Manually calculate the Raman Intensities

[lipelopesoliveira]

This PR introduces the new code to manually calculate the Raman intensity (total, perpendicular and parallel) using the small displacements approach and the polarizability tensor as a result of #4.

The code uses the Phono3py package to generate the dynamical matrix from the atomic forces and deal with the symmetry analysis.

There is now two scripts necessary to calculate the vibrational modes:

• generate_shift.py: Generates the input files for the cartesian displacements for all atoms in three directions (x, y, z) and in two polarizations (+, -);
• parse_phonon.py: Reads the results and calculates the vibrational modes, irreductive representations, and Raman intensities (total, perpendicular and parallel).

All the displacements generated by the first script are saved separately and can be executed independently.

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 0.0005 \
                  --UseOT \
                  --CalculateRaman \
                  --CalculateIR \
                  ${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 0.0005 \
                --CalculateRaman \
                --CalculateIR \
                --SaveVecs \
                ${OutputFolder}

The first script generate the inputs and execute the simulations for all displacements. The line containing the command to execute CP2K can be replaced by a command to submit a job on a HPC cluster.

The second script parse de results and generate the files with the Raman information:

• A VIBRATION_FILES folder containing the displacement vectors for all vibrational modes to be visualized on VESTA. The of the files follows the pattern: {FrameworkName}_{ModeNumber}_{IrreductiveRepresentation}_{Freq};
• A {FrameworkName}_all.axsf file containing all the displacement vectors in a single file to be visualized by XCrysDen;
• A {FrameworkName}_RamanTable.csv file containing the raman data;
• A {FrameworkName}_ RAMAN_Curve.csv` file containing the normalized (by total intensity) raman curve;

Closes #4

[lipelopesoliveira]

@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]

@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.

[neumannrf]

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

[lipelopesoliveira]

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

I'm still working on this.