def generate_pyscf(**kwargs):
sim_args, inp_args = Pyscf.separate_inputs(kwargs)
if not 'input' in sim_args:
if 'input_type' in inp_args:
input_type = inp_args.input_type
del inp_args.input_type
#end if
if 'prefix' not in inp_args and 'identifier' in sim_args:
inp_args['prefix'] = sim_args['identifier']
#end if
sim_args.input = generate_pyscf_input(**inp_args)
#end if
py = Pyscf(**sim_args)
return py
def test_empty_init():
from generic import obj
from pyscf_input import PyscfInput,generate_pyscf_input
ref = obj(
addendum = None,
allow_not_set = set([]),
checkpoint = False,
keywords = set([]),
prefix = None,
save_qmc = False,
template = None,
values = obj(),
)
pi = PyscfInput()
assert(object_eq(pi.to_obj(),ref))
pi2 = generate_pyscf_input()
assert(isinstance(pi2,PyscfInput))
assert(object_eq(pi,pi2))
def test_generate():
import os
from generic import obj
from physical_system import generate_physical_system
from pyscf_input import generate_pyscf_input
tpath = testing.setup_unit_test_output_directory('pyscf_input','test_generate')
# water molecule
xyz_path = os.path.join(tpath,'H2O.xyz')
template_path = os.path.join(tpath,'scf_template.py')
open(xyz_path,'w').write(h2o_xyz)
open(template_path,'w').write(scf_template)
system = generate_physical_system(
structure = xyz_path,
)
pi = generate_pyscf_input(
template = template_path,
system = system,
mole = obj(
basis = 'ccpvtz',
symmetry = True,
),
)
ref_system = '''
### generated system text ###
from pyscf import gto as gto_loc
mol = gto_loc.Mole()
mol.atom = {0}
O 0.00000000 0.00000000 0.00000000
H 0.00000000 0.75716000 0.58626000
H 0.00000000 0.75716000 -0.58626000
{0}
mol.basis = 'ccpvtz'
mol.unit = 'A'
mol.charge = 0
mol.spin = 0
mol.symmetry = True
mol.build()
### end generated system text ###
'''.format("'''")
assert(pi.template is not None)
assert(len(pi.values)==1 and 'system' in pi.values)
assert(text_eq(pi.values.system,ref_system))
ref_internal = obj(
addendum = None,
allow_not_set = set([]),
checkpoint = False,
keywords = set(['system']),
prefix = None,
save_qmc = False,
)
del pi.template
del pi.values
assert(object_eq(pi.to_obj(),ref_internal))
# diamond crystal
system = generate_physical_system(
units = 'A',
axes = '''1.785 1.785 0.000
0.000 1.785 1.785
1.785 0.000 1.785''',
elem_pos = '''
C 0.0000 0.0000 0.0000
C 0.8925 0.8925 0.8925
''',
kgrid = (1,1,1),
kshift = (0,0,0),
C = 4,
)
pi = generate_pyscf_input(
template = template_path,
system = system,
cell = obj(
basis = 'bfd-vdz',
ecp = 'bfd',
drop_exponent = 0.1,
verbose = 5,
),
)
ref_system = '''
### generated system text ###
from numpy import array
from pyscf.pbc import gto as gto_loc
cell = gto_loc.Cell()
cell.a = {0}
1.78500000 1.78500000 0.00000000
0.00000000 1.78500000 1.78500000
1.78500000 0.00000000 1.78500000
{0}
cell.basis = 'bfd-vdz'
cell.dimension = 3
cell.ecp = 'bfd'
cell.unit = 'A'
cell.atom = {0}
C 0.00000000 0.00000000 0.00000000
C 0.89250000 0.89250000 0.89250000
{0}
cell.drop_exponent = 0.1
cell.verbose = 5
cell.charge = 0
cell.spin = 0
cell.build()
kpts = array([
[0.0, 0.0, 0.0]])
### end generated system text ###
'''.format("'''")
assert(pi.template is not None)
assert(len(pi.values)==1 and 'system' in pi.values)
assert(text_eq(pi.values.system,ref_system))
del pi.template
del pi.values
assert(object_eq(pi.to_obj(),ref_internal))
# water molecule without template
xyz_path = os.path.join(tpath,'H2O.xyz')
open(xyz_path,'w').write(h2o_xyz)
system = generate_physical_system(
structure = xyz_path,
)
pi = generate_pyscf_input(
system = system,
mole = obj(
basis = 'ccpvtz',
symmetry = True,
),
calculation = obj(
method = 'RHF',
df_fitting = False,
),
)
ref_system = '''
### generated system text ###
from pyscf import gto as gto_loc
mol = gto_loc.Mole()
mol.atom = {0}
O 0.00000000 0.00000000 0.00000000
H 0.00000000 0.75716000 0.58626000
H 0.00000000 0.75716000 -0.58626000
{0}
mol.basis = 'ccpvtz'
mol.unit = 'A'
mol.charge = 0
mol.spin = 0
mol.symmetry = True
mol.build()
### end generated system text ###
'''.format("'''")
ref_calculation = '''
### generated calculation text ###
mf = scf.RHF(mol)
mf.tol = '1e-10'
e_scf = mf.kernel()
### end generated calculation text ###
'''.format("'''")
ref_pyscfimport = '''
### generated pyscfimport text ###
from pyscf import df, scf, dft
### end generated pyscfimport text ###
'''.format("'''")
ref_python_exe = 'python'
assert(len(pi.values)==4 and 'system' in pi.values)
assert(len(pi.values)==4 and 'calculation' in pi.values)
assert(len(pi.values)==4 and 'pyscfimport' in pi.values)
assert(len(pi.values)==4 and 'python_exe' in pi.values)
assert(text_eq(pi.values.system,ref_system))
assert(text_eq(pi.values.calculation,ref_calculation))
assert(text_eq(pi.values.pyscfimport,ref_pyscfimport))
assert(text_eq(pi.values.python_exe,ref_python_exe))
ref_internal = obj(
addendum = None,
allow_not_set = set([]),
checkpoint = False,
keywords = set(['system','calculation','pyscfimport','python_exe']),
prefix = None,
save_qmc = False,
)
del pi.values
del pi.calculation
del pi.template
assert(object_eq(pi.to_obj(),ref_internal))
# MnO crystal without template
poscar_path = os.path.join(tpath,'MnO.POSCAR')
open(poscar_path,'w').write(mno_poscar)
system = generate_physical_system(
structure = poscar_path,
elem = ['O','Mn'],
O = 6,
Mn = 15,
tiling = (1,1,1),
kgrid = (1,1,1),
kshift = (0,0,0),
)
pi = generate_pyscf_input(
system = system,
cell = obj(
basis = 'bfd-vdz',
ecp = 'bfd',
drop_exponent = 0.1,
verbose = 5,
),
python_exe = 'python3',
calculation = obj(
method = 'KRKSpU',
df_fitting = True,
xc = 'pbe',
tol = '1e-10',
df_method = 'GDF',
exxdiv = 'ewald',
u_idx = ['Mn 3d'],
u_val = [2.0],
C_ao_lo = 'minao',
),
)
ref_system = """
### generated system text ###
from numpy import array
from pyscf.pbc import gto as gto_loc
cell = gto_loc.Cell()
cell.a = '''
4.49453800 0.00000000 0.00000000
0.00000000 4.49453800 0.00000000
0.00000000 0.00000000 4.49453800
'''
cell.basis = 'bfd-vdz'
cell.dimension = 3
cell.ecp = 'bfd'
cell.unit = 'A'
cell.atom = '''
O 0.00000000 0.00000000 10.10043601
O 0.00000000 10.10043601 0.00000000
O 10.10043601 0.00000000 0.00000000
O 10.10043601 10.10043601 10.10043601
Mn 0.00000000 0.00000000 0.00000000
Mn 0.00000000 10.10043601 10.10043601
Mn 10.10043601 0.00000000 10.10043601
Mn 10.10043601 10.10043601 0.00000000
'''
cell.drop_exponent = 0.1
cell.verbose = 5
cell.charge = 0
cell.spin = 0
cell.build()
kpts = array([
[0.0, 0.0, 0.0]])
### end generated system text ###
""".format("'''")
ref_calculation = '''
### generated calculation text ###
mydf = df.GDF(cell)
mydf.auxbasis = 'weigend'
dfpath = 'df_ints.h5'
mydf._cderi_to_save = dfpath
mydf.build()
mf = dft.KRKSpU(cell,kpts,U_idx=array(['Mn 3d']),U_val=array([2.0]),C_ao_lo='minao').density_fit()
mf.exxdiv = 'ewald'
mf.xc = 'pbe'
mf.tol = '1e-10'
mf.with_df = mydf
e_scf = mf.kernel()
### end generated calculation text ###
'''.format("'''")
ref_pyscfimport = '''
### generated pyscfimport text ###
from pyscf.pbc import df, scf
### end generated pyscfimport text ###
'''.format("'''")
ref_python_exe = 'python3'
assert(len(pi.values)==4 and 'system' in pi.values)
assert(len(pi.values)==4 and 'calculation' in pi.values)
assert(len(pi.values)==4 and 'pyscfimport' in pi.values)
assert(len(pi.values)==4 and 'python_exe' in pi.values)
assert(text_eq(pi.values.system,ref_system))
assert(text_eq(pi.values.calculation,ref_calculation))
assert(text_eq(pi.values.pyscfimport,ref_pyscfimport))
assert(text_eq(pi.values.python_exe,ref_python_exe))
ref_internal = obj(
addendum = None,
allow_not_set = set([]),
checkpoint = False,
keywords = set(['system','calculation','pyscfimport','python_exe']),
prefix = None,
save_qmc = False,
)
del pi.values
del pi.calculation
del pi.template
assert(object_eq(pi.to_obj(),ref_internal))
def test_write():
import os
from generic import obj
from physical_system import generate_physical_system
from pyscf_input import generate_pyscf_input
tpath = testing.setup_unit_test_output_directory('pyscf_input','test_write')
# water molecule
xyz_path = os.path.join(tpath,'H2O.xyz')
template_path = os.path.join(tpath,'scf_template.py')
open(xyz_path,'w').write(h2o_xyz)
open(template_path,'w').write(scf_template)
system = generate_physical_system(
structure = xyz_path,
)
pi = generate_pyscf_input(
prefix = 'scf',
template = template_path,
system = system,
mole = obj(
verbose = 5,
basis = 'ccpvtz',
symmetry = True,
),
save_qmc = True,
)
write_path = os.path.join(tpath,'h2o.py')
pi.write(write_path)
assert(os.path.exists(write_path))
text = open(write_path,'r').read()
ref_text = '''
#! /usr/bin/env python3
from pyscf import scf
### generated system text ###
from pyscf import gto as gto_loc
mol = gto_loc.Mole()
mol.verbose = 5
mol.atom = {0}
O 0.00000000 0.00000000 0.00000000
H 0.00000000 0.75716000 0.58626000
H 0.00000000 0.75716000 -0.58626000
{0}
mol.basis = 'ccpvtz'
mol.unit = 'A'
mol.charge = 0
mol.spin = 0
mol.symmetry = True
mol.build()
### end generated system text ###
mf = scf.RHF(mol)
mf.kernel()
### generated conversion text ###
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(mol,mf,'scf')
### end generated conversion text ###
'''.format("'''")
assert(text_eq(text,ref_text))
# diamond crystal
system = generate_physical_system(
units = 'A',
axes = '''1.785 1.785 0.000
0.000 1.785 1.785
1.785 0.000 1.785''',
elem_pos = '''
C 0.0000 0.0000 0.0000
C 0.8925 0.8925 0.8925
''',
tiling = (2,1,1),
kgrid = (1,1,1),
kshift = (0,0,0),
C = 4,
)
pi = generate_pyscf_input(
prefix = 'scf',
template = template_path,
system = system,
cell = obj(
basis = 'bfd-vdz',
ecp = 'bfd',
drop_exponent = 0.1,
verbose = 5,
),
save_qmc = True,
)
write_path = os.path.join(tpath,'diamond.py')
pi.write(write_path)
assert(os.path.exists(write_path))
text = open(write_path,'r').read()
ref_text = '''
#! /usr/bin/env python3
from pyscf import scf
### generated system text ###
from numpy import array
from pyscf.pbc import gto as gto_loc
cell = gto_loc.Cell()
cell.a = {0}
1.78500000 1.78500000 0.00000000
0.00000000 1.78500000 1.78500000
1.78500000 0.00000000 1.78500000
{0}
cell.basis = 'bfd-vdz'
cell.dimension = 3
cell.ecp = 'bfd'
cell.unit = 'A'
cell.atom = {0}
C 0.00000000 0.00000000 0.00000000
C 0.89250000 0.89250000 0.89250000
{0}
cell.drop_exponent = 0.1
cell.verbose = 5
cell.charge = 0
cell.spin = 0
cell.build()
kpts = array([
[0.0, 0.0, 0.0] ,
[0.4656748546088228, 0.4656748546088228, -0.4656748546088228]])
### end generated system text ###
mf = scf.RHF(mol)
mf.kernel()
### generated conversion text ###
from PyscfToQmcpack import savetoqmcpack
savetoqmcpack(cell,mf,'scf',kpts)
### end generated conversion text ###
'''.format("'''")
text = text.replace('[',' [ ').replace(']',' ] ')
ref_text = ref_text.replace('[',' [ ').replace(']',' ] ')
assert(text_eq(text,ref_text))
def test_generate():
import os
from generic import obj
from physical_system import generate_physical_system
from pyscf_input import generate_pyscf_input
tpath = testing.setup_unit_test_output_directory('pyscf_input',
'test_generate')
# water molecule
xyz_path = os.path.join(tpath, 'H2O.xyz')
template_path = os.path.join(tpath, 'scf_template.py')
open(xyz_path, 'w').write(h2o_xyz)
open(template_path, 'w').write(scf_template)
system = generate_physical_system(structure=xyz_path, )
pi = generate_pyscf_input(
template=template_path,
system=system,
mole=obj(
basis='ccpvtz',
symmetry=True,
),
)
ref_system = '''
### generated system text ###
from pyscf import gto as gto_loc
mol = gto_loc.Mole()
mol.atom = {0}
O 0.00000000 0.00000000 0.00000000
H 0.00000000 0.75716000 0.58626000
H 0.00000000 0.75716000 -0.58626000
{0}
mol.basis = 'ccpvtz'
mol.unit = 'A'
mol.charge = 0
mol.spin = 0
mol.symmetry = True
mol.build()
### end generated system text ###
'''.format("'''")
assert (pi.template is not None)
assert (len(pi.values) == 1 and 'system' in pi.values)
assert (text_eq(pi.values.system, ref_system))
ref_internal = obj(
addendum=None,
allow_not_set=set([]),
checkpoint=False,
keywords=set(['system']),
prefix=None,
save_qmc=False,
)
del pi.template
del pi.values
assert (object_eq(pi.to_obj(), ref_internal))
# diamond crystal
system = generate_physical_system(
units='A',
axes='''1.785 1.785 0.000
0.000 1.785 1.785
1.785 0.000 1.785''',
elem_pos='''
C 0.0000 0.0000 0.0000
C 0.8925 0.8925 0.8925
''',
kgrid=(1, 1, 1),
kshift=(0, 0, 0),
C=4,
)
pi = generate_pyscf_input(
template=template_path,
system=system,
cell=obj(
basis='bfd-vdz',
ecp='bfd',
drop_exponent=0.1,
verbose=5,
),
)
ref_system = '''
### generated system text ###
from numpy import array
from pyscf.pbc import gto as gto_loc
cell = gto_loc.Cell()
cell.a = {0}
1.78500000 1.78500000 0.00000000
0.00000000 1.78500000 1.78500000
1.78500000 0.00000000 1.78500000
{0}
cell.basis = 'bfd-vdz'
cell.dimension = 3
cell.ecp = 'bfd'
cell.unit = 'A'
cell.atom = {0}
C 0.00000000 0.00000000 0.00000000
C 0.89250000 0.89250000 0.89250000
{0}
cell.drop_exponent = 0.1
cell.verbose = 5
cell.charge = 0
cell.spin = 0
cell.build()
kpts = array([
[0.0, 0.0, 0.0]])
### end generated system text ###
'''.format("'''")
assert (pi.template is not None)
assert (len(pi.values) == 1 and 'system' in pi.values)
assert (text_eq(pi.values.system, ref_system))
del pi.template
del pi.values
assert (object_eq(pi.to_obj(), ref_internal))