#!/usr/bin/python3
import numpy as np
from ..periodic_table import ELEMENTS
def _to_system_data_lower(lines):
system = {}
natoms = int(lines[0].split()[0])
cell = []
for idx, ii in enumerate(lines):
if "lattice" in ii or "Lattice" in ii or "LATTICE" in ii:
for kk in range(idx + 1, idx + 1 + 3):
vector = [float(jj) for jj in lines[kk].split()[0:3]]
cell.append(vector)
system["cells"] = np.array([cell])
coord = []
atomic_number = []
atom_numbs = []
for idx, ii in enumerate(lines):
if "Position" in ii or "POSITION" in ii or "position" in ii:
for kk in range(idx + 1, idx + 1 + natoms):
min = kk
for jj in range(kk + 1, idx + 1 + natoms):
if int(lines[jj].split()[0]) < int(lines[min].split()[0]):
min = jj
lines[min], lines[kk] = lines[kk], lines[min]
for gg in range(idx + 1, idx + 1 + natoms):
tmpv = [float(jj) for jj in lines[gg].split()[1:4]]
tmpv = np.matmul(np.array(tmpv), system["cells"][0])
coord.append(tmpv)
tmpn = int(lines[gg].split()[0])
atomic_number.append(tmpn)
for ii in np.unique(sorted(atomic_number)):
atom_numbs.append(atomic_number.count(ii))
system["atom_numbs"] = [int(ii) for ii in atom_numbs]
system["coords"] = np.array([coord])
system["orig"] = np.zeros(3)
atom_types = []
for idx, ii in enumerate(system["atom_numbs"]):
for jj in range(ii):
atom_types.append(idx)
system["atom_types"] = np.array(atom_types, dtype=int)
system["atom_names"] = [ELEMENTS[ii - 1] for ii in np.unique(sorted(atomic_number))]
return system
[docs]
def to_system_data(lines):
return _to_system_data_lower(lines)
[docs]
def from_system_data(system, f_idx=0, skip_zeros=True):
ret = ""
natoms = sum(system["atom_numbs"])
ret += "%d" % natoms
ret += "\n"
ret += "LATTICE"
ret += "\n"
for ii in system["cells"][f_idx]:
for jj in ii:
ret += "%.16e " % jj
ret += "\n"
ret += "POSITION"
ret += "\n"
atom_numbs = system["atom_numbs"]
atom_names = system["atom_names"]
atype = system["atom_types"]
posis = system["coords"][f_idx]
# atype_idx = [[idx,tt] for idx,tt in enumerate(atype)]
# sort_idx = np.argsort(atype, kind = 'mergesort')
sort_idx = np.lexsort((np.arange(len(atype)), atype))
atype = atype[sort_idx]
posis = posis[sort_idx]
symbal = []
for ii, jj in zip(atom_numbs, atom_names):
for kk in range(ii):
symbal.append(jj)
atomic_numbers = []
for ii in symbal:
atomic_numbers.append(ELEMENTS.index(ii) + 1)
posi_list = []
for jj, ii in zip(atomic_numbers, posis):
ii = np.matmul(ii, np.linalg.inv(system["cells"][0]))
posi_list.append("%d %15.10f %15.10f %15.10f 1 1 1" % (jj, ii[0], ii[1], ii[2]))
for kk in range(len(posi_list)):
min = kk
for jj in range(kk, len(posi_list)):
if int(posi_list[jj].split()[0]) < int(posi_list[min].split()[0]):
min = jj
posi_list[min], posi_list[kk] = posi_list[kk], posi_list[min]
posi_list.append("")
ret += "\n".join(posi_list)
return ret