def to_atoms(self):
#check if necessary input there & all makes sense
if self.has_key('GEOMETRY'):
block = self['geometry=']
#now create
atoms = Atoms(n=len(block))
field_list = [line.strip() for line in block]
field_list = [line.split() for line in block]
#Way this currently works any labels will be lost
#if want to use these for molecule specification
#will have to do something more clever
#label = re.compile('[0-9]')
#field_list = map(label.split, field_list[0])
elements = map(operator.itemgetter(0), field_list)
#Look up elements by atomic number
elements = [ not el.isdigit() and atomic_number(el) or el for el in elements ]
#Transfer positions to Atoms object
# Set the element and pos data
atoms.set_atoms(elements) #Elements still needs to be defined, farray is a function
atoms.pos[:,:] = farray([ [float(x) for x in row] \
for row in [field[1:4] for field in field_list]]).T
return atoms
def read_xml_output(xmlfile,energy_from=None, extract_forces=False, extract_dipole=False, datafile=None, cluster=None):
#parse an xml output file and return cluster with updated info
# datafile tells which energies, forces to look for, cluster Atoms object which gets returned, this is echoed in the xml file so can be left out
# If extract_forces is not given and the FORCE keyword is found in datafile, the default is to set extract_forces=True
log = logging.getLogger('molpro_driver')
if datafile is None:
datafile=MolproDatafile(xml=xmlfile)
if 'FORCE' in datafile:
extract_forces=True
energy_names = OrderedDict()
energy_names['CCSD(T)-F12'] = ["total energy"]
energy_names['CCSD(T)'] = ["total energy"]
energy_names['MP2'] = ["total energy"]
energy_names['DF-MP2'] = ["total energy"]
energy_names['DF-RMP2'] = ["energy"]
energy_names['RKS'] = ["Energy"]
energy_names['RHF'] = ["Energy"]
energy_names['DF-RHF'] = ["Energy"]
energy_names['HF'] = ["Energy"]
energy_names['DF-HF'] = ["Energy"]
#etc
gradient_names = OrderedDict()
gradient_names['CCSD(T)'] =[""]
gradient_names['RKS'] =['RKS GRADIENT']
gradient_names['MP2'] =['MP2 GRADIENT']
all_methods=OrderedDict()
all_methods['HF']=["RHF"]
all_methods['DF-HF']=["RHF"]
all_methods['RHF']=["RHF"]
all_methods['DF-RHF']=["RHF"]
all_methods['MP2']=["MP2"]
all_methods['DF-MP2']=["MP2"]
all_methods['DF-RMP2']=["DF-RMP2"]
all_methods['RKS']=["RKS"]
all_methods['CCSD(T)-F12']=["CCSD(T)-F12a","CCSD(T)-F12b"]
all_methods['CCSD(T)']=["CCSD(T)"]
if energy_from is None:
log.critical("don't know which energy to extract, use keyword energy_from with options "+str([all_methods[k] for k in iter(all_methods)]).replace('[','').replace(']',''))
#loop through datafile to look for methods.
calcs=[] #holds the keys for getting correct method, energy_name, gradient_name
data_keys_upper = [key.upper() for key in datafile._keys]
for key in all_methods._keys:
if key in data_keys_upper:
calcs.append(key)
dom = minidom.parse(xmlfile)
elements=[]
position_matrix=[]
cml = dom.documentElement.getElementsByTagName('cml:atomArray')
for l in cml[0].childNodes:
if l.nodeType== 1:
element=l.attributes['elementType'].value.encode('ascii','ignore')
elements.append(atomic_number(element))
posx = l.attributes['x3'].value.encode('ascii','ignore')
posy = l.attributes['y3'].value.encode('ascii','ignore')
posz = l.attributes['z3'].value.encode('ascii','ignore')
position_matrix.append([float(posx),float(posy),float(posz)])
if cluster is None:
cluster = Atoms(n=len(elements))
cluster.set_atoms(elements)
position_matrix=farray(position_matrix).T
if not 'ANGSTROM' in datafile._keys and not 'angstrom' in datafile._keys:
position_matrix = position_matrix * (1.0/0.529177249)
cluster.pos[:,:]=position_matrix
#note this leaves the lattice undefined
#now look for each of these energies in xml file
energy_found=False
props = dom.documentElement.getElementsByTagName('property')
for prop in props:
prop_name = prop.attributes['name'].value.encode('ascii','ignore')
prop_method = prop.attributes['method'].value.encode('ascii','ignore')
for calc in calcs:
if prop_name in energy_names[calc] and prop_method in all_methods[calc]:
energy_param_name="_".join([prop_method,prop_name])
energy_param_name=energy_param_name.replace(" ","_")
#log.info("found "+energy_param_name)
# dated routines for finding monomer pairs, triplets in Topology module
energy_param=prop.attributes['value'].value.encode('ascii','ignore')
my_energy=energy_param_name
i_en=1
while my_energy in cluster.params.iterkeys():
i_en+=1
my_energy='_'.join([energy_param_name,str(i_en)])
cluster.params[my_energy] = float(energy_param) * HARTREE
if prop_method == energy_from:
cluster.params['Energy']=float(energy_param) * HARTREE
energy_found=True
elif extract_dipole and prop_name=='Dipole moment':
dipole_param_name="_".join([prop_method,prop_name])
dipole_param_name=dipole_param_name.replace(" ","_")
log.info("found dipole moment: "+dipole_param_name)
dipole_param=prop.attributes['value'].value.encode('ascii','ignore')
cluster.params[dipole_param_name]=dipole_param
if not energy_found:
log.critical("couldn't find energy from "+energy_from+" prop method : "+prop_method)
# read gradients if requested
if extract_forces:
if not cluster.has_property('force'):
cluster.add_property('force', 0.0, n_cols=3)
grads = dom.documentElement.getElementsByTagName('gradient')
force_matrix = grads[0].childNodes[0].data.split('\n')
force_matrix = [str(i).split() for i in force_matrix]
for i in force_matrix:
try:
force_matrix.remove([])
except ValueError:
break
force_matrix = [[(-1.0 * HARTREE / BOHR) * float(j) for j in i]
for i in force_matrix]
cluster.force[:] =farray(force_matrix).T
if len(grads) != 1:
for k in range(1,len(grads)):
my_force='force%s'%str(k+1)
force_matrix = grads[k].childNodes[0].data.split('\n')
force_matrix = [str(i).split() for i in force_matrix]
for i in force_matrix:
try:
force_matrix.remove([])
except ValueError:
break
force_matrix = [[(-1.0 * HARTREE / BOHR) * float(j) for j in i]
for i in force_matrix]
cluster.add_property(my_force,farray(force_matrix).T)
return cluster
def param_to_xml(params, encoding='iso-8859-1'):
from xml.sax.saxutils import XMLGenerator
from StringIO import StringIO
output = StringIO()
xml = XMLGenerator(output, encoding)
xml.startDocument()
xml.startElement(
'TS_params', {
'cutoff': ' '.join([str(x) for x in params['rcut']]),
'n_types': str(params['nspecies']),
'betapol': str(params['betapol']),
'maxipol': str(params['maxipol']),
'tolpol': str(params['tolpol']),
'pred_order': str(params['pred_order']),
'yukalpha': str(params['yukalpha']),
'yuksmoothlength': str(params['yuksmoothlength']),
'tewald': params['tewald'] and 'T' or 'F',
'raggio': str(params['raggio']),
'a_ew': str(params['a_ew']),
'gcut': str(params['gcut']),
'iesr': ' '.join([str(x) for x in params.get('iesr', [0, 0, 0])])
})
ti_tj_to_index = {}
n = 0
for ti in range(params['nspecies']):
for tj in range(params['nspecies']):
if tj > ti: continue
ti_tj_to_index[(ti, tj)] = n
n += 1
for ti in range(params['nspecies']):
zi = atomic_number(params['species'][ti])
xml.startElement(
'per_type_data', {
'type': str(ti + 1),
'atomic_num': str(zi),
'pol': str(params['pol'][ti]),
'z': str(params['z'][ti])
})
xml.endElement('per_type_data')
for tj in range(params['nspecies']):
if tj > ti: continue
idx = ti_tj_to_index[(ti, tj)]
zj = atomic_number(params['species'][tj])
xml.startElement(
'per_pair_data', {
'atnum_i': str(zi),
'atnum_j': str(zj),
'D_ms': str(params['d_ms'][idx]),
'gamma_ms': str(params['gamma_ms'][idx]),
'R_ms': str(params['r_ms'][idx]),
'B_pol': str(params['bpol'][idx]),
'C_pol': str(params['cpol'][idx]),
})
xml.endElement('per_pair_data')
xml.endElement('TS_params')
xml.endDocument()
return output.getvalue()
def PosCelReader(basename=None,
pos='pos.in',
cel='cel.in',
force='force.in',
energy='energy.in',
stress='stress.in',
species_map={
'O': 1,
'Si': 2
},
cel_angstrom=False,
pos_angstrom=False,
rydberg=True,
format=None):
if basename is not None:
basename = os.path.splitext(basename)[0]
pos = '%s.pos' % basename
cel = '%s.cel' % basename
energy = '%s.ene' % basename
stress = '%s.str' % basename
force = '%s.for' % basename
doenergy = os.path.exists(energy)
doforce = os.path.exists(force)
dostress = os.path.exists(stress)
if isinstance(pos, str): pos = open(pos)
if isinstance(cel, str): cel = open(cel)
if doenergy and isinstance(energy, str): energy = open(energy)
if doforce and isinstance(force, str): force = open(force)
if dostress and isinstance(stress, str): stress = open(stress)
pos = iter(pos)
cel = iter(cel)
if doenergy: energy = iter(energy)
if doforce: force = iter(force)
if dostress: stress = iter(stress)
pos.next() # throw away blank line at start
if doforce: force.next()
rev_species_map = dict(zip(species_map.values(), species_map.keys()))
while True:
poslines = list(
itertools.takewhile(
lambda L: L.strip() != '' and not L.strip().startswith('STEP'),
pos))
if poslines == []:
break
cellines = list(itertools.islice(cel, 4))
#lattice = farray([ [float(x) for x in L.split()] for L in cellines[1:4] ]).T
lattice = fzeros((3, 3))
for i in (1, 2, 3):
lattice[:, i] = [float(x) for x in cellines[i].split()]
if not cel_angstrom: lattice *= BOHR
at = Atoms(n=len(poslines), lattice=lattice)
at.pos[:] = farray([[float(x) for x in L.split()[0:3]]
for L in poslines]).T
if not pos_angstrom: at.pos[:] *= BOHR
species = [rev_species_map[int(L.split()[3])] for L in poslines]
elements = [
not el.isdigit() and atomic_number(el) or el for el in species
]
at.set_atoms(elements)
if doenergy:
at.params['energy'] = float(energy.next().split()[0])
if rydberg:
at.params['energy'] *= RYDBERG
if dostress:
stress_lines = list(itertools.islice(stress, 4))
virial = farray([[float(x) for x in L.split()]
for L in stress_lines[1:4]])
virial *= at.cell_volume() / (10.0 * GPA)
at.params['virial'] = virial
if doforce:
at.add_property('force', 0.0, n_cols=3)
force_lines = list(
itertools.takewhile(lambda L: L.strip() != '', force))
if len(force_lines) != at.n:
raise ValueError("len(force_lines) (%d) != at.n (%d)" %
(len(force_lines), at.n))
at.force[:] = farray([[float(x) for x in L.split()[0:3]]
for L in force_lines]).T
if rydberg:
at.force[:] *= RYDBERG / BOHR
yield at