from qcldm.crystal_format.crystal_meta import CrystalMeta from qcldm.util.log_colorizer import init_log from qcldm.util.xyz_format import write_xyz from qcldm.structures.cluster_embedding import Cluster from qcldm.structures.bader_reader import read_baders from qcldm.structures.atom_vector import AtomKeys init_log(sys.argv) c = CrystalMeta() c.load('.') co = CrystalOut.from_file(c.out_file) dcm = CrystalMatrix.from_file(c.dm_file, co.cell, CrystalMatrix.DENSITY, 1e-3) ocm = CrystalMatrix.from_file(c.olp_file, co.cell, CrystalMatrix.OVERLAP, 1e-3) write_xyz(co.cell.cell, 'cell.xyz') #write_xyz(cm.cell.supercell, 'supercell.xyz') read_baders(co.cell) num = int(sys.argv[1]) layers = int(sys.argv[2]) electro = int(sys.argv[3]) center = co.cell.cell[num - 1] centers = [center] tmpshells = co.cell.neighbours.neighbours_cluster(centers, 2) for a in tmpshells[-1]: if a.name() != center.name(): centers.append(a)
#!/usr/bin/python import re, sys, math, logging sys.dont_write_bytecode = True from qcldm.openmx_format.dat_format import DAT_INPUT from qcldm.applications.openmx_rewriter import rewrite_files from qcldm.util.log_colorizer import init_log from qcldm.util.xyz_format import write_xyz from qcldm.matrix.matrix_reader import read_matrices from qcldm.structures.cluster_embedding import Cluster from qcldm.structures.bader_reader import read_baders init_log(sys.argv) d = DAT_INPUT.from_file('temporal_12345.input') write_xyz(d.cell.cell, 'cell.xyz') read_baders(d.cell) dm, olp, atoms = read_matrices(d.cell, 1e-3) num = int(sys.argv[1]) layers = int(sys.argv[2]) electro = int(sys.argv[3]) centers = [d.cell.cell[num - 1]] cluster = Cluster(d.cell, centers, layers, electro) cluster.estimate_charges(dm, olp) dirname = "cluster%d_%d_%d" % (num, layers, electro)
sys.dont_write_bytecode = True from qcldm.crystal_format.crystal_out import CrystalOut from qcldm.util.log_colorizer import init_log from qcldm.util.xyz_format import write_xyz from qcldm.structures.cluster_embedding import Cluster from qcldm.structures.atom_vector import AtomKeys init_log(sys.argv) co = CrystalOut.from_file('out') for a in co.cell.atoms: if a.name() == 'Yb': a.data()[AtomKeys.ESTIMATED_VALENCE] = 3 a.data()[AtomKeys.ESTIMATED_CHARGE] = 3 write_xyz(co.cell.cell, 'cell.xyz') write_xyz(co.cell.supercell, 'supercell.xyz') num = int(sys.argv[1]) layers = int(sys.argv[2]) electro = int(sys.argv[3]) centers = [co.cell.cell[num - 1]] cluster = Cluster(co.cell, centers, layers, electro) key = AtomKeys.MULLIKEN_CHARGE cluster.estimate_charges_dumb(key) dirname = "cluster_%d_%d_%d" % (num, layers, electro)
from qcldm.crystal_format.crystal_out import CrystalOut from qcldm.crystal_format.crystal_meta import CrystalMeta from qcldm.util.log_colorizer import init_log from qcldm.util.xyz_format import write_xyz from qcldm.embedding.cluster import Cluster from qcldm.embedding.embedding_settings import EmbeddingSettings from qcldm.structures.bader_reader import read_baders from qcldm.structures.atom_vector import AtomKeys init_log(sys.argv) c = CrystalMeta() c.load('.') co = CrystalOut.from_file(c.out_file) write_xyz(co.cell.cell, 'cell.xyz') write_xyz(co.cell.supercell, 'supercell.xyz') atoms = [] vectors = [6.91898051, 6.91898051, 6.06871692] zero = [-2.3, -3, -2.3] for a in co.cell.extended_cell(3): ok = True for k in range(3): if a.position()[k] < zero[k] or a.position( )[k] >= zero[k] + vectors[k]: ok = False break if ok: atoms.append(a) write_xyz(atoms, 'ortho1.xyz')