import xml.etree.ElementTree as ET
from xml.dom import minidom
import numpy as np
from ase import Atoms
from ase.utils import writer
[docs]def read_xsd(fd):
tree = ET.parse(fd)
root = tree.getroot()
atomtreeroot = root.find('AtomisticTreeRoot')
# if periodic system
if atomtreeroot.find('SymmetrySystem') is not None:
symmetrysystem = atomtreeroot.find('SymmetrySystem')
mappingset = symmetrysystem.find('MappingSet')
mappingfamily = mappingset.find('MappingFamily')
system = mappingfamily.find('IdentityMapping')
coords = []
cell = []
formula = ''
for atom in system:
if atom.tag == 'Atom3d':
symbol = atom.get('Components')
formula += symbol
xyz = atom.get('XYZ')
if xyz:
coord = [float(coord) for coord in xyz.split(',')]
else:
coord = [0.0, 0.0, 0.0]
coords.append(coord)
elif atom.tag == 'SpaceGroup':
avec = [float(vec) for vec in atom.get('AVector').split(',')]
bvec = [float(vec) for vec in atom.get('BVector').split(',')]
cvec = [float(vec) for vec in atom.get('CVector').split(',')]
cell.append(avec)
cell.append(bvec)
cell.append(cvec)
atoms = Atoms(formula, cell=cell, pbc=True)
atoms.set_scaled_positions(coords)
return atoms
# if non-periodic system
elif atomtreeroot.find('Molecule') is not None:
system = atomtreeroot.find('Molecule')
coords = []
formula = ''
for atom in system:
if atom.tag == 'Atom3d':
symbol = atom.get('Components')
formula += symbol
xyz = atom.get('XYZ')
coord = [float(coord) for coord in xyz.split(',')]
coords.append(coord)
atoms = Atoms(formula, pbc=False)
atoms.set_scaled_positions(coords)
return atoms
def CPK_or_BnS(element):
"""Determine how atom is visualized"""
if element in ['C', 'H', 'O', 'S', 'N']:
visualization_choice = 'Ball and Stick'
else:
visualization_choice = 'CPK'
return visualization_choice
def SetChild(parent, childname, props):
Child = ET.SubElement(parent, childname)
for key in props:
Child.set(key, props[key])
return Child
def SetBasicChilds():
"""
Basic property setup for Material Studio File
"""
XSD = ET.Element('XSD')
XSD.set('Version', '6.0')
ATR = SetChild(XSD, 'AtomisticTreeRoot', dict(
ID='1',
NumProperties='40',
NumChildren='1',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='AngleEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='BendBendEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='BendTorsionBendEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='BondEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Atom',
Name='EFGAsymmetry',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Atom',
Name='EFGQuadrupolarCoupling',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='ElectrostaticEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='GrowthFace',
Name='FaceMillerIndex',
Type='MillerIndex',
))
SetChild(ATR, 'Property', dict(
DefinedOn='GrowthFace',
Name='FacetTransparency',
Type='Float',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Bondable',
Name='Force',
Type='CoDirection',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='HydrogenBondEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Bondable',
Name='ImportOrder',
Type='UnsignedInteger',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='InversionEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Atom',
Name='IsBackboneAtom',
Type='Boolean',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Atom',
Name='IsChiralCenter',
Type='Boolean',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Atom',
Name='IsOutOfPlane',
Type='Boolean',
))
SetChild(ATR, 'Property', dict(
DefinedOn='BestFitLineMonitor',
Name='LineExtentPadding',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Linkage',
Name='LinkageGroupName',
Type='String',
))
SetChild(ATR, 'Property', dict(
DefinedOn='PropertyList',
Name='ListIdentifier',
Type='String',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Atom',
Name='NMRShielding',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='NonBondEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Bondable',
Name='NormalMode',
Type='Direction',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Bondable',
Name='NormalModeFrequency',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Bondable',
Name='OrbitalCutoffRadius',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='BestFitPlaneMonitor',
Name='PlaneExtentPadding',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='PotentialEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ScalarFieldBase',
Name='QuantizationValue',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='RestraintEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='SeparatedStretchStretchEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='Trajectory',
Name='SimulationStep',
Type='Integer',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='StretchBendStretchEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='StretchStretchEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='StretchTorsionStretchEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='TorsionBendBendEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='TorsionEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='TorsionStretchEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='ValenceCrossTermEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='ValenceDiagonalEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='ClassicalEnergyHolder',
Name='VanDerWaalsEnergy',
Type='Double',
))
SetChild(ATR, 'Property', dict(
DefinedOn='SymmetrySystem',
Name='_Stress',
Type='Matrix',
))
return ATR, XSD
def _write_xsd_html(images, connectivity=None):
ATR, XSD = SetBasicChilds()
natoms = len(images[0])
atom_element = images[0].get_chemical_symbols()
atom_cell = images[0].get_cell()
atom_positions = images[0].get_positions()
# Set up bonds
bonds = []
if connectivity is not None:
for i in range(connectivity.shape[0]):
for j in range(i + 1, connectivity.shape[0]):
if connectivity[i, j]:
bonds.append([i, j])
nbonds = len(bonds)
# non-periodic system
if not images[0].pbc.all():
Molecule = SetChild(ATR, 'Molecule', dict(
ID='2',
NumChildren=str(natoms + nbonds),
Name='Lattice="1.0',
))
# writing images[0]
for x in range(natoms):
Props = dict(
ID=str(x + 3),
Name=(atom_element[x] + str(x + 1)),
UserID=str(x + 1),
DisplayStyle=CPK_or_BnS(atom_element[x]),
XYZ=','.join('%1.16f' % xi for xi in atom_positions[x]),
Components=atom_element[x],
)
bondstr = []
for i, bond in enumerate(bonds):
if x in bond:
bondstr.append(str(i + 3 + natoms))
if bondstr:
Props['Connections'] = ','.join(bondstr)
SetChild(Molecule, 'Atom3d', Props)
for x in range(nbonds):
SetChild(Molecule, 'Bond', dict(
ID=str(x + 3 + natoms),
Connects='%i,%i' % (bonds[x][0] + 3, bonds[x][1] + 3),
))
# periodic system
else:
atom_positions = np.dot(atom_positions, np.linalg.inv(atom_cell))
Props = dict(
ID='2',
Mapping='3',
Children=','.join(map(str, range(4, natoms + nbonds + 5))),
Normalized='1',
Name='SymmSys',
UserID=str(natoms + 18),
XYZ='0.00000000000000,0.00000000000000,0.000000000000000',
OverspecificationTolerance='0.05',
PeriodicDisplayType='Original',
)
SymmSys = SetChild(ATR, 'SymmetrySystem', Props)
Props = dict(
ID=str(natoms + nbonds + 5),
SymmetryDefinition=str(natoms + 4),
ActiveSystem='2',
NumFamilies='1',
OwnsTotalConstraintMapping='1',
TotalConstraintMapping='3',
)
MappngSet = SetChild(SymmSys, 'MappingSet', Props)
Props = dict(ID=str(natoms + nbonds + 6), NumImageMappings='0')
MappngFamily = SetChild(MappngSet, 'MappingFamily', Props)
Props = dict(
ID=str(natoms + len(bonds) + 7),
Element='1,0,0,0,0,1,0,0,0,0,1,0',
Constraint='1,0,0,0,0,1,0,0,0,0,1,0',
MappedObjects=','.join(map(str, range(4, natoms + len(bonds) + 4))),
DefectObjects='%i,%i' % (natoms + nbonds + 4, natoms + nbonds + 8),
NumImages=str(natoms + len(bonds)),
NumDefects='2',
)
IdentMappng = SetChild(MappngFamily, 'IdentityMapping', Props)
SetChild(MappngFamily, 'MappingRepairs', {'NumRepairs': '0'})
# writing atoms
for x in range(natoms):
Props = dict(
ID=str(x + 4),
Mapping=str(natoms + len(bonds) + 7),
Parent='2',
Name=(atom_element[x] + str(x + 1)),
UserID=str(x + 1),
DisplayStyle=CPK_or_BnS(atom_element[x]),
Components=atom_element[x],
XYZ=','.join(['%1.16f' % xi for xi in atom_positions[x]]),
)
bondstr = []
for i, bond in enumerate(bonds):
if x in bond:
bondstr.append(str(i + 4 * natoms + 1))
if bondstr:
Props['Connections'] = ','.join(bondstr)
SetChild(IdentMappng, 'Atom3d', Props)
for x in range(len(bonds)):
SetChild(IdentMappng, 'Bond', dict(
ID=str(x + 4 + natoms + 1),
Mapping=str(natoms + len(bonds) + 7),
Parent='2',
Connects='%i,%i' % (bonds[x][0] + 4, bonds[x][1] + 4),
))
Props = dict(
ID=str(natoms + 4),
Parent='2',
Children=str(natoms + len(bonds) + 8),
DisplayStyle='Solid',
XYZ='0.00,0.00,0.00',
Color='0,0,0,0',
AVector=','.join(['%1.16f' % atom_cell[0, x] for x in range(3)]),
BVector=','.join(['%1.16f' % atom_cell[1, x] for x in range(3)]),
CVector=','.join(['%1.16f' % atom_cell[2, x] for x in range(3)]),
OrientationBase='C along Z, B in YZ plane',
Centering='3D Primitive-Centered',
Lattice='3D Triclinic',
GroupName='GroupName',
Operators='1,0,0,0,0,1,0,0,0,0,1,0',
DisplayRange='0,1,0,1,0,1',
LineThickness='2',
CylinderRadius='0.2',
LabelAxes='1',
ActiveSystem='2',
ITNumber='1',
LongName='P 1',
Qualifier='Origin-1',
SchoenfliesName='C1-1',
System='Triclinic',
Class='1',
)
SetChild(IdentMappng, 'SpaceGroup', Props)
SetChild(IdentMappng, 'ReciprocalLattice3D', dict(
ID=str(natoms + len(bonds) + 8),
Parent=str(natoms + 4),
))
SetChild(MappngSet, 'InfiniteMapping', dict(
ID='3',
Element='1,0,0,0,0,1,0,0,0,0,1,0',
MappedObjects='2',
))
return XSD, ATR
[docs]@writer
def write_xsd(fd, images, connectivity=None):
"""Takes Atoms object, and write materials studio file
atoms: Atoms object
filename: path of the output file
connectivity: number of atoms by number of atoms matrix for connectivity
between atoms (0 not connected, 1 connected)
note: material studio file cannot use a partial periodic system. If partial
perodic system was inputted, full periodicity was assumed.
"""
if hasattr(images, 'get_positions'):
images = [images]
XSD, ATR = _write_xsd_html(images, connectivity)
# Return a pretty-printed XML string for the Element.
rough_string = ET.tostring(XSD, 'utf-8')
reparsed = minidom.parseString(rough_string)
Document = reparsed.toprettyxml(indent='\t')
fd.write(Document)