import os import sys import numpy as np import matplotlib.pyplot as plt import tkinter as tk #from pymatgen.core import Composition from pymatgen.core import Lattice, Structure, Site from tklib.tkapplication import tkApplication from tklib.tkfile import tkFile from tklib.tkutils import get_ext, getarg, getintarg, getfloatarg, pint, pfloat, terminate from tklib.tkutils import split_file_path, replace_path from tklib.tkwrapper.tktqdm import tqdm from tklib.tkcrystal.tkcrystal import tkCrystal from tklib.tkcrystal.tkpymatgen import tkPymatgenVASP, tkPymatgen from tklib.tkcrystal.tkalamode import read_input, read_taudata, read_log, read_kpoints, read_properties, cal_contrib, convert_k_list, convert_k from tklib.tkgraphic.tkplotevent import tkPlotEvent, RangeSelector from tklib.tkgraphic.tkplot_pyplot import select_plt, tkPlot_pyplot from tklib.tkgraphic.tkplot_tkinter import tkPlot_tkinter from tklib.tkgui.tksimple_gui import tkWidgets, CustomDialog_with_config """ Convert ALAMODE .xyz to CIF """ plugin_ver = "structure:0.2" #================================ # global parameters #================================ default_ext = ".xyz" input_type = "ALAMODE .xyz" output_type = "CIF" #============================= # Treat argments #============================= def initialize(app = None, cparams = None): cparams.debug = 0 inputfile = 'anime.in' logfile = 'k25.log' infile = 'vmd_data_k25_k2/ik2.anime01.xyz' outfile = 'structure.cif' symprec = 1.0e-5 draw_range = "2,2,2" max_distance = 2.75 atom_alpha = 0.5 displacement = 0.2 sleep = 0.01 time_step = 0.05 nstep = 100 kr = 200.0 bond_r = 3.0 vector_r = 1.5 vector_length = 2.0 arrow_length_ratio = 0.3 fontsize = 16 legend_fontsize = 12 app.add_argument(opt = '--inputfile', type = "str", defval = inputfile) app.add_argument(opt = '--logfile', type = "str", defval = logfile) app.add_argument(opt = '--infile', type = "str", defval = infile) app.add_argument(opt = '--outfile', type = "str", defval = outfile) app.add_argument(opt = '--symprec', type = "float", defval = symprec) app.add_argument(opt = '--draw_range', type = "str", defval = draw_range) app.add_argument(opt = '--max_distance', type = "float", defval = max_distance) app.add_argument(opt = '--atom_alpha', type = "float", defval = atom_alpha) app.add_argument(opt = '--displacement', type = "float", defval = displacement) app.add_argument(opt = '--sleep', type = "float", defval = sleep) app.add_argument(opt = '--time_step', type = "float", defval = time_step) app.add_argument(opt = '--nstep', type = "int", defval = nstep) app.add_argument(opt = '--kr', type = "float", defval = kr) app.add_argument(opt = '--bond_r', type = "float", defval = bond_r) app.add_argument(opt = '--vector_r', type = "float", defval = vector_r) app.add_argument(opt = '--vector_length', type = "float", defval = vector_length) app.add_argument(opt = '--arrow_length_ratio', type = "float", defval = arrow_length_ratio) app.add_argument(opt = '--coordinate', type = "str", defval = 'fc') app.add_argument(opt = '--site_name', type = "str", defval = 'as') app.add_argument(opt = '--fontsize', type = "int", defval = fontsize) app.add_argument(opt = '--legend_fontsize', type = "int", defval = legend_fontsize) def get_base_path(infile): vasp = tkVASP() if os.path.isfile(infile): base_path = vasp.getdir(infile) else: base_path = infile return vasp, base_path def check_exist(path, print_level = 0): f = os.path.isfile(path) if not f: if print_level: print(f"Error in check_file_type(): [{path}] does not exist") return None return True def check_file_type(infile, inf = None, app = None, cparams = None, print_level = 0): if not os.path.isfile(infile) and not os.path.isdir(infile): return None #f"Error: file [{infile}] does not exist" ext = get_ext(infile).lower() if ext == default_ext: return {"file_type": input_type} return {"file_type": "VASP POSCAR"} def get_output_path(infile, inf = None, app = None, cparams = None): cparams.outfile = app.replace_path(infile, template = ["{dirname}", "{filebody}.cif"]) return cparams.outfile def get_input_type(inf = None, app = None, cparams = None): return {"file_type": input_type} def get_output_type(inf = None, app = None, cparams = None): return {"file_type": output_type} def read_data(infile, app = None, cparams = None, print_level = 0): infile = os.path.abspath(infile) if print_level >= 1: print("") print("ALAMODE input file path: ", cparams.inputfile) print("ALAMODE log file path : ", cparams.logfile) print("ALAMODE .xyz file path : ", cparams.infile) dirname, basename, filebody, ext = split_file_path(infile, check_dir = True) sample_name = filebody pm = tkPymatgen() print() print(f"Read log file [{cparams.inputfile}]") inf_input = read_input(cparams.inputfile, print_level = 1) if inf_input is None: if print_level: print() print(f"Error in alamode_xyz2cif.read_data(): Can not read input file [{cparams.inputfile}]") print() return None # print("inf_input=", inf_input) print() print(f"Read log file [{cparams.logfile}]") inf_log, kp_list, kp_list_ik = read_log(cparams.logfile) if inf_log is None: if print_level: print() print(f"Error in alamode_xyz2cif.read_data(): Can not read log file [{cparams.logfile}]") print() return None if inf_input["aij"]: aij_input = inf_input["aij"] aij = inf_log["aij"] paij = inf_log["paij"] haij = inf_log.get("haij", None) else: latt = inf_input["latt"] aij = Lattice.from_parameters(*latt) paij = None haij = None _cry = tkCrystal() latt_aij_input = _cry.calculate_lattice_parameters_from_vector(aij_input) latt_aij = _cry.calculate_lattice_parameters_from_vector(aij) latt_paij = _cry.calculate_lattice_parameters_from_vector(paij) latt_haij = _cry.calculate_lattice_parameters_from_vector(haij) if print_level: print("input aij =", aij_input) print("supercell aij=", aij) print("primitive cell aij=", paij) print("harmonic supercell aij=", haij) print("input lattice parameters =", latt_aij_input) print("supercell lattice parameters =", latt_aij) print("primitive cell lattice parameters =", latt_paij) print("harmonic supercell lattice parameters=", latt_haij) print() print(f"Read xyz file [{cparams.infile}]") fin = tkFile(app.cparams.infile, "r") if fin is None or fin.fp is None: if print_level: print() print(f"Error in alamode_xyz2cif.read_data(): Can not read [{cparams.xyzfile}]") print() return None symprec = cparams.get("symprec", 1.0e-4) istructure = 0 crystal_list = [] structure_list = [] while True: line = fin.readline() if not line: break cry = tkCrystal() cry.SetSampleName(sample_name) cry.SetCrystalName(sample_name) cry.set_lattice_vectors(aij) latt = cry.lattice_parameters() lattice_obj = Lattice.from_parameters(*latt) structure = Structure(lattice_obj, [], []) nsites = pint(line) line = fin.readline() _aa = line.split('(', 1) imode = pint(_aa[1]) _aa2 = _aa[1].split(')', 1) _aa3 = _aa2[0].split() kx = pfloat(_aa3[0]) ky = pfloat(_aa3[1]) kz = pfloat(_aa3[2]) _aa4 = _aa2[1].split('=') f = pfloat(_aa4[1], strict = False) istep = pint(_aa4[-1]) # print("nsite=", nsites, imode) # print("k=", kx, ky, kz) # print("f=", f) # print("istep=", istep) print(f"istructure={istructure}") for i in tqdm(range(nsites)): line = fin.readline() if not line: break _aa = line.split() atom_name = _aa[0] x = float(_aa[1]) y = float(_aa[2]) z = float(_aa[3]) cry.AddAtomSite(name = atom_name, pos = [x, y, z]) cry.expand_coordinates() crystal_list.append(cry) atom_sites = cry.atom_site_list() for i in range(nsites): site = atom_sites[i] atom_name = site.atom_name_only() pos = site.position() structure.append(atom_name, pos, coords_are_cartesian = True) formula, reduced_formula = pm.chemical_formula(structure) iSPG, SPG_name, symmetrized_structure = pm.symmetrize(structure, symprec) structure_list.append(structure) istructure += 1 if istructure >= 2: break nstructures = len(structure_list) if nstructures >= 2: if print_level: print() print("Calculate velocities") for istr, structure in enumerate(structure_list): if istr == 0: i = 0 j = 1 div = 1 elif istr == nstructures - 1: i = istr - 1 j = istr div = 1 else: i = istr - 1 j = istr + 1 div = 2 structure_i = structure_list[i] structure_j = structure_list[j] sites = structure.sites for isite in range(len(sites)): site = structure.sites[isite] site_i = structure_i.sites[isite] site_j = structure_j.sites[isite] pos_i = site_i.coords pos_j = site_j.coords vx = (pos_j[0] - pos_i[0]) / div vy = (pos_j[1] - pos_i[1]) / div vz = (pos_j[2] - pos_i[2]) / div # print("v=", istr, vx, vy, vz) site.properties["velocity"] = [vx, vy, vz] if print_level > 1: # cry.print_inf() print("last structure:") print(structure) inf = {} inf["data_list_type"] = "[tkCIF]" inf["filename"] = infile inf["filenames"] = [infile] inf["sample_name"] = reduced_formula inf["meta"] = [] #[inf_list] inf["pymatgen"] = pm inf["crystal_list"] = crystal_list inf["structure_list"] = structure_list inf["aij_input"] = aij_input inf["aij"] = aij inf["paij"] = paij inf["haij"] = haij inf["lattice_parameter(aij_input)"] = latt_aij_input inf["lattice_parameter(aij)"] = latt_aij inf["lattice_parameter(paij)"] = latt_paij inf["lattice_parameter(haij)"] = latt_haij return inf def print_data(inf, app = None, cparams = None, print_level = 1): for i, structure in enumerate(inf["structure_list"]): print() print(f"icrystal={i}") # cry.print_inf() print(structure) def save_data(outfiles, inf, app = None, cparams = None, print_level = 0): if type(outfiles) == str: outfile = outfiles else: outfile = outfiles[0] structure = inf["structure_list"][0] pm = inf["pymatgen"] print() print(f"Save structure to [{outfile}]") pm.to(outfile, structure, symprec = cparams.symprec, print_level = print_level) return True def draw(tkplt, inf, app = None, cparams = None, ax = None, animation = True, stop_callback = None, print_level = 0): max_distance = cparams.max_distance draw_range = [pfloat(s) for s in cparams.draw_range.split(',')] print() print("Draw configuration:") # print(f"draw_range: ", draw_range) print(f"max_distance: {max_distance}") structure = inf["structure_list"][0] pm = tkPymatgen() latt_aij_input = inf["lattice_parameter(aij_input)"] latt_aij = inf["lattice_parameter(aij_input)"] # latt_paij = inf["lattice_parameter(paij)"] # latt_haij = inf["lattice_parameter(haij)"] # nx = draw_range[0] * latt_aij_input[0] / latt_haij[0] # ny = draw_range[1] * latt_aij_input[1] / latt_haij[1] # nz = draw_range[2] * latt_aij_input[2] / latt_haij[2] nx, ny, nz = draw_range print(f"Input lattice parameters: ", latt_aij_input) print(f"Draw range: x in (0, {nx:.2f}) x in (0, {ny:.2f}) x in (0, {nz:.2f})") lattice_obj = Lattice.from_parameters(*latt_aij_input) # lattice_obj = Lattice.from_parameters(*latt_paij) structure_draw = Structure(lattice_obj, [], []) eps = 0.1 sites = structure.sites i = 0 for site in sites: x, y, z = site.coords if x < -eps or nx * latt_aij_input[0] + eps < x: continue if y < -eps or ny * latt_aij_input[1] + eps < y: continue if z < -eps or nz * latt_aij_input[2] + eps < z: continue atom_name = site.specie.symbol structure_draw.append(atom_name, site.coords, coords_are_cartesian = True) structure_draw.sites[i].properties = site.properties.copy() i += 1 if print_level: print() print("Draw structre:") print(structure_draw) pm.draw_structure(tkplt, ax, structure_draw, draw_range = [[0, nx], [0, ny], [0, nz]], max_distance = max_distance, kr = cparams.kr, atom_alpha = cparams.atom_alpha, bond_r = cparams.bond_r, vector_r = cparams.vector_r, vector_length = cparams.vector_length, arrow_length_ratio = cparams.arrow_length_ratio, displacement = cparams.displacement, animation = animation, stop_callback = stop_callback, sleep = cparams.sleep, time_step = cparams.time_step, nstep = cparams.nstep, fontsize = cparams.fontsize, legend_fontsize = cparams.legend_fontsize) # pm.draw_structure(ax, structure, draw_range = [[0, nx], [0, ny], [0, nz]], max_distance = max_distance) # plt.pause(1.0e-4) def create_window(app, cparams, tkplt, fig, axes, inf): tkplt.create_window(fig) tkplt.add_toolbar() wg = tkWidgets(parent = tkplt.parent, plt = plt) wg.set_font(size = 14) notebook = wg.add_tab() page1_frame = wg.add_page(notebook, title = "main") # page2_frame = wg.add_page(notebook, title = "configure") top_frame = tk.Frame(page1_frame) #tkplt.parent) top_frame.pack(side = tk.TOP, expand = True, fill = "both") left_frame = tk.Frame(top_frame) left_frame.pack(side = tk.LEFT, anchor = "n", expand = True, fill = "x") canvas_frame = tk.Frame(top_frame) canvas = tkplt.add_canvas(fig, parent = canvas_frame) canvas_frame.pack(side = tk.LEFT, expand = True, fill = "both") def save_figure(fig, outfile = "figure.png"): print() print(f"Save figure to [{outfile}]") fig.savefig(outfile) def redraw(): wg.update_variables() for key in cparams.__dict__.keys(): if key in wg.vars.keys(): setattr(cparams, key, getattr(wg.vars, key)) axes[0].clear() draw(tkplt, inf, app = app, cparams = cparams, ax = axes[0], animation = False, print_level = 1) tkplt.draw() def get_animation_stop(wg): return wg.stop_animation def animation_start(): print() print("Start animation") wg.update_variables() for key in cparams.__dict__.keys(): if key in wg.vars.keys(): setattr(cparams, key, getattr(wg.vars, key)) wg.stop_animation = False axes[0].clear() draw(tkplt, inf, app = app, cparams = cparams, ax = axes[0], animation = True, stop_callback = lambda: get_animation_stop(wg), print_level = 1) tkplt.draw() def animation_stop(): print() print("Stop animation") wg.stop_animation = True tkplt.draw() tkplt.add_toolbar_button(text = "Redraw", command = redraw) tkplt.add_toolbar_button(text = "Animation start", command = animation_start) tkplt.add_toolbar_button(text = "Animation stop", command = animation_stop) tkplt.add_toolbar_button(text = "Save figure", command = lambda: save_figure(fig)) wg.vars.update(**cparams.__dict__) def on_click(): # show_varibles(config) wg.update_variables() print("clicked", wg.vars.Vg_min, wg.vars.Vg_max, wg.vars.Vd_min, wg.vars.Vd_max) # button1 = tk.Button(left_frame, text = "test")#, command = command) widgets = [ [{"type": "label", "label": "input file: "}, {"type": "entry","varname": "inputfile", "vartype": "str", "width": 20, "state": "readonly", "expand": True, "fill": "x"} ], [{"type": "label", "label": "log file: "}, {"type": "entry","varname": "logfile", "vartype": "str", "width": 20, "state": "readonly", "expand": True, "fill": "x"} ], [{"type": "label", "label": "xyz file: "}, {"type": "entry","varname": "infile", "vartype": "str", "width": 20, "state": "readonly", "expand": True, "fill": "x"} ], [{"type": "label", "label": "Draw range:"}, {"type": "entry","varname": "draw_range", "vartype": "str", "width": 20} ], [{"type": "label", "label": "Atom:"}], [{"type": "label", "label": " atomic radius coefficient:"}, {"type": "entry","varname": "kr", "vartype": "float", "width": 10}, {"type": "label", "label": "alpha:"}, {"type": "entry","varname": "atom_alpha", "vartype": "float", "width": 10}, ], [{"type": "label", "label": "Chemical bond:"}], [{"type": "label", "label": " max bond length:"}, {"type": "entry","varname": "max_distance", "vartype": "float", "width": 10} ], [{"type": "label", "label": " radius:"}, {"type": "entry","varname": "bond_r", "vartype": "float", "width": 10}, ], [{"type": "label", "label": "Displacement:"}], [{"type": "label", "label": " vector length:"}, {"type": "entry","varname": "vector_length", "vartype": "float", "width": 10}, {"type": "label", "label": " radius:"}, {"type": "entry","varname": "vector_r", "vartype": "float", "width": 10} ], [{"type": "label", "label": " arrow head ratio:"}, {"type": "entry","varname": "arrow_length_ratio", "vartype": "float", "width": 10} ], [{"type": "label", "label": "One shot draw:"}, {"type": "button", "name": "redraw", "text": "redraw", "anchor": "w", "command": redraw}, ], [{"type": "label", "label": "Animation:"}, {"type": "button", "name": "animation_start", "text": "start", "anchor": "w", "command": animation_start}, {"type": "button", "name": "animation_stop", "text": "stop", "anchor": "w", "command": animation_stop}, ], [{"type": "label", "label": " sleep:"}, {"type": "entry","varname": "sleep", "vartype": "float", "width": 10}, {"type": "label", "label": "time step:"}, {"type": "entry","varname": "time_step", "vartype": "float", "width": 10}, {"type": "label", "label": "nstep:"}, {"type": "entry","varname": "nstep", "vartype": "int", "width": 10} ], ] widgets_frame, config_left_pain = wg.add_widgets(parent = left_frame, widgets = widgets, side = "top", expand = True, fill = "x") draw(tkplt, inf, app = app, cparams = cparams, ax = axes[0], animation = False, print_level = 1) return wg, widgets_frame, config_left_pain def plot_data(inf, app = None, cparams = None, print_level = 0): tkplt, root, tkpyplot = select_plt(use_tkinter = 1, plt = plt, parent = None, title = "Phonon animation") fig, axes = tkplt.subplots(1, 1, figsize = (8, 8), dpi = 100, projection = '3d', tight_layout = False) # ax = fig.add_subplot(111, projection = '3d') ax = axes[0] plot_event = tkPlotEvent(plt) wg, widgets_frame, config_left_pain = create_window(app, cparams, tkplt, fig, axes, inf) tkplt.pause(1.0e-5) root.mainloop() # input("\nPress ENTER to terminate>>\n") def convert(inf, app = None, cparams = None, print_level = 0): return inf def main(): #================================================================== # Initialize parameters #================================================================== app = tkApplication(globals = globals(), locals = locals()) # app = tkApplication(usage_str = usage_str, globals = globals(), locals = locals()) cparams = app.get_params() app.cparams = cparams initialize(app, cparams) # update_vars(app, cparams) app.update_vars(cparams, apply_default = True) # vasp, base_path = get_base_path(cparams.infile) base_path = os.path.dirname(cparams.infile) print("") print( "==========================================================================") print(" Convert ALAMODE .xyz file to CIF") print( "==========================================================================") print(f"ALAMODE input file: {cparams.inputfile}") print(f"ALAMODE log file : {cparams.logfile}") print(f"ALAMODE .xyz file : {cparams.infile}") print(f"Output file : {cparams.outfile}") # print(f"base_path : {base_path}") # logfile = os.path.join(base_path, "poscar2cif-out.txt") logfile = app.replace_path(cparams.infile, template = ["{dirname}", "{filebody}-out.txt"]) print(f"Open logfile [{logfile}]") app.redirect(targets = ["stdout", logfile], mode = 'w') cparams.outfile = get_output_path(cparams.infile, app = app, cparams = cparams) print(f"Output CIF file : {cparams.outfile}") file_type = check_file_type(cparams.infile, print_level = 1) if file_type is None: app.terminate(f"Error: [{cparams.infile}] invalid file type", usage = "built-in") if 'Error' in file_type: app.terminate(file_type, usage = usage) inf = read_data(cparams.infile, app = app, cparams = cparams, print_level = 2) # print_data(inf) # inf = convert(inf, cparams = cparams, print_level = 1) save_data([cparams.outfile], inf, cparams = cparams, print_level = 9) plot_data(inf, cparams = cparams, print_level = 0) app.terminate(usage = 'built-in') if __name__ == "__main__": main()