def outputMolecule(singleMol, dataDir):
molecule = Molecule([], [])
for site in singleMol:
molecule.append(str(site.specie), site.coords)
xyzObj = XYZ(molecule)
os.chdir(dataDir)
os.system('mkdir singleMolecule')
xyzObj.write_file(dataDir + '/singleMolecule/singleMol.xyz')
def getAllMols(supercell, bondDict):
# molList is the list of pymatgen Molecule object
# tmpMol is pyatgen Molecule object
molList = []
while len(supercell.sites) != 0:
# function getCentralSingleMol returns a dictionary
# the keys are the index of each sites in supercell
print('length of supercell:', len(supercell.sites))
molsites = Molecule([], [])
molindex = list()
tmpMol = getCentralSingleMol(supercell, bondDict)
for siteIndex in tmpMol.keys():
molsites.append(str(tmpMol[siteIndex].specie),
tmpMol[siteIndex].coords)
molindex.append(siteIndex)
supercell.remove_sites(molindex)
molList += [molsites]
return molList
def outputMolecule(singleMol, dataDir):
molecule = Molecule([], [])
singlemolpath = os.path.join(dataDir, 'singlemolecule')
for siteIndex in singleMol.keys():
molecule.append(str(singleMol[siteIndex].specie), singleMol[siteIndex].coords)
xyzObj = XYZ(molecule)
if "singleMol.xyz" in os.listdir(singlemolpath):
decision = None
print('You have one \'singleMol.xyz\' file inside the single molecule path.')
print('This previous file will be overwritten.')
while decision != 'Y' and decision != 'N':
decision = input('Do you want to proceed? Y for yes, N for no.')
if decision == 'Y':
xyzObj.write_file(os.path.join(singlemolpath, 'singleMol.xyz'))
print('The single molecule structure is saved under:', os.path.join(dataDir, 'singlemolecule.singleMol.xyz'))
elif decision == 'N':
print('The previous file is not changed. ')
sys.exit()
else:
print('Not eligible response!!!\n')
else:
xyzObj.write_file(os.path.join(singlemolpath, 'singleMol.xyz'))
print('The single molecule structure is saved under:', os.path.join(dataDir, 'singlemolecule/singleMol.xyz'))
from pymatgen import Molecule
import os
import numpy as np
inpath = "./data/crystals"
namelist = os.listdir(inpath)
outpath = "./data/singmol"
nocando = []
for name in namelist:
structID = name[:-3]
print(structID)
struct = read(os.path.join(inpath, name))
struct = AseAtomsAdaptor.get_structure(struct)
struct.make_supercell([4, 5, 7])
bondDict = getBondDict(struct, bondCutoff)
print(bondDict)
try:
singleMol = getCentralSingleMol(struct, bondDict)
#singleMol.to(filename=outpath+"/"+structID+".xyz")
mol = Molecule([], [])
for site in singleMol.items():
mol.append(str(site[1].specie), site[1].coords)
mol.to(filename=outpath + "/" + structID + "xyz")
except:
nocando.append(structID)
print(nocando)
nocando = np.array(nocando)
np.savetxt('nocandolist.csv', nocando, delimiter=' ', fmt='%s')
