def main(ingname=""):
"""Get the energy from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "energy (eV);<energy as a string>", ex:
"energy (eV); 3.0"
Returns last E0 energy for a VASP run.
Returns last E0 energy for all images for a VASP neb.
Returns "N/A" otherwise.
"""
trymeta = "%s/metadata.txt" % ingname
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if 'induce' in ingname: #skip inducedefect ingredients
myprogram = "None"
if 'vasp' in myprogram:
if os.path.isdir("%s/01" % ingname):
estr = "energies (eV)"
for subdir in dirutil.immediate_subdirs(ingname):
mychecker = VaspChecker(name="%s/%s" % (ingname, subdir))
estr = estr + ";%3.3f" % mychecker.get_energy_from_energy_file()
return estr
else:
mychecker = VaspChecker(name=ingname)
return "energy (eV);%3.3f" % mychecker.get_energy_from_energy_file()
else:
return "energy (eV);N/A"
def main(ingname=""):
"""Get the energy from an ingredient.
Args:
ingname <str>: Ingredient name, full path
Returns:
<string>: "energy (eV);<energy as a string>", ex:
"energy (eV); 3.0"
Returns last E0 energy for a VASP run.
Returns last E0 energy for all images for a VASP neb.
Returns "N/A" otherwise.
"""
trymeta = "%s/metadata.txt" % ingname
if os.path.isfile(trymeta):
mymeta = Metadata(metafile=trymeta)
myprogram = mymeta.read_data("program")
else:
myprogram = "None"
if 'induce' in ingname: #skip inducedefect ingredients
myprogram = "None"
if 'vasp' in myprogram:
if os.path.isdir("%s/01" % ingname):
estr = "energies (eV)"
for subdir in dirutil.immediate_subdirs(ingname):
mychecker = VaspChecker(name="%s/%s" % (ingname, subdir))
estr = estr + ";%3.3f" % mychecker.get_energy_from_energy_file(
)
return estr
else:
mychecker = VaspChecker(name=ingname)
return "energy (eV);%3.3f" % mychecker.get_energy_from_energy_file(
)
else:
return "energy (eV);N/A"
def evaluate_ga_vasp_and_update(self, childname=""):
"""Evaluate the Genetic Algorithm VASP ingredient.
"""
raise NotImplementedError
childpath = os.path.join(os.path.dirname(self.keywords['name']), childname)
from mastlib.amy_ga_code import fitness_evaluation
from MAST.ingredients.checker import VaspChecker
from MAST.utility import MASTFile
dircontents = os.listdir(self.keywords['name'])
subfolders = list()
for diritem in dircontents:
fulldir = os.path.join(self.keywords['name'],diritem)
if os.path.isdir(fulldir) and diritem.isdigit():
subfolders.append(fulldir)
energylist = list()
structurelist = list()
for subfolder in subfolders:
mychecker = VaspChecker(subfolder, self.keywords['program_keys'], self.keywords['structure'])
mystructure = mychecker.get_final_structure_from_directory()
structurelist.append(mystructure)
myenergy = mychecker.get_energy_from_energy_file()
energylist.append(myenergy)
[fitoutput, fitstructure] = fitness_evaluation.evaluate(structurelist, energylist)
#If output is a structure or xyz file, could just write it directly.
fitfile = MASTFile()
fitfile.data = fitoutput
import time
timestamp = time.strftime("%Y%m%d_%H%M%S")
outputname = "my_output_%s" % timestamp
outputstrname = "my_structure_%s" % timestamp
fitfile.to_file(os.path.join(childpath, outputname))
fitstructure.write_file(os.path.join(childpath, outputstrname))
return " %s and %s written in %s" % (outputname, outputstrname, childpath)
def evaluate_ga_vasp_and_update(self, childname=""):
"""Evaluate the Genetic Algorithm VASP ingredient.
"""
raise NotImplementedError
childpath = os.path.join(os.path.dirname(self.keywords['name']),
childname)
from mastlib.amy_ga_code import fitness_evaluation
from MAST.ingredients.checker import VaspChecker
from MAST.utility import MASTFile
dircontents = os.listdir(self.keywords['name'])
subfolders = list()
for diritem in dircontents:
fulldir = os.path.join(self.keywords['name'], diritem)
if os.path.isdir(fulldir) and diritem.isdigit():
subfolders.append(fulldir)
energylist = list()
structurelist = list()
for subfolder in subfolders:
mychecker = VaspChecker(subfolder, self.keywords['program_keys'],
self.keywords['structure'])
mystructure = mychecker.get_final_structure_from_directory()
structurelist.append(mystructure)
myenergy = mychecker.get_energy_from_energy_file()
energylist.append(myenergy)
[fitoutput,
fitstructure] = fitness_evaluation.evaluate(structurelist, energylist)
#If output is a structure or xyz file, could just write it directly.
fitfile = MASTFile()
fitfile.data = fitoutput
import time
timestamp = time.strftime("%Y%m%d_%H%M%S")
outputname = "my_output_%s" % timestamp
outputstrname = "my_structure_%s" % timestamp
fitfile.to_file(os.path.join(childpath, outputname))
fitstructure.write_file(os.path.join(childpath, outputstrname))
return " %s and %s written in %s" % (outputname, outputstrname,
childpath)
def get_total_energy(self, directory):
"""Returns the total energy from a directory"""
abspath = '%s/%s/' % (self.recdir, directory)
mychecker = VaspChecker(name=abspath)
return mychecker.get_energy_from_energy_file()
def get_total_energy(self, directory):
"""Returns the total energy from a directory"""
abspath = '%s/%s/' % (self.recdir, directory)
mychecker = VaspChecker(name=abspath)
return mychecker.get_energy_from_energy_file()
