Open pkruzikova opened 9 months ago
potpaw
folder with the LDA potentials and the potpaw_PBE
folder with the GGA PBE potentials in their pyiron resources: https://github.com/pyiron/pyiron-resources/tree/main/vasp/potentials potentials_vasp.csv
specifies all potentials while potentials_vasp_lda_default.csv
specifies the default potentials for each element for the LDA functional and potentials_vasp_pbe_default.csv
analogous for GGA PBE. To generate the csv files for a new release of VASP potentials you can use the following code:
import os
import glob
import pandas
import numpy as np
from mendeleev.fetch import fetch_table
path = "/path/to/vasp_potentials" # change this to match your path
# https://www.vasp.at/wiki/index.php/Available_PAW_potentials
elements_dict = {
"H": "H",
"He": "He",
"Li": "Li_sv",
"Be": "Be",
"B": "B",
"C": "C",
"N": "N",
"O": "O",
"F": "F",
"Ne": "Ne",
"Na": "Na_pv",
"Mg": "Mg",
"Al": "Al",
"Si": "Si",
"P": "P",
"S": "S",
"Cl": "Cl",
"Ar": "Ar",
"K": "K_sv",
"Ca": "Ca_sv",
"Sc": "Sc_sv",
"Ti": "Ti_sv",
"V": "V_sv",
"Cr": "Cr_pv",
"Mn": "Mn_pv",
"Fe": "Fe",
"Co": "Co",
"Ni": "Ni",
"Cu": "Cu",
"Zn": "Zn",
"Ga": "Ga_d",
"Ge": "Ge_d",
"As": "As",
"Se": "Se",
"Br": "Br",
"Kr": "Kr",
"Rb": "Rb_sv",
"Sr": "Sr_sv",
"Y": "Y_sv",
"Zr": "Zr_sv",
"Nb": "Nb_sv",
"Mo": "Mo_sv",
"Tc": "Tc_pv",
"Ru": "Ru_pv",
"Rh": "Rh_pv",
"Pd": "Pd",
"Ag": "Ag",
"Cd": "Cd",
"In": "In_d",
"Sn": "Sn_d",
"Sb": "Sb",
"Te": "Te",
"I": "I",
"Xe": "Xe",
"Cs": "Cs_sv",
"Ba": "Ba_sv",
"La": "La",
"Ce": "Ce",
"Pr": "Pr_3",
"Nd": "Nd_3",
"Pm": "Pm_3",
"Sm": "Sm_3",
"Eu": "Eu_2",
"Gd": "Gd_3",
"Tb": "Tb_3",
"Dy": "Dy_3",
"Ho": "Ho_3",
"Er": "Er_3",
"Tm": "Tm_3",
"Yb": "Yb_2",
"Lu": "Lu_3",
"Hf": "Hf_pv",
"Ta": "Ta_pv",
"W": "W_sv",
"Re": "Re",
"Os": "Os",
"Ir": "Ir",
"Pt": "Pt",
"Au": "Au",
"Hg": "Hg",
"Tl": "Tl_d",
"Pb": "Pb_d",
"Bi": "Bi_d",
"Po": "Po_d",
"At": "At",
"Rn": "Rn",
"Fr": "Fr_sv",
"Ra": "Ra_sv",
"Ac": "Ac",
"Th": "Th",
"Pa": "Pa",
"U": "U",
"Np": "Np",
"Pu": "Pu",
"Am": "Am",
"Cm": "Cm"
}
if __name__ == "__main__":
potcar_lst = [name for name in glob.glob(path + '/*/*/POTCAR')]
file_name_lst = [p.split(path)[-1][1:] for p in potcar_lst]
model_lst = ["gga-pbe" if "/potpaw_PBE/" in p else "lda" for p in potcar_lst]
filename_lst = [p.split("/")[-2] for p in potcar_lst]
species_lst = [[p.split("_")[0]] for p in filename_lst]
name_lst = [s+"-"+m for s, m in zip(filename_lst, model_lst)]
encut_recommended_lst, electrons_lst = [], []
for potcar_file in potcar_lst:
with open(potcar_file, "r") as f:
content = f.readlines()
for l in content:
if "ENMAX" in l:
encut_low = float(l.split()[2].replace(";", ""))
if "ZVAL" in l:
zval_electron = float(l.split()[5])
encut_recommended_lst.append(encut_low)
electrons_lst.append(zval_electron)
df = pandas.DataFrame({
"Filename": file_name_lst,
"Model": model_lst,
"Name": name_lst,
"Species": species_lst,
"n_elect": electrons_lst,
"ENMAX": encut_recommended_lst
})
df_mendeleev = fetch_table('elements')
ind = np.array([l[0] in df_mendeleev.symbol.values for l in df.Species])
df_lda = pandas.DataFrame({"Element": elements_dict.keys(), "Name": [v + "-lda" for k, v in elements_dict.items()]})
df_lda.set_index("Element", inplace=True)
df_lda.sort_index(inplace=True)
df_pbe = pandas.DataFrame({"Element": elements_dict.keys(), "Name": [v + "-gga-pbe" for k, v in elements_dict.items()]})
df_pbe.set_index("Element", inplace=True)
df_pbe.sort_index(inplace=True)
df_pbe.to_csv("potentials_vasp_pbe_default.csv")
df_lda.to_csv("potentials_vasp_lda_default.csv")
df[ind].to_csv("potentials_vasp.csv")
Having access to the VASP installation on our cluster, and the potentials files, I just need a little more detailed instructions than are available here. Some questions I have include
Thanks!