| 修訂 | 222a7b36ea78813caff0622ef392bcd20069a5a4 (tree) |
|---|---|
| 時間 | 2018-12-27 18:31:48 |
| 作者 |  mitsuaki1987 <kawamitsuaki@gmai...> |
| Commiter | mitsuaki1987 |
Add script to generate QE input from cif file
.gitignore (diff)
doc/index.html (diff) src/energy.F90 (diff)
tool/cif2qe.py (diff)| @@ -1,7 +1,8 @@ | ||
| 1 | -*.o | |
| 2 | -*.mod | |
| 3 | -*.x | |
| 4 | -make.inc | |
| 5 | -*~ | |
| 6 | -doc/html/ | |
| 7 | -*.a | |
| 1 | +*.o | |
| 2 | +*.mod | |
| 3 | +*.x | |
| 4 | +make.inc | |
| 5 | +*~ | |
| 6 | +doc/html/ | |
| 7 | +*.a | |
| 8 | +tool/__pycache__ |
| @@ -0,0 +1,110 @@ | ||
| 1 | +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> | |
| 2 | +<html lang="ja"> | |
| 3 | + <head> | |
| 4 | + <meta name="Content-Language" content="ja"> | |
| 5 | + <meta http-equiv="Content-Style-Type" content="text/css"> | |
| 6 | + <meta http-equiv="Content-Script-Type" content="text/javascript"> | |
| 7 | + <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> | |
| 8 | + <meta http-equiv="Pragma" content="no-cache"> | |
| 9 | + <meta http-equiv="Cache-Control" content="no-cache"> | |
| 10 | + <title>Web page for Numerical Analysis for Material Science 2 (DFT part)</title> | |
| 11 | + </head> | |
| 12 | + | |
| 13 | + <body bgcolor="CCFFCC"> | |
| 14 | + <h1> | |
| 15 | + <p>Numerical Analysis for Material Science 2 (DFT part)</p> | |
| 16 | + <p>物質科学のための計算数理 2 (DFT part)</p> | |
| 17 | + </h1> | |
| 18 | + <hr> | |
| 19 | + | |
| 20 | + <h2><a href="./html/index.html">Source browser</a></h2> | |
| 21 | + <h2><a href="https://osdn.net/projects/educational-pwdft/scm/git/pwdft/">Git browser</a></h2> | |
| 22 | + <h2> | |
| 23 | + <code> | |
| 24 | + $ git clone git://git.osdn.net/gitroot/educational-pwdft/pwdft.git | |
| 25 | + </code> | |
| 26 | + </h2> | |
| 27 | + | |
| 28 | + <ul> | |
| 29 | + <li> | |
| 30 | + <h2>8th : Basics of DFT calculation | |
| 31 | + (<a href="2018W-8.pptx">PPTX</a> / <a href="2018W-8.pdf">PDF</a>)</h2> | |
| 32 | + <h3> | |
| 33 | + <ul> | |
| 34 | + <li>Hohenberg-Kohn theorem</li> | |
| 35 | + <li>Kohn-Sham method</li> | |
| 36 | + <li>Local density approximation</li> | |
| 37 | + <li>Bloch theorem</li> | |
| 38 | + <li>Hands-on of QuantumESPRESSO : MgB<sub>2</sub></li> | |
| 39 | + </ul> | |
| 40 | + </h3> | |
| 41 | + </li> | |
| 42 | + <li> | |
| 43 | + <h2> | |
| 44 | + 9th : Solution of Kohn-Sham eq. | |
| 45 | + (<a href="2018W-9.pptx">PPTX</a> / <a href="2018W-9.pdf">PDF</a>) | |
| 46 | + </h2> | |
| 47 | + <h3> | |
| 48 | + <ul> | |
| 49 | + <li>Plane wave representation of Kohn-Sham eq.</li> | |
| 50 | + <li>Direct diagonalization</li> | |
| 51 | + <li>Iterative method : LOBPCG</li> | |
| 52 | + </ul> | |
| 53 | + </h3> | |
| 54 | + </li> | |
| 55 | + <li> | |
| 56 | + <h2> | |
| 57 | + 10th : DFT self-consistent loop | |
| 58 | + (<a href="2018W-10.pptx">PPTX</a> / <a href="2018W-10.pdf">PDF</a>) | |
| 59 | + </h2> | |
| 60 | + <h3> | |
| 61 | + <ul> | |
| 62 | + <li>SCF loop</li> | |
| 63 | + <li>Kohn-Sham potential</li> | |
| 64 | + <li>Broyden method</li> | |
| 65 | + <li>Plot volumetric (grid) data</li> | |
| 66 | + </ul> | |
| 67 | + </h3> | |
| 68 | + </li> | |
| 69 | + <li> | |
| 70 | + <h2> | |
| 71 | + 11th Total energy | |
| 72 | + (<a href="2018W-11.pptx">PPTX</a> / <a href="2018W-11.pdf">PDF</a>) | |
| 73 | + </h2> | |
| 74 | + <h3> | |
| 75 | + <ul> | |
| 76 | + <li>Total energy</li> | |
| 77 | + <li>Ewald sum</li> | |
| 78 | + <li>Tetrahedron method</li> | |
| 79 | + <li>Fermi surface</li> | |
| 80 | + </ul> | |
| 81 | + </h3> | |
| 82 | + </li> | |
| 83 | + <li> | |
| 84 | + <h2> | |
| 85 | + 12th : Advanced topics | |
| 86 | + (<a href="2018W-12.pptx">PPTX</a> / <a href="2018W-12.pdf">PDF</a>) | |
| 87 | + </h2> | |
| 88 | + <h3> | |
| 89 | + <ul> | |
| 90 | + <li>Non-local pseudopotentials</li> | |
| 91 | + <li>Generalized gradient approximation</li> | |
| 92 | + <li>Spin density functional theory</li> | |
| 93 | + </ul> | |
| 94 | + </h3> | |
| 95 | + </li> | |
| 96 | + <li> | |
| 97 | + <h2> | |
| 98 | + 13th : Practical calculation | |
| 99 | + (<a href="2018W-13.pptx">PPTX</a> / <a href="2018W-13.pdf">PDF</a>) | |
| 100 | + </h2> | |
| 101 | + <h3> | |
| 102 | + <ul> | |
| 103 | + <li>CIF file and structure database</li> | |
| 104 | + </ul> | |
| 105 | + </h3> | |
| 106 | + </li> | |
| 107 | + </ul> | |
| 108 | + | |
| 109 | + </body> | |
| 110 | +</html> |
| @@ -155,7 +155,7 @@ contains | ||
| 155 | 155 | norm = sqrt(dot_product(bvec(1:3,ii), bvec(1:3,ii))) |
| 156 | 156 | eta = eta + norm |
| 157 | 157 | end do |
| 158 | - eta = eta / 3.0d0 | |
| 158 | + eta = eta / 3.0d0 / sqrt(2.0d0) / sqrt(2.0d0*pi) | |
| 159 | 159 | write(*,*) " Ewald eta [Bohr^-1] : ", eta |
| 160 | 160 | ! |
| 161 | 161 | ! Reciprocal space |
| @@ -232,7 +232,7 @@ contains | ||
| 232 | 232 | ! |
| 233 | 233 | end do |
| 234 | 234 | ! |
| 235 | - write(*,*) " Eward energy : ", Eew*htr2ev | |
| 235 | + write(*,*) " Ewald energy : ", Eew*htr2ev | |
| 236 | 236 | Etot = Etot + Eew |
| 237 | 237 | ! |
| 238 | 238 | end subroutine ewald |
| @@ -0,0 +1,280 @@ | ||
| 1 | +#!/usr/bin/python3 | |
| 2 | +import sys | |
| 3 | +import pymatgen | |
| 4 | +import seekpath | |
| 5 | +import numpy | |
| 6 | +from pymatgen.core.periodic_table import get_el_sp | |
| 7 | +import json | |
| 8 | + | |
| 9 | + | |
| 10 | +def write_atom(f, avec, typ, nat, pos, atom): | |
| 11 | + print("CELL_PARAMETERS angstrom", file=f) | |
| 12 | + for ii in range(3): | |
| 13 | + print(" %f %f %f" % (avec[ii, 0], avec[ii, 1], avec[ii, 2]), file=f) | |
| 14 | + print("ATOMIC_SPECIES", file=f) | |
| 15 | + for ityp in typ: | |
| 16 | + print(" %s %f %s" % (ityp, pymatgen.Element(ityp).atomic_mass, sssp[str(ityp)]["filename"]), file=f) | |
| 17 | + print("ATOMIC_POSITIONS crystal", file=f) | |
| 18 | + for iat in range(nat): | |
| 19 | + print(" %s %f %f %f" % ( | |
| 20 | + atom[iat], pos[iat][0], pos[iat][1], pos[iat][2]), file=f) | |
| 21 | + | |
| 22 | + | |
| 23 | +def write_middle(f, nat, ntyp, ecutwfc, ecutrho, psdir): | |
| 24 | + print(" pseudo_dir = \'%s/\'" % psdir, file=f) | |
| 25 | + print("/", file=f) | |
| 26 | + print("&SYSTEM", file=f) | |
| 27 | + print(" ibrav = 0", file=f) | |
| 28 | + print(" nat = %d" % nat, file=f) | |
| 29 | + print(" ntyp = %d" % ntyp, file=f) | |
| 30 | + print(" ecutwfc = %f" % ecutwfc, file=f) | |
| 31 | + print(" ecutrho = %f" % ecutrho, file=f) | |
| 32 | + | |
| 33 | + | |
| 34 | +if __name__ == '__main__': | |
| 35 | + | |
| 36 | + args = sys.argv | |
| 37 | + if len(args) < 2: | |
| 38 | + print("Usage:") | |
| 39 | + print("$ cif2qe.py cif-file pseudo-directory [dk_path] [dk_grid]") | |
| 40 | + print("Default:") | |
| 41 | + print("$ cif2qe.py cif-file pseudo-directory 0.1 0.2") | |
| 42 | + exit(0) | |
| 43 | + # | |
| 44 | + # CIF parser | |
| 45 | + # | |
| 46 | + structure = pymatgen.Structure.from_file(args[1]) | |
| 47 | + # | |
| 48 | + # Default value | |
| 49 | + # | |
| 50 | + dk_path = 0.1 | |
| 51 | + dk_grid = 0.2 | |
| 52 | + # | |
| 53 | + psdir = args[2] | |
| 54 | + f = open(psdir + '/sssp_efficiency.json', 'r') | |
| 55 | + sssp = json.load(f) | |
| 56 | + # | |
| 57 | + if len(args) > 3: | |
| 58 | + dk_path = float(args[3]) | |
| 59 | + if len(args) > 4: | |
| 60 | + dk_grid = float(args[4]) | |
| 61 | + # | |
| 62 | + print(" dk for band : {0}".format(dk_path)) | |
| 63 | + print(" dk for grid : {0}".format(dk_grid)) | |
| 64 | + | |
| 65 | + structure.remove_oxidation_states() | |
| 66 | + | |
| 67 | + # | |
| 68 | + # Band path and primitive lattice | |
| 69 | + # | |
| 70 | + skp = seekpath.get_explicit_k_path((structure.lattice.matrix, structure.frac_coords, | |
| 71 | + [pymatgen.Element(str(spc)).number for spc in structure.species]), | |
| 72 | + reference_distance=dk_path) | |
| 73 | + # | |
| 74 | + # Lattice information | |
| 75 | + # | |
| 76 | + avec = skp["primitive_lattice"] | |
| 77 | + bvec = skp["reciprocal_primitive_lattice"] | |
| 78 | + pos = skp["primitive_positions"] | |
| 79 | + nat = len(skp["primitive_types"]) | |
| 80 | + atom = [str(get_el_sp(iat)) for iat in skp["primitive_types"]] | |
| 81 | + typ = set(atom) | |
| 82 | + ntyp = len(typ) | |
| 83 | + typ = set(atom) | |
| 84 | + # | |
| 85 | + # WFC and Rho cutoff | |
| 86 | + # | |
| 87 | + ecutwfc = 0.0 | |
| 88 | + ecutrho = 0.0 | |
| 89 | + for ityp in typ: | |
| 90 | + if ecutwfc < sssp[str(ityp)]["cutoff"]: | |
| 91 | + ecutwfc = sssp[str(ityp)]["cutoff"] | |
| 92 | + if ecutrho < sssp[str(ityp)]["cutoff"] * sssp[str(ityp)]['dual']: | |
| 93 | + ecutrho = sssp[str(ityp)]["cutoff"] * sssp[str(ityp)]['dual'] | |
| 94 | + # | |
| 95 | + # k and q grid | |
| 96 | + # | |
| 97 | + nk = numpy.zeros(3, numpy.int_) | |
| 98 | + for ii in range(3): | |
| 99 | + norm = numpy.sqrt(numpy.dot(bvec[ii][:], bvec[ii][:])) | |
| 100 | + nk[ii] = round(norm / dk_grid) | |
| 101 | + print(norm) | |
| 102 | + print("SCF k-grid : ", nk[0], nk[1], nk[2]) | |
| 103 | + # | |
| 104 | + # Band path | |
| 105 | + # | |
| 106 | + print("Band path") | |
| 107 | + for ipath in range(len(skp["path"])): | |
| 108 | + start = skp["explicit_segments"][ipath][0] | |
| 109 | + final = skp["explicit_segments"][ipath][1] - 1 | |
| 110 | + print("%5d %8s %10.5f %10.5f %10.5f %8s %10.5f %10.5f %10.5f" % ( | |
| 111 | + final - start + 1, | |
| 112 | + skp["explicit_kpoints_labels"][start], | |
| 113 | + skp["explicit_kpoints_rel"][start][0], | |
| 114 | + skp["explicit_kpoints_rel"][start][1], | |
| 115 | + skp["explicit_kpoints_rel"][start][2], | |
| 116 | + skp["explicit_kpoints_labels"][final], | |
| 117 | + skp["explicit_kpoints_rel"][final][0], | |
| 118 | + skp["explicit_kpoints_rel"][final][1], | |
| 119 | + skp["explicit_kpoints_rel"][final][2])) | |
| 120 | + # | |
| 121 | + # Number of electrons | |
| 122 | + # | |
| 123 | + nbnd = len(atom)*10 | |
| 124 | + # | |
| 125 | + # scf.in : Charge density | |
| 126 | + # | |
| 127 | + with open("scf.in", 'w') as f: | |
| 128 | + print("&CONTROL", file=f) | |
| 129 | + print(" calculation = \'scf\'", file=f) | |
| 130 | + write_middle(f, nat, ntyp, ecutwfc, ecutrho, psdir) | |
| 131 | + print(" occupations = \'tetrahedra_opt\'", file=f) | |
| 132 | + print("/", file=f) | |
| 133 | + # | |
| 134 | + print("&ELECTRONS", file=f) | |
| 135 | + print(" mixing_beta = 0.3", file=f) | |
| 136 | + print(" conv_thr = %e" % (float(nat)*1.0e-10), file=f) | |
| 137 | + print("/", file=f) | |
| 138 | + write_atom(f, avec, typ, nat, pos, atom) | |
| 139 | + print("K_POINTS automatic", file=f) | |
| 140 | + print(" %d %d %d 0 0 0" % (nk[0], nk[1], nk[2]), file=f) | |
| 141 | + # | |
| 142 | + # nscf.in : Dense k grid | |
| 143 | + # | |
| 144 | + with open("nscf.in", 'w') as f: | |
| 145 | + print("&CONTROL", file=f) | |
| 146 | + print(" calculation = \'nscf\'", file=f) | |
| 147 | + write_middle(f, nat, ntyp, ecutwfc, ecutrho, psdir) | |
| 148 | + print(" occupations = \'tetrahedra_opt\'", file=f) | |
| 149 | + print(" nbnd = %d" % nbnd, file=f) | |
| 150 | + print(" la2f = .true.", file=f) | |
| 151 | + print("/", file=f) | |
| 152 | + print("&ELECTRONS", file=f) | |
| 153 | + print("/", file=f) | |
| 154 | + write_atom(f, avec, typ, nat, pos, atom) | |
| 155 | + print("K_POINTS automatic", file=f) | |
| 156 | + print(" %d %d %d 0 0 0" % (nk[0]*2, nk[1]*2, nk[2]*2), file=f) | |
| 157 | + # | |
| 158 | + # band.in : Plot band | |
| 159 | + # | |
| 160 | + with open("band.in", 'w') as f: | |
| 161 | + print("&CONTROL", file=f) | |
| 162 | + print(" calculation = \'bands\'", file=f) | |
| 163 | + write_middle(f, nat, ntyp, ecutwfc, ecutrho, psdir) | |
| 164 | + print(" nbnd = %d" % nbnd, file=f) | |
| 165 | + print("/", file=f) | |
| 166 | + print("&ELECTRONS", file=f) | |
| 167 | + print("/", file=f) | |
| 168 | + write_atom(f, avec, typ, nat, pos, atom) | |
| 169 | + print("K_POINTS crystal", file=f) | |
| 170 | + print(len(skp["explicit_kpoints_rel"]), file=f) | |
| 171 | + for ik in range(len(skp["explicit_kpoints_rel"])): | |
| 172 | + print(" %f %f %f 1.0" % ( | |
| 173 | + skp["explicit_kpoints_rel"][ik][0], | |
| 174 | + skp["explicit_kpoints_rel"][ik][1], | |
| 175 | + skp["explicit_kpoints_rel"][ik][2]), | |
| 176 | + file=f) | |
| 177 | + # | |
| 178 | + # bands.in : Read by bands.x | |
| 179 | + # | |
| 180 | + with open("bands.in", 'w') as f: | |
| 181 | + print("&BANDS", file=f) | |
| 182 | + print(" lsym = .false.", file=f) | |
| 183 | + print("/", file=f) | |
| 184 | + # | |
| 185 | + # proj.in : Read by projwfc.x | |
| 186 | + # | |
| 187 | + with open("proj.in", 'w') as f: | |
| 188 | + print("&PROJWFC", file=f) | |
| 189 | + print(" emin = ", file=f) | |
| 190 | + print(" emax = ", file=f) | |
| 191 | + print(" deltae = 0.1", file=f) | |
| 192 | + print("/", file=f) | |
| 193 | + # | |
| 194 | + # pp.in : Plot Kohn-Sham orbitals | |
| 195 | + # | |
| 196 | + with open("pp.in", 'w') as f: | |
| 197 | + print("&INPUTPP ", file=f) | |
| 198 | + print(" plot_num = 7", file=f) | |
| 199 | + print(" kpoint = 1", file=f) | |
| 200 | + print(" kband(1) = %d" % 1, file=f) | |
| 201 | + print(" kband(2) = %d" % nbnd, file=f) | |
| 202 | + print(" lsign = .true.", file=f) | |
| 203 | + print("/", file=f) | |
| 204 | + print("&PLOT ", file=f) | |
| 205 | + print(" iflag = 3", file=f) | |
| 206 | + print(" output_format = 5", file=f) | |
| 207 | + print(" fileout = \".xsf\"", file=f) | |
| 208 | + print("/", file=f) | |
| 209 | + # | |
| 210 | + # band.gp : Gnuplot script | |
| 211 | + # | |
| 212 | + with open("band.gp", 'w') as f: | |
| 213 | + print("set terminal pdf color enhanced \\", file=f) | |
| 214 | + print("dashed dl 0.5 size 8.0cm, 6.0cm", file=f) | |
| 215 | + print("set output \"band.pdf\"", file=f) | |
| 216 | + print("#", file=f) | |
| 217 | + n_sym_points = 1 | |
| 218 | + final = 0 | |
| 219 | + x0 = numpy.linalg.norm(avec[0, :]) * 0.5 / numpy.pi | |
| 220 | + print("x%d = %f" % (n_sym_points, x0*skp["explicit_kpoints_linearcoord"][final]), file=f) | |
| 221 | + for ipath in range(len(skp["path"])): | |
| 222 | + start = skp["explicit_segments"][ipath][0] | |
| 223 | + if start != final: | |
| 224 | + n_sym_points += 1 | |
| 225 | + print("x%d = %f" % (n_sym_points, x0*skp["explicit_kpoints_linearcoord"][start]), file=f) | |
| 226 | + n_sym_points += 1 | |
| 227 | + final = skp["explicit_segments"][ipath][1] - 1 | |
| 228 | + print("x%d = %f" % (n_sym_points, x0*skp["explicit_kpoints_linearcoord"][final]), file=f) | |
| 229 | + print("#", file=f) | |
| 230 | + print("set border lw 2", file=f) | |
| 231 | + print("#", file=f) | |
| 232 | + print("set style line 1 lt 1 lw 2 lc 0 dashtype 2", file=f) | |
| 233 | + print("set style line 2 lt 1 lw 2 lc 0", file=f) | |
| 234 | + print("set style line 3 lt 1 lw 1 lc 1", file=f) | |
| 235 | + print("#", file=f) | |
| 236 | + print("set ytics scale 3.0, -0.5 font \'Cmr10,18\'", file=f) | |
| 237 | + print("set xtics( \\", file=f) | |
| 238 | + n_sym_points = 1 | |
| 239 | + final = 0 | |
| 240 | + label_f = skp["explicit_kpoints_labels"][final] | |
| 241 | + if label_f == "GAMMA": | |
| 242 | + label_f = "\\241" | |
| 243 | + print("\"%s\" x%d" % (label_f, n_sym_points), end="", file=f) | |
| 244 | + for ipath in range(len(skp["path"])): | |
| 245 | + start = skp["explicit_segments"][ipath][0] | |
| 246 | + label_s = skp["explicit_kpoints_labels"][start] | |
| 247 | + if label_s == "GAMMA": | |
| 248 | + label_s = "\\241" | |
| 249 | + label_f = skp["explicit_kpoints_labels"][final] | |
| 250 | + if label_f == "GAMMA": | |
| 251 | + label_f = "\\241" | |
| 252 | + if start != final: | |
| 253 | + n_sym_points += 1 | |
| 254 | + print(", \\\n\"%s%s\" x%d" % (label_f, label_s, n_sym_points), end="", file=f) | |
| 255 | + n_sym_points += 1 | |
| 256 | + final = skp["explicit_segments"][ipath][1] - 1 | |
| 257 | + label_f = skp["explicit_kpoints_labels"][final] | |
| 258 | + if label_f == "GAMMA": | |
| 259 | + label_f = "\\241" | |
| 260 | + print(", \\\n\"%s\" x%d" % (label_f, n_sym_points), end="", file=f) | |
| 261 | + print(") \\\noffset 0.0, 0.0 font \'Cmr10,18\'", file=f) | |
| 262 | + print("#", file=f) | |
| 263 | + print("set grid xtics ls 2 front", file=f) | |
| 264 | + print("#", file=f) | |
| 265 | + print("unset key", file=f) | |
| 266 | + print("#", file=f) | |
| 267 | + print("set xzeroaxis ls 1", file=f) | |
| 268 | + print("#", file=f) | |
| 269 | + print("set ylabel \"Energy from {/Cmmi10 \\042}_F [eV]\" offset - 0.5, 0.0 font \'Cmr10,18\'", file=f) | |
| 270 | + print("#", file=f) | |
| 271 | + n_sym_points = 1 | |
| 272 | + final = 0 | |
| 273 | + for ipath in range(len(skp["path"])): | |
| 274 | + start = skp["explicit_segments"][ipath][0] | |
| 275 | + if start == final: | |
| 276 | + n_sym_points += 1 | |
| 277 | + final = skp["explicit_segments"][ipath][1] - 1 | |
| 278 | + else: | |
| 279 | + break | |
| 280 | + print("plot[:][emin:emax] \"bands.out.gnu\" u 1:($2-ef) w l ls 3", file=f) |
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