Sep 9, 2024
14eabd5
Fix missing line
lipelopesoliveira Sep 9, 2024
35148cd
Add 'SZV', 'TZVP' as options for basis set
lipelopesoliveira Sep 9, 2024
8c3ed83
Use the developed function to save cif files
lipelopesoliveira Sep 9, 2024
da3f8a4
Add the molecular dynamics to the documentation
lipelopesoliveira Sep 9, 2024
93b2343
Fix parallel and perpendicular raman equations
lipelopesoliveira Sep 9, 2024
29ea654
Remove the dictionary parameters from create_input_file function.
lipelopesoliveira Sep 9, 2024
0df792c
Fix error on the saving of the vibrabional modes on axsf format.
lipelopesoliveira Sep 25, 2024
a3a65da
Save the vibrational modes in ChemJson format
lipelopesoliveira Sep 27, 2024
8a886f6
Add the Resolution option for raman curve generation
lipelopesoliveira Sep 29, 2024
a38fc89
Add CurveLimits option to specify Raman/IR spectrum plot limits
lipelopesoliveira Feb 8, 2025
7b9366f
Replace print statements with warnings for polarizability tensor checks
lipelopesoliveira Feb 8, 2025
b45bf2e
Move the code to calculate Raman Tensor Placzek Invariants to the ca…
lipelopesoliveira Feb 8, 2025
8417b20
Add function to calculate Raman intensity and refactor usage in phono…
lipelopesoliveira Feb 8, 2025
2278bcb
Add functions to save vibrational modes and Raman data, including CSV…
lipelopesoliveira Feb 8, 2025
e27afa3
Fix formatting issues in parse_phonon.py by correcting dictionary syntax
lipelopesoliveira Feb 8, 2025
f38fdf4
Add informative print statement and fix input file naming in generate…
lipelopesoliveira Feb 8, 2025
997bc85
Refactor save_raman_data function call for improved readability and p…
lipelopesoliveira Feb 8, 2025
a7a159f
Add header documentation and print statement for scripts
lipelopesoliveira Feb 9, 2025
584da0e
Remove author name from header documentation in constants.py
lipelopesoliveira Feb 9, 2025
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7 changes: 5 additions & 2 deletions bin/charge_density.py
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@

from modules.calculate_properties import get_CellParameters, get_AtomicPositions
from modules.atom_data import BASIS_SET, PSEUDO_POTENTIALS
from modules.constants import header

# Required parameters
parser = argparse.ArgumentParser(description='Create the CP2K simulation input.')
Expand Down Expand Up @@ -96,7 +97,7 @@
default='DZVP',
action='store',
required=False,
choices=['DZVP', 'TZV2P'],
choices=['SZV', 'DZVP', 'TZVP', 'TZV2P'],
metavar='BASIS_SET',
help='Gaussian basis set type.')
parser.add_argument('--MaxSCFycles',
Expand Down Expand Up @@ -223,6 +224,8 @@
# Parse the arguments
arg = parser.parse_args()

print(header.format('CP2K Input Creator'))

# Read the cif file and get the lattice parameters and atomic positions
cif_filename = os.path.join(arg.output_folder, arg.FrameworkName + '.cif')

Expand All @@ -236,7 +239,7 @@

Kind_List = []

for i, specie in enumerate(set(AtomicTypes)):
for specie in set(AtomicTypes):
Kind_List.append({
"_": specie,
'element': specie,
Expand Down
3 changes: 3 additions & 0 deletions bin/chargemol.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@

from modules.calculate_properties import get_CellParameters, get_AtomicPositions
from modules.atom_data import ATOMIC_NUMBER, CORE_NUM
from modules.constants import header

# Required parameters
parser = argparse.ArgumentParser(description='Create the Chargemol simulation input.')
Expand Down Expand Up @@ -42,6 +43,8 @@

arg = parser.parse_args()

print(header.format('Chargemol Input Creator'))

# Calculate self-consistent properties
cif_filename = os.path.join(arg.output_folder, arg.FrameworkName + '.cif')

Expand Down
3 changes: 3 additions & 0 deletions bin/convert_file.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@

import argparse

from modules.constants import header
from modules.io_files import (readCIF, saveCIF,
readChemicalJSON, saveChemicalJSON,
readGJF, saveGJF,
Expand Down Expand Up @@ -46,6 +47,8 @@
# Parse the arguments
arg = parser.parse_args()

print(header.format('Structure Converter'))

# Dictionary containing the function to read files
read_dict = {
'cif': readCIF,
Expand Down
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