dlmonte_python_setup/Supercell.py at master · jrhmanning/dlmonte_python_setup · GitHub

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conversion = {
    '1.147' : 'Zn',
    '-0.63': 'O',
    '-1.30': 'O\_Zn',
    '0.72' : 'C\_OO',
    '-0.071' : 'C\_COO',
    '-0.102' : 'C',
    '0.118' : 'H'
}

def printcoords(atomlist, name='IRMOF1', number=424):
    output='MOLECULE {0:s} {1:10d} {2:10d}\n'.format(name, number, number)
    for i in atomlist:
        output += '{0:10s}c\n{1:15.7f}{2:15.7f}{3:15.7f}  0\n'.format(i[0], i[1], i[2], i[3])

    return output

def convertcoords(rawlist):
    output = []
    for i in rawlist:
        output.append([conversion[i[5]], float(i[1]), float(i[2]), float(i[3])])
    return output

def offset(list, x=False, y=False, z=False):
    output = []
    for i in list:
        element = []
        element.append(i[0])
        element.append(i[1]+box[0] if x else i[1])
        element.append(i[2]+box[1] if y else i[2])
        element.append(i[3]+box[2] if z else i[3])
        output.append(element)
    return output

input = "IRMOF1step0.mol"
alldata = []
with open(input, 'r') as f:
    for line in f:
        alldata.append(line.split())

coords = []
for i in alldata[4:-8:]:
    coords.append(i)
box = []
for i in alldata[-1]:
    box.append(float(i))
print(box)
#print(coords[-1])
for i in coords:
    if i[5] == '-1.30':
        print(i)

basicunit = convertcoords(coords)
unit001 = offset(basicunit, False, False, True)
unit010 = offset(basicunit, False, True, False)
unit100 = offset(basicunit, True, False, False)
unit110 = offset(basicunit, True, True, False)
unit101 = offset(basicunit, True, False, True)
unit011 = offset(basicunit, False, True, True)
unit111 = offset(basicunit, True, True, True)
cell000 = printcoords(basicunit)

with open('testconfig.txt', 'w') as f:
    f.write('Test Autogenerated supercell\n   0   1\n')
    f.write('{0:15.7f}{1:15.7f}{2:15.7f}\n'.format(box[0]*2, 0., 0.))
    f.write('{1:15.7f}{0:15.7f}{2:15.7f}\n'.format(box[1]*2, 0., 0.))
    f.write('{2:15.7f}{1:15.7f}{0:15.7f}\n'.format(box[2]*2, 0., 0.))
    f.write('NUMMOL 2 6000 8\n')
    f.write('''MOLECULE Nitrogen         3         3
 N        c
      9.9188610      9.4992033      9.2883771     0
 M        c
      9.7441457      9.1889227      9.7075434     0
 N        c
     10.5043414      8.8264009     10.4777255     0
''')
    f.write(printcoords(basicunit) + '\n')
    f.write(printcoords(unit001) + '\n')
    f.write(printcoords(unit010) + '\n')
    f.write(printcoords(unit100) + '\n')
    f.write(printcoords(unit011) + '\n')
    f.write(printcoords(unit101) + '\n')
    f.write(printcoords(unit110) + '\n')
    f.write(printcoords(unit111))