def from_configuration_dir(cls,
configuration_dir,
calctype,
auto=True,
sort=True):
"""returns a instance of the Neb class instantited with a single configuration"""
# change config_dir to configuration_dir all over
proj = Project(configuration_dir)
sel = Selection(proj, "EMPTY", "config", False)
split_path = configuration_dir.split(os.path.sep)
index = split_path.index("training_data")
name = '/'.join(split_path[index + 1:])
sel.data = pandas.DataFrame({
"name": name,
"selected": 1
},
index=range(1))
# try:
# os.mkdir(os.path.join(proj.path, ".casm/tmp"))
# except:
# pass
# sel_config = sel.saveas(os.path.join(proj.path, ".casm/tmp", configname.replace('/', '.')), True)
obj = cls(sel, calctype, auto, sort)
return obj
"tolerance" : 0.001
},
"incremental_conditions" : {
"param_chem_pot" : {
"a" : 0.0
},
"temperature" : -100.0,
"tolerance" : 0.001
}
}
with open('../example_grand_canonical/metropolis_grand_canonical.json','r') as f:
input = json.load(f)
cwd = os.getcwd()
proj = Project()
index = 0
for xi in np.arange(-3.,0.,0.1):
path = 'path.' + str(index)
tinput = copy.deepcopy(input)
tinput['driver'] = d
tinput['driver']['initial_conditions']['param_chem_pot']['a'] = xi
tinput['driver']['final_conditions']['param_chem_pot']['a'] = xi
os.mkdir(path)
os.chdir(path)
with open('input.json','w') as f:
json.dump(tinput, f)
# attributes to hall[indiv_i]: # # "dft_gs" : DFT calculated ground states # "clex_gs" : predicted ground states # "gs_missing" : DFT ground states that are not predicted ground states # "gs_spurious" : Predicted ground states that are not DFT ground states # "uncalculated" : Predicted ground states and near ground states that have not been calculated # "below_hull" : All configurations predicted below the prediction of the DFT hull # "ranged_rms": root-mean-square error calculated for the subset of configurations # whose DFT formation energy lies within some range of the DFT convex hull. # Currently calculated for ranges 0.001, 0.005, 0.01, 0.05, 0.1, 0.5 eV/unit cell # indiv_i = 0 checkhull(input, hall, indices=[indiv_i]) proj = Project() # make sure ECI are saved into CASM project indiv = hall[indiv_i] write_eci(proj, hall[0].eci, to_json(indiv_i, hall[indiv_i])) ### Get data for plotting # query properties from CASM sel = Selection(proj, selection, all=False) comp_a = 'comp(a)' is_calculated = 'is_calculated' dft_Ef = 'formation_energy' clex_Ef = 'clex(formation_energy)' sel.query([comp_a, is_calculated, dft_Ef, clex_Ef])
def main(argv = None):
if argv is None:
argv = sys.argv[1:]
parser = argparse.ArgumentParser(description = 'Submit calculations for CASM')
parser.add_argument('-c', '--configs', help=configs_help, type=str, default="MASTER")
parser.add_argument('--path', help=path_help, type=str, default=None)
parser.add_argument('-m','--method', help=method_help, type=str, default=None)
parser.add_argument('--run', help=run_help, action="store_true", default=False)
parser.add_argument('--submit', help=submit_help, action="store_true", default=False)
parser.add_argument('--setup', help=setup_help, action="store_true", default=False)
parser.add_argument('--report', help=report_help, action="store_true", default=False)
args = parser.parse_args(argv)
if args.path is None:
args.path = getcwd()
try:
proj = Project(abspath(args.path))
sel = Selection(proj, args.configs, all=False)
if sel.data["configname"] is not None:
configname=sel.data["configname"][0]
casm_settings=proj.settings
if casm_settings == None:
raise casm.qewrapper.QEWrapperError("Not in a CASM project. The file '.casm' directory was not found.")
casm_directories=proj.dir
print(" Reading relax.json settings file")
sys.stdout.flush()
setfile = casm_directories.settings_path_crawl("relax.json",configname,casm_settings.default_clex)
if setfile == None:
raise casm.qewrapper.QEWrapperError("Could not find \"relax.json\" in an appropriate \"settings\" directory")
sys.stdout.flush()
else:
print("Using "+str(setfile)+" as settings...")
settings = casm.qewrapper.read_settings(setfile)
if settings["software"] is None:
settings["software"]="vasp"
software=settings["software"]
print("Relevant software is:", software)
if args.setup:
sel.write_pos()
for configname in sel.data["configname"]:
if software == "quantumespresso":
relaxation = casm.qewrapper.Relax(proj.dir.configuration_dir(configname))
elif software == "lammps":
relaxation = casm.lammpswrapper.Relax(proj.dir.configuration_dir(configname))
else:
relaxation = Relax(proj.dir.configuration_dir(configname))
relaxation.setup()
elif args.submit:
sel.write_pos()
for configname in sel.data["configname"]:
if software == "quantumespresso":
relaxation = casm.qewrapper.Relax(proj.dir.configuration_dir(configname))
elif software == "lammps":
relaxation = casm.lammpswrapper.Relax(proj.dir.configuration_dir(configname))
else:
relaxation = Relax(proj.dir.configuration_dir(configname))
relaxation.submit()
elif args.run:
sel.write_pos()
for configname in sel.data["configname"]:
if software == "quantumespresso":
relaxation = casm.qewrapper.Relax(proj.dir.configuration_dir(configname))
elif software == "lammps":
relaxation = casm.lammpswrapper.Relax(proj.dir.configuration_dir(configname))
else:
relaxation = Relax(proj.dir.configuration_dir(configname))
relaxation.run()
elif args.report:
for configname in sel.data["configname"]:
configdir = proj.dir.configuration_dir(configname)
clex = proj.settings.default_clex
calcdir = proj.dir.calctype_dir(configname, clex)
finaldir = join(calcdir, "run.final")
try:
if software == "quantumespresso":
if settings["outfilename"] is None:
print("WARNING: No output file specified in relax.json using default outfilename of std.out")
settings["outfilename"]="std.out"
outfilename = settings["outfilename"]
output = casm.qewrapper.Relax.properties(finaldir,outfilename)
elif software == "lammps":
output = casm.lammpswrapper.Relax.properties(calcdir)
else:
output = Relax.properties(finaldir)
calc_props = proj.dir.calculated_properties(configname, clex)
print("writing:", calc_props)
with open(calc_props, 'wb') as f:
f.write(six.u(json.dumps(output, cls=noindent.NoIndentEncoder, indent=2)).encode('utf-8'))
#compat.dump(json, output, calc_props, 'w', cls=noindent.NoIndentEncoder, indent=4, sort_keys=True)
except:
print(("Unable to report properties for directory {}.\n"
"Please verify that it contains a completed calculation.".format(configdir)))
except Exception as e:
print(e)
sys.exit(1)
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
parser = argparse.ArgumentParser(
description='Submit calculations for CASM')
parser.add_argument('-c',
'--configs',
help=configs_help,
type=str,
default="MASTER")
parser.add_argument('-t',
'--type',
help=configtype_help,
type=str,
default="config")
parser.add_argument('--calctype', help=calctype_help, type=str, default="")
parser.add_argument('--path', help=path_help, type=str, default=None)
parser.add_argument('--run',
help=run_help,
action="store_true",
default=False)
parser.add_argument('--submit',
help=submit_help,
action="store_true",
default=False)
parser.add_argument('--setup',
help=setup_help,
action="store_true",
default=False)
parser.add_argument('--report',
help=report_help,
action="store_true",
default=False)
args = parser.parse_args(argv)
if args.path is None:
args.path = getcwd()
try:
proj = Project(abspath(args.path))
sel = Selection(proj, args.configs, args.type, all=False)
if args.calctype == "":
#get default calctype
args.calctype = proj.settings.default_clex.calctype
global_settings = json.load(
open(
join(proj.dir.calctype_settings_dir(args.calctype),
"calc.json")))
software = global_settings["software"]
method = global_settings["method"]
# Construct with Selection:
# - This provides access to the Project, via sel.proj
# - From the project you can make calls to run interpolation and query lattice relaxations
calculator = available_calculators[software][method](sel,
args.calctype)
if args.setup:
calculator.setup()
elif args.submit:
calculator.submit()
elif args.run:
calculator.run()
elif args.report:
calculator.report()
except Exception as e:
print(e)
sys.exit(1)
},
"incremental_conditions": {
"param_chem_pot": {
"a": 0.0
},
"temperature": -100.0,
"tolerance": 0.001
}
}
with open('../example_grand_canonical/metropolis_grand_canonical.json',
'r') as f:
input = json.load(f)
cwd = os.getcwd()
proj = Project()
index = 0
for xi in np.arange(-3., 0., 0.1):
path = 'path.' + str(index)
tinput = copy.deepcopy(input)
tinput['driver'] = d
tinput['driver']['initial_conditions']['param_chem_pot']['a'] = xi
tinput['driver']['final_conditions']['param_chem_pot']['a'] = xi
os.mkdir(path)
os.chdir(path)
with open('input.json', 'w') as f:
json.dump(tinput, f)
def monte_cmd(input):
global proj
if proj is None:
proj = Project()
stdout, stderr, returncode = proj.command('monte -s input.json')
print stdout