dpgen.data.tools package

dpgen.data.tools package#

Submodules#

dpgen.data.tools.bcc module#

dpgen.data.tools.bcc.gen_box()[source]#
dpgen.data.tools.bcc.numb_atoms()[source]#
dpgen.data.tools.bcc.poscar_unit(latt)[source]#

dpgen.data.tools.cessp2force_lin module#

dpgen.data.tools.cessp2force_lin.Parser()[source]#
dpgen.data.tools.cessp2force_lin.get_outcar_files(directory, recursive)[source]#
dpgen.data.tools.cessp2force_lin.process_outcar_file_v5_dev(outcars, data, numbers, types, max_types, elements=None, windex=None, fout='potfit.configs')[source]#
dpgen.data.tools.cessp2force_lin.scan_outcar_file(file_handle)[source]#
dpgen.data.tools.cessp2force_lin.uniq(seq)[source]#

dpgen.data.tools.create_random_disturb module#

dpgen.data.tools.create_random_disturb.RandomDisturbParser()[source]#
dpgen.data.tools.create_random_disturb.create_disturbs_abacus_dev(fin, nfile, dmax=1.0, etmax=0.1, ofmt='abacus', dstyle='uniform', write_d=False, diag=0)[source]#
dpgen.data.tools.create_random_disturb.create_disturbs_ase(fin, nfile, dmax=1.0, ofmt='lmp', dstyle='uniform', write_d=False)[source]#
dpgen.data.tools.create_random_disturb.create_disturbs_ase_dev(fin, nfile, dmax=1.0, etmax=0.1, ofmt='lmp', dstyle='uniform', write_d=False, diag=0)[source]#
dpgen.data.tools.create_random_disturb.create_disturbs_atomsk(fin, nfile, dmax=1.0, ofmt='lmp')[source]#
dpgen.data.tools.create_random_disturb.create_random_alloys(fin, alloy_dist, ifmt='vasp', ofmt='vasp')[source]#

In fact, atomsk also gives us the convinient tool to do this.

dpgen.data.tools.create_random_disturb.gen_random_disturb(dmax, a, b, dstyle='uniform')[source]#
dpgen.data.tools.create_random_disturb.gen_random_emat(etmax, diag=0)[source]#
dpgen.data.tools.create_random_disturb.random_range(a, b, ndata=1)[source]#

dpgen.data.tools.diamond module#

dpgen.data.tools.diamond.gen_box()[source]#
dpgen.data.tools.diamond.numb_atoms()[source]#
dpgen.data.tools.diamond.poscar_unit(latt)[source]#

dpgen.data.tools.fcc module#

dpgen.data.tools.fcc.gen_box()[source]#
dpgen.data.tools.fcc.numb_atoms()[source]#
dpgen.data.tools.fcc.poscar_unit(latt)[source]#

dpgen.data.tools.hcp module#

dpgen.data.tools.hcp.gen_box()[source]#
dpgen.data.tools.hcp.numb_atoms()[source]#
dpgen.data.tools.hcp.poscar_unit(latt)[source]#

dpgen.data.tools.io_lammps module#

ASE Atoms convert to LAMMPS configuration Some functions are adapted from ASE lammpsrun.py.

dpgen.data.tools.io_lammps.ase2lammpsdata(atoms, typeids=None, fout='out.lmp')[source]#
dpgen.data.tools.io_lammps.car2dir(v, Ainv)[source]#

Cartesian to direct coordinates.

dpgen.data.tools.io_lammps.convert_cell(ase_cell)[source]#

Convert a parallel piped (forming right hand basis) to lower triangular matrix LAMMPS can accept. This function transposes cell matrix so the bases are column vectors.

dpgen.data.tools.io_lammps.convert_forces(forces0, cell0, cell_new)[source]#
dpgen.data.tools.io_lammps.convert_positions(pos0, cell0, cell_new, direct=False)[source]#
dpgen.data.tools.io_lammps.convert_stress(s6_0, cell0, cell_new)[source]#
dpgen.data.tools.io_lammps.dir2car(v, A)[source]#

Direct to cartesian coordinates.

dpgen.data.tools.io_lammps.get_atoms_ntypes(atoms)[source]#
dpgen.data.tools.io_lammps.get_typeid(typeids, csymbol)[source]#
dpgen.data.tools.io_lammps.is_upper_triangular(mat)[source]#

Test if 3x3 matrix is upper triangular LAMMPS has a rule for cell matrix definition.

dpgen.data.tools.io_lammps.set_atoms_typeids(atoms)[source]#
dpgen.data.tools.io_lammps.set_atoms_typeids_with_atomic_numbers(atoms)[source]#
dpgen.data.tools.io_lammps.stress6_to_stress9(s6)[source]#
dpgen.data.tools.io_lammps.stress9_to_stress6(s9)[source]#

dpgen.data.tools.ovito_file_convert module#

dpgen.data.tools.poscar_copy module#

dpgen.data.tools.sc module#

dpgen.data.tools.sc.gen_box()[source]#
dpgen.data.tools.sc.numb_atoms()[source]#
dpgen.data.tools.sc.poscar_unit(latt)[source]#