import os import glob import re from collections import OrderedDict from tklib.tkcrystal.tkvasp import tkVASP image_exts = ['.png', '.ico', '.jpeg', '.jpg', '.bmp'] text_exts = ['.txt', '.md'] html_exts = ['.html', '.htm'] csv_exts = ['.csv'] excel_exts = ['.xlsx', '.xlsm'] word_exts = [".docx"] pdf_exts = [".pdf"] def search_reference_files(base_dir, search_dir): fmask = os.path.join(search_dir, "*") files = sorted(glob.glob(fmask, recursive=False)) image_files = [] text_files = [] html_files = [] pdf_files = [] files_list = [] for f in files: #fの拡張子を取得 ext = os.path.splitext(f)[1].lower() #fのパスを、base_dirに対する相対パスにする rel_path = os.path.relpath(f, base_dir) if ext in image_exts: image_files.append(rel_path) elif ext in text_exts: text_files.append(rel_path) elif ext in html_exts: html_files.append(rel_path) elif ext in pdf_exts: pdf_files.append(rel_path) return { "image_files": image_files, "text_files": text_files, "html_files": html_files, "pdf_files": pdf_files } def flatten_dict(d, sep=':', parent_key = '', escape_keys = True, prefix = ""): """ 階層的な辞書をフラットな辞書に変換する関数。 """ items = {} for k, v in d.items(): if parent_key is None or parent_key == "": new_key = k else: new_key = f"{parent_key}{sep}{k}" if prefix != "": new_key = f"{prefix}{sep}{new_key}" if escape_keys: new_key = re.sub(r'[^a-zA-Z0-9_]', '_', new_key) if isinstance(v, dict): items.update(flatten_dict(v, sep, new_key, True, "")) else: items[new_key] = v return items def is_cardir(path): if not os.path.isdir(path): return False if not os.path.isfile(os.path.join(path, 'INCAR')): return False if not os.path.isfile(os.path.join(path, 'POSCAR')): return False if not os.path.isfile(os.path.join(path, 'OUTCAR')): return False return True def read_inf(car_dir, print_level=1): vasp = tkVASP() # inf = vasp.read_files(car_dir, ["INCAR", "POSCAR", "POTCAR", "KPOINTS", "CONTCAR", "VASPRUN", "OUTCAR", "DOSCAR", "EIGENVAL", "EIGENVAL_OPT"], inf = vasp.read_files(car_dir, ["INCAR", "POSCAR", "POTCAR", "KPOINTS", "CONTCAR", "OUTCAR", "DOSCAR", "EIGENVAL", "EIGENVAL_OPT"], EF = 0.0, normalize_E = True, unit = '/cm3', data_for_bandedges = None, exit_by_error = False, print_level = 1, terminate = None) inf_meta = {} inf_compare = {} inf_func = {} outcarinf = inf.get("OUTCAR", {}) if outcarinf is None or outcarinf == {}: return inf, inf_meta, inf_compare, inf_func for key in ["compiler", "mpi", "ncores_k", "ncores_bandf", "Total CPU time", "User time", "System time", "Elapsed time"]: val = outcarinf.get(key, None) if val is not None: inf_meta[key] = val print() print("POSCAR:") inf_poscar = inf["POSCAR"] cry = inf_poscar["crystal"] a, b, c, alpha, beta, gamma = cry.LatticeParameters() Vcell = cry.Volume() print(" cell: {:12.8f} {:12.8f} {:12.8f} A {:10.6f} {:10.6f} {:10.6f}".format(a, b, c, alpha, beta, gamma)) print(" volume: {:12.6f} A^-3".format(Vcell)) inf["InitialStructure:LatticeParameters"] = inf["POSCAR"]["LatticeParameters"] inf["InitialStructure:Vcell"] = inf_poscar["Vcell"] inf["InitialStructure:nAtomTypes"] = inf_poscar["nAtomTypes"] inf["InitialStructure:AtomTypes"] = inf_poscar["AtomTypes"] inf["InitialStructure:nAtomSites"] = inf_poscar["nAtomSites"] inf["InitialStructure:AtomSites"] = inf_poscar["AtomSites"] if "CONTCAR" in inf.keys(): if print_level: print() print("CONTCAR:") inf_contcar = inf.get("CONTCAR", None) if inf_contcar: cry = inf_contcar["crystal"] a, b, c, alpha, beta, gamma = cry.LatticeParameters() Vcell = cry.Volume() for key in ['a', 'b', 'c', 'alpha', 'beta', 'gamma', "Vcell"]: inf_compare[key] = locals()[key] inf_func[key] = lambda x1, x2, eps = 1.0e-6: check_difference(x1, x2, eps) if print_level: print(" cell: {:12.8f} {:12.8f} {:12.8f} A {:10.6f} {:10.6f} {:10.6f}".format(a, b, c, alpha, beta, gamma)) print(" volume: {:12.6f} A^-3".format(Vcell)) inf["FinalStructure:LatticeParameters"] = inf_contcar["LatticeParameters"] inf["FinalStructure:Vcell"] = inf_contcar["Vcell"] inf["FinalStructure:nAtomTypes"] = inf_contcar["nAtomTypes"] inf["FinalStructure:AtomTypes"] = inf_contcar["AtomTypes"] inf["FinalStructure:nAtomSites"] = inf_contcar["nAtomSites"] inf["FinalStructure:AtomSites"] = inf_contcar["AtomSites"] if "OUTCAR" in inf.keys(): if print_level: print() print("OUTCAR:") outcarinf = inf.get("OUTCAR", None) if outcarinf is None: return inf, inf_meta, inf_compare, inf_func ISPIN = outcarinf["ISPIN"] EF = outcarinf.get("EF", "") TOTEN = outcarinf.get("TOTEN", "") # final_charges = outcarinf.get("Final_charges", "") for key in ['EF', "TOTEN"]: inf_compare[key] = locals()[key] inf_func[key] = lambda x1, x2, eps = 1.0e-4: check_difference(x1, x2, eps) born_charges = outcarinf.get("born_charges", None) if born_charges: for iion, bc in enumerate(born_charges): for i in range(3): for j in range(3): key = f"born_charges[{iion}][{i}][{j}]" inf_compare[key] = bc[i][j] inf_func[key] = lambda x1, x2, eps = 1.0e-4: check_difference(x1, x2, eps) piezo_static_localeff = outcarinf.get("piezo_static_localeff", None) if piezo_static_localeff: idx_str = ["XX", "YY", "ZZ", "XY", "YZ", "ZX"] for i in range(3): for j in range(6): key = f"piezo_static[{i}][{idx_str[j]}]" inf_compare[key] = piezo_static_localeff[i][j] inf_func[key] = lambda x1, x2, eps = 1.0e-4: check_difference(x1, x2, eps) eps_static_localeff = outcarinf.get("eps_static_localeff", None) if eps_static_localeff: for i in range(3): for j in range(3): key = f"eps_static_e[{i}][{j}]" inf_compare[key] = eps_static_localeff[i][j] inf_func[key] = lambda x1, x2, eps = 1.0e-4: check_difference(x1, x2, eps) eps_static_ionic = outcarinf.get("eps_static_ionic", None) if eps_static_ionic: for i in range(3): for j in range(3): key = f"eps_static_ionic[{i}][{j}]" inf_compare[key] = eps_static_ionic[i][j] inf_func[key] = lambda x1, x2, eps = 1.0e-4: check_difference(x1, x2, eps) if print_level: print(f"ISPIN: {ISPIN}") print(f"EF: {EF} eV") print(f"TOTEN: {TOTEN} eV") if "EIGENVAL" in inf.keys(): if print_level: print() print("EIGENVAL:") eigenvalinf = inf.get("EIGENVAL", None) if eigenvalinf: nk = eigenvalinf["nk"] nLevels = eigenvalinf["nLevels"] if print_level: print("k points in EIGENVAL:") print("nk=", nk) print("nLevels=", nLevels) bandedgeinf = vasp.find_band_edges_from_eigenval(EF0 = EF, eigenvalinf = eigenvalinf, ISPIN = ISPIN, print_level = print_level) if bandedgeinf.get('EV', None) is None: print(f"Warning in read_inf.read_inf(): Could not get band edges") inf["EIGENVAL:EV"] = None inf["EIGENVAL:EC"] = None inf["EIGENVAL:Eg"] = None else: EV = bandedgeinf["EV"] EC = bandedgeinf["EC"] Eg = bandedgeinf["Eg"] for key in ["EV", "EC", "Eg"]: inf_compare[key] = locals()[key] inf_func[key] = lambda x1, x2, eps = 1.0e-6: check_difference(x1, x2, eps) inf["EIGENVAL:EV"] = EV inf["EIGENVAL:EC"] = EC inf["EIGENVAL:Eg"] = Eg if print_level: print(f"EV: {EV} eV") print(f"EC: {EC} eV") print(f"Eg: {Eg} eV") """ print() print("EIGENVAL_OPT:") eigenvaloptinf = inf["EIGENVAL_OPT"] nk = eigenvaloptinf.get("nk", "") nLevels = eigenvaloptinf.get("nLevels", "") print("k points in EIGENVAL_OPT:") print("nk=", nk) print("nLevels=", nLevels) """ """ if "DOSCAR" in inf.keys(): if print_level: print() print("DOSCAR:") dosinf = inf["DOSCAR"] E_raw = dosinf["E"] dos_raw = dosinf["TotalDOS"] nDOS = dosinf["nE"] Emin = E_raw[0] Emax = E_raw[nDOS-1] Estep = (E_raw[nDOS-1] - E_raw[0]) / (nDOS - 1) if print_level: print(" DOS E range: {} - {}, {} eV step".format(Emin, Emax, Estep)) """ return inf # return inf, inf_meta, inf_compare, inf_func def read_inf_all(base_dir, subdirs, args, print_level = 1): if subdirs is None or subdirs == "": files_list = search_reference_files( base_dir = base_dir, search_dir = base_dir) # print("files_list=", files_list) replace_dict = {} replace_dict["ImageFiles"] = files_list["image_files"] replace_dict["TextFiles"] = files_list["text_files"] replace_dict["HTMLFiles"] = files_list["html_files"] replace_dict["PDFFiles"] = files_list["pdf_files"] inf = read_inf(base_dir, print_level = print_level) replace_dict2 = flatten_dict(inf, escape_keys = True, prefix = args.prefix) replace_dict.update(replace_dict2) else: replace_dict = {} replace_dict["base_dir"] = base_dir replace_dict["base_path"] = os.path.abspath(base_dir) replace_dict["subdirs"] = subdirs replace_dict["subdirs_searched"] = None replace_dict["prefix"] = args.prefix replace_dict["template_path"] = args.template_file replace_dict["SYSTEM_Source"] = None replace_dict["SYSTEM"] = None replace_dict["InitialStructure_Source"] = None replace_dict["InitialStructure_LatticeParameters"] = None replace_dict["InitialStructure_Vcell"] = None replace_dict["InitialStructure_nAtomTypes"] = None replace_dict["InitialStructure_AtomTypes"] = None replace_dict["InitialStructure_nAtomSites"] = None replace_dict["InitialStructure_AtomSites"] = None replace_dict["RelaxedStructure_Source"] = None replace_dict["RelaxedStructure_LatticeParameters"] = None replace_dict["RelaxedStructure_Vcell"] = None replace_dict["RelaxedStructure_nAtomTypes"] = None replace_dict["RelaxedStructure_AtomTypes"] = None replace_dict["RelaxedStructure_nAtomSites"] = None replace_dict["RelaxedStructure_AtomSites"] = None files_list = search_reference_files(base_dir = base_dir, search_dir = base_dir) # print("files_list=", files_list) replace_dict["ImageFiles"] = files_list["image_files"] replace_dict["TextFiles"] = files_list["text_files"] replace_dict["HTMLFiles"] = files_list["html_files"] replace_dict["PDFFiles"] = files_list["pdf_files"] _a = subdirs.split(",") files_dict = OrderedDict() for dir in _a: print(f"**split subdirs [{dir}]") fmask = os.path.join(base_dir, dir) for file in glob.glob(fmask): files_dict[file] = "" dirs = list(files_dict.keys()) dirs = [path for path in dirs if is_cardir(path)] print() print("base_dir:", base_dir) print("Sub directories to search:", dirs) inf_dict = {} subdirs_inf = [] subdirs_inf_added = {} for d in dirs: car_dir = d # car_dir = os.path.join(base_dir, d) files_list = search_reference_files(base_dir = base_dir, search_dir = car_dir) inf_base = {} inf_base["ImageFiles"] = files_list["image_files"] inf_base["TextFiles"] = files_list["text_files"] inf_base["HTMLFiles"] = files_list["html_files"] inf_base["PDFFiles"] = files_list["pdf_files"] inf2 = read_inf(car_dir, print_level=1) if inf2: prefix = os.path.basename(d) fullpath = os.path.abspath(car_dir) directory = os.path.dirname(fullpath) base_name = os.path.basename(fullpath) # print(f"{prefix=}") # print(f"{fullpath=}") # print(f"{directory=}") # print(f"{base_name=}") if subdirs_inf_added.get(fullpath, None) is None: subdirs_inf.append({ "path": fullpath, "dir": directory, "last_dir": base_name }) subdirs_inf_added[fullpath] = True #inf2のkeyは、Jinja2互換ではない (:などが使われている) inf_dict[prefix] = inf2 inf_base.update(inf2) #replace_dictのkeyは、Jinja2互換になる replace_dict2 = flatten_dict(inf_base, escape_keys = True, prefix = prefix) replace_dict.update(replace_dict2) replace_dict["subdirs_searched"] = subdirs_inf print() print(f"Search global parameters from {list(inf_dict.keys())}:") # globalな設定 (初期構造をどのsubdirからとるかなど) inf_incar = None for key in ["MD", "VCRelax1", "VCRelax", "SCFDFT", "SCF", "DOS", "BandX", "Phonon"]: if inf_dict.get(key, None): print(f" SYSTEM is taken from [{key}]") inf_incar = inf_dict.get(key) break replace_dict["SYSTEM_Source"] = key replace_dict["SYSTEM"] = inf_incar["INCAR"]["SYSTEM"] inf_istruct = None for key in ["MD", "VCRelax1", "VCRelax", "SCFDFT", "SCF", "DOS", "BandX", "Phonon"]: if inf_dict.get(key, None): print(f" Initial structure is taken from [{key}]") inf_istruct = inf_dict.get(key) break if inf_istruct: replace_dict["InitialStructure_Source"] = key replace_dict["InitialStructure_LatticeParameters"] = inf_istruct["InitialStructure:LatticeParameters"] replace_dict["InitialStructure_Vcell"] = inf_istruct["InitialStructure:Vcell"] replace_dict["InitialStructure_nAtomTypes"] = inf_istruct["InitialStructure:nAtomTypes"] replace_dict["InitialStructure_AtomTypes"] = inf_istruct["InitialStructure:AtomTypes"] replace_dict["InitialStructure_nAtomSites"] = inf_istruct["InitialStructure:nAtomSites"] replace_dict["InitialStructure_AtomSites"] = inf_istruct["InitialStructure:AtomSites"] inf_rstruct = None for key in [f"VCRelax", "VCRelax1"]: # print("check fin: ", key) if inf_dict.get(key, None): print(f" Relaxed structure is taken from [{key}]") inf_rstruct = inf_dict.get(key) break # print("inf_rstruct:", inf_rstruct) if inf_rstruct: replace_dict["RelaxedStructure_Source"] = key replace_dict["RelaxedStructure_LatticeParameters"] = inf_rstruct["FinalStructure:LatticeParameters"] replace_dict["RelaxedStructure_Vcell"] = inf_rstruct["FinalStructure:Vcell"] replace_dict["RelaxedStructure_nAtomTypes"] = inf_rstruct["FinalStructure:nAtomTypes"] replace_dict["RelaxedStructure_AtomTypes"] = inf_rstruct["FinalStructure:AtomTypes"] replace_dict["RelaxedStructure_nAtomSites"] = inf_rstruct["FinalStructure:nAtomSites"] replace_dict["RelaxedStructure_AtomSites"] = inf_rstruct["FinalStructure:AtomSites"] return replace_dict