fitsnap

The code generates a SNAP potential in LAMMPS format from the fitting of reference energies and/or atomic forces.

Citation

A. Lunghi, S. Sanvito, A unified picture of the covalent bond within quantumaccurate force fields: From organic molecules to metallic complexes’ reactivity. Sci. Adv. 5, eaaw2210 (2019)

Usage

The execution of the code with no command-line arguments prints out the available keywords. fitsnap.x

 -inp <lammps_input_file_heading>
 -datas <dataset_info_file>
 -pot_fix <LAMMPS_potential_file>
 -pot_fit <SNAP_potential_info_file>
 -ener perform the fitting of reference energies
 -force perform the fitting of reference energies
 -skip_fit does not perform a fitting but simply test the potential
 -compress <value of L2 norm constraint>
 -E0 <it can be either 1 or 0. Use 1 if all the training geometries contain the same number of atoms/atomic kind and 0 in any other case.>
 -refine <max new configurations> <MD temperature> <threshold for Gaussian metric>
 
 <lammps_input_file_heading>: Input file necessary to initialize a LAMMPS simulation.

 <dataset_info_file>: Contain the information about the training set used to fit SNAP.
 
 Line1: $(N: number of lammps' data files)
 Line2: $(name of data file 1) $(number of configurations) $(name of .xyz file containing all the geometries) $(if keyword -ener, name of .xyz file containing all the energies) $(if keyword -force, name of the file containing all the forces) $(weight)
 Line3: $(name of data file 2) $(number of configurations) $(name of .xyz file containing all the geometries) $(if keyword -ener, name of .xyz file containing all the energies) $(if keyword -force, name of the file containing all the forces) $(weight)
 ...For each LAMMPS data file
 
 The energies file should contain 1 column of numbers
 The structures file should contain a list of geometries in the xyz format
 The forces file should contain a list of forces in the xyz format but without the atomic labels column.
 

 <LAMMPS_potential_file>: Input file to set up a potantial in LAMMPS, including the SNAP potential that needs to be determined.

 <SNAP_potential_info_file>: File containing all the information on the SNAP potential to be determined.

 Line1: $(Radial Cutoff), $(Order of the bispectrum component 2J), $(Number of bispectrum components for the selected order), 0
 Line2: $(Number of atomic kinds)
 Line3: $(Label atomic kind 1) 1 $(element radius) $(weight) $(sigma gaussian metric)
 Line4: $(Label atomic kind 3) 2 $(element radius) $(weight) $(sigma gaussian metric)
 Line5: $(Label atomic kind 3) 3 $(element radius) $(weight) $(sigma gaussian metric)
 ...For each atomic kind
 
 Example: 
 
 Generation of SNAP potential for Water using 100 configurations and energies. 
 The SNAP potential is constructed for the Oxygen and Hydrogen atomic kinds using a bispectrum order of 2J=8 (56 parameters per kind).
 
 Command: "fitsnap.x -inp lammps_inp -datas data_file -pot_fix pot.fix -pot_fit pot.fit -ener"
 
 lammps_inp: 
      units real
      atom_style atomic
      pair_style snap
      
 data_file:
      1
      data.Water 100 Water.xyz Water.ener 1.0
 
 pot.fix:
      pair_coeff * * snapcoeff O H snapparam O H
      
 pot.fit:
      3.1000 8 56 0
      2
      O 1 0.5 1.0 1.0
      H 2 0.5 1.0 1.0