def read_xsf(self, filepath, component=None):
component = self.process_component_name(component)
vlog('Reading density data from XSF file for component "{}"'.format(
component),
time=True)
if isinstance(filepath, XsfFile):
vlog('XSF file already loaded, reusing data.')
xsf = filepath
copy_values = True
else:
vlog('Loading data from file', n=1, time=True)
vlog('file location: {}'.format(filepath), n=2)
vlog('memory before: ', n=2, mem=True)
xsf = XsfFile(filepath)
vlog('load complete', n=2, time=True)
vlog('memory after: ', n=2, mem=True)
copy_values = False
#end if
# read structure
if not self.has_attribute('structure'):
vlog('Reading structure from XSF data', n=1, time=True)
s = Structure()
s.read_xsf(xsf)
self.set_attribute('structure', s)
#end if
# read grid
if not self.has_attribute('grid'):
vlog('Reading grid from XSF data', n=1, time=True)
g = read_grid(xsf)
self.set_attribute('grid', g)
self.set_attribute('distance_units', 'B')
#end if
# read values
xsf.remove_ghost()
d = xsf.get_density()
values = d.values_noghost.ravel()
if copy_values:
values = values.copy()
#end if
# create grid function for component
vlog('Constructing grid function from XSF data', n=1, time=True)
f = grid_function(
type='parallelotope',
grid=self.grid,
values=values,
copy=False,
)
self.set_attribute(component, f)
self.set_attribute('distance_units', 'A')
vlog('Read complete', n=1, time=True)
vlog('Current memory:', n=1, mem=True)
def test_chgcar_file():
import os
from fileio import XsfFile
from fileio import PoscarFile
from fileio import ChgcarFile
tpath = testing.setup_unit_test_output_directory('fileio','test_chgcarfile')
files = get_files()
empty = ChgcarFile()
assert(not empty.is_valid())
# get reference poscar and xsf files
p = PoscarFile(files['VO2_R_48.POSCAR'])
x = XsfFile(files['VO2_R_48_dens.xsf'])
# create and test reference chgcar file
ref = ChgcarFile()
ref.incorporate_xsf(x)
assert(ref.is_valid())
assert(object_eq(ref.poscar,p))
# test read
f = ChgcarFile(files['VO2_R_48_dens.CHGCAR'])
assert(f.is_valid())
assert(object_eq(f,ref))
# test write
outfile = os.path.join(tpath,'test.CHGCAR')
f.write(outfile)
f2 = ChgcarFile(outfile)
assert(f2.is_valid())
assert(object_eq(f2,ref))
def test_xsffile():
import os
import numpy as np
from fileio import XsfFile
tpath = testing.setup_unit_test_output_directory('fileio','test_xsffile')
files = get_files()
# test empty initialization
empty = XsfFile()
assert(not empty.is_valid())
# populate reference object
ref = XsfFile()
ref.set(
elem = np.array([8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,
8,8,8,8,8,8,8,8,8,8,8,8,23,23,23,23,23,
23,23,23,23,23,23,23,23,23,23,23],dtype=int),
filetype = 'xsf',
periodicity = 'crystal',
pos = np.array([
[ 1.36683546, 1.36683546, 0. ],
[ 3.18776454, 3.18776454, 0. ],
[ 3.64413546, 0.91046454, 1.4264 ],
[ 5.46506454, -0.91046454, 1.4264 ],
[ 1.36683546, 1.36683546, 2.8528 ],
[ 3.18776454, 3.18776454, 2.8528 ],
[ 3.64413546, 0.91046454, 4.2792 ],
[ 5.46506454, -0.91046454, 4.2792 ],
[ 5.92143546, 1.36683546, 0. ],
[ 3.18776454, -1.36683546, 0. ],
[ 3.64413546, -3.64413546, 1.4264 ],
[ 0.91046454, -0.91046454, 1.4264 ],
[ 5.92143546, 1.36683546, 2.8528 ],
[ 3.18776454, -1.36683546, 2.8528 ],
[ 3.64413546, -3.64413546, 4.2792 ],
[ 0.91046454, -0.91046454, 4.2792 ],
[ 1.36683546, 1.36683546, 5.7056 ],
[ 3.18776454, 3.18776454, 5.7056 ],
[ 3.64413546, 0.91046454, 7.132 ],
[ 5.46506454, -0.91046454, 7.132 ],
[ 1.36683546, 1.36683546, 8.5584 ],
[ 3.18776454, 3.18776454, 8.5584 ],
[ 3.64413546, 0.91046454, 9.9848 ],
[ 5.46506454, -0.91046454, 9.9848 ],
[ 5.92143546, 1.36683546, 5.7056 ],
[ 3.18776454, -1.36683546, 5.7056 ],
[ 3.64413546, -3.64413546, 7.132 ],
[ 0.91046454, -0.91046454, 7.132 ],
[ 5.92143546, 1.36683546, 8.5584 ],
[ 3.18776454, -1.36683546, 8.5584 ],
[ 3.64413546, -3.64413546, 9.9848 ],
[ 0.91046454, -0.91046454, 9.9848 ],
[ 0. , 0. , 0. ],
[ 2.2773 , 2.2773 , 1.4264 ],
[ 0. , 0. , 2.8528 ],
[ 2.2773 , 2.2773 , 4.2792 ],
[ 4.5546 , 0. , 0. ],
[ 2.2773 , -2.2773 , 1.4264 ],
[ 4.5546 , 0. , 2.8528 ],
[ 2.2773 , -2.2773 , 4.2792 ],
[ 0. , 0. , 5.7056 ],
[ 2.2773 , 2.2773 , 7.132 ],
[ 0. , 0. , 8.5584 ],
[ 2.2773 , 2.2773 , 9.9848 ],
[ 4.5546 , 0. , 5.7056 ],
[ 2.2773 , -2.2773 , 7.132 ],
[ 4.5546 , 0. , 8.5584 ],
[ 2.2773 , -2.2773 , 9.9848 ]
],dtype=float),
primvec = np.array([
[ 4.5546, -4.5546, 0. ],
[ 4.5546, 4.5546, 0. ],
[ 0. , 0. , 11.4112]
],dtype=float),
)
assert(ref.is_valid())
# test read
f = XsfFile(files['VO2_R_48.xsf'])
assert(f.is_valid())
assert(object_eq(f,ref))
# test write
outfile = os.path.join(tpath,'test.xsf')
f.write(outfile)
f2 = XsfFile(outfile)
assert(f2.is_valid())
assert(object_eq(f2,ref))
def test_poscar_file():
import os
import numpy as np
from fileio import PoscarFile
tpath = testing.setup_unit_test_output_directory('fileio','test_poscarfile')
files = get_files()
# test empty initialization
empty = PoscarFile()
assert(not empty.is_valid())
# populate reference object
ref = PoscarFile()
ref.set(
axes = np.array([
[ 4.5546, -4.5546, 0. ],
[ 4.5546, 4.5546, 0. ],
[ 0. , 0. , 11.4112]
],dtype=float),
coord = 'cartesian',
description = 'System cell and coordinates',
dynamic = None,
elem = np.array(['O', 'V'],dtype=str),
elem_count = np.array([32, 16],dtype=int),
pos = np.array([
[ 1.36683546, 1.36683546, 0. ],
[ 3.18776454, 3.18776454, 0. ],
[ 3.64413546, 0.91046454, 1.4264 ],
[ 5.46506454, -0.91046454, 1.4264 ],
[ 1.36683546, 1.36683546, 2.8528 ],
[ 3.18776454, 3.18776454, 2.8528 ],
[ 3.64413546, 0.91046454, 4.2792 ],
[ 5.46506454, -0.91046454, 4.2792 ],
[ 5.92143546, 1.36683546, 0. ],
[ 3.18776454, -1.36683546, 0. ],
[ 3.64413546, -3.64413546, 1.4264 ],
[ 0.91046454, -0.91046454, 1.4264 ],
[ 5.92143546, 1.36683546, 2.8528 ],
[ 3.18776454, -1.36683546, 2.8528 ],
[ 3.64413546, -3.64413546, 4.2792 ],
[ 0.91046454, -0.91046454, 4.2792 ],
[ 1.36683546, 1.36683546, 5.7056 ],
[ 3.18776454, 3.18776454, 5.7056 ],
[ 3.64413546, 0.91046454, 7.132 ],
[ 5.46506454, -0.91046454, 7.132 ],
[ 1.36683546, 1.36683546, 8.5584 ],
[ 3.18776454, 3.18776454, 8.5584 ],
[ 3.64413546, 0.91046454, 9.9848 ],
[ 5.46506454, -0.91046454, 9.9848 ],
[ 5.92143546, 1.36683546, 5.7056 ],
[ 3.18776454, -1.36683546, 5.7056 ],
[ 3.64413546, -3.64413546, 7.132 ],
[ 0.91046454, -0.91046454, 7.132 ],
[ 5.92143546, 1.36683546, 8.5584 ],
[ 3.18776454, -1.36683546, 8.5584 ],
[ 3.64413546, -3.64413546, 9.9848 ],
[ 0.91046454, -0.91046454, 9.9848 ],
[ 0. , 0. , 0. ],
[ 2.2773 , 2.2773 , 1.4264 ],
[ 0. , 0. , 2.8528 ],
[ 2.2773 , 2.2773 , 4.2792 ],
[ 4.5546 , 0. , 0. ],
[ 2.2773 , -2.2773 , 1.4264 ],
[ 4.5546 , 0. , 2.8528 ],
[ 2.2773 , -2.2773 , 4.2792 ],
[ 0. , 0. , 5.7056 ],
[ 2.2773 , 2.2773 , 7.132 ],
[ 0. , 0. , 8.5584 ],
[ 2.2773 , 2.2773 , 9.9848 ],
[ 4.5546 , 0. , 5.7056 ],
[ 2.2773 , -2.2773 , 7.132 ],
[ 4.5546 , 0. , 8.5584 ],
[ 2.2773 , -2.2773 , 9.9848 ]
],dtype=float),
scale = 1.0,
vel = None,
vel_coord = None,
)
# test read
f = PoscarFile(files['VO2_R_48.POSCAR'])
assert(f.is_valid())
assert(object_eq(f,ref))
# test write
outfile = os.path.join(tpath,'test.POSCAR')
f.write(outfile)
f2 = PoscarFile(outfile)
assert(f2.is_valid())
assert(object_eq(f2,ref))
# test incorporate xsf
from fileio import XsfFile
x = XsfFile(files['VO2_R_48.xsf'])
f = PoscarFile()
f.incorporate_xsf(x)
assert(f.is_valid())
assert(object_eq(f,ref))
def test_xsffile_density():
import os
import numpy as np
from fileio import XsfFile
tpath = testing.setup_unit_test_output_directory('fileio','test_xsffile_density')
files = get_files()
ref = XsfFile(files['VO2_R_48.xsf'])
grid = 3,5,7
dens = 0.01*np.arange(np.prod(grid),dtype=float)
dens.shape=grid
ref.add_density(ref.primvec,dens,add_ghost=True)
assert(ref.is_valid())
f = XsfFile(files['VO2_R_48_dens.xsf'])
assert(f.is_valid())
assert(object_eq(f,ref))
d = f.get_density().values
assert(isinstance(d,np.ndarray))
assert(d.shape==(4,6,8))
outfile = os.path.join(tpath,'test_density.xsf')
f.write(outfile)
f2 = XsfFile(outfile)
assert(f2.is_valid())
assert(object_eq(f2,ref))