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