def write_vasp_input(dirpath,
incarfile,
prim_kpointsfile,
prim_poscarfile,
super_poscarfile,
speciesfile,
sort=True,
extra_input_files=[],
strict_kpoints=False):
""" Write VASP input files in directory 'dirpath' """
print "Setting up VASP input files:", dirpath
# read prim and prim kpoints
print " Reading KPOINTS:", prim_kpointsfile
prim_kpoints = kpoints.Kpoints(prim_kpointsfile)
if prim_poscarfile != None:
print " Reading KPOINTS reference POSCAR:", prim_poscarfile
prim = poscar.Poscar(prim_poscarfile)
else:
prim = None
# read species, super poscar, incar, and generate super kpoints
print " Reading SPECIES:", speciesfile
species_settings = species.species_settings(speciesfile)
print " Reading supercell POS:", super_poscarfile
super = poscar.Poscar(super_poscarfile, species_settings)
print " Reading INCAR:", incarfile
super_incar = incar.Incar(incarfile, species_settings, super, sort)
print " Generating supercell KPOINTS"
if strict_kpoints:
super_kpoints = prim_kpoints
else:
super_kpoints = prim_kpoints.super_kpoints(prim, super)
# write main input files
print " Writing supercell POSCAR:", os.path.join(dirpath, 'POSCAR')
super.write(os.path.join(dirpath, 'POSCAR'), sort)
print " Writing INCAR:", os.path.join(dirpath, 'INCAR')
super_incar.write(os.path.join(dirpath, 'INCAR'))
print " Writing supercell KPOINTS:", os.path.join(dirpath, 'KPOINTS')
super_kpoints.write(os.path.join(dirpath, 'KPOINTS'))
print " Writing POTCAR:", os.path.join(dirpath, 'POTCAR')
write_potcar(os.path.join(dirpath, 'POTCAR'), super, species_settings,
sort)
# copy extra input files
if len(extra_input_files):
print " Copying extra input files",
for s in extra_input_files:
print " ", s
shutil.copy(s, dirpath)
print " DONE\n"
sys.stdout.flush()
def write_quantum_espresso_input(dirpath,
infilename,
super_poscarfile,
speciesfile,
sort=True,
extra_input_files=[],
strict_kpoints=False):
""" Write Quantum Espresso input files in directory 'dirpath' """
print "Setting up Quantum Espresso input files:", dirpath
# read Infile for K_POINTS, CELL_PARAMETERS, and generate super kpoints
print " Reading Infile:", infilename
myinfile = infile.Infile(infilename, None, None, sort)
print " Reading SPECIES:", speciesfile
species_settings = species.species_settings(speciesfile)
print " Reading K_POINTS from:", infilename
prim_kpoints = myinfile.cards["K_POINTS"]
print " Reading K_POINTS reference positions from CELL_PARAMETERS:", infilename
prim = poscar.Poscar(infilename, species_settings)
print " Reading supercell POS:", super_poscarfile
super = poscar.Poscar(super_poscarfile, species_settings)
print " Generating supercell KPOINTS"
if strict_kpoints:
super_kpoints = prim_kpoints
else:
super_kpoints = prim_kpoints.super_kpoints(prim, super)
#get raw infile name (without directories)
directories = re.split("/", infilename)
if len(directories) > 1:
infilename = directories[-1]
# write main input file
print " Writing supercell positions to Infile"
myinfile.rewrite_poscar_info(super)
print " Writing supercell K_POINTS to Infile"
myinfile.cards["K_POINTS"] = super_kpoints
print " Writing Infile:", os.path.join(dirpath, infilename)
myinfile.write(os.path.join(dirpath, infilename))
# copy extra input files
print " Copying extra input files",
for s in extra_input_files:
print s,
shutil.copy(s, dirpath)
print ""
print "Quantum Espresso input files complete\n"
sys.stdout.flush()
def __init__(self, incarfile, prim_kpointsfile, prim_poscarfile, super_poscarfile, speciesfile, sort=False):
""" Construct a VaspIO object
Args:
incarfile: path to INCAR file
prim_kpointsfile: path to primitive KPOINTS file
prim_poscarfile: path to primitive POSCAR file
super_poscarfile: path to POSCAR file for this configuration
speciesfile: path to SPECIES file
This functions reads the input files and generates self.kpoints appropriate for self.poscar
given that 'prim_kpointsfile' is for 'prim_poscarfile'.
"""
prim = poscar.Poscar(prim_poscarfile)
prim_kpoints = kpoints.Kpoints(prim_kpointsfile)
self.species = species.species_settings(speciesfile)
self.poscar = poscar.Poscar(super_poscarfile, self.species)
self.incar = incar.Incar(incarfile, self.species, self.poscar, sort)
self.kpoints = prim_kpoints.super_kpoints(prim, self.poscar)
#!/usr/bin/python
import sys
import io
import os
import logging
import numpy as np
testdir = os.path.dirname(__file__)
srcdir = '../parsevasp'
sys.path.insert(0, os.path.abspath(os.path.join(testdir, srcdir)))
import poscar
logging.basicConfig(level=logging.DEBUG)
logger = logging.getLogger('Testing')
poscar = poscar.Poscar(file_path = testdir + "/POSCAREXT")
poscar.modify("unitcell", np.array([[2.0, 0.0, 0.0],
[0.0, 2.0, 0.0],
[0.0, 0.0, 2.0]]))
poscar.delete_site(2)
poscar.write(file_path = testdir + "/POSCAREXTMOD")
def iter_read(self):
""" Create a QErun object from an outfile """
myoutfile = outfile.Outfile(self.outfilename)
pos = poscar.Poscar(self.outfilename)
self.is_complete = myoutfile.complete
self.all_e_0 = myoutfile.E
self.total_energy = self.all_e_0[-1]
self.lattice = pos._lattice.tolist()
self.rec_lat = pos._reciprocal_lattice
self.coord_mode = pos.coord_mode
self.atom_type = pos.type_atoms
self.atoms_per_type = pos.num_atoms
self.elec_conv = True
###Read things that haven't been taken care of by other functions
### i.e. efermi, dos_lm, Band, DOS, dos, forces, nstep
if os.path.isfile(self.outfilename):
if self.outfilename.split(".")[-1].lower() == "gz":
f = gzip.open(self.outfilename)
else:
f = open(self.outfilename)
elif os.path.isfile(self.outfilename+".gz"):
f = gzip.open(self.outfilename+".gz")
else:
raise QErunError("file not found: " + self.outfilename)
line=f.readline()
m = re.search("Final en.*",line)
while not m and self.elec_conv:
line = f.readline()
if line=='':
self.elec_conv = False
line = line.strip()
m = re.search("Final en.*",line)
f.seek(0)
line=f.readline()
m = re.search("highest occupied level.*",line)
if not m:
while not m:
line = f.readline()
if line=='':
raise QErunError("EOF reach without finding highest occupied level")
line = line.strip()
m = re.search("highest occupied level.*",line)
try:
self.efermi = float(line.split()[-1])
except ValueError:
raise QErunError("could not convert efermi to float")
line=f.readline()
m = re.search("Forces acting on atoms.*",line)
if not m:
while not m:
line = f.readline()
if line=='':
raise QErunError("EOF reach without finding Forces acting on atoms")
line = line.strip()
m = re.search("Forces acting on atoms.*",line)
forces=[]
f.readline()
for i in range(sum(self.atoms_per_type)):
line=f.readline().split()
forces+=[[float(line[-3]),float(line[-2]),float(line[-1])]]
f.close()
#Band & DOS stuff not implemented
#parse basis from poscar object into 2d list
names=[]
for site in pos.basis:
names+= [site.occ_alias]
sortednames=sorted(names,key=lambda x: self.atom_type.index(x))
indexmap=sorted(range(len(names)),key=lambda x: sortednames.index(names[x]))
rawlist=[]
for site in pos.basis:
rawlist += [site.position]
#make sure basis and forces correspond
self.basis = map(lambda x:rawlist[x].tolist() ,indexmap)
self.forces = map(lambda x:forces[x] ,indexmap)