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qmcpack/nexus/library/crystal.py

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Python
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##################################################################
## (c) Copyright 2015- by Jaron T. Krogel ##
##################################################################
import os
from generic import obj
from periodic_table import pt as ptable
from pseudopotential import GaussianPP
from nexus_base import nexus_noncore
from simulation import Simulation
from developer import error
molecule_symm_text = '''
1 1 C1
2 1b Ci
3 2x C2x
4 2y C2y
5 2z C2z
6 mx Csx
7 my Csy
8 mz Csz
9 2/mx C2hx
10 2/my C2hy
11 2/mz C2hz
12 222 D2
13 2mm C2vx
14 m2m C2vy
15 mm2 C2vz
16 mmm D2h
17 4 C4
18 4b S4
19 4/m C4h
20 422 D4
21 4mm C4v
22 4b2m D2d
23 4bm2 D2d
24 4/mmm D4h
25 3 C3
26 3b C3i
27 321 D3
28 312 D3
29 3m1 C3v
30 31m C3v
31 3bm1 D3d
32 3b1m D3d
33 6 C6
34 6b C3h
35 6/m C6h
36 622 D6
37 6mm C6v
38 6bm2 D3h
39 6b2m D3h
40 6/mmm D6h
41 23 T
42 m3b Th
43 432 O
44 4b3m Td
45 m3bm Oh
46 235 I
47 m3b5b Ih
'''
symm_map = obj(
molecule = obj(),
polymer = obj(),
slab = obj(),
crystal = obj(),
)
smap = symm_map.molecule
for line in molecule_symm_text.splitlines():
ls = line.strip()
if len(ls)>0:
index,hm,schoen = line.split()
index = int(index)
smap[hm] = index
smap[schoen] = index
# default to x direction if exists
if hm.endswith('x'):
smap[hm[:-1]] = index
#end if
if schoen.endswith('x'):
smap[schoen[:-1]] = index
#end if
#end if
#end for
def write_geometry(title,bcond,system,symmetry=1,pseudo=True):
t = '{0}\n{1}\n'.format(title,bcond.upper())
bcond = bcond.lower()
if not bcond in symm_map:
error('unknown boundary conditions: {0}'.format(bcond))
#end if
smap = symm_map[bcond]
if isinstance(symmetry,int):
t += str(symmetry)+'\n'
elif symmetry in symm_map:
t += str(smap[symmetry])+'\n'
else:
error('symmetry {0} is unknown'.format(symmetry),'write_geometry')
#end if
s = system.structure.copy()
s.change_units('A')
t += '{0}\n'.format(len(s.elem))
if pseudo:
an_base = 200 # for 'conventional' atomic numbers
else:
an_base = 0
#end if
for n in xrange(len(s.elem)):
e = s.elem[n]
p = s.pos[n]
conv_atomic_number = ptable[e].atomic_number+an_base
t += '{0} {1: 12.8f} {2: 12.8f} {3: 12.8f}\n'.format(conv_atomic_number,p[0],p[1],p[2])
#end for
t+='END\n'
return t
#end def write_geometry
def write_basis(pseudos,occupations,formats):
s = ''
if len(pseudos)!=len(occupations):
error('must provide one set of occupations for each pseudopotential','write_basis')
#end if
if len(pseudos)!=len(formats):
error('must specify file format for each pseudopotential','write_basis')
#end if
for n in range(len(pseudos)):
pp = GaussianPP(pseudos[n],format=formats[n])
s += pp.write_text(format='crystal',occ=occupations[n])
#end for
s += '99 0\n'
s += 'END\n'
return s
#end def write_basis
def write_hamiltonian(theory = None,
system = None,
spinlock_cycles = 100,
levshift = None,
levshift_lock = 1,
maxcycle = None,
):
s = ''
theory = theory.lower().strip()
dft_functionals = set(['pbe0'])
known_theories = set(['rhf','uhf']) | dft_functionals
if theory in known_theories:
if theory not in dft_functionals:
s+=theory.upper()+'\n'
else:
s+='DFT\n'+theory.upper()+'\nSPIN\nEND\n'
#end if
else:
error('unknown theory: '+theory,'write_hamiltonian')
#end if
if system!=None:
s+='SPINLOCK\n{0} {1}\n'.format(system.net_spin,spinlock_cycles)
#end if
if levshift!=None:
s+='LEVSHIFT\n{0} {1}\n'.format(levshift,levshift_lock)
#end if
if maxcycle!=None:
s+='MAXCYCLE\n{0}\n'.format(maxcycle)
#end if
s += 'END\n'
return s
#end def write_hamiltonian
class CrystalSim: None
class PropertiesSim: None
from simulation import GenericSimulation
class Crystal_1(GenericSimulation,CrystalSim):
generic_identifier = 'crystal'
application = 'crystal'
infile_extension = '.d12'
application_results = set(['orbitals'])
def check_result(self,result_name,sim):
return result_name=='orbitals'
#end def check_result
def get_result(self,result_name,sim):
result = obj() # its up to the other application how to handle crystal
if result_name!='orbitals':
self.error('ability to get result '+result_name+' has not been implemented')
#end if
return result
#end def get_result
def incorporate_result(self,result_name,result,sim):
self.error('ability to incorporate result '+result_name+' has not been implemented')
#end def incorporate_result
def app_command(self):
return self.app_name+'<'+self.infile
#end def app_command
#end class Crystal_1
from simulation import generate_simulation,input_template_dev
def gen_crystal_molecule_sim(
identifier = 'crystal',
path = None,
job = None,
title = 'atom',
system = None,
pseudos = None,
occupations = None,
formats = None,
theory = None,
levshift = None,
maxcycle = None,
):
required = obj(path=path,system=system,pseudos=pseudos,occupations=occupations,formats=formats,theory=theory,job=job)
for k,v in required.iteritems():
if v is None:
error(k+' is a required input','gen_crystal_molecule_sim')
#end if
#end for
pseudos_in = pseudos
pseudos = []
for pp in pseudos_in:
pseudos.append(os.path.join(nexus_noncore.pseudo_dir,pp))
#end for
crys_input = input_template_dev()
crys_input.read_text(
write_geometry(
title = title,
bcond = 'molecule',
system = system
)+
write_basis(
pseudos = pseudos,
occupations = occupations,
formats = formats,
)+
write_hamiltonian(
theory = theory,
system = system,
levshift = levshift,
maxcycle = maxcycle
)
)
#crys = generate_simulation(
# identifier = identifier,
# path = path,
# job = job(cores=1,serial=True,app_command='crystal<{0}.d12>&{0}.out&'.format(identifier)),
# input = crys_input,
# infile = '{0}.d12'.format(identifier),
# outfile = '{0}.out'.format(identifier),
# )
crys = Crystal_1(
identifier = identifier,
path = path,
job = job,
input = crys_input,
)
return crys
#end def gen_crystal_molecule_sim
class Properties_1(GenericSimulation,PropertiesSim): # same implementation, not 'is a'
generic_identifier = 'properties'
application = 'properties'
infile_extension = '.d3'
application_results = set(['orbitals'])
def check_result(self,result_name,sim):
return result_name=='orbitals'
#end def check_result
def get_result(self,result_name,sim):
result = obj() # its up to the other application how to handle crystal
if result_name!='orbitals':
self.error('ability to get result '+result_name+' has not been implemented')
#end if
return result
#end def get_result
def incorporate_result(self,result_name,result,sim):
if result_name!='orbitals' or not isinstance(sim,Crystal_1):
self.error('ability to incorporate result '+result_name+' has not been implemented')
#end if
#end def incorporate_result
def app_command(self):
return self.app_name+'<'+self.infile
#end def app_command
#end class Properties_1
molecule_text = '''
NEWK
1 0
CRYAPI_OUT
END
'''
periodic_text = '''
NEWK
0 0
1 0
CRYAPI_OUT
END
'''
def gen_properties(**kwargs):
if 'systype' not in kwargs:
error('systype is a required input','gen_properties')
#end if
systype = kwargs['systype']
del kwargs['systype']
if systype=='molecule_qmc':
text = molecule_text
elif systype=='periodic_qmc':
text = periodic_text
else:
error('invalid systype encountered\nsystype provided: {0}\nvalid options are: molecule_qmc, periodic_qmc'.format(systype))
#end if
sim_args,inp_args = Simulation.separate_inputs(kwargs)
if len(inp_args)>0:
error('invalid arguments encountered\ninvalid keywords: {0}'.format(sorted(inp_args.keys())),'gen_properties')
#end if
if not 'input' in sim_args:
sim_args.input = input_template_dev(text=text.strip())
#end if
prop = Properties_1(**sim_args)
return prop
#end def gen_properties
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