def get_volumetric_data(self, filename='CHG', **kwargs):
'''Read filename to read the volumetric data in it.
Supported filenames are CHG, CHGCAR, and LOCPOT.
'''
atoms = self.get_atoms()
vd = VaspChargeDensity(filename)
data = np.array(vd.chg)
n0, n1, n2 = data[0].shape
s0 = 1.0 / n0
s1 = 1.0 / n1
s2 = 1.0 / n2
X, Y, Z = np.mgrid[0.0:1.0:s0, 0.0:1.0:s1, 0.0:1.0:s2]
C = np.column_stack([X.ravel(), Y.ravel(), Z.ravel()])
uc = atoms.get_cell()
real = np.dot(C, uc)
# now convert arrays back to unitcell shape
x = np.reshape(real[:, 0], (n0, n1, n2))
y = np.reshape(real[:, 1], (n0, n1, n2))
z = np.reshape(real[:, 2], (n0, n1, n2))
return x, y, z, data
def chg_at_point(
chgfile,
xred1,
):
"""
Return the the value of charge density at coordinate xred1; Actually it provides charge density for the closest grid point
Most probably the units are (el/A^3)
chgfile - full path to the file with charge density
xred1 - reduced coordinate;
RETURN:
Charge density at given point
"""
vasp_charge = VaspChargeDensity(chgfile)
density = vasp_charge.chg[-1]
atoms = vasp_charge.atoms[-1]
del vasp_charge
# print density[0][0][0]
ngridpts = numpy.array(density.shape) # size of grid
print('Size of grid', ngridpts)
# rprimd = atoms.get_cell()
# print rprimd
# xred1 = [0.5, 0.5, 0.5]
# rprimd_lengths=numpy.sqrt(numpy.dot(rprimd,rprimd.transpose()).diagonal()) #length of cell vectors
i, j, k = [int(round(x * (n - 1))) for x, n in zip(xred1, ngridpts)
] # corresponding to xred1 point
print(i, j, k)
print('Density at xred', xred1, 'is', density[i][j][k])
return density[i][j][k]
def get_charge_density(self, spin=0):
"""Returns x, y, and z coordinate and charge density arrays.
:param int spin:
:returns: x, y, z, charge density arrays
:rtype: 3-d numpy arrays
Relies on :func:`ase.calculators.vasp.VaspChargeDensity`.
"""
atoms = self.get_atoms()
vcd = VaspChargeDensity()
cd = np.array(vcd.chg[spin])
n0, n1, n2 = cd.shape
s0 = 1.0 / n0
s1 = 1.0 / n1
s2 = 1.0 / n2
X, Y, Z = np.mgrid[0.0:1.0:s0, 0.0:1.0:s1, 0.0:1.0:s2]
C = np.column_stack([X.ravel(), Y.ravel(), Z.ravel()])
uc = atoms.get_cell()
real = np.dot(C, uc)
# now convert arrays back to unitcell shape
x = np.reshape(real[:, 0], (n0, n1, n2))
y = np.reshape(real[:, 1], (n0, n1, n2))
z = np.reshape(real[:, 2], (n0, n1, n2))
return x, y, z, cd
def get_volumetric_data(self, filename='CHG', **kwargs):
"""Read filename to read the volumetric data in it.
Supported filenames are CHG, CHGCAR, and LOCPOT.
"""
atoms = self.get_atoms()
vd = VaspChargeDensity(filename)
data = np.array(vd.chg)
n0, n1, n2 = data[0].shape
s0 = np.linspace(0, 1, num=n0, endpoint=False)
s1 = np.linspace(0, 1, num=n1, endpoint=False)
s2 = np.linspace(0, 1, num=n2, endpoint=False)
X, Y, Z = np.meshgrid(s0, s1, s2)
C = np.column_stack([X.ravel(), Y.ravel(), Z.ravel()])
uc = atoms.get_cell()
real = np.dot(C, uc)
# now convert arrays back to unitcell shape
x = np.reshape(real[:, 0], (n0, n1, n2))
y = np.reshape(real[:, 1], (n0, n1, n2))
z = np.reshape(real[:, 2], (n0, n1, n2))
return x, y, z, data
def load(loc, axis="Z"):
global average, latticelength, ngridpts, idir, direction
LOCPOTfile = loc + '/LOCPOT'
direction = axis
vasp_charge = VaspChargeDensity(filename=LOCPOTfile)
atoms = vasp_charge.atoms[-1]
cell = atoms.cell
potl = vasp_charge.chg[-1] * atoms.get_volume()
latticelength = np.dot(cell, cell.T).diagonal()**0.5
ngridpts = np.array(potl.shape)
if direction == "X":
idir = 0
elif direction == "Y":
idir = 1
else:
idir = 2
average = np.zeros(ngridpts[idir], np.float)
for ipt in range(ngridpts[idir]):
if direction == "X":
average[ipt] = potl[ipt, :, :].sum()
elif direction == "Y":
average[ipt] = potl[:, ipt, :].sum()
else:
average[ipt] = potl[:, :, ipt].sum()
average /= ngridpts[(idir + 1) % 3] * ngridpts[(idir + 2) % 3]
def from_file(file_path):
data = VaspChargeDensity(file_path)
density = data.chg[-1]
atoms = data.atoms[-1]
ngridpts = np.array(density.shape)
totalgridpts = ngridpts.prod()
unitcell = atoms.get_cell()
return VaspDens(density, atoms, ngridpts, unitcell)
def read_vasp_density(density_file):
data = VaspChargeDensity(density_file)
density = data.chg[-1]
atoms = data.atoms[-1]
ngridpts = np.array(density.shape)
totalgridpts = ngridpts.prod()
unitcell = atoms.get_cell()
return data, density, atoms, ngridpts, totalgridpts, unitcell
def chg_at_z_direct(cl, k_p=20, plot=None, filetype='CHGCAR'):
"""
Return the the value of charge density or electrostatic potential along z direction of slab;
chgfile - full path to the file with charge density
cl - Calculation() with slab structure;
it is needed for the definition of the correct coordinates of points in a structure in which will be calculated of el/stat pot
RETURN:
List of z-coordinates and respective average value of electrostatic pot in the z slice.
"""
from siman.picture_functions import fit_and_plot
if filetype == 'CHGCAR':
chgfile = cl.get_chg_file()
else:
chgfile = cl.get_file(filetype=filetype)
st = cl.end
vasp_charge = VaspChargeDensity(chgfile)
density = vasp_charge.chg[-1]
atoms = vasp_charge.atoms[-1]
del vasp_charge
ngridpts = np.array(density.shape) # size of grid
# print ('Size of grid', ngridpts)
z = int(cl.vlength[2] * 10)
elst = []
z_coord = []
xred1 = [0, 0, 0]
for n3 in range(0, z):
dens = 0
# for more accurate calculation of electrostatic pot, it is needed to split the z-sliced plane into a grid of points k_p (20 x 20)
# and find the average value for the slice
for n1 in range(0, k_p):
for n2 in range(0, k_p):
xred1[0] = n1 / k_p
xred1[1] = n2 / k_p
xred1[2] = n3 / z
i, j, k = [
int(round(x * (n - 1))) for x, n in zip(xred1, ngridpts)
] # corresponding to xred1 point
dens += density[i][j][k] * st.vol
elst.append(dens / k_p**2 * st.vol)
z_coord.append(n3 / 10)
if plot:
# print(z_coord, elst)
fit_and_plot(a=(z_coord, elst, '-b'),
xlabel='Z coordinate, $\AA$',
ylabel='Potential, eV',
filename='figs/' + st.id[0] + '_pot')
return z_coord, elst
def locpot_mean(fname="LOCPOT",
axis='z',
savefile='locpot.dat',
outcar="OUTCAR"):
'''
Reads the LOCPOT file and calculate the average potential along `axis`.
@in: See function argument.
@out:
- xvals: grid data along selected axis;
- mean: averaged potential corresponding to `xvals`.
'''
def get_efermi(outcar="OUTCAR"):
if not os.path.isfile(outcar):
logger.warning("OUTCAR file not found. E-fermi set to 0.0eV")
return None
txt = open(outcar).read()
efermi = re.search(
r'E-fermi :\s*([-+]?[0-9]+[.]?[0-9]*([eE][-+]?[0-9]+)?)',
txt).groups()[0]
logger.info("Found E-fermi = {}".format(efermi))
return float(efermi)
logger.info("Loading LOCPOT file {}".format(fname))
locd = VaspChargeDensity(fname)
cell = locd.atoms[0].cell
latlens = np.linalg.norm(cell, axis=1)
vol = np.linalg.det(cell)
iaxis = ['x', 'y', 'z'].index(axis.lower())
axes = [0, 1, 2]
axes.remove(iaxis)
axes = tuple(axes)
locpot = locd.chg[0]
# must multiply with cell volume, similar to CHGCAR
logger.info("Calculating workfunction along {} axis".format(axis))
mean = np.mean(locpot, axes) * vol
xvals = np.linspace(0, latlens[iaxis], locpot.shape[iaxis])
# save to 'locpot.dat'
efermi = get_efermi(outcar)
logger.info("Saving raw data to {}".format(savefile))
if efermi is None:
np.savetxt(savefile,
np.c_[xvals, mean],
fmt='%13.5f',
header='Distance(A) Potential(eV) # E-fermi not corrected')
else:
mean -= efermi
np.savetxt(
savefile,
np.c_[xvals, mean],
fmt='%13.5f',
header='Distance(A) Potential(eV) # E-fermi shifted to 0.0eV')
return (xvals, mean)
def read_chgcar(INDATA, CONTCAR='CONTCAR'):
print('Input data: ', INDATA)
print('Read ', INDATA)
print(datetime.datetime.now())
rho = VaspChargeDensity(INDATA)
print(datetime.datetime.now())
return rho
def _read_vasp(filecontent):
# Write to tmp file and read using ASE
tmpfd, tmppath = tempfile.mkstemp(prefix="tmpdeepdft")
tmpfile = os.fdopen(tmpfd, "wb")
tmpfile.write(filecontent)
tmpfile.close()
vasp_charge = VaspChargeDensity(filename=tmppath)
os.remove(tmppath)
density = vasp_charge.chg[-1] # separate density
atoms = vasp_charge.atoms[-1] # separate atom positions
return density, atoms, np.zeros(3) # TODO: Can we always assume origin at 0,0,0?
def get_s(chgcar='CHGCAR'):
chg = VaspChargeDensity(chgcar)
abc = np.shape(chg.chg[-1])
dx = abc[0] / np.shape(chg.chg[0])[0]
dy = abc[1] / np.shape(chg.chg[0])[1]
dz = abc[2] / np.shape(chg.chg[0])[2]
v_chg_gr = np.gradient(chg.chg[0], dx, dy, dz)
chg_grad = np.sqrt(
np.square(v_chg_gr[0]) + np.square(v_chg_gr[1]) +
np.square(v_chg_gr[2]))
s = chg_grad / (2 * (3. * pi**2 * chg.chg[0])**1. / 3 * chg.chg[0])
return s
def plan_avg_ase(filename='LOCPOT'):
import numpy as np
from ase.calculators.vasp import VaspChargeDensity
locpot = VaspChargeDensity(filename)
# For LOCPOT files we multiply by the volume to get back to eV
if 'LOCPOT' in filename:
avg_c = [
np.average(locpot.chg[0][:, :, i] * locpot.atoms[0].get_volume())
for i in range(0,
np.shape(locpot.chg)[3])
]
else:
avg_c = [
np.average(locpot.chg[0][:, :, i])
for i in range(0,
np.shape(locpot.chg)[3])
]
return avg_c
def write_chg_file(self):
"""Write the charge input file for the vdW calculation."""
fd = open('%s.chargeden' % self.name, 'w')
fd.write('lattice\n')
cell = self.atoms.get_cell()
for n in range(3):
fd.write(' %14.7f %14.7f %14.7f\n' %
(cell[n, 0], cell[n, 1], cell[n, 2]))
fd.write('Mesh\n')
if self.calc_name == 'vasp':
from ase.calculators.vasp import VaspChargeDensity
charge = VaspChargeDensity('CHGCAR')
elif self.calc_name == 'aims':
from ase.io.cube import read_cube
charge = read_cube('total_density.cube', read_data=True)
a, b, c = charge.chg[0].shape
charge = charge.chg[0].T.ravel()
charge *= self.atoms.get_volume()
fd.write(' %5d %5d %5d\n' % (a, b, c))
fd.write('Density\n')
for c in charge:
fd.write('%17.15E\n' % c)
fd.close()
print("\n** ERROR: Must specify the name of file on command line.")
print("eg. chgdiff.py CHGCAR")
print("Only one file name are allowed")
sys.exit(0)
if not os.path.isfile(prm.CHGCAR[0]):
print("\n** ERROR: Input file %s was not found." % prm.CHGCAR[0])
sys.exit(0)
# Read information from command line
# First specify location of CHGCAR
CHGCARfile = prm.CHGCAR[0].lstrip()
# Open geometry and density class objects
#-----------------------------------------
vasp_charge = VaspChargeDensity(filename=CHGCARfile)
if len(vasp_charge.chgdiff) == 3:
spin = 3
print("\nReading spin orbital potential data from file %s ... " %
CHGCARfile,
end='')
sys.stdout.flush()
atoms = vasp_charge.atoms[-1]
potl_total = vasp_charge.chg[-1]
potl_x = vasp_charge.chgdiff[0]
potl_y = vasp_charge.chgdiff[1]
potl_z = vasp_charge.chgdiff[2]
if not potl_total.shape == potl_x.shape == potl_y.shape == potl_z.shape:
print("\n**ERROR: Two sets of data are not on the same grid.")
print("Data from data block 1 on %dx%dx%d grid." %
(potl_total.shape[0], potl_total.shape[1], potl_total.shape[2]))
# for step in range(1,20):
for step in [14,]:
# distance = 4.5+step/10.
# distance = 4.7+step/4.
distance = 4+step/4.
#First option is to read data from a CHGCAR file and then interpolate density onto
#an arbitrary plane
if option=="1":
# Ask which file to plot
# inputstr=raw_input("Enter filename of CHGCAR format file containing data:\n")
print "Reading charge/potential data from file...",
sys.stdout.flush()
# Read density and atoms
vasp_charge = VaspChargeDensity(filename = inputstr)
density = vasp_charge.chg[-1]
atoms = vasp_charge.atoms[-1]
del vasp_charge
print "Done.\n"
# Read size of grid
ngridpts = numpy.array(density.shape)
# Read total number of grid points
totgridpts = ngridpts.prod()
# Read scaling factor and unit cell
unit_cell=atoms.get_cell()
# Take Fourier transform of density
from ChargeDensity.image_file_process import charge_file_crop_2d
from CrystalToolkit.geometry_properties import symmetry_order_2d, rectangle_transform_2d
from CrystalToolkit.vasp_chgcar import chgcar_file_slice_2d, charge_file_2d_reformat
file_chgcar = sys.argv[1]
stru = Chgcar.from_file(file_chgcar).poscar.structure
'''
# find the symmetry order of the 2D structure
with open('data.json') as json_file:
symmetry_data = json.load(json_file)
point_group_list = symmetry_data['point_group_list']
symmetry_order_2d(structure=stru, point_group_list=point_group_list)
'''
# slice the vasp chgcar file into 2D
vasp_charge = VaspChargeDensity(filename=file_chgcar)
density = vasp_charge.chg[-1]
atoms = vasp_charge.atoms[-1]
*_, chgden_2d = chgcar_file_slice_2d(density=density, atoms=atoms)
# change to RGB values, type must be unit 8 otherwise PIL will complain
chgden_2d = (255.0 / chgden_2d.max() * (chgden_2d - chgden_2d.min())).astype(
np.uint8)
file_png = file_chgcar.replace('chgcar', 'png')
Image.fromarray(chgden_2d).save(file_png)
#cv2.imwrite(file_png, chgden_2d)
#charge_file_2d_reformat(filein=file_chgcar.replace('chgcar', 'chgtile'))
if_transform, alat, blat = rectangle_transform_2d(structure=stru)
if if_transform:
im = cv2.imread(file_png, 0)
#======================================
atom1 = 2 # atom in the center
atom2 = 1 # atom from the plane
atom3 = 0 # second atom in the plain
npx = 90 # number of point to sample the plane in x
npy = 90 # number of point to sample the plane in y
angle = radians(-144) # rotate the final plot around the central atom
#angle= radians(0)
start = time.time()
sys.stdout.write("Reading CHGCAR... ")
sys.stdout.flush()
CHGCAR = VaspChargeDensity("CHGCAR")
end = time.time()
print "finished. {0}".format(end - start)
cell = CHGCAR.atoms[0].cell
nx, ny, nz = np.shape(CHGCAR.chg[0])
ncell = cell / np.array([nx, ny, nz])
# define plane =================================
p1 = CHGCAR.atoms[0].get_scaled_positions()[atom1]
p2 = CHGCAR.atoms[0].get_scaled_positions()[atom2]
p3 = CHGCAR.atoms[0].get_scaled_positions()[atom3]
# get normal to the plane
v1 = p2 - p1
v2 = p3 - p1
# Check that files exist
for name in sys.argv[1:]:
if not os.path.isfile(name):
print "\n** ERROR: Input file %s was not found." % name
sys.exit(0)
# Read information from command line
# First specify location of CHGCAR file with reference density
CHGCARfile1 = sys.argv[1].lstrip()
# Open geometry and density class objects
#-----------------------------------------
print "Reading density data from file %s ..." % CHGCARfile1,
sys.stdout.flush()
vasp_charge1 = VaspChargeDensity(filename=CHGCARfile1)
chg1 = vasp_charge1.chg[-1]
atoms1 = vasp_charge1.atoms[-1]
del vasp_charge1
print "done."
chgadd = chg1
for CHGCARfile2 in sys.argv[2:]:
CHGCARfile2 = CHGCARfile2.strip()
print "Reading density data from file %s ..." % CHGCARfile2,
sys.stdout.flush()
vasp_charge2 = VaspChargeDensity(filename=CHGCARfile2)
chg2 = vasp_charge2.chg[-1]
del vasp_charge2
print "done."
print "\n**ERROR: Two sets of data are not on the same grid."
print "Data from file %s on %dx%dx%d grid." % (CHGCARfile1,chg1.shape[0],chg1.shape[1],chg1.shape[2])
print "Data from file %s on %dx%dx%d grid.\n" % (CHGCARfile2,chg2.shape[0],chg2.shape[1],chg2.shape[2])
sys.exit(0)
else:
print "Adding data from file %s ..." % CHGCARfile2,
sys.stdout.flush()
# Add charge density
#-----------------
chgadd += chg2
print "done."
zero = raw_input("Set negative values of the added charge density to zero (Yes/No): ")
vasp_charge_add = VaspChargeDensity(filename=None)
vasp_charge_add.atoms=[atoms1,]
vasp_charge_add.chg=[chgadd,]
# Print out charge density
#--------------------------
# Check whether CHGADD exists
if os.path.isfile("./CHGADD"):
print "\n**WARNING: A file called CHGADD already exists in this directory."
yesno=raw_input("Type y to continue and overwrite it, any other key to stop\n")
if yesno!="y":
sys.exit(0)
print "Writing added density data to file CHGADD ...",
sys.stdout.flush()
sys.exit(0)
if not os.path.isfile(prm.OUTCAR):
print("\n** ERROR: Input file %s was not found." % prm.CHGCAR)
sys.exit(0)
# Read information from command line
# First specify location of CHGCAR
CHGCARfile = prm.CHGCAR.lstrip()
OUTCARfile = prm.OUTCAR.lstrip()
# Open geometry and density class objects
#-----------------------------------------
vasp_charge = VaspChargeDensity(filename = CHGCARfile)
potl = vasp_charge.chg[-1]
atoms = vasp_charge.atoms[-1]
del vasp_charge
# Open outcar to find zval and ions_per_type
#-----------------------------------------
with open(OUTCARfile) as search:
for line in search:
line = line.rstrip() # remove '\n' at end of line
if "ZVAL" in line:
ZVAL = line.split()[2:]
elif "ions per type" in line:
ions_per_type = line.split()[4:]
# Check that files exist
for name in sys.argv[1:]:
if not os.path.isfile(name):
print "\n** ERROR: Input file %s was not found." % name
sys.exit(0)
# Read information from command line
# First specify location of CHGCAR file with reference density
CHGCARfile1 = sys.argv[1].lstrip()
# Open geometry and density class objects
#-----------------------------------------
print "Reading potential data from file %s ..." % CHGCARfile1,
sys.stdout.flush()
vasp_charge1 = VaspChargeDensity(filename=CHGCARfile1)
chg1 = vasp_charge1.chg[-1]
atoms1 = vasp_charge1.atoms[-1]
del vasp_charge1
print "done."
chgdiff = chg1
for CHGCARfile2 in sys.argv[2:]:
CHGCARfile2 = CHGCARfile2.strip()
print "Reading potential data from file %s ..." % CHGCARfile2,
sys.stdout.flush()
vasp_charge2 = VaspChargeDensity(filename=CHGCARfile2)
chg2 = vasp_charge2.chg[-1]
del vasp_charge2
print "done."
spin_cut_off = 0.4
density_cut_off = 0.15
rotation = '24x, 34y, 14z'
#rotation = '0x, 0y, 0z'
run_povray = True
pov_name = 'NiO_marching_cubes.pov'
ini_name = 'NiO_marching_cubes.ini'
#########################
from ase.calculators.vasp import VaspChargeDensity
vchg = VaspChargeDensity('CHGCAR')
atoms = vchg.atoms[0]
kwargs = { # For povray files only
'pause': False, # Pause when done rendering (only if display)
'transparent': False, # Transparent background
'canvas_width': None, # Width of canvas in pixels
'canvas_height': 1024, # Height of canvas in pixels
'show_unit_cell': 1,
'camera_dist': 25.0, # Distance from camera to front atom
'camera_type': 'orthographic angle 35', # 'perspective angle 20'
'radii': atoms.positions.shape[0] * [0.3],
'textures': len(atoms) * ['ase3']
}
# some more options:
#'image_plane' : None, # Distance from front atom to image plane
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from ase.calculators.vasp import VaspChargeDensity
print("-" * 86)
starttime = time.perf_counter()
print("Starting the program at")
print(time.strftime("%Y-%m-%d %H:%M:%S"))
print("-" * 86)
# Check if the PARCHG exists and import charge density data from it.
# If not, enter the filename of CHGCAR/PARCHG format file containing charge density data.
if os.path.exists("PARCHG"):
print("PARCHG file already exists, reading data now...\n")
vasp_charge = VaspChargeDensity('PARCHG')
density = vasp_charge.chg[-1]
atoms = vasp_charge.atoms[-1]
del vasp_charge
print("Done!\n")
else:
active = True
while active:
inputstr1 = input(
"Enter the filename of CHGCAR/PARCHG format file containing data:")
if os.path.exists(inputstr1):
print("\nReading charge density data from %s...\n" % inputstr1)
vasp_charge = VaspChargeDensity(filename=inputstr1)
density = vasp_charge.chg[-1]
atoms = vasp_charge.atoms[-1]
dest='outfile',
help='Output to file \
named by this argument. If omitted, defaults to a file chgfile0_op_chgfile1')
parser.add_option('-w',
'--which-cell',
dest='wcell',
help='Take the \
embedded supercell information from which charge density file. Must be \
either 0 or 1.')
(options, args) = parser.parse_args()
chgf1 = args[0]
chgf2 = args[2]
op = args[1]
chg1 = VaspChargeDensity(chgf1)
chg2 = VaspChargeDensity(chgf2)
if options.wcell:
wcell = int(options.wcell)
if wcell == 0:
chga = chg1
elif wcell == 1:
chga = chg2
else:
print 'Error, invalid argument to -w option'
sys.exit(1)
else:
chga = chg1
if len(chg1.chg) != len(chg2.chg):
opt_diff = options.diff
opt_grad = options.gradient
two_files_involved = (opt_diff)
####### READING THE FILE #############
if (iformat == "cube"):
if (two_files_involved):
field, atoms = read_cube(sys.argv[num - 2], read_data=True)
field2, atoms2 = read_cube(sys.argv[num - 1], read_data=True)
if (atoms == atoms2):
print "WARRNING: geometries of the system are not the same"
else:
field, atoms = read_cube(sys.argv[num - 1], read_data=True)
elif (iformat == "locpot"):
locpot = VaspChargeDensity(filename=sys.argv[num - 1])
field = locpot.chg[-1]
atoms = locpot.atoms[-1]
del locpot
####### MANIPULATE #############
get = options.get
# Calculate Gradient of the fild
if (opt_grad != None):
# if(get == "diffx" or get == "diffy" or get == "diffz"):
cell = np.array(atoms.get_cell())
shape = np.array(field.shape)
dr = np.empty(3)
for i in range(3):
if (shape[i] % 2 == 1):
if not os.path.isfile(sys.argv[1]):
print "\n** ERROR: Input file %s was not found." % sys.argv[1]
sys.exit(0)
if not os.path.isfile(sys.argv[2]):
print "\n** ERROR: Input file %s was not found." % sys.argv[1]
sys.exit(0)
# Read information from command line
# First specify location of LOCPOT
LOCPOTfile = sys.argv[1].lstrip()
OUTCARfile = sys.argv[2].lstrip()
# Open geometry and density class objects
#-----------------------------------------
vasp_charge = VaspChargeDensity(filename=LOCPOTfile)
potl = vasp_charge.chg[-1]
atoms = vasp_charge.atoms[-1]
del vasp_charge
# Open outcar to find zval and ions_per_type
#-----------------------------------------
with open(OUTCARfile) as search:
for line in search:
line = line.rstrip() # remove '\n' at end of line
if "ZVAL" in line:
ZVAL = line.split()[2:]
elif "ions per type" in line:
ions_per_type = line.split()[4:]
print "\nElectronic part"
def chgarith(chgf1, chgf2, op, filename, wcell):
# chgf1 = args[0]
# chgf2 = args[2]
# op = args[1]
chg1 = VaspChargeDensity(chgf1)
chg2 = VaspChargeDensity(chgf2)
# if options.wcell:
# wcell = int(options.wcell)
if wcell == 0:
chga = chg1
elif wcell == 1:
chga = chg2
# else:
# print ('Error, invalid argument to -w option')
# sys.exit(1)
# else:
# chga = chg1
if len(chg1.chg) != len(chg2.chg):
print(
'Number of images in charge density files not equal. Using just the final images in both files.'
)
print('len(chg.chg)', len(chg1.chg), len(chg2.chg))
chg1.chg = [chg1.chg[-1]]
chg1.atoms = [chg1.atoms[-1]]
if chg1.is_spin_polarized():
chg1.chgdiff = [chg1.chgdiff[-1]]
chg2.chgdiff = [chg2.chgdiff[-1]]
chg2.chg = [chg2.chg[-1]]
chg2.atoms = [chg2.atoms[-1]]
newchg = VaspChargeDensity(None)
print('Start charge manipul')
for i, atchg in enumerate(chg1.chg):
c1 = atchg
c2 = chg2.chg[i]
newchg.atoms.append(chga.atoms[i].copy())
if op == '+':
nc = c1 + c2
oplong = '_add_'
elif op == '-':
nc = c1 - c2
oplong = '_sub_'
elif op == '*':
nc = c1 * c2
oplong = '_mult_'
elif op == '/':
nc = c1 / c2
oplong = '_div_'
elif op == 'avg':
nc = (c1 + c2) / 2
oplong = '_avg_'
newchg.chg.append(nc)
if chg1.is_spin_polarized():
print('Spin polarized')
for i, cd in enumerate(chg1.chgdiff):
cd2 = chg2.chgdiff[i]
if op == '+':
nd = cd + cd2
elif op == '-':
nd = cd - cd2
elif op == '*':
nd = cd * cd2
elif op == '/':
nd = cd / cd2
elif op == 'avg':
nd = (cd + cd2) / 2
newchg.chgdiff.append(nd)
# Screw doing anything fancy with the augmentation charges
# Just take them from the same file as the embedded atoms object.
newchg.aug = chga.aug
newchg.augdiff = chga.augdiff
# if options.outfile:
# fname = options.outfile
# else:
# from os.path import basename
# fname = basename(chgf1) + oplong + basename(chgf2)
newchg.write(filename)
return filename
# --------------------------------------------------------
if chg2.shape != chg1.shape:
print "\n**ERROR: Two sets of data are not on the same grid."
print "Data from file %s on %dx%dx%d grid." % (CHGCARfile1, chg1.shape[0], chg1.shape[1], chg1.shape[2])
print "Data from file %s on %dx%dx%d grid.\n" % (CHGCARfile2, chg2.shape[0], chg2.shape[1], chg2.shape[2])
sys.exit(0)
else:
print "Subtracting data from file %s ..." % CHGCARfile2,
sys.stdout.flush()
# Take difference
# -----------------
chgdiff = chgdiff - chg2
print "done."
vasp_charge_diff = VaspChargeDensity(filename=None)
vasp_charge_diff.atoms = [atoms1]
vasp_charge_diff.chg = [chgdiff]
# Print out charge density
# --------------------------
# Check whether CHGDIFF exists
if os.path.isfile("./CHGDIFF"):
print "\n**WARNING: A file called CHGDIFF already exists in this directory."
yesno = raw_input("Type y to continue and overwrite it, any other key to stop\n")
if yesno != "y":
sys.exit(0)
print "Writing density difference data to file CHGDIFF ...",
sys.stdout.flush()
print "eg. splitparchg.py PARCHG ."
sys.exit(0)
if not os.path.isfile(sys.argv[1]):
print "\n** ERROR: Input file %s was not found." % sys.argv[1]
sys.exit(0)
# Read information from command line
# First specify location of PARCHG
PARCHGfile = sys.argv[1].lstrip()
# Open geometry and density class objects
#-----------------------------------------
print "Reading potential data from file %s ..." % PARCHGfile,
sys.stdout.flush()
vasp_charge_data = VaspChargeDensity(filename=PARCHGfile)
print "done."
# Check data is spin polarised
if not vasp_charge_data.is_spin_polarized():
print "\n** ERROR: Input file does not contain spin polarised data."
sys.exit(0)
# Make Atoms object and arrays of density data
geomdata = vasp_charge_data.atoms[-1]
parchg_sum = vasp_charge_data.chg[-1]
parchg_diff = vasp_charge_data.chgdiff[-1]
# Read in potential data
#------------------------
ngridpts = numpy.array(parchg_sum.shape)
totgridpts = ngridpts.prod()
print "Potential stored on a %dx%dx%d grid" % (ngridpts[0],ngridpts[1],ngridpts[2])