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# Generate the data visualized in web-page: water.png
import numpy as np
from doc.documentation.directmin import tools_and_data
from ase import Atoms
from gpaw import LCAO, ConvergenceError
from ase.parallel import paropen
from gpaw.mpi import world
from gpaw.atom.basis import BasisMaker
from gpaw import setup_paths
setup_paths.insert(0, '.')
for symbol in ['H', 'O']:
bm = BasisMaker.from_symbol(symbol, xc='PBE')
basis = bm.generate(zetacount=3, polarizationcount=2)
basis.write_xml()
positions = tools_and_data.positions
L = 9.8553729
r = [[1, 1, 1],
[2, 1, 1],
[2, 2, 1]]
calc_args = {'xc': 'PBE', 'h': 0.2,
'convergence': {'density': 1.0e-6,
'eigenstates': 100},
'maxiter': 333, 'basis': 'tzdp',
'mode': LCAO(), 'symmetry': 'off',
'parallel': {'domain': world.size}}
# Results (total energy, number of iterations) obtained
# in a previous calculation. Used to compare with the
# current results.
saved_results = tools_and_data.wm_saved_results
eig_string = ['scf', 'dm']
t = np.zeros(2)
iters = np.zeros(2)
with paropen('water-results.txt', 'w') as fd:
for i, x in enumerate(r):
atoms = Atoms('32(OH2)', positions=positions)
atoms.set_cell((L, L, L))
atoms.set_pbc(1)
atoms = atoms.repeat(x)
name = str(len(atoms) // 3) + '_H2Omlcls'
try:
for dm in [0, 1]:
txt = name + '_' + eig_string[dm] + '.txt'
tools_and_data.set_calc(atoms, calc_args, txt, dm)
e, iters[dm], t[dm] = \
tools_and_data.get_energy_and_iters(atoms, dm)
# Compare with saved results from previous calculation
e_diff_saved_calc = abs(saved_results[dm][i, 0] - e)
iters_diff_saved_calc = \
abs(saved_results[dm][i, 1] - iters[dm])
tools_and_data.compare_calculated_and_saved_results(
e_diff_saved_calc, iters_diff_saved_calc,
eig_string, name, dm)
# Ratio of elapsed times per iteration
# 2 is added to account for the diagonalization
# performed at the beginning and at the end of etdm
ratio_per_iter = (t[0] / iters[0]) / (t[1] / (iters[1] + 2))
print("{}\t{}\t{}".format(
len(atoms), t[0] / t[1], ratio_per_iter),
flush=True, file=fd)
except ConvergenceError:
print("{}\t{}\t{}".format(
len(atoms), None, None),
flush=True, file=fd)
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