Manually calculate the Raman Intensities #13

lipelopesoliveira · 2024-04-04T21:49:38Z

Manual Raman Intensity Calculation Using Small Displacements Approach

This pull request introduces a new set of tools designed to manually calculate Raman intensities (total, perpendicular, and parallel) using the small displacements approach. The calculation leverages the polarizability tensor, as outlined in issue #4, and incorporates symmetry analysis through the Phono3py package. This package is used to generate the dynamical matrix from atomic forces, enabling accurate vibrational mode analysis.

Key Features

Raman Intensity Calculation:
- Implements manual calculation of Raman intensities (total, perpendicular, and parallel) based on small atomic displacements and the resulting polarizability tensor.
Phono3py Integration: Utilizes the Phono3py package for:
- Generating the dynamical matrix from atomic forces.
- Performing symmetry analysis critical for vibrational mode calculations.

After running the scripts, the following files and directories are produced:

VIBRATION_FILES
- Contains displacement vectors for all vibrational modes. Files are named following the pattern:
  {FrameworkName}_{ModeNumber}_{IrreductiveRepresentation}_{Freq}.axsf
  These files can be visualized using VESTA.
All Displacements File:
- A single file named {FrameworkName}_all.axsf that consolidates all displacement vectors. This file is suitable for visualization in XCrysDen.
Raman Data CSV:
- A file called {FrameworkName}_RamanTable.csv that tabulates the computed Raman intensities and related data.
Normalized Raman Curve CSV:
- A file named {FrameworkName}_RAMAN_Curve.csv that contains the normalized Raman curve, with intensities normalized by the total intensity and a given half width for the peaks.

Usage and Execution

Prepare Input Files:
- Run generate_shift.py to create the necessary displacement input files. Note: The default command line for executing CP2K within this script can be modified to fit HPC cluster job submission requirements.
Run Simulations:
- Execute the generated displacement files independently in three directions (x, y, z) and in two polarization (+, -). Each displacement is designed to run as a standalone simulation.
Parse and Analyze Results:
- After simulations complete, run parse_phonon.py to:
  - Read simulation outputs.
  - Calculate vibrational modes and irreducible representations.
  - Compute Raman intensities and generate all output files described above.

Below there is an example of two scripts that can execute the workflow completely.

#!/bin/bash

# Define environment variables
export PATH=$PATH:/home/felipe/Github/electronic-structure-experiment/bin

export CP2K_DIR=/home/felipe/lib/cp2k-2023.2
export CP2K_DATA_DIR=${CP2K_DIR}/data

export OMP_NUM_THREADS=1

# Define specific variables
FrameworkName='HKUST_1'
OutputFolder=$PWD
NProcs=25

# Load the CP2K setup script
source ${CP2K_DIR}/tools/toolchain/install/setup

# First ensure that the CIF file has all atoms explicitly defined in a P1 primitive cell
echo -e "\nCreating primitive P1 cell..."
mv -v ${OutputFolder}/${FrameworkName}.cif ${OutputFolder}/${FrameworkName}_original.cif
pmg structure --convert --filename ${OutputFolder}/${FrameworkName}_original.cif ${OutputFolder}/${FrameworkName}_prim.cif
mv -v ${OutputFolder}/${FrameworkName}_prim.cif ${OutputFolder}/${FrameworkName}.cif

echo -e "\nCreating CP2K input file..."
generate_shift.py --FrameworkName ${FrameworkName} \
                  --Functional "PBE" \
                  --DispersionCorrection "DFTD3(BJ)" \
                  --PWCutoff 1200 \
                  --BasisSet "TZV2P" \
                  --UnitCell "1,1,1" \
                  --dR 0.005 \
                  --UseOT \
                  --CalculateRaman \
                  ${OutputFolder}

FOLDER_LIST=$(ls -d */)

# List the folders in the current directory and iterate over it
for folder in $FOLDER_LIST; do
    echo "Running the cp2k program for the folder $folder"
    # Change to the folder
    cd $folder
    # Remove the \ from the folder name
    folder=$(echo $folder | tr -d '/')
    # Run the cp2k program
    mpirun -np 25 $CP2K_DIR/exe/local/cp2k.psmp -i ${FrameworkName}_${folder}.inp -o ${FrameworkName}_${folder}.out
    # Return to the parent directory
    cd ..
done

#!/bin/bash

# Define environment variables
export PATH=$PATH:/home/felipe/Github/electronic-structure-experiment/bin

export CP2K_DIR=/home/felipe/lib/cp2k-2023.2
export CP2K_DATA_DIR=${CP2K_DIR}/data

export OMP_NUM_THREADS=1

# Define specific variables
FrameworkName='HKUST_1'
OutputFolder=$PWD
NProcs=25

# Load the CP2K setup script
source ${CP2K_DIR}/tools/toolchain/install/setup

echo -e "\nCreating RASPA P1 cell input file..."
parse_phonon.py --FrameworkName ${FrameworkName} \
                --UnitCell "1,1,1" \
                --dR 0.005 \
                --CalculateRaman \
                --SaveVecs \
                --CurveLimits '0,4000' \
                --Resolution 0.1 \
                --HalfWidth 5.0 \
                ${OutputFolder}

Closes #4

lipelopesoliveira · 2024-04-04T21:51:18Z

@pcostacarvalho can you test this new workflow for Raman simulations with the HKUST-1 structure on CCC? In case you need some help just let me know and we can schedule a meeting.

neumannrf

Thanks, @lipelopesoliveira !!! 👏 👏 👏

This will bring an amazing productivity gain. I would even suggest to include the Shell script in the PR description as a file in the repository. Maybe @pcostacarvalho can do that after figuring out the appropriate command for the LSF cluster we have.

bin/generate_shift.py

bin/modules/calculate_properties.py

bin/modules/constants.py

bin/parse_phonon.py

neumannrf · 2024-04-05T18:36:18Z

@lipelopesoliveira Which of these packages need to be added to environment.yml: phono3py or phonopy?

Even though you cited phono3py in the text above, the imports all point to phonopy.

…cular dynamics

…imization

neumannrf · 2024-09-19T17:48:37Z

@lipelopesoliveira Is it time already to merge this branch, or are you still working on it?

lipelopesoliveira · 2024-09-23T16:21:45Z

@lipelopesoliveira Is it time already to merge this branch, or are you still working on it?

I'm still working on this.

…culate_properties

…n parsing

… output and spectrum calculation

…_shift.py and calculate_properties.py

…arameter clarity in parse_phonon.py

lipelopesoliveira · 2025-02-09T15:08:25Z

@neumannrf This is a tentative for closing this PR. There is still two functionalities that are not implemented:

Calculation of IR spectra using the manual method
Independent calculation of phonon dispersion curves and thermodynamic properties
Use of symmetry to reduce the number of calculations

The first two are not urgent so I'll let it for the future. The third one could help a lot right now, but unfortunately implement it will require a lot more time than I anticipated, so maybe in a few weeks when I will have more time to dedicate to it I can come back and implement it.

I tested most of the things here on my computer and everything seems to be working. But if @pcostacarvalho have some time to spare it would be good to double check the code with some simple examples just to make sure that I didn't broke anything.

There still some things that I would like to implement, such as unit tests and a better documentation with more examples. But as people says: "The perfect is the enemy of the good..."

Add the new code to manually calculate the Raman Intensities

4742e7c

lipelopesoliveira added the enhancement New feature or request label Apr 4, 2024

lipelopesoliveira requested review from pcostacarvalho and m-estevesf April 4, 2024 21:49

lipelopesoliveira self-assigned this Apr 4, 2024

neumannrf requested changes Apr 5, 2024

View reviewed changes

lipelopesoliveira added 19 commits April 24, 2024 17:41

Fix documentation and add tests for pol tensor

9d1aeae

Correct the diff_cross_section function

05c831e

Add phono3py on the environment file

2a28880

Add Raman Cross Section on the output files

1bfe20e

Fix name of the pol. tensor file

2ae379e

Fix possible error on readChemicalJSON function.

600c308

Add the modules to create the input and parse the results of the mole…

6d3aebf

…cular dynamics

Add other DispersionCorrection methods and improve the parsing of opt…

d4377c9

…imization

Improve the saving of the AXSF format

1cd83bb

Move some codes to the parse_cp2k module

2912862

Fix the molecular_dynamics module

b4a8cde

Fix error on get_forces of Raman

fb4f0c9

Fix small errors

d0437d6

Fix missing line

14eabd5

Add 'SZV', 'TZVP' as options for basis set

35148cd

Use the developed function to save cif files

8c3ed83

Add the molecular dynamics to the documentation

da3f8a4

Fix parallel and perpendicular raman equations

93b2343

Remove the dictionary parameters from create_input_file function.

29ea654

Fix error on the saving of the vibrabional modes on axsf format.

0df792c

lipelopesoliveira added 12 commits September 27, 2024 10:45

Save the vibrational modes in ChemJson format

a3a65da

Add the Resolution option for raman curve generation

8a886f6

Add CurveLimits option to specify Raman/IR spectrum plot limits

a38fc89

Replace print statements with warnings for polarizability tensor checks

7b9366f

Move the code to calculate Raman Tensor Placzek Invariants to the cal…

b45bf2e

…culate_properties

Add function to calculate Raman intensity and refactor usage in phono…

8417b20

…n parsing

Add functions to save vibrational modes and Raman data, including CSV…

2278bcb

… output and spectrum calculation

Fix formatting issues in parse_phonon.py by correcting dictionary syntax

e27afa3

Add informative print statement and fix input file naming in generate…

f38fdf4

…_shift.py and calculate_properties.py

Refactor save_raman_data function call for improved readability and p…

997bc85

…arameter clarity in parse_phonon.py

Add header documentation and print statement for scripts

a7a159f

Remove author name from header documentation in constants.py

584da0e

lipelopesoliveira requested a review from neumannrf February 9, 2025 14:52

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Manually calculate the Raman Intensities #13

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Manual Raman Intensity Calculation Using Small Displacements Approach

Key Features

Usage and Execution

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