def test_water_cost_dist_fc():
fn_chk = context.get_fn('test/water_hessian.chk')
sample = load_chk(fn_chk)
system = System(pos=sample['pos'], numbers=sample['numbers'], ffatypes=['O', 'H', 'H'])
system.detect_bonds()
fn_pars = context.get_fn('test/parameters_water.txt')
parameters = Parameters.from_file(fn_pars)
del parameters.sections['FIXQ']
del parameters.sections['DAMPDISP']
del parameters.sections['EXPREP']
rules = [ScaleRule('BONDFUES', 'PARS', 'O\s*H', 2)]
mods = [ParameterModifier(rules)]
pt = ParameterTransform(parameters, mods)
simulations = [GeoOptHessianSimulation('only', system)]
tests = [FCTest(kjmol/angstrom**2, sample['pos'], sample['hessian'].reshape(9, 9), simulations[0], BondGroup(system))]
assert tests[0].icgroup.cases == [[1, 0], [2, 0]]
cost = CostFunction(pt, {'all': tests})
x = np.array([1.0])
assert abs(cost(x) - np.log(0.5*(5159.1871966 - 4.0088096730e+03)**2)) < 1
x = np.array([1.1])
assert abs(cost(x) - np.log(0.5*(5159.1871966 - 1.1*4.0088096730e+03)**2)) < 1
x = np.array([0.8])
assert abs(cost(x) - np.log(0.5*(5159.1871966 - 0.8*4.0088096730e+03)**2)) < 1
def test_water_cost_angle_fc():
fn_chk = context.get_fn('test/water_hessian.chk')
sample = load_chk(fn_chk)
system = System(pos=sample['pos'], numbers=sample['numbers'], ffatypes=['O', 'H', 'H'])
system.detect_bonds()
fn_pars = context.get_fn('test/parameters_water.txt')
parameters = Parameters.from_file(fn_pars)
del parameters.sections['FIXQ']
del parameters.sections['DAMPDISP']
del parameters.sections['EXPREP']
rules = [ScaleRule('BENDCHARM', 'PARS', 'O\s*H', 3)]
mods = [ParameterModifier(rules)]
pt = ParameterTransform(parameters, mods)
simulations = [GeoOptHessianSimulation('only', system)]
tests = [FCTest(kjmol, sample['pos'], sample['hessian'].reshape(9, 9), simulations[0], BendGroup(system))]
assert tests[0].icgroup.cases == [[2, 0, 1]]
cost = CostFunction(pt, {'all': tests})
x = np.array([1.0])
assert abs(cost(x) - np.log(0.5*(394.59354836 - 302.068346061)**2)) < 1
x = np.array([1.1])
assert abs(cost(x) - np.log(0.5*(394.59354836 - 1.1*302.068346061)**2)) < 1
x = np.array([0.8])
assert abs(cost(x) - np.log(0.5*(394.59354836 - 0.8*302.068346061)**2)) < 1
def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
with path('quickff.data.systems.uio66-zr-brick', 'system.chk') as fn:
data = load_chk(fn)
system = System(data['numbers'],data['pos'],charges=data['charges'],
ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai', coords=system.pos.copy(),
grad=data['gradient'], hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,fn_yaff=fn_yaff,fn_sys=fn_sys,log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s"%("Basename","Cross FC","Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0,1]:
fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
if fc_diag==0.0: assert fc==0.0
def test_uio66zrbrick_crossterms():
with log.section('NOSETEST', 2):
# Load input data for a ficticious system of an isolated
# UiO-66 brick
name = 'uio66-zr-brick/system.chk'
fn = context.get_fn(os.path.join('systems', name))
data = load_chk(fn)
system = System(data['numbers'],data['pos'],charges=data['charges'],
ffatypes=data['ffatypes'],bonds=data['bonds'],radii=data['radii'])
system.set_standard_masses()
ai = SecondOrderTaylor('ai', coords=system.pos.copy(),
grad=data['gradient'], hess=data['hessian'])
# Run QuickFF
with tmpdir('test_uio66') as dn:
fn_yaff = os.path.join(dn, 'pars_cov.txt')
fn_sys = os.path.join(dn, 'system.chk')
fn_log = os.path.join(dn, 'quickff.log')
program = DeriveFF(system, ai, Settings(consistent_cross_rvs=True,
remove_dysfunctional_cross=True,fn_yaff=fn_yaff,fn_sys=fn_sys,log_file=fn_log))
program.run()
# Check force constants of cross terms and corresponding diagonal terms
print("%50s %15s %15s"%("Basename","Cross FC","Diag FC"))
for term in program.valence.terms:
if not term.is_master(): continue
if term.basename.startswith('Cross'):
fc = program.valence.get_params(term.index, only='fc')
for i in [0,1]:
fc_diag = program.valence.get_params(term.diag_term_indexes[i], only='fc')
print("%50s %15.6f %15.6f %50s" % (term.basename,fc,fc_diag,program.valence.terms[term.diag_term_indexes[i]].basename))
if fc_diag==0.0: assert fc==0.0
def check_data(testname, data0, dtype):
with tmpdir(__name__, testname) as dn:
fn_test = os.path.join(dn, 'test.chk')
dump_chk(fn_test, data0)
data1 = load_chk(fn_test)
assert data0.keys() == data1.keys()
assert data0['values'] == data1['values']
assert isinstance(data1['values'], dtype)
def check_data_array(testname, data0, dtype):
with tmpdir(__name__, testname) as dn:
fn_test = os.path.join(dn, 'test.chk')
dump_chk(fn_test, data0)
data1 = load_chk(fn_test)
assert data0.keys() == data1.keys()
assert data1['values'].dtype == dtype
assert (np.asarray(data0['values'], dtype=dtype) == data1['values']).all()
def from_file(cls, *fns, **user_kwargs):
"""Construct a new System instance from one or more files
**Arguments:**
fn1, fn2, ...
A list of filenames that are read in order. Information in later
files overrides information in earlier files.
**Optional arguments:**
Any argument from the default constructor ``__init__``. These must be
given with keywords.
**Supported file formats**
.xyz
Standard Cartesian coordinates file (in angstroms). Atomic
positions and atomic numbers are read from this file. If the
title consists of 3, 6 or 9 numbers, each group of three numbers
is interpreted as a cell vector (in angstroms). A guess of the
bonds will be made based on inter-atomic distances.
.psf
Atom types and bonds are read from this file
.chk
Internal text-based checkpoint format. It just contains a
dictionary with the constructor arguments.
"""
with log.section('SYS'):
kwargs = {}
for fn in fns:
if fn.endswith('.xyz'):
from molmod import Molecule
mol = Molecule.from_file(fn)
kwargs['numbers'] = mol.numbers.copy()
kwargs['pos'] = mol.coordinates.copy()
elif fn.endswith('.psf'):
from molmod.io import PSFFile
psf = PSFFile(fn)
kwargs['ffatypes'] = psf.atom_types
kwargs['bonds'] = np.array(psf.bonds, copy=False)
kwargs['charges'] = np.array(psf.charges, copy=False)
elif fn.endswith('.chk'):
from molmod.io import load_chk
allowed_keys = [
'numbers', 'pos', 'scopes', 'scope_ids', 'ffatypes',
'ffatype_ids', 'bonds', 'rvecs', 'charges', 'radii',
'dipoles','radii2','masses',
]
for key, value in load_chk(fn).iteritems():
if key in allowed_keys:
kwargs.update({key: value})
elif fn.endswith('.h5'):
with h5.File(fn, 'r') as f:
return cls.from_hdf5(f)
else:
raise IOError('Can not read from file \'%s\'.' % fn)
if log.do_high:
log('Read system parameters from %s.' % fn)
kwargs.update(user_kwargs)
return cls(**kwargs)
def from_file(cls, *fns, **user_kwargs):
"""Construct a new System instance from one or more files
**Arguments:**
fn1, fn2, ...
A list of filenames that are read in order. Information in later
files overrides information in earlier files.
**Optional arguments:**
Any argument from the default constructor ``__init__``. These must be
given with keywords.
**Supported file formats**
.xyz
Standard Cartesian coordinates file (in angstroms). Atomic
positions and atomic numbers are read from this file. If the
title consists of 3, 6 or 9 numbers, each group of three numbers
is interpreted as a cell vector (in angstroms). A guess of the
bonds will be made based on inter-atomic distances.
.psf
Atom types and bonds are read from this file
.chk
Internal text-based checkpoint format. It just contains a
dictionary with the constructor arguments.
"""
with log.section('SYS'):
kwargs = {}
for fn in fns:
if fn.endswith('.xyz'):
from molmod import Molecule
mol = Molecule.from_file(fn)
kwargs['numbers'] = mol.numbers.copy()
kwargs['pos'] = mol.coordinates.copy()
elif fn.endswith('.psf'):
from molmod.io import PSFFile
psf = PSFFile(fn)
kwargs['ffatypes'] = psf.atom_types
kwargs['bonds'] = np.array(psf.bonds, copy=False)
kwargs['charges'] = np.array(psf.charges, copy=False)
elif fn.endswith('.chk'):
from molmod.io import load_chk
allowed_keys = [
'numbers',
'pos',
'scopes',
'scope_ids',
'ffatypes',
'ffatype_ids',
'bonds',
'rvecs',
'charges',
'radii',
'valence_charges',
'dipoles',
'radii2',
'masses',
]
for key, value in load_chk(fn).items():
if key in allowed_keys:
kwargs.update({key: value})
elif fn.endswith('.h5'):
with h5.File(fn, 'r') as f:
return cls.from_hdf5(f)
else:
raise IOError('Can not read from file \'%s\'.' % fn)
if log.do_high:
log('Read system parameters from %s.' % fn)
kwargs.update(user_kwargs)
return cls(**kwargs)
