Davis Computational Spectroscopy Workflow

The Davis Computational Spectroscopy workflow (DCS-Flow) was designed to connect and automate different material sciences tools which facilitate the use and comparison of electronic methods such as DFT, DFTB; molecular mechanics method such as molecular dynamics to simulate the structure and dynamics of materials properties for improved structure property prediction. DCS-Flow provides an efficient workflow to create databases of inelastic neutron scattering (INS) simulations

Installation

1. DCSflow

git clone https://github.com/moule-group/DCSflow.git
cd DCSflow
conda create -n dcsflow
pip install .

2. DFTB+

Install DFTB:

    conda install 'dftbplus=*=nompi_*'

Then download and extract the parameter set mio-1-1 at https://github.com/dftbparams/mio/releases

3. Oclimax

Download the file oclimax from the page https://sites.google.com/site/ornliceman/download

If using Shifter instead of Docker, modify the file and replace the run and convert functions with:

run() 
{
        CMD="shifter --image=docker:ornliceman/oclimax oclimax $1 ${@:2}"
        command $CMD
}

convert()
{
        CMD="shifter --image=docker:ornliceman/oclimax 2climax.py $1 ${@:2}"
        command $CMD
}

4. Append environmental variables

In ~/.bashrc, add:

export DFTB_PREFIX="your_path/mio-1-1/" # SK files for DFTB
export VASP_PP_PATH="your_path" # VASP PP path
export PATH="your_path/oclimax/bin":$PATH # Oclimax path

Description

There are 2 Methods for simulating the INS spectrum. One is finite displacement method (FD) and the other is molecular dynamics method (MD). The theory of these 2 methods are written in the "Theory" section. Currently, there are 2 calculators in DCS-flow: VASP and DFTB+.

Documentation

Workflows

(a) DFT-FD: Relaxation --> Phonon --> Oclimax

(b) DFTB-FD: Relaxation --> Phonon --> Oclimax

(c) DFT-MD: Relaxation --> Nvt-md --> Nve-md --> Oclimax

(d) DFTB-MD: Relaxation --> Nvt-md --> Nve-md --> Oclimax

Options (defaults are bolded)

Command	Explanation	DFT-FD	DFTB-FD	DFT-MD	DFTB-MD
-w	workflow (int)	1	2	3	4
-r	relaxation (boolean)	True/False	True/False	True/False	True/False
-p	phonons (boolean)	True/False	True/False	N/A	N/A
-nvt	NVT-MD (boolean), apply when workflow = 3 or 4	N/A	N/A	True/False	True/False
-nve	NVE-MD (boolean), apply when workflow = 3 or 4	N/A	N/A	True/False	True/False
-o	oclimax (boolean)	True/False	True/False	True/False	True/False
-l	Running VASP in local machine, apply when workflow = 1 or 3 (boolean)	True/False	N/A	True/False	N/A
-g	Running VASP on HPC GPU mode, apply when workflow = 1 or 3 (boolean). If Flase, run on CPU mode	True/False	N/A	True/False	N/A
-a	If -g, set your account # in slurm script (str)	your account #	N/A	your account #	N/A
-t	If -g, set time limit on HPC	01:00:00	N/A	01:00:00	N/A
-H	srun setting for VASP simulation, i.e.: srun -n 8 -c 32 -G 8 --cpu-bind=cores --gpu-bind=none vasp_std"	8 32 8	N/A	8 32 8	N/A
-f	Converge if forces on all atoms < fmax	Float 1e-2	Float 1e-2	Float 1e-2	Float 1e-2
-t1	Initial temperature for MD simulation (K)	N/A	N/A	Float 150.0	Float 150.0
-t2	Final temperature for MD simulation (K), currently not under usage	N/A	N/A	Float 150.0	N/A
-k	Kpoints for simulation. We recommend increase K-grid in relaxation	1 1 1	1 1 1	1 1 1	1 1 1
-s	Supercell size	2 2 2	2 2 2	2 2 2	2 2 2
-d	Apply dispersion correction, refer to vasp docs. For DFTB, only support DFT-D3 (Becke-Johnson) if -d > 0	int 12	int 12	int 12	int 12
-m	The mesh grid running phonopy mesh	8 8 8	8 8 8	N/A	N/A
-n1	Number of NVT MD steps, apply when workflow = 3 or 4	N/A	N/A	int 4000	int 4000
-n2	Number of NVE MD steps for each loop, apply when workflow = 3 or 4	N/A	N/A	int 4000	int 4000
-step	Multiple of NVE-MD steps; (i.e. 4000*steps is the total steps for NVE-MD)	N/A	N/A	int 10	int 10

Usage:

Specify workflow using -w, and then specify the steps you are running (relaxation: -r; phonon: -p; NVTMD: -nvt; NVEMD: -nve; Oclimax:-o).

Example: DFTB-FD relaxation

dcsflow -w 2 -r

Theory

1. Finite Displacement Method (Phonopy)

2. Molecular Dynamics Method