Source code for dpti.lib.lammps

#!/usr/bin/env python3

import numpy as np




def get_natoms(filename):
    with open(filename) as fp:
        lines = fp.read().split("\n")
    for ii in lines:
        if "atoms" in ii:
            natoms = int(ii.split()[0])
            return natoms
    raise RuntimeError("cannot find key word 'atoms' in " + filename)



def _is_n_number(inputs, nn):
    words = inputs.split()
    if len(words) != nn:
        return False, None
    res = []
    for ii in words:
        try:
            res.append(float(ii))
        except ValueError:
            return False, None
    return True, res




def get_thermo(filename):
    with open(filename) as fp:
        fc = fp.read().split("\n")
    for sl in range(len(fc)):
        if "Step " in fc[sl]:
            break
    nwords = len(fc[sl + 1].split())
    data = []
    for el in range(sl + 1, len(fc)):
        flag, res = _is_n_number(fc[el], nwords)
        if not flag:
            break
        else:
            data.append(res)
    data = np.array(data)
    return data





def get_thermo_old(filename):
    with open(filename) as fp:
        fc = fp.read().split("\n")
    for sl in range(len(fc)):
        if "Step KinEng PotEng TotEng" in fc[sl]:
            break
    for el in range(len(fc)):
        if "Loop time of" in fc[el]:
            break
    data = []
    for ii in range(sl + 1, el):
        data.append([float(jj) for jj in fc[ii].split()])
    data = np.array(data)
    return data





def get_last_dump(dump):
    with open(dump) as fp:
        lines = fp.read().split("\n")
    lines = lines[:-1]
    step_idx = -1
    for idx, ii in enumerate(lines):
        if "ITEM: TIMESTEP" in ii:
            step_idx = idx
    if step_idx == -1:
        raise RuntimeError("cannot find timestep in lammps dump, something wrong")
    return "\n".join(lines[step_idx:])