def test___init__(self):
"""check BVSCalculator.__init__()
"""
self.assertEqual(1e-5, self.bvc.valenceprecision)
bvc1 = BVSCalculator(valenceprecision=1e-4)
self.assertEqual(1e-4, bvc1.valenceprecision)
return
def setUp(self):
self.bvc = BVSCalculator()
if not hasattr(self, 'rutile'):
type(self).rutile = loadDiffPyStructure('rutile.cif')
# rutile.cif does not have charge data, we need to add them here
iondict = {'Ti': 'Ti4+', 'O': 'O2-'}
for a in self.rutile:
a.element = iondict[a.element]
return
def test_pickling(self):
'''check pickling and unpickling of BVSCalculator.
'''
bvsc = BVSCalculator()
bvsc.rmin = 0.1
bvsc.rmax = 12.3
bvsc.valenceprecision = 0.3e-4
spkl = pickle.dumps(bvsc)
bvsc1 = pickle.loads(spkl)
self.assertFalse(bvsc is bvsc1)
for a in bvsc._namesOfDoubleAttributes():
self.assertEqual(getattr(bvsc, a), getattr(bvsc1, a))
self.assertRaises(RuntimeError, pickle_with_attr, bvsc, foo='bar')
return
def test_pickling(self):
'''check pickling and unpickling of BVSCalculator.
'''
bvsc = BVSCalculator()
bvsc.rmin = 0.1
bvsc.rmax = 12.3
bvsc.valenceprecision = 0.3e-4
bvsc.foobar = 'asdf'
spkl = cPickle.dumps(bvsc)
bvsc1 = cPickle.loads(spkl)
self.failIf(bvsc is bvsc1)
for a in bvsc._namesOfDoubleAttributes():
self.assertEqual(getattr(bvsc, a), getattr(bvsc1, a))
self.assertEqual('asdf', bvsc1.foobar)
return
def __init__(self, parset, sig=1, scaled=False):
"""Initialize the Restraint.
parset -- SrRealParSet that creates this BVSRestraint.
sig -- The uncertainty on the BVS (default 1).
scaled -- A flag indicating if the restraint is scaled
(multiplied) by the unrestrained point-average chi^2
(chi^2/numpoints) (bool, default False).
"""
from diffpy.srreal.bvscalculator import BVSCalculator
self._calc = BVSCalculator()
self._parset = parset
self.sig = float(sig)
self.scaled = bool(scaled)
return
def test_bvs_to_xarray(db):
stru = db["Ni_stru"]
calc = BVSCalculator()
calc(stru)
arr = bvs_to_xarray(calc)
print(arr)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Calculation of bond valence sums using diffpy.srreal module included in
DiffPy-CMI.
'''
from __future__ import print_function
from diffpy.Structure import loadStructure
from diffpy.srreal.bvscalculator import BVSCalculator
# load crystal structure data from a CIF file
nacl = loadStructure('NaCl.cif')
# create bond valence sum calculator object
bvsc = BVSCalculator()
# calculate BVS and print the expected and actual valences
vsim = bvsc(nacl)
print('Calculate bond valence sums for NaCl "bvsc(nacl)"')
print('expected "bvsc.valences":\n ', bvsc.valences)
print('calculated "bvsc.value":\n ' , vsim)
print('difference "bvsc.bvdiff":\n ', bvsc.bvdiff)
print('root mean square difference "bvsc.bvrmsdiff":', bvsc.bvrmsdiff)
print()
# create new BVS calculator with a custom bond valence parameters
bvsc2 = BVSCalculator()
# Use alternate value for the Na+ Cl- bond valence parameters from
# http://www.iucr.org/__data/assets/file/0018/59004/bvparm2011.cif
