def test_read_cif():
"""
Read La2CuO4 structure from a CIF file.
"""
from structure import read_structure, generate_structure
files = get_files()
# Read from CIF file
s = read_structure(files['La2CuO4_ICSD69312.cif'])
ref = generate_structure(
units='A',
axes=[[2.665, 0., -6.5525], [0., 5.4126, 0.], [2.665, 0., 6.5525]],
elem='La La La La Cu Cu O O O O O O O O'.split(),
pos=[[2.665, 5.37038172,
-1.8071795], [2.665, 2.74851828, 4.7453205],
[2.665, 2.66408172, -4.7453205],
[2.665, 0.04221828, 1.8071795], [0., 0., 0.],
[2.665, 2.7063, 0.], [1.3325, 1.35315, -0.128429],
[3.9975, 4.05945, 0.128429], [3.9975, 1.35315, -0.128429],
[1.3325, 4.05945, 0.128429], [2.665, 0.23490684, -4.1398695],
[2.665, 2.47139316,
2.4126305], [2.665, 2.94120684, -2.4126305],
[2.665, 5.17769316, 4.1398695]],
)
assert (structure_same(s, ref))
def test_bounding_box():
import numpy as np
from structure import generate_structure, read_structure
files = get_files()
h2o = generate_structure(
elem=['O', 'H', 'H'],
pos=[[0.000000, 0.000000, 0.000000], [0.000000, -0.757160, 0.586260],
[0.000000, 0.757160, 0.586260]],
units='A', # Angstroms
)
# add a box by hand to the water molecule
h2o_diy = h2o.copy()
h2o_diy.set_axes(8.0 * np.eye(3))
assert (value_eq(h2o_diy.axes, 8. * np.eye(3)))
# automatically add a bounding box to the water molecule
h2o_auto = h2o.copy()
h2o_auto.bounding_box(box='cubic', minsize=8.0)
assert (value_eq(h2o_auto.axes, 8. * np.eye(3)))
assert (value_eq(tuple(h2o_auto.pos[-1]), (4., 4.75716, 4.29313)))
s = read_structure(files['coronene.xyz'])
# make a bounding box that is at least 5 A from the nearest atom
s.bounding_box(mindist=5.0)
ref_axes = np.array([[16.4035, 0., 0.], [0., 16.3786, 0.], [0., 0., 10.]])
assert (value_eq(s.axes, ref_axes))
assert (value_eq(s.pos[:, 2].min(), 5.0))
assert (value_eq(s.pos[:, 2].max(), 5.0))
def test_read_write():
"""
Write/read conventional diamond cell to/from XYZ, XSF, and POSCAR formats.
"""
import os
from structure import generate_structure, read_structure
tpath = testing.setup_unit_test_output_directory('structure',
'test_read_write')
d8 = generate_structure(
structure='diamond',
cell='conv',
)
# Write an XYZ file
xyz_file = os.path.join(tpath, 'diamond8.xyz')
d8.write(xyz_file)
# Write an XSF file
xsf_file = os.path.join(tpath, 'diamond8.xsf')
d8.write(xsf_file)
# Write a POSCAR file
poscar_file = os.path.join(tpath, 'diamond8.POSCAR')
d8.write(poscar_file)
# Read an XYZ file
d8_xyz = read_structure(xyz_file) # no cell info
assert (value_eq(d8_xyz.elem, d8.elem))
assert (value_eq(d8_xyz.pos, d8.pos))
# Read an XSF file
d8_xsf = read_structure(xsf_file)
assert (structure_same(d8_xsf, d8))
# Read a POSCAR file
d8_poscar = read_structure(poscar_file)
assert (structure_same(d8_poscar, d8))
def demo_read_cif():
"""
Read La2CuO4 structure from a CIF file.
"""
# Note: this demo requires PyCifRW
# Read from CIF file
s = read_structure('La2CuO4_ICSD69312.cif')
# Print out the structure
print('La2CuO4 in POSCAR format:')
print(s.write_poscar())
def demo_read():
"""
Read conventional diamond cell from XYZ, XSF, and POSCAR formats.
"""
# Read an XYZ file
d8_xyz = read_structure('diamond8.xyz') # no cell info
# Read an XSF file
d8_xsf = read_structure('diamond8.xsf')
# Read a POSCAR file
d8_poscar = read_structure('diamond8.POSCAR')
# Compare with the reference structure
d8 = generate_structure(
structure='diamond',
cell='conv',
)
def struct_same(s1, s2, axes=True):
same = True
same &= value_eq(s1.elem, s2.elem)
same &= value_eq(s1.pos, s2.pos)
if axes:
same &= value_eq(s1.axes, s2.axes)
#end if
return same
#end def struct_same
print('\nXYZ valid? {}'.format(struct_same(d8_xyz, d8, axes=False)))
print('\nXSF valid? {}'.format(struct_same(d8_xsf, d8)))
print('\nPOSCAR valid? {}'.format(struct_same(d8_poscar, d8)))
def demo_coronene_box():
"""
Place coronene in a well apportioned box.
"""
s = read_structure('./coronene.xyz')
# make a bounding box that is at least 5 A from the nearest atom
s.bounding_box(mindist=5.0)
# print the resulting box
print(s.axes)
# plot the coronene molecule with an automatic box
plt.figure(tight_layout=True)
s.plot2d_ax(0, 1, 'k', lw=2)
s.plot2d_pos(0, 1, 'bo')
plt.axis('equal')
plt.xlabel('x (A)')
plt.ylabel('y (A)')
plt.title('demo coronene box: box with minimum distance')
plt.show()
def generate_physical_system(**kwargs):
for var, val in ps_defaults.items():
if not var in kwargs:
kwargs[var] = val
#end if
#end for
type = kwargs['type']
if type == 'atom' or type == 'dimer' or type == 'trimer':
del kwargs['kshift']
del kwargs['tiling']
#if not 'units' in kwargs:
# kwargs['units'] = 'B'
##end if
tiling = None
else:
tiling = kwargs['tiling']
#end if
if 'structure' in kwargs:
s = kwargs['structure']
is_str = isinstance(s, str)
if is_str:
if os.path.exists(s):
if 'elem' in kwargs:
s = read_structure(s, elem=kwargs['elem'])
else:
s = read_structure(s)
#end if
if 'axes' in kwargs:
s.reset_axes(kwargs['axes'])
#end if
kwargs['structure'] = s
else:
slow = s.lower()
format = None
if '.' in slow:
format = slow.rsplit('.')[1]
elif 'poscar' in slow:
format = 'poscar'
#end if
is_path = '/' in s
is_file = format in set('xyz xsf poscar cif fhi-aims'.split())
if is_path or is_file:
PhysicalSystem.class_error(
'user provided structure file does not exist\nstructure file path: '
+ s, 'generate_physical_system')
#end if
#end if
#end if
#end if
generation_info = obj()
generation_info.transfer_from(deepcopy(kwargs))
net_charge = kwargs['net_charge']
net_spin = kwargs['net_spin']
tiled_spin = kwargs['tiled_spin']
extensive = kwargs['extensive']
del kwargs['net_spin']
del kwargs['net_charge']
del kwargs['tiled_spin']
del kwargs['extensive']
if 'particles' in kwargs:
particles = kwargs['particles']
del kwargs['particles']
else:
generation_info.particles = None
#end if
pretile = kwargs['pretile']
del kwargs['pretile']
valency = dict()
remove = []
for var in kwargs:
#if var in Matter.elements:
if is_element(var):
valency[var] = kwargs[var]
remove.append(var)
#end if
#end if
generation_info.valency = deepcopy(valency)
for var in remove:
del kwargs[var]
#end for
if pretile is None:
structure = generate_structure(**kwargs)
else:
for d in range(len(pretile)):
if tiling[d] % pretile[d] != 0:
PhysicalSystem.class_error(
'pretile does not divide evenly into tiling\n tiling provided: {0}\n pretile provided: {1}'
.format(tiling, pretile), 'generate_physical_system')
#end if
#end for
tiling = tuple(array(tiling) // array(pretile))
kwargs['tiling'] = pretile
pre = generate_structure(**kwargs)
pre.remove_folded_structure()
structure = pre.tile(tiling)
#end if
if tiling != None and tiling != (1, 1, 1) and structure.has_folded():
fps = PhysicalSystem(structure=structure.folded_structure,
net_charge=net_charge,
net_spin=net_spin,
**valency)
structure.remove_folded()
folded_structure = fps.structure
if extensive:
ncells = int(round(structure.volume() / folded_structure.volume()))
net_charge = ncells * net_charge
if not isinstance(net_spin, str):
net_spin = ncells * net_spin
#end if
#end if
if tiled_spin != None:
net_spin = tiled_spin
#end if
ps = PhysicalSystem(structure=structure,
net_charge=net_charge,
net_spin=net_spin,
**valency)
structure.set_folded(folded_structure)
ps.folded_system = fps
else:
ps = PhysicalSystem(structure=structure,
net_charge=net_charge,
net_spin=net_spin,
**valency)
#end if
ps.generation_info = generation_info
return ps
def generate_physical_system(**kwargs):
for var,val in ps_defaults.iteritems():
if not var in kwargs:
kwargs[var] = val
#end if
#end for
type = kwargs['type']
if type=='atom' or type=='dimer' or type=='trimer':
del kwargs['kshift']
del kwargs['tiling']
#if not 'units' in kwargs:
# kwargs['units'] = 'B'
##end if
tiling = None
else:
tiling = kwargs['tiling']
#end if
if 'structure' in kwargs:
s = kwargs['structure']
is_str = isinstance(s,str)
if is_str and os.path.exists(s):# and '.' in os.path.split(s)[1]:
if 'elem' in kwargs:
print 'system using elem'
kwargs['structure'] = read_structure(s,elem=kwargs['elem'])
else:
kwargs['structure'] = read_structure(s)
#end if
elif is_str and '/' in s:
PhysicalSystem.class_error('path provided for structure file does not exist: '+s,'generate_physical_system')
#end if
#end if
generation_info = obj()
generation_info.transfer_from(deepcopy(kwargs))
net_charge = kwargs['net_charge']
net_spin = kwargs['net_spin']
tiled_spin = kwargs['tiled_spin']
extensive = kwargs['extensive']
del kwargs['net_spin']
del kwargs['net_charge']
del kwargs['tiled_spin']
del kwargs['extensive']
if 'particles' in kwargs:
particles = kwargs['particles']
del kwargs['particles']
else:
generation_info.particles = None
#end if
pretile = kwargs['pretile']
del kwargs['pretile']
valency = dict()
remove = []
for var in kwargs:
#if var in Matter.elements:
if is_element(var):
valency[var] = kwargs[var]
remove.append(var)
#end if
#end if
generation_info.valency = deepcopy(valency)
for var in remove:
del kwargs[var]
#end for
if pretile is None:
structure = generate_structure(**kwargs)
else:
for d in range(len(pretile)):
if tiling[d]%pretile[d]!=0:
PhysicalSystem.class_error('pretile does not divide evenly into tiling\n tiling provided: {0}\n pretile provided: {1}'.format(tiling,pretile),'generate_physical_system')
#end if
#end for
tiling = tuple(array(tiling)/array(pretile))
kwargs['tiling'] = pretile
pre = generate_structure(**kwargs)
pre.remove_folded_structure()
structure = pre.tile(tiling)
#end if
if tiling!=None and tiling!=(1,1,1):
fps = PhysicalSystem(
structure = structure.folded_structure,
net_charge = net_charge,
net_spin = net_spin,
**valency
)
structure.remove_folded()
folded_structure = fps.structure
if extensive:
ncells = int(round(structure.volume()/folded_structure.volume()))
net_charge = ncells*net_charge
net_spin = ncells*net_spin
#end if
if tiled_spin!=None:
net_spin = tiled_spin
#end if
ps = PhysicalSystem(
structure = structure,
net_charge = net_charge,
net_spin = net_spin,
**valency
)
structure.set_folded(folded_structure)
ps.folded_system = fps
else:
ps = PhysicalSystem(
structure = structure,
net_charge = net_charge,
net_spin = net_spin,
**valency
)
#end if
ps.generation_info = generation_info
return ps
def test_input():
# imports
import os
import numpy as np
import pwscf_input as pwi
from generic import obj
from structure import read_structure
from physical_system import generate_physical_system
from pwscf_input import check_new_variables,check_section_classes
from pwscf_input import PwscfInput,generate_pwscf_input
# directories
tpath = testing.setup_unit_test_output_directory('pwscf_input','test_input')
# files
files = get_files()
# divert logging function
divert_nexus_log()
# definitions
def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'):
pw_same = object_eq(pw1_,pw2_,int_as_float=True)
if not pw_same:
d,d1,d2 = object_diff(pw1_,pw2_,full=True,int_as_float=True)
diff = obj({l1:obj(d1),l2:obj(d2)})
failed(str(diff))
#end if
#end def check_pw_same
# test internal spec
check_new_variables(exit=False)
check_section_classes(exit=False)
# test compose
compositions = obj()
# based on sample_inputs/Fe_start_ns_eig.in
pw = PwscfInput()
pw.control.set(
calculation = 'scf' ,
restart_mode = 'from_scratch' ,
wf_collect = True ,
outdir = './output' ,
pseudo_dir = '../pseudo/' ,
prefix = 'fe' ,
etot_conv_thr = 1.0e-9 ,
forc_conv_thr = 1.0e-6 ,
tstress = True ,
tprnfor = True ,
)
pw.system.set(
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100 ,
ecutrho = 300 ,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005 ,
smearing = 'methfessel-paxton' ,
nspin = 2 ,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True ,
)
pw.system.set({
'celldm(1)' : 15,
'starting_magnetization(1)' : 0.9,
'hubbard_u(1)' : 3.1,
'starting_ns_eigenvalue(1,2,1)' : 0.0,
'starting_ns_eigenvalue(2,2,1)' : 0.0476060,
'starting_ns_eigenvalue(3,2,1)' : 0.0476060,
'starting_ns_eigenvalue(4,2,1)' : 0.9654373,
'starting_ns_eigenvalue(5,2,1)' : 0.9954307,
})
pw.electrons.set(
conv_thr = 1.0e-9 ,
mixing_beta = 0.7 ,
diagonalization = 'david' ,
mixing_fixed_ns = 500,
)
pw.atomic_species.set(
atoms = ['Fe'],
masses = obj(Fe=58.69000),
pseudopotentials = obj(Fe='Fe.pbe-nd-rrkjus.UPF'),
)
pw.atomic_positions.set(
specifier = 'angstrom',
atoms = ['Fe','Fe'],
positions = np.array([
[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000],
]),
)
pw.k_points.set(
specifier = 'automatic',
grid = np.array((1,1,1)),
shift = np.array((1,1,1)),
)
compositions['Fe_start_ns_eig.in'] = pw
# test read
pwr = PwscfInput(files['Fe_start_ns_eig.in'])
pwc = pw.copy()
pwc.standardize_types()
check_pw_same(pwc,pwr,'compose','read')
# test write
infile = os.path.join(tpath,'pwscf.in')
pw.write(infile)
pw2 = PwscfInput()
pw2.read(infile)
check_pw_same(pw2,pwr)
# test read/write/read
reads = obj()
for infile in input_files:
read_path = files[infile]
write_path = os.path.join(tpath,infile)
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw = PwscfInput(read_path)
pw.write(write_path)
pw2 = PwscfInput(write_path)
check_pw_same(pw,pw2,'read','write/read')
reads[infile] = pw
#end for
# test generate
generations = obj()
# based on sample_inputs/VO2_M1_afm.in
infile = 'VO2_M1_afm.in'
struct_file = files['VO2_M1_afm.xsf']
read_path = files[infile]
write_path = os.path.join(tpath,infile)
s = read_structure(struct_file)
s.elem[0] = 'V1'
s.elem[1] = 'V2'
s.elem[2] = 'V1'
s.elem[3] = 'V2'
vo2 = generate_physical_system(
structure = s,
V1 = 13,
V2 = 13,
O = 6,
)
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
disk_io = 'low',
verbosity = 'high',
wf_collect = True,
input_dft = 'lda',
hubbard_u = obj(V1=3.5,V2=3.5),
ecutwfc = 350,
bandfac = 1.3,
nosym = True,
occupations = 'smearing',
smearing = 'fermi-dirac',
degauss = 0.0001,
nspin = 2,
start_mag = obj(V1=1.0,V2=-1.0),
diagonalization = 'david',
conv_thr = 1e-8,
mixing_beta = 0.2,
electron_maxstep = 1000,
system = vo2,
pseudos = ['V.opt.upf','O.opt.upf'],
kgrid = (6,6,6),
kshift = (0,0,0),
# added for reverse compatibility
celldm = {1:1.0},
cell_option = 'alat',
positions_option = 'alat',
)
generations[infile] = pw
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw2 = PwscfInput(read_path)
pw3 = PwscfInput(write_path)
check_pw_same(pw2,pw3,'generate','read')
# based on sample_inputs/Fe_start_ns_eig.in
infile = 'Fe_start_ns_eig.in'
read_path = files[infile]
write_path = os.path.join(tpath,infile)
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
restart_mode = 'from_scratch',
wf_collect = True,
outdir = './output',
pseudo_dir = '../pseudo/',
prefix = 'fe',
etot_conv_thr = 1.0e-9,
forc_conv_thr = 1.0e-6,
tstress = True,
tprnfor = True,
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100,
ecutrho = 300,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005,
smearing = 'methfessel-paxton',
nspin = 2,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True,
conv_thr = 1.0e-9,
mixing_beta = 0.7,
diagonalization = 'david',
mixing_fixed_ns = 500,
mass = obj(Fe=58.69000),
pseudos = ['Fe.pbe-nd-rrkjus.UPF'],
elem = ['Fe','Fe'],
pos = [[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000]],
pos_specifier = 'angstrom',
kgrid = np.array((1,1,1)),
kshift = np.array((1,1,1)),
)
pw.system.set({
'celldm(1)' : 15,
'starting_magnetization(1)' : 0.9,
'hubbard_u(1)' : 3.1,
'starting_ns_eigenvalue(1,2,1)' : 0.0,
'starting_ns_eigenvalue(2,2,1)' : 0.0476060,
'starting_ns_eigenvalue(3,2,1)' : 0.0476060,
'starting_ns_eigenvalue(4,2,1)' : 0.9654373,
'starting_ns_eigenvalue(5,2,1)' : 0.9954307,
})
generations[infile] = pw
pw2 = compositions[infile]
check_pw_same(pw,pw2,'generate','compose')
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw3 = PwscfInput(write_path)
pw4 = reads[infile]
check_pw_same(pw3,pw4,'generate','read')
# based on sample_inputs/Fe_start_ns_eig.in
# variant that uses direct pwscf array input
pw = generate_pwscf_input(
selector = 'generic',
calculation = 'scf',
restart_mode = 'from_scratch',
wf_collect = True,
outdir = './output',
pseudo_dir = '../pseudo/',
prefix = 'fe',
etot_conv_thr = 1.0e-9,
forc_conv_thr = 1.0e-6,
tstress = True,
tprnfor = True,
ibrav = 1,
nat = 2,
ntyp = 1,
ecutwfc = 100,
ecutrho = 300,
nbnd = 18,
occupations = 'smearing',
degauss = 0.0005,
smearing = 'methfessel-paxton',
nspin = 2,
assume_isolated = 'martyna-tuckerman',
lda_plus_u = True,
conv_thr = 1.0e-9,
mixing_beta = 0.7,
diagonalization = 'david',
mixing_fixed_ns = 500,
mass = obj(Fe=58.69000),
pseudos = ['Fe.pbe-nd-rrkjus.UPF'],
elem = ['Fe','Fe'],
pos = [[2.070000000, 0.000000000, 0.000000000],
[0.000000000, 0.000000000, 0.000000000]],
pos_specifier = 'angstrom',
kgrid = np.array((1,1,1)),
kshift = np.array((1,1,1)),
starting_ns_eigenvalue = {(1,2,1) : 0.0,
(2,2,1) : 0.0476060,
(3,2,1) : 0.0476060,
(4,2,1) : 0.9654373,
(5,2,1) : 0.9954307,},
celldm = {1 : 15 },
starting_magnetization = {1 : 0.9},
hubbard_u = {1 : 3.1},
)
pwg = pw.copy()
pwg.standardize_types()
generations[infile] = pw
pw2 = compositions[infile].copy()
pw2.standardize_types()
check_pw_same(pwg,pw2,'generate','compose')
pw3 = reads[infile]
check_pw_same(pwg,pw3,'generate','read')
if os.path.exists(write_path):
os.remove(write_path)
#end if
pw.write(write_path)
pw4 = PwscfInput(write_path)
check_pw_same(pwg,pw3,'generate','write')
# restore logging function
restore_nexus_log()