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)