Examples
Example 1: Workflow on local machine
The following example shows the complete workflow run on a local machine.
Calculate transfer integral between pairs of molecules (Javerage):
First, create a folder containing the geometry file (.cif, .gen, .sdf, or .xyz). The folder used in this example, named Anthracene, can be downloaded from the Uploads Folder.
In the Anthracene folder, unwrap the structure to whole molecules, and calculate the transfer integral between each unique pair of molecules in the system, using the following command.
elph --javerage
Once the job has completed, the following files and folders can be found in the Anthracene folder.
1/ A/ 950158.cif atom_mapping.json J_C.json
2/ B/ all_pairs.json J_A.json
3/ C/ all_pairs.xyz J_B.json
The J files (J_A.json, J_B.json, J_C.json) present the transfer integral in meV of each pair described in all_pairs.json.
Calculate the variance of transfer integrals (Sigma):
Before calculating Sigma, which is the variance of the transfer integral due to vibrations in the system, the phonons have to be computed. DCS-Flow calculates the phonon modes as the second part of its own workflow (2-phonons).
Copy the following files to the Anthracene folder
FORCE_SETS phonopy_params.yaml
Calculate the variance (Sigma) within the finite differences method using the command
elph --sigma
After the job is done, the following files and folders will be written in the Anthracene folder.
1/displacements/... A/displacements/... A_disp_js.npz Sigma_A.json phonon.npz
2/displacements/... B/displacements/... B_disp_js.npz Sigma_B.json
3/displacements/... C/displacements/... C_disp_js.npz Sigma_A.json
The Sigma files (Sigma_A.json, Sigma_B.json, Sigma_C.json) present the variance of the transfer integral in meV of each pair
Calculate the mobility
Create the lattice and parameters files, lattice.jsonand params.json, with the command
elph --write_files
Edit the files to match the following values
lattice.json:
{
"nmuc": 2,
"coordmol": [
[0.0, 0.0, 0.0],
[0.5, 0.5, 0.0]
],
"unitcell": [
[1.0, 0.0, 0.0],
[0.0, 1.7321, 0.0],
[0.0, 0.0, 1000.0]
],
"supercell": [16, 16, 1],
"unique": 6,
"uniqinter": [
[1, 1, 1, 0, 0, 1],
[2, 2, 1, 0, 0, 1],
[1, 2, 0, 0, 0, 3],
[2, 1, 1, 0, 0, 2],
[2, 1, 0, 1, 0, 2],
[2, 1, 1, 1, 0, 3]
]
}
params.json:
{
"javg": [0.058, 0.058, 0.058],
"sigma": [0.029, 0.029, 0.029],
"nrepeat": 50,
"iseed": 3987187,
"invtau": 0.005,
"temp": 0.025
}
Use the following command to calculate the mobility (in cm2/(V . s))
elph --mobility
Visualize Sigma
In order to visualize the atomic contributions to Sigma, run
elph --view atoms
Or to visualize the 3 highest contributing phonon modes to Sigma, used
elph --view modes 3
Example 2: Workflow on NERSC
The following example shows the complete workflow run on the NERSC supercomputer.
Calculate transfer integral between pairs of molecules (Javerage):
Upload the Anthracene folder to NERSC using a file transfer software like Globus. The folder should contain the .cif file and the following run script (run.py)
#!/bin/bash
#SBATCH -J anthracene
#SBATCH -q debug
#SBATCH -N 1
#SBATCH -t 00:30:00
#SBATCH -C knl
#SBATCH --output=out.out
#SBATCH --error=err.out
#SBATCH --open-mode=append
#Print output before end of run
export PYTHONUNBUFFERED=1
export GAUSSIAN_BASIS='3-21G*'
export GAUSSIAN_CORES=12
#run the application:
eval $'elph --javerage'
Unwrap the structure to whole molecules, and submit the jobs to calculate the transfer integral between each unique pair of molecules in the system, by submitting the run script.
sbatch run.py
The script will submit a job for each molecule and pair of molecules (1, 2, 3, A, B, C). Check the progress of the submitted jobs using
sqs
Once all the jobs are done, read the calculated transfer integrals submitting the same run script changing the last line to
eval $'elph --read_javg'
After this, the following files and folders can be found in the Anthracene folder.
1/ A/ 950158.cif J_A.json atom_mapping.json
2/ B/ all_pairs.json J_B.json err.out
3/ C/ all_pairs.xyz J_C.json out.out
The J files (J_A.json, J_B.json, J_C.json) present the transfer integral in meV of each pair described in all_pairs.json.
Calculate the variance of transfer integrals (Sigma):
The phonons in the system have to be precomputed. DCS-Flow calculates the phonon modes as the second part of its own workflow (2-phonons).
Upload the following files to the Anthracene folder
FORCE_SETS phonopy_params.yaml
Calculate the variance (Sigma) within the finite differences method submitting the run script with the updated command (depending on the size of the system 30 minutes in the debug queue is not enough to submit all the jobs, consider using -q as ‘regular’ and -t 01:00:00 or more)
eval $'elph --sigma'
A job for each displaced atom will be submitted. After all jobs are done, read the result submitting the run script with (this takes less than 10 minutes)
eval $'elph --read_sigma'
The following files and folders will be written in the Anthracene folder.
1/displacements/... A/displacements/... A_disp_js.npz Sigma_A.json phonon.npz
2/displacements/... B/displacements/... B_disp_js.npz Sigma_B.json
3/displacements/... C/displacements/... C_disp_js.npz Sigma_A.json
The Sigma files (Sigma_A.json, Sigma_B.json, Sigma_C.json) present the variance of the transfer integral in meV of each pair.
Calculate the mobility
Create the lattice and parameters files, lattice.jsonand params.json, with the command
elph --write_files
Edit the files to match the following values
lattice.json:
{
"nmuc": 2,
"coordmol": [
[0.0, 0.0, 0.0],
[0.5, 0.5, 0.0]
],
"unitcell": [
[1.0, 0.0, 0.0],
[0.0, 1.7321, 0.0],
[0.0, 0.0, 1000.0]
],
"supercell": [16, 16, 1],
"unique": 6,
"uniqinter": [
[1, 1, 1, 0, 0, 1],
[2, 2, 1, 0, 0, 1],
[1, 2, 0, 0, 0, 3],
[2, 1, 1, 0, 0, 2],
[2, 1, 0, 1, 0, 2],
[2, 1, 1, 1, 0, 3]
]
}
params.json:
{
"javg": [0.058, 0.058, 0.058],
"sigma": [0.029, 0.029, 0.029],
"nrepeat": 50,
"iseed": 3987187,
"invtau": 0.005,
"temp": 0.025
}
Submit the run script to calculate the mobility (in cm2/(V . s)) by updating the command to
eval $'elph --mobility'