def write_vtk(self, name='trilinear', gpts=None):
"""
Write data into vtk file with given number of grid points.
Parameters:
gpts - number of grid points to all directions. Default
is the number of DFT grid points.
"""
if gpts == None:
gpts = self.n
R = [np.linspace(0, self.grids[i][-1], gpts[i]) for i in range(3)]
nx, ny, nz = (gpts[0], gpts[1], gpts[2])
of = open('%s.vtk' % name, 'w')
print("# vtk DataFile Version 2.0", file=of)
print("Trilinear interpolation", file=of)
print("ASCII", file=of)
print("DATASET RECTILINEAR_GRID", file=of)
print("DIMENSIONS %i %i %i" % (nx, ny, nz), file=of)
print("X_COORDINATES %i double" % nx, file=of)
print(mix.a2s(R[0]), file=of)
print("Y_COORDINATES %i double" % ny, file=of)
print(mix.a2s(R[1]), file=of)
print("Z_COORDINATES %i double" % nz, file=of)
print(mix.a2s(R[2]), file=of)
print("POINT_DATA %i" % (nx * ny * nz), file=of)
print("SCALARS data double", file=of)
print("LOOKUP_TABLE default", file=of)
for k in range(nz):
for j in range(ny):
for i in range(nx):
r = vec([R[0][i], R[1][j], R[2][k]])
print(self(r), file=of)
of.close()
def atoms_vtk(atoms, scalars={}, vectors={}, filename=None):
'''
vtk output of atoms
@param filename: vtk output file name
@param atoms: atoms object
@param scalars: dictionary of atoms' scalar properties
@param vectors: dictionary of atoms' vector properties
'''
if filename == None:
filename = atoms.get_name() + '.vtk'
N = len(atoms)
f = open(filename, 'w')
f.write('# vtk DataFile Version 2.0 \nAtoms %s\n' % atoms.get_name())
f.write('ASCII \nDATASET UNSTRUCTURED_GRID\n')
f.write('POINTS %i double \n ' % N)
fmt = '%20.14f' #output format for floats
# Point data (atom coordinates) and cell data (bonds)
for r in atoms.get_positions():
f.write('%s\n' % mix.a2s(r, fmt=fmt))
# First the data related to atoms
f.write('POINT_DATA %i\n' % N)
for scalar in scalars:
print('SCALARS %s double 1\nLOOKUP_TABLE default' % scalar, file=f)
for value in scalars[scalar]:
print('%12.6f' % (value * 1.0), file=f)
for vector in vectors:
print('VECTORS %s double\n' % vector, file=f)
for value in properties:
print(mix.a2s(value, fmt=fmt), file=f)
f.close()
def rectilinear_vtk(grid, data, fname):
""" Write data in rectilinear grid into .vtk file.
parameters:
-----------
grid: grid[:,{0,1,2}] x-, y-, and z-grids
data: data on this regular grid.
fname: output file name
"""
f = open(fname, 'w')
nx, ny, nz = len(grid[0][:]), len(grid[1][:]), len(grid[2][:])
print("# vtk DataFile Version 2.0", file=f)
print("...some rectilinear grid data.", file=f)
print("ASCII", file=f)
print("DATASET RECTILINEAR_GRID", file=f)
print("DIMENSIONS %i %i %i" % (nx, ny, nz), file=f)
print("X_COORDINATES %i double" % nx, file=f)
print(mix.a2s(grid[0][:]), file=f)
print("Y_COORDINATES %i double" % ny, file=f)
print(mix.a2s(grid[1][:]), file=f)
print("Z_COORDINATES %i double" % nz, file=f)
print(mix.a2s(grid[2][:]), file=f)
print("POINT_DATA %i" % (nx * ny * nz), file=f)
print("SCALARS some_data double", file=f)
print("LOOKUP_TABLE default", file=f)
for k in range(nz):
for j in range(ny):
for i in range(nx):
print(data[i, j, k], file=f)
print('min ... max=', min(data.flatten()), '...', max(data.flatten()))
f.close()
def atoms_vtk(atoms,scalars={},vectors={},filename=None):
'''
vtk output of atoms
@param filename: vtk output file name
@param atoms: atoms object
@param scalars: dictionary of atoms' scalar properties
@param vectors: dictionary of atoms' vector properties
'''
if filename==None:
filename=atoms.get_name()+'.vtk'
N=len(atoms)
f=open(filename,'w')
f.write('# vtk DataFile Version 2.0 \nAtoms %s\n' %atoms.get_name())
f.write('ASCII \nDATASET UNSTRUCTURED_GRID\n')
f.write('POINTS %i double \n ' %N)
fmt='%20.14f' #output format for floats
# Point data (atom coordinates) and cell data (bonds)
for r in atoms.get_positions():
f.write('%s\n' %mix.a2s(r,fmt=fmt))
# First the data related to atoms
f.write('POINT_DATA %i\n' %N)
for scalar in scalars:
print>>f, 'SCALARS %s double 1\nLOOKUP_TABLE default' %scalar
for value in scalars[scalar]:
print>>f, '%12.6f' %(value*1.0)
for vector in vectors:
print>>f, 'VECTORS %s double\n' %vector
for value in properties:
print>>f, mix.a2s(value,fmt=fmt)
f.close()
def rectilinear_vtk(grid,data,fname):
""" Write data in rectilinear grid into .vtk file.
parameters:
-----------
grid: grid[:,{0,1,2}] x-, y-, and z-grids
data: data on this regular grid.
fname: output file name
"""
f=open(fname,'w')
nx, ny, nz=len(grid[0][:]), len(grid[1][:]), len(grid[2][:])
print>>f,"# vtk DataFile Version 2.0"
print>>f,"...some rectilinear grid data."
print>>f,"ASCII"
print>>f,"DATASET RECTILINEAR_GRID"
print>>f,"DIMENSIONS %i %i %i" %(nx,ny,nz)
print>>f,"X_COORDINATES %i double" %nx
print>>f,mix.a2s(grid[0][:])
print>>f,"Y_COORDINATES %i double" %ny
print>>f,mix.a2s(grid[1][:])
print>>f,"Z_COORDINATES %i double" %nz
print>>f,mix.a2s(grid[2][:])
print>>f,"POINT_DATA %i" %(nx*ny*nz)
print>>f,"SCALARS some_data double"
print>>f,"LOOKUP_TABLE default"
for k in range(nz):
for j in range(ny):
for i in range(nx):
print>>f, data[i,j,k]
print 'min ... max=',min(data.flatten()),'...',max(data.flatten())
f.close()
def write_vtk(self, file=None):
""" vtk output of atoms (all scalar and vector properties) """
if file == None:
file = self.get_name() + '.vtk'
N = len(self)
f = open(file, 'w')
f.write('# vtk DataFile Version 2.0 \nAtoms %s\n' % self.get_name())
f.write('ASCII \nDATASET UNSTRUCTURED_GRID\n')
f.write('POINTS %i double \n ' % N)
fmt = '%20.14f' #output format for floats
# Point data (atom coordinates) and cell data (bonds)
if self.get('nbonds') == None:
self.construct_bonds()
nb = self.get('nbonds')
bonds = self.get('bonds')
for r in self.get_positions():
f.write('%s\n' % mix.a2s(r, fmt=fmt))
f.write('CELLS %i %i\n' % (nb, 3 * nb))
for bond in bonds:
f.write('2 %i %i\n' % (bond['i'], bond['j']))
f.write('CELL_TYPES %i\n' % nb)
for bond in bonds:
f.write('3\n')
# First the data related to atoms
f.write('POINT_DATA %i\n' % N)
self.set('velocities', self.get_velocities())
for property in self.list_properties():
properties = self.get(property)
try:
tp = type(properties[0])
except:
continue
if tp == type(vec([])) or tp == type([]):
if not isinstance(properties[0], (int, float)): continue
print('VECTORS %s double\n' % property, file=f)
for value in properties:
print(mix.a2s(value, fmt=fmt), file=f)
else:
try:
x = float(properties[0])
except:
continue
print('SCALARS %s double 1\nLOOKUP_TABLE default' % property,
file=f)
for value in properties:
print('%12.6f' % (value * 1.0), file=f)
# Then data related to bonds
print('CELL_DATA %i' % nb, file=f)
print('SCALARS bond_length double 1\nLOOKUP_TABLE default', file=f)
for bond in bonds:
f.write('%f\n' % bond['length'])
f.close()
def write_vtk(self,file=None):
""" vtk output of atoms (all scalar and vector properties) """
if file==None:
file=self.get_name()+'.vtk'
N=len(self)
f=open(file,'w')
f.write('# vtk DataFile Version 2.0 \nAtoms %s\n' %self.get_name())
f.write('ASCII \nDATASET UNSTRUCTURED_GRID\n')
f.write('POINTS %i double \n ' %N)
fmt='%20.14f' #output format for floats
# Point data (atom coordinates) and cell data (bonds)
if self.get('nbonds')==None:
self.construct_bonds()
nb=self.get('nbonds')
bonds=self.get('bonds')
for r in self.get_positions():
f.write('%s\n' %mix.a2s(r,fmt=fmt))
f.write('CELLS %i %i\n' %(nb,3*nb))
for bond in bonds:
f.write( '2 %i %i\n' %(bond['i'],bond['j']) )
f.write('CELL_TYPES %i\n' %nb)
for bond in bonds:
f.write('3\n')
# First the data related to atoms
f.write('POINT_DATA %i\n' %N)
self.set('velocities',self.get_velocities())
for property in self.list_properties():
properties=self.get(property)
try:
tp=type(properties[0])
except:
continue
if tp==type(vec([])) or tp==type([]):
if not isinstance(properties[0],(int,float)): continue
print>>f, 'VECTORS %s double\n' %property
for value in properties:
print>>f, mix.a2s(value,fmt=fmt)
else:
try:
x=float(properties[0])
except:
continue
print>>f, 'SCALARS %s double 1\nLOOKUP_TABLE default' %property
for value in properties:
print>>f, '%12.6f' %(value*1.0)
# Then data related to bonds
print>>f, 'CELL_DATA %i' %nb
print>>f, 'SCALARS bond_length double 1\nLOOKUP_TABLE default'
for bond in bonds:
f.write( '%f\n' %bond['length'] )
f.close()
def write_vtk(self,name='trilinear',gpts=None):
"""
Write data into vtk file with given number of grid points.
Parameters:
gpts - number of grid points to all directions. Default
is the number of DFT grid points.
"""
if gpts==None:
gpts=self.n
R=[np.linspace(0,self.grids[i][-1],gpts[i]) for i in range(3)]
nx,ny,nz=(gpts[0],gpts[1],gpts[2])
of=open('%s.vtk' %name,'w')
print>>of,"# vtk DataFile Version 2.0"
print>>of,"Trilinear interpolation"
print>>of,"ASCII"
print>>of,"DATASET RECTILINEAR_GRID"
print>>of,"DIMENSIONS %i %i %i" %(nx,ny,nz)
print>>of,"X_COORDINATES %i double" %nx
print>>of,mix.a2s(R[0])
print>>of,"Y_COORDINATES %i double" %ny
print>>of,mix.a2s(R[1])
print>>of,"Z_COORDINATES %i double" %nz
print>>of,mix.a2s(R[2])
print>>of,"POINT_DATA %i" %(nx*ny*nz)
print>>of,"SCALARS data double"
print>>of,"LOOKUP_TABLE default"
for k in range(nz):
for j in range(ny):
for i in range(nx):
r=vec([R[0][i],R[1][j],R[2][k]])
print>>of, self(r)
of.close()