import numpy as np from maptool.core.analysis import rdf from dpdata import System ls = System('dump_npt_470.atom', fmt='lammps/dump', type_map=['Li']) sls = ls.sub_system(range(int(0.5 * len(ls)), len(ls))) pmg_sts = sls.to_pymatgen_structure() d = [st.density for st in pmg_sts] print(np.std(d)) print(np.mean(d)) rdf, radii = rdf(pmg_sts, 10, 200, (0, 10)) ret = np.vstack((radii, rdf)).T print(ret.shape) np.savetxt('rn.txt', ret)
import numpy as np from maptool.core.analysis import rdf from dpdata import System ls = System('dump_nvt_470.atom', fmt='lammps/dump', type_map=['Li']) sls = ls.sub_system(range(1000, len(ls))) pmg_sts = sls.to_pymatgen_structure() d = [st.density for st in pmg_sts] print(np.mean(d))