def castep_structure(filename, extension):
#Get structure attributes
if pure:
atoms = casread(filename)
nAtoms = atoms.get_global_number_of_atoms()
elems = ' '.join(atoms.get_chemical_symbols())
cell = atoms.get_cell()
posns = atoms.get_scaled_positions()
else:
extension = filename.split(".")[-1]
assert extension in ["cell", "castep"], "Mixtures are only supported\
if they are .cell or .castep files."
if extension == "cell":
atoms = rc.readcell(filename)
elif extension == "castep":
atoms = rc.readcas(filename)
else:
ValueError("Could not read the file since it was a mixture and not\
a .cell or .castep file.")
nAtoms = atoms.Nions
elems = ' '.join(atoms.get_elements())
cell = atoms.get_cell()
posns = atoms.get_posns()
if verbose:
print("Number of atoms:", nAtoms)
print("Lattice vectors: ", cell)
print("Fractional positions: ", posns)
latvecs = [' '.join([str(c) for c in cell[i, :]])+'\r\n' for i in \
range(3)]
return nAtoms, elems, cell, posns, latvecs
def get_structure(cellname): cas = rc.readcell(cellname) pureatoms = cas.extract_struc() kpoints, offset = cas.get_kpoints() constrs = cas.get_cell_constrs() psps = cas.get_psps() return pureatoms, kpoints, offset, constrs, psps
rtn_dist=False)
pinchatoms.set_chemical_symbols(fixelems)
pinchatoms.set_positions(pinchposnew)
return pinchatoms
##########################################################################
if __name__ == '__main__':
""" Run from the command line, pinch the second cell to match the first """
cellfile0 = sys.argv[1]
cellfile1 = sys.argv[2]
# Load the fixed cell (incl generating pure structure)
if '.cell' in cellfile0:
mix0 = rc.readcell(cellfile0)
elif '.castep' in cellfile0:
mix0 = rc.readcas(cellfile0)
mixatoms0 = mix0.extract_struc()
mixkey0 = mix0.get_mixkey()
mapping0 = mixmap.mixmap(mixatoms0, mixkey0)
pureatoms0 = mapping0.mix2pure(mixatoms0)
posns0 = pureatoms0.get_positions()
Nions = len(pureatoms0)
# Load the cell to be pinched (incl generating pure structure)
mix1 = rc.readcell(cellfile1)
mixatoms1 = mix1.extract_struc()
mixkey1 = mix1.get_mixkey()
mapping1 = mixmap.mixmap(mixatoms1, mixkey1)
pureatoms1 = mapping1.mix2pure(mixatoms1)
""" A silly script to test that all the functionality works.
Running this script should test that most functions and classes run without
errors (although as yet no checks test that the results are sensible). """
########################################################
########################################################
###################################
# Manipulating pure & mixed cells #
###################################
# Read mix cell
print('\n\n\nMix Cell\n\n\n')
cas = rc.readcell('examples/Ca2.15Sr0.85Ti2O7_Amam.cell')
print(cas.get_kpoints())
print(cas.get_psps())
print(cas.get_elements())
print(cas.get_init_spin())
print(cas.get_mixkey())
print(cas.get_posns())
print(cas.get_ext_press())
print(cas.get_cell_constrs())
print(cas.get_cell())
mixkey = cas.get_mixkey()
########################################################
#!/usr/bin/env python3 import sys import mixmap import readmixcastep as rc import numpy as np cellfile = sys.argv[1] shift = np.array([float(s) for s in sys.argv[2:5]]) # frac coords cas = rc.readcell(cellfile) mixatoms = cas.extract_struc() mixkey = cas.get_mixkey() mapping = mixmap.mixmap(mixatoms, mixkey) posns = mixatoms.get_scaled_positions() posns += shift mixatoms.set_scaled_positions(posns) mapping.casprint(mixatoms, cellfile)
#!/usr/bin/env python3
import mixmap
import readmixcastep as rc
import sys
""" Command line tool to quickly get a pure cell file from a solid soln. """
# Load the input file (accepts .castep or .cell)
casfile = str(sys.argv[1])
if '.castep' in casfile:
chem = casfile.replace('.castep', '')
cas = rc.readcas(casfile)
elif '.cell' in casfile:
chem = casfile.replace('.cell', '')
cas = rc.readcell(casfile)
# Extract calculation parameters and convert from mix to pure structure
mixatom = cas.extract_struc(iteration=None)
mixkey = cas.get_mixkey(iteration=None)
press = cas.get_ext_press()
kpoints, offset = cas.get_kpoints()
pseudos = cas.get_psps()
constraints = cas.get_cell_constrs()
mapping = mixmap.mixmap(mixatom, mixkey)
pureatom = mapping.mix2pure(mixatom)
# Write the pure cell (always with the same handle plus the suffix _nonSS)
mapping.setcellparams(pressure=press,
cell_constrs=constraints,
pseudos=pseudos,
kpoints=kpoints,