LINEAR Tutorial

LINEAR Tutorial

This tutorial uses the MatPL [source root/example/SiC] example to demonstrate training, testing, LAMMPS simulation, and other operations for a Linear model. The example directory is organized as follows.

SiC
  ├── 1_300_MOVEMENT
  ├── 2_300_MOVEMENT
  ├── atom.config
  ├── linear_test.json
  ├── linear_train.json
  ├── train.job
  ├── linear_lmps
  └── MD
      └── MOVEMENT

• linear_train.json is the input file for training the Linear force field.
• linear_test.json is the input file for testing the Linear force field.
• train.job is an example Slurm job script for training.
• The linear_lmps directory contains a LAMMPS MD example for the Linear force field:
  • Force-field file: forcefield.ff
  • Initial structure: lmp.config
  • Control file: in.lammps
  • Example Slurm script: runcpu.job

train

Run the following command in the SiC directory to start training: Example etot.input input file:

MatPL train linear_train.json
# Alternatively, update the environment variables and submit the training job through Slurm: sbatch train.job

Input file description

The contents of linear_train.json are shown below. For descriptions of the Linear parameters, see the Parameter Reference:

{   
    "train_data":["./1_300_MOVEMENT", "./2_300_MOVEMENT"],
    "valid_data":["./1_300_MOVEMENT"],
    "format":"pwmat/movement",
    "model_type": "Linear",
    "atom_type":[14, 6]
}

After the program runs, it creates a forcefield directory in the working directory:

forcefield
├── forcefield.ff
├── fread_dfeat            
│   ├── energyL*           
│   ├── forceL*            
│   ├── linear*            
│   ├── weight_feat.*      
│   ├── energyL*           
│   ├── ...           
│   ├── feat*          
│   ├── weight_feat.*          
│   └── linear_fitB.ntype     
├── input          
│   └── *feature.in     
└── (output)                     
    └── grid*   # Used for features 1 and 2

test

MatPL test linear_test.json

The contents of test.json are shown below. For parameter descriptions, see the Parameter Reference.

{   
    "test_movement_file":["./MD/MOVEMENT"],
    "format": "pwmat/movement",
    "model_type": "Linear",
    "atom_type":[14, 6]
}

Note that the MOVEMENT file must be placed in a directory named MD; otherwise, it cannot be detected. After testing, the test_result force-field directory contains the following files:

lammps MD

For installation and usage of the LAMMPS interface for Linear models, see lammps-fortran.

Use the trained *.ff force-field file for the LAMMPS simulation. Add the following settings to the LAMMPS input file:

pair_style      matpl
pair_coeff      * * 1 1 forcefield.ff 14 6

The first 1 selects a force field generated by the Linear model, and the second 1 specifies that one force-field file is read. forcefield.ff is the force-field file generated by MatPL, while 14 and 6 are the atomic numbers of Si and C, respectively.