How to use the pyscal.traj_process.read_lammps_dump function in pyscal

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github srmnitc / pyscal / src / pyscal / core.py View on Github external
self.box = boxdims

                    if triclinic:
                        #we have to input rotation matrix and the inverse rotation matrix
                        rot = box.T
                        rotinv = np.linalg.inv(rot)
                        self.assign_triclinic_params(rot, rotinv)
                else:
                    raise IOError("input file %s not found"%filename)

                #now remove filenames
                for file in filenames:
                    os.remove(file)

            elif os.path.exists(filename):
                atoms, boxdims, box, triclinic = ptp.read_lammps_dump(filename, compressed=compressed, check_triclinic=True, box_vectors=True, customkeys=customkeys)
                self.atoms = atoms
                self.box = boxdims

                if triclinic:
                    rot = box.T
                    rotinv = np.linalg.inv(rot)
                    self.assign_triclinic_params(rot, rotinv)
            else:
                raise IOError("input file %s not found"%filename)


        elif format == 'poscar':
            if os.path.exists(filename):
                atoms, boxdims = ptp.read_poscar(filename, compressed=compressed)
                self.atoms = atoms
                self.box = boxdims
github srmnitc / pyscal / src / pyscal / core.py View on Github external
#check customkeys and assign a variable
            customread = (len(customkeys) > 0)

            if frame != -1:
                #split the traj and returns set of filenames
                filenames = ptp.split_traj_lammps_dump(filename, compressed=compressed)

                #reassign filename
                try:
                    filename = filenames[frame]
                except:
                    raise IOError("frame %d is not found in the trajectory"%frame)

                #now if file exists
                if os.path.exists(filename):
                    atoms, boxdims, box, triclinic = ptp.read_lammps_dump(filename, compressed=compressed, check_triclinic=True, box_vectors=True, customkeys=customkeys)
                    self.atoms = atoms
                    self.box = boxdims

                    if triclinic:
                        #we have to input rotation matrix and the inverse rotation matrix
                        rot = box.T
                        rotinv = np.linalg.inv(rot)
                        self.assign_triclinic_params(rot, rotinv)
                else:
                    raise IOError("input file %s not found"%filename)

                #now remove filenames
                for file in filenames:
                    os.remove(file)

            elif os.path.exists(filename):