Source code for hiphive.input_output.gpumd

import numpy as np
from itertools import permutations, product

[docs]def write_fcs_gpumd(fname_fc: str, fname_clusters: str, fcs, order: int, tol: float = 1e-10): """ Writes force constants of given order in GPUMD format. Parameters ---------- fname_fc name of file which contains the lookup force constants fname_clusters name of file which contains the clusters and the force constant lookup index fcs force constants order force constants for this order will be written to file tol if the norm of a force constant term is less than this value it will be excluded from the output; if two force-constants differ by this value or less, they are considered equal. """ cluster_lookup, fc_lookup = _get_lookup_data_smart(fcs, order, tol) _write_clusters(fname_clusters, cluster_lookup, order) _write_fc_lookup(fname_fc, fc_lookup, order)
def _write_fc_lookup(fname, fc_lookup, order): """ Writes the lookup force constants to file """ fmt = '{}' + ' {}'*order with open(fname, 'w') as f: f.write(str(len(fc_lookup)) + '\n\n') for fc in fc_lookup: for xyz in product(range(3), repeat=order): f.write(fmt.format(*xyz, fc[xyz])+'\n') f.write('\n') def _write_clusters(fname, cluster_lookup, order): """ Writes the cluster lookup to file """ fmt = '{}' + ' {}'*order with open(fname, 'w') as f: f.write(str(len(cluster_lookup)) + '\n\n') for c, i in cluster_lookup.items(): line = fmt.format(*c, i) + '\n' f.write(line) def _get_clusters(fcs, order: int, tol: float): """ Collect all relevant clusters; for 2nd and 3rd-order force constants all permutations are included. """ if order in [2, 3]: clusters = [] for c in fcs._fc_dict.keys(): if len(c) == order and np.linalg.norm(fcs[c]) > tol: for ci in permutations(c): clusters.append(ci) clusters = list(sorted(set(clusters))) else: clusters = [c for c in fcs._fc_dict.keys() if len(c) == order and np.linalg.norm(fcs[c]) > tol] # noqa return clusters def _get_lookup_data_naive(fcs, order: int, tol: float): """ Groups force constants for a given order into groups for which the force constant is identical. """ fc_lookup = [] cluster_lookup = dict() clusters = _get_clusters(fcs, order, tol) for c in clusters: fc1 = fcs[c] if np.linalg.norm(fc1) < tol: continue for i, fc2 in enumerate(fc_lookup): if np.linalg.norm(fc1 - fc2) < tol: cluster_lookup[c] = i break else: cluster_lookup[c] = len(fc_lookup) fc_lookup.append(fc1) return cluster_lookup, fc_lookup def _get_lookup_data_smart(fcs, order: int, tol: float): """ Groups force constants for a given order into groups for which the force constant is identical. """ fc_lookup = [] cluster_lookup = dict() axis = tuple(range(1, order+1)) clusters = _get_clusters(fcs, order, tol) fc_all = np.array([fcs[c] for c in clusters]) indices = list(range(len(clusters))) while len(indices) > 0: i = indices[0] delta = fc_all[indices] - fc_all[i] delta_norm = np.sqrt(np.sum(delta**2, axis=axis)) inds_to_del = [indices[x] for x in np.where(delta_norm < tol)[0]] assert i in inds_to_del fc_lookup.append(fc_all[i]) for j in inds_to_del: indices.remove(j) cluster_lookup[clusters[j]] = len(fc_lookup)-1 return cluster_lookup, fc_lookup
[docs]def write_fcp_txt(fname: str, path: str, n_types: int, max_order: int, heat_current_order: int = 2): """ Write driver potential file for GPUMD. Parameters ---------- fname file name path path to directory with force constant file n_types number of atom types max_order maximum order of the force constant potential heat_current_order heat current order used in thermal conductivity Format is a simple file containing the following fcp number_of_atom_types highest_force_order heat_current_order path_to_force_constant_files which in practice for a binary system with a sixth order model, consider third-order heat-currents, would mean fcp 2 6 3 /path/to/your/folder """ with open(fname, 'w') as f: f.write('fcp {}\n'.format(n_types)) f.write('{} {}\n'.format(max_order, heat_current_order)) f.write('{}'.format(path.rstrip('/'))) # without a trailing '/'
[docs]def write_r0(fname, atoms): """ Write GPUMD r0 file, with reference atomic positions. Parameters ---------- fname : str name of file to which to write the atomic positions atoms : ase.Atoms input structure """ line = '{} {} {}\n' with open(fname, 'w') as f: for a in atoms: f.write(line.format(*a.position))