Initinal commit /lps-lii-ps4-iodide-geometry
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佐久間 美波
Executable
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#!/usr/bin/env python
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# ./dump2cube_edge_corner.py -i 050Li3PS4-050LiI.lammpstrj -m 160 160 160 -cut 8
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import numpy as np
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import argparse
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import re
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import os
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import time
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description = """This is a test program"""
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par = argparse.ArgumentParser(description=description)
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par.add_argument('-i', '--trjfile', default="", required=True,
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help='input trjfile')
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par.add_argument('-m', '--mesh', default=(30, 30, 30), required=False,
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nargs=3, type=int, help='mesh grid')
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par.add_argument('-cut', '--cutoff', default=7, required=False,
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type=float, help='mesh grid')
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args = par.parse_args()
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ang_borr = 0.5291772109217
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dirname = os.path.dirname(__file__)
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class LammpsTrj():
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def __init__(self):
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"""
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trjファイルを読み込んで、原子数、lattice、ステップ数を格納
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"""
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with open(args.trjfile) as o:
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data = o.read().split()
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self.atoms = int(data[7]) # 原子数
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data = np.array(data).reshape(-1, self.atoms*7+32)
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self.lattices = data[:, 17:23].astype(float) # (step, 6)
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self.data = data[:, 32:] # 座標データ
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self.steps = data.shape[0]
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self.mesh = args.mesh
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self.cutoff = args.cutoff
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def setLattice(self, lat):
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"""
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latticeの形によって操作を分岐
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self.M, self.M_を作成
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"""
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if lat.shape[0] == 6:
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M = np.array([[lat[1]-lat[0], 0, 0],
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[0, lat[3]-lat[2], 0],
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[0, 0, lat[5]-lat[4]]]).astype(float)
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if lat.shape[0] == 9:
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xlo_bound, xhi_bound, xy = lat[0, 0], lat[0, 1], lat[0, 2]
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ylo_bound, yhi_bound, xz = lat[1, 0], lat[1, 1], lat[1, 2]
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zlo_bound, zhi_bound, yz = lat[2, 0], lat[2, 1], lat[2, 2]
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xlo = xlo_bound - np.min([0.0, xy, xz, xy+xz])
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xhi = xhi_bound - np.max([0.0, xy, xz, xy+xz])
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ylo = ylo_bound - np.min([0.0, yz])
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yhi = yhi_bound - np.max([0.0, yz])
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zlo = zlo_bound
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zhi = zhi_bound
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lx = xhi - xlo
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ly = yhi - ylo
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lz = zhi - zlo
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a = lx
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b = np.sqrt(ly**2 + xy**2)
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c = np.sqrt(lz**2 + xz**2 + yz**2)
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alpha = np.arccos((xy*xz + ly*yz)/b/c)
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beta = np.arccos(xz/c)
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gamma = np.arccos(xy/b)
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v1 = [a, 0, 0]
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v2 = [b*np.cos(gamma), b*np.sin(gamma), 0]
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v3 = [c*np.cos(beta),
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c*(np.cos(alpha)-np.cos(beta)*np.cos(gamma))/np.sin(gamma),
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c*np.sqrt(1+2*np.cos(alpha)*np.cos(beta)*np.cos(gamma)
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- np.cos(alpha)**2-np.cos(beta)**2
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- np.cos(gamma)**2 / np.sin(gamma))]
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M = np.array([v1, v2, v3])
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return M
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def getOnestep(self, step):
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"""
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引数のstepにおける座標を、原子ごとにself.elems(辞書)に格納する
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"""
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step_data = self.data[step, :].reshape(self.atoms, -1) # (atoms, 6)
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self.M = self.setLattice(self.lattices[step])
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self.M_ = np.linalg.inv(self.M)
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self.elems = {}
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for e in np.unique(step_data[:, 2]):
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d = step_data[step_data[:, 2] == e, 3:].astype(float)
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dxyz = d[:, 0:3]
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dxyz = dxyz @ self.M_
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dxyz = dxyz - np.floor(dxyz)
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d[:, 0:3] = dxyz
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self.elems[e] = d
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return self.elems
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def makeCube(self, trjfile):
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"""
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P原子ごとに最も近い4つのI原子を選出し、Edge/Corner分類および回転を行う
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"""
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self.li_coords_list = []
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self.i_coords_list = []
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self.i_zero_coords_list = []
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self.i_corner_coords_list = []
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self.i_edge_coords_list = []
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self.i_three_coords_list = []
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self.li_hist = None
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self.i_hist = None
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self.i_hist_zero = None
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self.i_hist_corner = None
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self.i_hist_edge = None
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self.i_hist_three = None
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count_p = 0
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I_S_CUTOFF = 4.7 # Edge/Corner判定用距離 (Angstrom)
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for step in range(self.steps):
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print(f"processing {step} step")
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self.elems = self.getOnestep(step)
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elems_ = {k: v.copy() for k, v in self.elems.items()}
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for p_data in elems_["P"]:
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# P原子に最も近い4つのI原子を特定
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i_diffs = elems_["I"][:, 0:3] - p_data[0:3]
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i_diffs = i_diffs - np.around(i_diffs)
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i_diffs_abs = i_diffs @ self.M
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distances = np.linalg.norm(i_diffs_abs, axis=1)
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sorted_indices = np.argsort(distances)
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closest_Is = elems_["I"][sorted_indices[:4]]
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closer_Is = elems_["I"][sorted_indices[:15]]
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nearest_I_coords = closest_Is[0]
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# 着目P原子と同じPS4を構成するS原子を取得
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s_data = elems_["S"][elems_["S"][:, 3] == p_data[3]]
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# --- 距離によるSの配置決定 ---
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si_diff = s_data[:, 0:3] - nearest_I_coords[0:3]
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si_diff = si_diff - np.around(si_diff)
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si_diff = np.linalg.norm(si_diff @ self.M, axis=1)
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n_S_idx = np.argmax(si_diff)
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s_indices = [0, 1, 2, 3]
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s_indices.remove(n_S_idx)
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n2_S_idx = s_indices[0]
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s_xyz = s_data[:, 0:3] - p_data[0:3]
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s_xyz = s_xyz - np.round(s_xyz)
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s_xyz = s_xyz @ self.M
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# --- 座標の回転行列を作成 ---
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theta = np.arctan2(s_xyz[n_S_idx][0], s_xyz[n_S_idx][1])
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self.Mat_z = np.array([[np.cos(-theta), np.sin(-theta), 0],
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[-np.sin(-theta), np.cos(-theta), 0],
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[0, 0, 1]])
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s_xyz = (self.Mat_z @ s_xyz.T).T
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theta2 = np.arctan2(s_xyz[n_S_idx][1], s_xyz[n_S_idx][2])
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self.Mat_x = np.array([[1, 0, 0],
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[0, np.cos(-theta2), np.sin(-theta2)],
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[0, -np.sin(-theta2), np.cos(-theta2)]])
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s_xyz = (self.Mat_x @ s_xyz.T).T
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theta3 = np.arctan2(s_xyz[n2_S_idx][0], s_xyz[n2_S_idx][1])
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self.Mat_z2 = np.array([[np.cos(-theta3), np.sin(-theta3), 0],
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[-np.sin(-theta3), np.cos(-theta3), 0],
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[0, 0, 1]])
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s_xyz = (self.Mat_z2 @ s_xyz.T).T
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self.s_xyz = s_xyz
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p_xyz = np.array([0, 0, 0])
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self.ps4_coord = np.vstack((p_xyz, s_xyz)) / ang_borr
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def rotate_coords(coords_fractional):
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if len(coords_fractional) == 0:
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return np.array([])
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rot_xyz = coords_fractional[:, 0:3] - p_data[0:3]
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rot_xyz = rot_xyz - np.round(rot_xyz)
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rot_xyz = rot_xyz @ self.M
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rot_xyz = (self.Mat_z @ rot_xyz.T).T
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rot_xyz = (self.Mat_x @ rot_xyz.T).T
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rot_xyz = (self.Mat_z2 @ rot_xyz.T).T
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return rot_xyz
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# --- I原子のEdge/Corner判定と振り分け ---
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zero_Is = []
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edge_Is = []
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corner_Is = []
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three_Is = []
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other_Is = []
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for i_coord in closer_Is:
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diff_si = s_data[:, 0:3] - i_coord[0:3]
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diff_si = diff_si - np.around(diff_si)
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diff_si_abs = diff_si @ self.M
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dists = np.linalg.norm(diff_si_abs, axis=1)
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# 距離がCUTOFF以下のS原子の数をカウント
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close_S_count = np.sum(dists <= I_S_CUTOFF)
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if close_S_count == 0:
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zero_Is.append(i_coord)
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elif close_S_count == 1:
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corner_Is.append(i_coord)
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elif close_S_count == 2:
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edge_Is.append(i_coord)
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elif close_S_count == 3:
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three_Is.append(i_coord)
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elif close_S_count > 3:
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other_Is.append(i_coord)
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# 判定結果に基づいてそれぞれのリストに追加
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if len(zero_Is) > 0:
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self.i_zero_coords_list.extend(
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rotate_coords(np.array(zero_Is)).tolist())
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if len(edge_Is) > 0:
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self.i_edge_coords_list.extend(
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rotate_coords(np.array(edge_Is)).tolist())
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if len(corner_Is) > 0:
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self.i_corner_coords_list.extend(
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rotate_coords(np.array(corner_Is)).tolist())
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if len(three_Is) > 0:
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self.i_three_coords_list.extend(
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rotate_coords(np.array(three_Is)).tolist())
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# 全体のI用リストにも追加
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self.i_coords_list.extend(rotate_coords(closest_Is).tolist())
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count_p += 1
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print("Calculating Histograms...")
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volume = (self.cutoff*2)**3
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bounds = [[-(self.cutoff)/ang_borr, (self.cutoff)/ang_borr]] * 3
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# I (全体のI原子数で割ることで、Edge/Cornerの比率も反映させる)
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total_I_num = len(self.i_coords_list)
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if total_I_num > 0:
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# I (All)
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print("num_I_all: ", total_I_num)
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i_arr = np.array(self.i_coords_list) / ang_borr
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i_hist, _ = np.histogramdd(i_arr, bins=self.mesh, range=bounds)
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self.i_hist = i_hist.ravel() / total_I_num / volume
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# I (zero)
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if len(self.i_zero_coords_list) > 0:
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print("num_I_zero: ", len(self.i_zero_coords_list))
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i_arr_zero = np.array(self.i_zero_coords_list) / ang_borr
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i_hist_zero, _ = np.histogramdd(
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i_arr_zero, bins=self.mesh, range=bounds)
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self.i_hist_zero = i_hist_zero.ravel() / total_I_num / volume
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# I (Corner)
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if len(self.i_corner_coords_list) > 0:
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print("num_I_corner: ", len(self.i_corner_coords_list))
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i_arr_corner = np.array(self.i_corner_coords_list) / ang_borr
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i_hist_corner, _ = np.histogramdd(
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i_arr_corner, bins=self.mesh, range=bounds)
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self.i_hist_corner = i_hist_corner.ravel() / total_I_num / volume
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# I (Edge)
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if len(self.i_edge_coords_list) > 0:
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print("num_I_edge: ", len(self.i_edge_coords_list))
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i_arr_edge = np.array(self.i_edge_coords_list) / ang_borr
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i_hist_edge, _ = np.histogramdd(
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i_arr_edge, bins=self.mesh, range=bounds)
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self.i_hist_edge = i_hist_edge.ravel() / total_I_num / volume
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# I (Three)
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if len(self.i_three_coords_list) > 0:
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print("num_I_three: ", len(self.i_three_coords_list))
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i_arr_three = np.array(self.i_three_coords_list) / ang_borr
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i_hist_three, _ = np.histogramdd(
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i_arr_three, bins=self.mesh, range=bounds)
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self.i_hist_three = i_hist_three.ravel() / total_I_num / volume
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def outputCube(self):
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output_start_time = time.time()
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base = re.match(r"(\d{3}.*?LiI).*?",
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args.trjfile.split("/")[-1]).group(1)
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self.atomsDic = {'I': '53', 'Li': '3', 'P': '15', 'S': '16'}
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def get_header():
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body = f"created from {__file__}, {args}\n"
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body += "Contains the selected quantity on a FFT grid\n"
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origin = [-(self.cutoff)/ang_borr] * 3
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body += "{:>5d}{:>12.7f}{:>12.7f}{:>12.7f}\n".format(5, *origin)
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body += "{:>5d}{:>12.7f}{:>12.7f}{:>12.7f}\n".format(
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self.mesh[0], (self.cutoff*2)/self.mesh[0]/ang_borr, 0, 0)
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body += "{:>5d}{:>12.7f}{:>12.7f}{:>12.7f}\n".format(
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self.mesh[1], 0, (self.cutoff*2)/self.mesh[1]/ang_borr, 0)
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body += "{:>5d}{:>12.7f}{:>12.7f}{:>12.7f}\n".format(
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self.mesh[2], 0, 0, (self.cutoff*2)/self.mesh[2]/ang_borr)
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body += "{:>5d}{:>12.7f}{:>12.7f}{:>12.7f}{:>12.7f}\n".format(
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int(self.atomsDic["P"]), float(self.atomsDic["P"]), *self.ps4_coord[0])
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for s_coord in self.ps4_coord[1:5]:
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body += "{:>5d}{:>12.7f}{:>12.7f}{:>12.7f}{:>12.7f}\n".format(
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int(self.atomsDic["S"]), float(self.atomsDic["S"]), *s_coord)
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return body
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def save_cube(hist_data, suffix):
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if hist_data is None:
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return
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body = get_header()
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for idx, r in enumerate(hist_data):
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if idx % 6 == 5:
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body += "{:>13.5E}\n".format(r)
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else:
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body += "{:>13.5E}".format(r)
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if idx % 6 != 5:
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body += "\n" # 最後の行で改行がない場合用
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outfile = f"{dirname}/{base}_PS4_{suffix}.cube"
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with open(outfile, "w") as o:
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o.write(body)
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print(f"{outfile} was created.")
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save_cube(self.li_hist, "Li")
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save_cube(self.i_hist, "I_All")
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save_cube(self.i_hist_zero, "I_zero")
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save_cube(self.i_hist_corner, "I_corner")
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save_cube(self.i_hist_edge, "I_edge")
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save_cube(self.i_hist_three, "I_three")
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output_end_time = time.time()
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print(f"output_time : {output_end_time - output_start_time:.2f} s")
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if __name__ == "__main__":
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trj = LammpsTrj()
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trj.makeCube(args.trjfile)
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trj.outputCube()
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