def get_structure_from_file(self, myfilepath=""):
"""Get the structure from a specified file path.
For LAMMPS, this is a trajectory-type file.
Args:
myfilepath <str>: File path for structure.
"""
dir = os.path.dirname(myfilepath)
if dir == '':
dir = os.getcwd()
filelist = os.listdir(dir)
atomsymbolsfile = None
for onefile in filelist:
if 'atom_symbols' in onefile:
atomsymbolsfile = os.path.join(dir, onefile)
#Read the atom types from the atoms symbol file
f = open(atomsymbolsfile, 'r')
atomslist = list()
for line in f.readlines():
atomslist.append(line.strip())
f.close()
if "DATA" in myfilepath:
atms = read_lammps_data(myfilepath, atomslist)
elif "TRAJECTORY" in myfilepath:
atms, velocities, forces = read_lammps_trajectory(
myfilepath, -1, atomslist)
else:
raise MASTError(
self.__class__.__name__,
"Unknown file type for receiving structure from LAMMPS: %s" %
myfilepath)
return AseAtomsAdaptor.get_structure(atms)
def get_structure_from_file(self, myfilepath=""):
"""Get the structure from a specified file path.
For LAMMPS, this is a trajectory-type file.
Args:
myfilepath <str>: File path for structure.
"""
dir = os.path.dirname(myfilepath)
if dir == '':
dir = os.getcwd()
filelist = os.listdir(dir)
atomsymbolsfile = None
for onefile in filelist:
if 'atom_symbols' in onefile:
atomsymbolsfile = os.path.join(dir, onefile)
#Read the atom types from the atoms symbol file
f = open(atomsymbolsfile, 'r')
atomslist = list()
for line in f.readlines():
atomslist.append(line.strip())
f.close()
if "DATA" in myfilepath:
atms = read_lammps_data(myfilepath,atomslist)
elif "TRAJECTORY" in myfilepath:
atms,velocities,forces = read_lammps_trajectory(myfilepath,-1,atomslist)
else:
raise MASTError(self.__class__.__name__,
"Unknown file type for receiving structure from LAMMPS: %s" % myfilepath)
return AseAtomsAdaptor.get_structure(atms)
def get_initial_structure_from_directory(self, mydir=""):
"""Get the structure from a specified file path.
For LAMMPS, this is a data-type file.
Args:
myfilepath <str>: File path for structure.
"""
dir = os.path.dirname(myfilepath)
filelist = os.listdir(dir)
atomsymbolsfile = None
for onefile in filelist:
if 'atom_symbols' in onefile:
atomsymbolsfile = os.path.join(dir, onefile)
#Read the atom types from the atoms symbol file
f = open(atomsymbolsfile)
atomslist = list()
for line in f.readlines():
atomslist.append(line.strip())
f.close()
atms = read_lammps_data(myfilepath, atomslist)
return AseAtomsAdaptor.get_structure(atms)
def get_initial_structure_from_directory(self,mydir=""):
"""Get the structure from a specified file path.
For LAMMPS, this is a data-type file.
Args:
myfilepath <str>: File path for structure.
"""
dir = os.path.dirname(myfilepath)
filelist = os.listdir(dir)
atomsymbolsfile = None
for onefile in filelist:
if 'atom_symbols' in onefile:
atomsymbolsfile = os.path.join(dir, onefile)
#Read the atom types from the atoms symbol file
f = open(atomsymbolsfile)
atomslist = list()
for line in f.readlines():
atomslist.append(line.strip())
f.close()
atms = read_lammps_data(myfilepath,atomslist)
return AseAtomsAdaptor.get_structure(atms)