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# creates: H.rst, H.png
# ... and all the rest.
import gzip
import json
import sys
import matplotlib.pyplot as plt
import numpy as np
from ase.data import atomic_names, atomic_numbers
from ase.units import Hartree
from ase.utils import plural
RST = """\
.. Computer generated reST (make_setup_pages.py)
.. index:: {name}
.. _{name}:
================
{name}
================
PAW-potentials:
.. csv-table::
:header: name, valence electrons, frozen core electrons
{table}"""
RST1 = """
{electrons}
====================
Radial cutoffs and eigenvalues:
.. csv-table::
:header: id, occ, eig [eV], cutoff [Bohr]
{table1}
The figure shows convergence of the absolute FCC-energy (blue lines)
and BCC-FCC energy difference (orange lines) relative
to converged numbers (plane-wave calculation at 1200 eV).
.. image:: {dataset}.png
.. csv-table::
:header: mode, E(FCC) [eV/atom], E(BCC) [eV/atom], E(BCC)-E(FCC) [eV/atom]
{table2}
Egg-box errors in finite-difference mode:
.. csv-table::
:header: grid-spacing [Å], energy variation [meV]
{table3}"""
def rst(names, data):
symbol = names[0]
Z = atomic_numbers[symbol]
name = atomic_names[Z]
table = ''
rst = RST
for name in names:
dct = data[name]
_, _, kind = name.partition('.')
kind = kind or 'default'
nv, txt = rst1(dct, name, symbol)
if kind != 'default':
kind = f"``'{kind}'``"
table += f' {kind},{nv},{Z - nv}\n'
rst += txt
with open(symbol + '.rst', 'w') as fd:
fd.write(rst.format(table=table, name=name))
def rst1(dct, name, symbol):
table1 = ''
nv = 0
for n, l, f, e, rcut in dct['nlfer']:
n, l, f = (int(x) for x in [n, l, f])
if n == -1:
n = ''
table1 += f" {n}{'spdf'[l]},{f},{e * Hartree:.3f},"
if rcut:
table1 += f'{rcut:.2f}'
nv += f
table1 += '\n'
_, _, eegg = dct['eggbox']
if eegg:
table3 = ''
for h, energies in eegg:
E = [e for h, e in energies]
e = np.ptp(E)
table3 += f' {h:.2f},{1000 * e:.3f}\n'
else:
table3 = ' -,-\n'
fig = plt.figure(figsize=(8, 5))
_, _, _, _, xfcc, yfcc = dct['fcc-pw']
_, _, _, _, xbcc, ybcc = dct['bcc-pw']
yfcc = np.array(yfcc)
efcc0 = yfcc[0]
ebcc0 = ybcc[0]
table2 = (' PW(ecut=1200),' +
f'{efcc0:.3f},{ebcc0:.3f},{ebcc0 - efcc0:.3f}\n')
n = min(len(yfcc), len(ybcc))
dy = ybcc[:n] - yfcc[:n]
dy -= dy[0]
ax1 = plt.subplot(121)
ax1.semilogy(xfcc[1:len(yfcc)], abs(yfcc[1:] - yfcc[0]),
'C0-', label='PW, E(FCC)')
ax1.semilogy(xfcc[1:n], abs(dy[1:]), 'C1--', label='PW, E(BCC)-E(FCC)')
plt.xlabel('Planewave cutoff [eV]')
plt.ylabel('Error [eV/atom]')
plt.legend(loc='best')
ax2 = plt.subplot(122, sharey=ax1)
for mode, style in [('fd', 's'), ('lcao', 'o')]:
_, _, _, _, hfcc, efcc = dct[f'fcc-{mode}']
_, _, _, _, hbcc, ebcc = dct[f'bcc-{mode}']
efcc = np.array(efcc) - efcc0
ebcc = np.array(ebcc) - ebcc0
ax2.semilogy(hfcc[:len(efcc)], abs(efcc), f'C0{style}-',
label=f'{mode.upper()}, E(FCC)')
H = []
de = []
for hf, ef in zip(hfcc, efcc):
_, hb, eb = min((abs(hb - hf), hb, eb)
for hb, eb in zip(hbcc, ebcc))
H.append((hf + hb) / 2)
de.append(abs(eb - ef))
ax2.semilogy(H, de, f'C1{style}--',
label=f'{mode.upper()}, E(BCC)-E(FCC)')
if len(efcc) > 0:
table2 += (
f' "{mode.upper()}(h={hfcc[0]:.2f},{hbcc[0]:.2f})",' +
f'{efcc[0] + efcc0:.3f},' +
f'{ebcc[0] + ebcc0:.3f},' +
f'{ebcc[0] + ebcc0 - efcc[0] - efcc0:.3f}\n')
plt.xlabel('grid-spacing [Å]')
plt.legend(loc='best')
plt.setp(ax2.get_yticklabels(), visible=False)
plt.tight_layout()
plt.subplots_adjust(wspace=0)
plt.savefig(name + '.png')
plt.close(fig)
nv = dct['nvalence']
return nv, RST1.format(electrons=plural(nv, 'valence electron'),
table1=table1,
table2=table2,
table3=table3,
symbol=symbol,
dataset=name)
def main(symbols=None):
with gzip.open('potentials.json.gz', 'rt') as fd:
data = json.load(fd)
for symbol in symbols or data:
if '.' not in symbol:
print(symbol, end='')
sys.stdout.flush()
rst([symbol] + [name for name in data
if name.startswith(symbol + '.')],
data)
print()
# if __name__ == '__main__':
if 1:
# main(['In'])
main()
|
