def setup(self):
""" Setup initial relaxation run
Uses the following files from the most local .../settings/calctype.name directory:
INCAR: VASP input settings
KPOINTS: VASP kpoints settings
POSCAR: reference for KPOINTS if KPOINTS mode is not A/AUTO/Automatic
SPECIES: info for each species such as which POTCAR files to use, MAGMOM, GGA+U, etc.
Uses the following files from the .../config directory:
POS: structure of the configuration to be relaxed
"""
incarfile = casm.settings_path("INCAR",self.casm_settings["curr_calctype"],self.configdir)
prim_kpointsfile = casm.settings_path("KPOINTS",self.casm_settings["curr_calctype"],self.configdir)
prim_poscarfile = casm.settings_path("POSCAR",self.casm_settings["curr_calctype"],self.configdir)
super_poscarfile = os.path.join(self.configdir,"POS")
speciesfile = casm.settings_path("SPECIES",self.casm_settings["curr_calctype"],self.configdir)
if incarfile == None or not os.path.isfile(incarfile):
raise vasp.VaspError("Relax.setup failed. No incar file: '" + incarfile + "'")
if prim_kpointsfile == None or not os.path.isfile(prim_kpointsfile):
raise vasp.VaspError("Relax.setup failed. No kpoints file: '" + prim_kpointsfile + "'")
if prim_poscarfile == None or not os.path.isfile(prim_poscarfile):
# raise vasp.VaspError("Relax.setup failed. No prim poscar file: '" + prim_poscarfile + "'")
warnings.warn("No prim poscar file: '" + prim_poscarfile + "', I hope your KPOINTS mode is A/AUTO/Automatic \
or this will fail!!!", vasp.VaspWarning)
prim_poscarfile = None
if super_poscarfile == None or not os.path.isfile(super_poscarfile):
raise vasp.VaspError("Relax.setup failed. No pos file: '" + super_poscarfile + "'")
if speciesfile == None or not os.path.isfile(speciesfile):
raise vasp.VaspError("Relax.setup failed. No species file: '" + speciesfile + "'")
sys.stdout.flush()
vasp.io.write_vasp_input(self.calcdir, incarfile, prim_kpointsfile, prim_poscarfile, super_poscarfile, speciesfile, self.sort)
def setup(self):
""" Setup initial relaxation run
Uses the following files from the most local .../settings/calctype.name directory:
INCAR: VASP input settings
KPOINTS: VASP kpoints settings
POSCAR: reference for KPOINTS if KPOINTS mode is not A/AUTO/Automatic
SPECIES: info for each species such as which POTCAR files to use, MAGMOM, GGA+U, etc.
Uses the following files from the .../config directory:
POS: structure of the configuration to be relaxed
"""
incarfile = casm.settings_path("INCAR",
self.casm_settings["curr_calctype"],
self.configdir)
prim_kpointsfile = casm.settings_path(
"KPOINTS", self.casm_settings["curr_calctype"], self.configdir)
prim_poscarfile = casm.settings_path(
"POSCAR", self.casm_settings["curr_calctype"], self.configdir)
super_poscarfile = os.path.join(self.configdir, "POS")
speciesfile = casm.settings_path("SPECIES",
self.casm_settings["curr_calctype"],
self.configdir)
if incarfile == None or not os.path.isfile(incarfile):
raise vasp.VaspError("Relax.setup failed. No incar file: '" +
incarfile + "'")
if prim_kpointsfile == None or not os.path.isfile(prim_kpointsfile):
raise vasp.VaspError("Relax.setup failed. No kpoints file: '" +
prim_kpointsfile + "'")
if prim_poscarfile == None or not os.path.isfile(prim_poscarfile):
# raise vasp.VaspError("Relax.setup failed. No prim poscar file: '" + prim_poscarfile + "'")
warnings.warn(
"No prim poscar file: '" + prim_poscarfile +
"', I hope your KPOINTS mode is A/AUTO/Automatic \
or this will fail!!!", vasp.VaspWarning)
prim_poscarfile = None
if super_poscarfile == None or not os.path.isfile(super_poscarfile):
raise vasp.VaspError("Relax.setup failed. No pos file: '" +
super_poscarfile + "'")
if speciesfile == None or not os.path.isfile(speciesfile):
raise vasp.VaspError("Relax.setup failed. No species file: '" +
speciesfile + "'")
sys.stdout.flush()
vasp.io.write_vasp_input(self.calcdir, incarfile, prim_kpointsfile,
prim_poscarfile, super_poscarfile,
speciesfile, self.sort)
def report(self):
"""Report final results to properties.calc.json file in configuration directory."""
outputfile = os.path.join(self.calcdir, "properties.calc.json")
if os.path.isfile(outputfile):
with open(outputfile, 'r') as file:
output = json.load(file)
else:
output = dict()
vrun = vasp.io.Vasprun( os.path.join(self.calcdir, "run.final", "vasprun.xml") )
# the calculation is run on the 'sorted' POSCAR, need to report results 'unsorted'
if self.sort:
super_poscarfile = os.path.join(self.configdir,"POS")
speciesfile = casm.settings_path("SPECIES",self.casm_settings["curr_calctype"],self.configdir)
species_settings = vasp.io.species_settings(speciesfile)
super = vasp.io.Poscar(super_poscarfile, species_settings)
unsort_dict = super.unsort_dict()
else:
# fake unsort_dict (unsort_dict[i] == i)
unsort_dict = dict(zip(range(0,len(vrun.basis)),range(0,len(vrun.basis))))
print unsort_dict
# unsort_dict:
# Returns 'unsort_dict', for which: unsorted_dict[orig_index] == sorted_index;
# unsorted_dict[sorted_index] == orig_index
# For example:
# 'unsort_dict[0]' returns the index into the unsorted POSCAR of the first atom in the sorted POSCAR
results = dict()
results["is_complete"] = vrun.is_complete
results["atom_type"] = super.type_atoms
results["atoms_per_type"] = super.num_atoms
results["coord_mode"] = vrun.coord_mode
# as lists
results["relaxed_forces"] = [ None for i in range(len(vrun.forces))]
for i, v in enumerate(vrun.forces):
results["relaxed_forces"][unsort_dict[i] ] = vrun.forces[i]
results["relaxed_lattice"] = vrun.lattice
results["relaxed_basis"] = [ None for i in range(len(vrun.basis))]
for i, v in enumerate(vrun.basis):
results["relaxed_basis"][unsort_dict[i] ] = vrun.basis[i]
results["relaxed_energy"] = vrun.total_energy
with open(outputfile, 'w') as file:
json.dump(results, file, indent=4, sort_keys=True)
print "Wrote " + outputfile
sys.stdout.flush()
def report(self):
"""Report final results to properties.calc.json file in configuration directory."""
outputfile = os.path.join(self.calcdir, "properties.calc.json")
if os.path.isfile(outputfile):
with open(outputfile, 'r') as file:
output = json.load(file)
else:
output = dict()
vrun = vasp.io.Vasprun( os.path.join(self.calcdir, "run.final", "vasprun.xml") )
# the calculation is run on the 'sorted' POSCAR, need to report results 'unsorted'
if self.sort:
super_poscarfile = os.path.join(self.configdir,"POS")
speciesfile = casm.settings_path("SPECIES",self.casm_settings["curr_calctype"],self.configdir)
species_settings = vasp.io.species_settings(speciesfile)
super = vasp.io.Poscar(super_poscarfile, species_settings)
unsort_dict = super.unsort_dict()
else:
# fake unsort_dict (unsort_dict[i] == i)
unsort_dict = dict(zip(range(0,len(vrun.basis)),range(0,len(vrun.basis))))
print unsort_dict
# unsort_dict:
# Returns 'unsort_dict', for which: unsorted_dict[orig_index] == sorted_index;
# unsorted_dict[sorted_index] == orig_index
# For example:
# 'unsort_dict[0]' returns the index into the unsorted POSCAR of the first atom in the sorted POSCAR
results = dict()
results["is_complete"] = vrun.is_complete
results["atom_type"] = super.type_atoms
results["atoms_per_type"] = super.num_atoms
results["coord_mode"] = vrun.coord_mode
# as lists
results["relaxed_forces"] = [ None for i in range(len(vrun.forces))]
for i, v in enumerate(vrun.forces):
results["relaxed_forces"][unsort_dict[i] ] = casm.NoIndent(vrun.forces[i])
results["relaxed_lattice"] = [casm.NoIndent(v) for v in vrun.lattice]
results["relaxed_basis"] = [ None for i in range(len(vrun.basis))]
for i, v in enumerate(vrun.basis):
results["relaxed_basis"][unsort_dict[i] ] = casm.NoIndent(vrun.basis[i])
results["relaxed_energy"] = vrun.total_energy
with open(outputfile, 'w') as file:
file.write(json.dumps(results, file, cls=casm.NoIndentEncoder, indent=4, sort_keys=True))
print "Wrote " + outputfile
sys.stdout.flush()
def __init__(self, configdir = None, convtype = None, auto = True, sort = True):
"""
Construct a VASP convergence job object.
Args:
configdir: path to configuration
convtype: type of convergence (e.g. 'kpoints' or 'encut')
auto: True if using pbs module's JobDB to manage pbs jobs
"""
if configdir == None:
configdir = os.getcwd()
print "Reading CASM settings"
self.casm_settings = casm.casm_settings(configdir)
if self.casm_settings == None:
raise vaspwrapper.VaspWrapperError("Not in a CASM project. The file '.casm/project_settings.json' was not found.")
print "Constructing a CASM VASPWrapper Converge object"
sys.stdout.flush()
print " Setting up directories"
sys.stdout.flush()
# store path to .../config, if not existing raise
self.configdir = os.path.abspath(configdir)
if not os.path.isdir(self.configdir):
raise vasp.VaspError("Error in casm.vasp.relax: Did not find directory: " + self.configdir)
sys.stdout.flush()
# store path to .../config/calctype.name, and create if not existing
self.calcdir = os.path.join(self.configdir, self.casm_settings["curr_calctype"])
try:
os.mkdir(self.calcdir)
except:
pass
# read the settings json file
print " Reading converge.json settings file"
sys.stdout.flush()
setfile = casm.settings_path("converge.json",self.casm_settings["curr_calctype"],self.configdir)
if setfile == None:
raise vaspwrapper.VaspWrapperError("Could not find .../settings/" + self.casm_settings["curr_calctype"] + "/converge.json file.")
sys.stdout.flush()
self.settings = vaspwrapper.read_settings(setfile)
# add required keys to settings if not present
if not "ncore" in self.settings:
self.settings["ncore"] = None
if not "npar" in self.settings:
self.settings["npar"] = None
if not "kpar" in self.settings:
self.settings["kpar"] = None
if not "vasp_cmd" in self.settings:
self.settings["vasp_cmd"] = None
if not "ncpus" in self.settings:
self.settings["ncpus"] = None
if not "encut" in self.settings:
self.settings["encut"] = None
if not "kpoints" in self.settings:
self.settings["kpoints"] = None
if not "nrg_convergence" in self.settings:
self.settings["nrg_convergence"] = None
if not "run_limit" in self.settings:
self.settings["run_limit"] = None
self.auto = auto
self.sort = sort
print "VASP Converge object constructed\n"
sys.stdout.flush()
def __init__(self, configdir=None, auto = True, sort = True):
"""
Construct a VASP relaxation job object.
Args:
configdir: path to configuration
auto: True if using pbs module's JobDB to manage pbs jobs
"""
if configdir == None:
configdir = os.getcwd()
print "Reading CASM settings"
self.casm_settings = casm.casm_settings(configdir)
if self.casm_settings == None:
raise vaspwrapper.VaspWrapperError("Not in a CASM project. The file '.casm' directory was not found.")
print "Constructing a CASM VASPWrapper Relax object"
sys.stdout.flush()
print " Setting up directories"
sys.stdout.flush()
# store path to .../config, if not existing raise
self.configdir = os.path.abspath(configdir)
if not os.path.isdir(self.configdir):
raise vasp.VaspError("Error in casm.vasp.relax: Did not find directory: " + self.configdir)
sys.stdout.flush()
# store path to .../config/calctype.name, and create if not existing
self.calcdir = os.path.join(self.configdir, self.casm_settings["curr_calctype"])
try:
os.mkdir(self.calcdir)
except:
pass
# read the settings json file
print " Reading relax.json settings file"
sys.stdout.flush()
setfile = casm.settings_path("relax.json",self.casm_settings["curr_calctype"],self.configdir)
if setfile == None:
raise vaspwrapper.VaspWrapperError("Could not find .../settings/" + self.casm_settings["curr_calctype"] + "/relax.json file.")
sys.stdout.flush()
self.settings = vaspwrapper.read_settings(setfile)
# add required keys to settings if not present
if not "ncore" in self.settings:
self.settings["ncore"] = None
if not "npar" in self.settings:
self.settings["npar"] = None
if not "kpar" in self.settings:
self.settings["kpar"] = None
if not "vasp_cmd" in self.settings:
self.settings["vasp_cmd"] = None
if not "ncpus" in self.settings:
self.settings["ncpus"] = None
if not "run_limit" in self.settings:
self.settings["run_limit"] = None
self.auto = auto
self.sort = sort
print "VASP Relax object constructed\n"
sys.stdout.flush()
