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)
cluster = Cluster(co.cell, centers, layers, electro)
key = AtomKeys.BADER_CHARGE
cluster.estimate_charges_mulliken(dcm.matrix, ocm.matrix, key)
dirname = "cluster_test%d_%d_%d" % (num, layers, electro)
cluster.write_structure(dirname)
cluster.write_charges(key, dirname)
cluster.write_embedding(key, dirname)
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)
cluster.write_structure(dirname)
cluster.write_charges(dirname)
cluster.write_embedding(dirname)
rewrite_files(d, cluster, dirname)
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)
cluster.write_structure(dirname)
cluster.write_charges(key, dirname)
cluster.write_embedding(key, dirname)
import re, sys, math, logging
sys.dont_write_bytecode = True
from qcldm.openmx_format.dat_format import DAT_INPUT
from qcldm.util.log_colorizer import init_log
from qcldm.util.xyz_format import write_xyz
from qcldm.structures.cluster_embedding import Cluster
init_log(sys.argv)
d = DAT_INPUT.from_file('test.dat')
write_xyz(d.cell.cell, 'cell.xyz')
num = int(sys.argv[1])
layers = int(sys.argv[2])
electro = int(sys.argv[3])
center = d.cell.cell[num - 1]
centers = [center]
tmpshells = d.cell.neighbours.neighbours_cluster(centers, 2)
for a in tmpshells[-1]:
if a.name() != center.name():
centers.append(a)
cluster = Cluster(d.cell, centers, layers, electro)
dirname = "cluster_test%d_%d_%d" % (num, layers, electro)
cluster.load_atoms_dummy()
cluster.write_structure(dirname)