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cmp_unito_crystal_parsers.py
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cmp_unito_crystal_parsers.py
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"""
Compare the parsing results for the
two different unito CRYSTAL parsers:
* ejplugins by Chris Sewell
* pycrystal by Evgeny Blokhin
"""
from __future__ import division
import os
import sys
import random
import logging
import math
import time
from datetime import timedelta
import numpy as np
from ase import Atoms
from ase.geometry import distance
from ase.ga.standard_comparators import InteratomicDistanceComparator
from ase.calculators.calculator import Calculator
from ejplugins.crystal import CrystalOutputPlugin
from pycrystal import CRYSTOUT, CRYSTOUT_Error
logging.getLogger('ejplugins.crystal').setLevel(logging.ERROR)
Ejpcry = CrystalOutputPlugin()
allowed_dt = timedelta(seconds=30)
cmp_atoms = InteratomicDistanceComparator(mic=True)
starttime = time.time()
class Mock(Calculator):
def __init__(self, *args, **kwargs):
Calculator.__init__(self)
def get_property(self, *args, **kwargs):
return 42
for root, dirs, files in os.walk(sys.argv[1]):
# NB beware of the broken links (clean e.g. find . -type l -exec rm -f {} \;)
for filename in files:
target = root + os.sep + filename
if not CRYSTOUT.acceptable(target):
continue
logging.info("*"*25 + root + os.sep + filename + "*"*25)
skipped = False
# Parsing with ejp
tic = time.time()
with open(target) as fp:
try:
ejp_result = Ejpcry.read_file(fp, log_warnings=False)
except Exception as err:
logging.error("EJP FAILED TO PARSE: %s" % str(err))
skipped = True
ejp_perf = round(time.time() - tic, 3)
# Parsing with pcy
tic = time.time()
try:
pcy_result = CRYSTOUT(target)
except CRYSTOUT_Error as err:
logging.error("PCY FAILED TO PARSE: %s" % str(err))
skipped = True
pcy_perf = round(time.time() - tic, 3)
if skipped:
continue
logging.info("PERFORMANCE: %1.1f" % (ejp_perf / pcy_perf))
if not pcy_result['prog']:
logging.error("NOT A KNOWN CODE VERSION")
continue
# NB conversion accuracy issues (codata vs. ASE)
if ejp_result['final'].get('energy') and pcy_result['energy'] is not None:
if abs(ejp_result['final']['energy']['total_corrected']['magnitude'] -
pcy_result['energy']) > 0.0001: # eV
logging.critical("TOTAL ENERGIES: %s VS. %s" % (
ejp_result['final']['energy']['total_corrected']['magnitude'],
pcy_result['energy']
))
elif pcy_result['energy'] is None:
logging.critical("PCY MISSED ENERGY")
continue
else:
logging.error("EJP MISSED ENERGY")
continue
# Comparison by SCF
if abs(len(ejp_result['initial']['scf']) - len(pcy_result['convergence'])) < 2:
tstep = random.randint(0, len(ejp_result['initial']['scf']) - 1)
de = ejp_result['initial']['scf'][tstep - 1]['energy']['total']['magnitude'] - \
ejp_result['initial']['scf'][tstep]['energy']['total']['magnitude']
if de != 0 and not math.isnan(de):
power = int(math.floor(math.log(abs(de), 10)))
if abs(power - pcy_result['convergence'][tstep]) > 1:
logging.critical("TOTAL DE IN CONV: %s VS. %s" % (
power,
pcy_result['convergence'][-1]
))
else:
logging.critical("NUMBERS OF THE CONV STEPS DIFFER: %s VS. %s" % (
len(ejp_result['initial']['scf']),
len(pcy_result['convergence'])
))
# Comparison by running time
pcy_d = timedelta(hours=float(pcy_result['duration'] or 0))
dsplit = map(int, ejp_result['meta']['elapsed_time'].split(':'))
ejp_d = timedelta(hours=dsplit[0], minutes=dsplit[1], seconds=dsplit[2])
if abs(pcy_d - ejp_d) > allowed_dt:
logging.critical("TIME: %s VS. %s" % (pcy_d, ejp_d))
# NB alpha+beta require ECP subtracting, so we omit
magmoms = pcy_result['structures'][-1].get_initial_magnetic_moments()
if magmoms.any():
if magmoms.tolist() != ejp_result['mulliken']['alpha-beta_electrons']['charges']:
logging.critical("NON-EQUAL MAGMOMS")
# Comparison by opt steps
if ejp_result['optimisation'] and pcy_result['optgeom']:
if abs(len(ejp_result['optimisation']) - len(pcy_result['optgeom'])) < 2:
tstep = random.randint(0, min([
len(ejp_result['optimisation']),
len(pcy_result['optgeom'])
]) - 1)
if abs(ejp_result['optimisation'][tstep]['energy']['total_corrected']['magnitude'] -
pcy_result['optgeom'][tstep][-1]) > 0.0001: # eV
logging.critical("TOTAL ENERGIES IN OPT: %s VS. %s" % (
ejp_result['optimisation'][tstep]['energy']['total_corrected']['magnitude'],
pcy_result['optgeom'][tstep][-1]
))
else:
logging.critical("NUMBERS OF THE OPT STEPS DIFFER: %s VS. %s" % (
len(ejp_result['optimisation']),
len(pcy_result['optgeom'])
))
# Structure comparison
if ejp_result['final']['primitive_cell'].get('cell_vectors') and \
ejp_result['final']['primitive_cell'].get('ccoords'):
try:
ejp_struct = Atoms(
symbols=[
''.join([c for c in el if not c.isdigit()]).capitalize()
for el in ejp_result['final']['primitive_cell']['symbols']
], # NB atomic_numbers may contain ECPs
cell=[
ejp_result['final']['primitive_cell']['cell_vectors']['a']['magnitude'],
ejp_result['final']['primitive_cell']['cell_vectors']['b']['magnitude'],
ejp_result['final']['primitive_cell']['cell_vectors']['c']['magnitude']
],
positions=ejp_result['final']['primitive_cell']['ccoords']['magnitude'],
pbc=ejp_result['final']['primitive_cell']['pbc']
)
except KeyError:
logging.critical("PROBLEMATIC STRUCTURE: %s" %
ejp_result['final']['primitive_cell']['symbols'])
continue
if not all(ejp_struct.get_pbc()): # account non-periodic directions
adjust, cellpar = False, ejp_struct.get_cell_lengths_and_angles()
for n in range(3):
if cellpar[n] > CRYSTOUT.PERIODIC_LIMIT:
adjust, cellpar[n] = True, CRYSTOUT.PERIODIC_LIMIT
if adjust:
ejp_struct.set_cell(cellpar)
else:
logging.critical("CANNOT GET EJP STRUCTURE")
continue
pcy_struct = pcy_result['structures'][-1]
args = np.argsort(ejp_struct.positions[:, 2])
ejp_struct = ejp_struct[args]
args = np.argsort(pcy_struct.positions[:, 2])
pcy_struct = pcy_struct[args]
if len(ejp_struct) != len(pcy_struct):
logging.critical("N_ATOMS: %s VS. %s" % (len(ejp_struct), len(pcy_struct)))
continue
ejp_symbs, pcy_symbs = set(ejp_struct.get_chemical_symbols()), set(pcy_struct.get_chemical_symbols())
if ejp_symbs != pcy_symbs:
logging.info("DIFFERENT SYMBOLS: %s VS. %s" % (ejp_symbs, pcy_symbs))
continue
ejp_struct.calc, pcy_struct.calc = Mock(), Mock() # code below does not work without this
if cmp_atoms.looks_like(ejp_struct, pcy_struct):
dd = distance(pcy_struct, ejp_struct)
if dd > 2:
logging.info("STRUCTURE DIFF IS VERY BIG: %s" % dd)
else:
logging.critical("STRUCTURES ARE DIFFERENT")
logging.info("Done in %1.2f sc" % (time.time() - starttime))