def test_cell_distances1_exclude_b():
cell = Cell(np.zeros((0,3),float))
pos0 = np.array([
[1.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
[2.0, 0.0, 0.0],
])
# Zeroth
output = np.zeros(3, float)
cell.compute_distances(output, pos0)
assert output[0] == 1
assert output[1] == 1
assert output[2] == 2
# First
output = np.zeros(2, float)
exclude = np.array([[1,0]])
cell.compute_distances(output, pos0, pairs=exclude)
assert output[0] == 1
assert output[1] == 2
# Second
output = np.zeros(1, float)
exclude = np.array([[1,0],[2,1]])
cell.compute_distances(output, pos0, pairs=exclude)
assert output[0] == 1
# Third
output = np.zeros(1, float)
exclude = np.array([[2,1],[1,0]])
with assert_raises(ValueError):
cell.compute_distances(output, pos0, pairs=exclude)
def test_cell_distances2_exclude_a():
cell = Cell(np.zeros((0, 3), float))
pos0 = np.array([
[0.0, 0.0, 0.0],
])
pos1 = np.array([
[0.0, 0.0, 1.0],
])
# Zeroth
output = np.zeros(1, float)
cell.compute_distances(output, pos0, pos1)
assert output[0] == 1
# First
output = np.zeros(0, float)
exclude = np.array([[0, 0]])
cell.compute_distances(output, pos0, pos1, pairs=exclude)
# Second
output = np.zeros(0, float)
for exclude in np.array([[-1, 0]]), np.array([[0, -1]]), np.array(
[[0, 5]]), np.array([[1, 0]]):
print exclude
try:
cell.compute_distances(output, pos0, pos1, pairs=exclude)
assert False
except ValueError:
pass
def test_cell_distances1_exclude_a():
cell = Cell(np.zeros((0, 3), float))
pos0 = np.array([
[1.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
])
# First
output = np.zeros(1, float)
exclude = np.zeros((0, 2), int)
cell.compute_distances(output, pos0, pairs=exclude)
assert output[0] == 1
# Second
output = np.zeros(0, float)
exclude = np.array([[1, 0]])
cell.compute_distances(output, pos0, pairs=exclude)
# Third
output = np.zeros(0, float)
exclude = np.array([[0, 1]])
try:
cell.compute_distances(output, pos0, pairs=exclude)
assert False
except ValueError:
pass
def test_cell_distances2_exclude_a():
cell = Cell(np.zeros((0,3),float))
pos0 = np.array([
[0.0, 0.0, 0.0],
])
pos1 = np.array([
[0.0, 0.0, 1.0],
])
# Zeroth
output = np.zeros(1, float)
cell.compute_distances(output, pos0, pos1)
assert output[0] == 1
# First
output = np.zeros(0, float)
exclude = np.array([[0,0]])
cell.compute_distances(output, pos0, pos1, pairs=exclude)
# Second
output = np.zeros(0, float)
for exclude in np.array([[-1,0]]), np.array([[0,-1]]), np.array([[0,5]]), np.array([[1,0]]):
print exclude
try:
cell.compute_distances(output, pos0, pos1, pairs=exclude)
assert False
except ValueError:
pass
def test_cell_distances1_exclude_a():
cell = Cell(np.zeros((0,3),float))
pos0 = np.array([
[1.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
])
# First
output = np.zeros(1, float)
exclude = np.zeros((0,2),int)
cell.compute_distances(output, pos0, pairs=exclude)
assert output[0] == 1
# Second
output = np.zeros(0, float)
exclude = np.array([[1,0]])
cell.compute_distances(output, pos0, pairs=exclude)
# Third
output = np.zeros(0, float)
exclude = np.array([[0,1]])
try:
cell.compute_distances(output, pos0, pairs=exclude)
assert False
except ValueError:
pass
def test_cell_distances2_exclude_b():
cell = Cell(np.zeros((0, 3), float))
pos0 = np.array([
[0.0, 0.0, 0.0],
[0.0, 0.0, 1.0],
])
pos1 = np.array([
[0.0, 0.0, 1.0],
[0.0, 0.0, 2.0],
])
# Zeroth
output = np.zeros(4, float)
cell.compute_distances(output, pos0, pos1)
assert output[0] == 1
assert output[1] == 2
assert output[2] == 0
assert output[3] == 1
# First
output = np.zeros(3, float)
exclude = np.array([[0, 0]])
cell.compute_distances(output, pos0, pos1, pairs=exclude)
assert output[0] == 2
assert output[1] == 0
assert output[2] == 1
# Second
output = np.zeros(2, float)
exclude = np.array([[0, 0], [1, 1]])
cell.compute_distances(output, pos0, pos1, pairs=exclude)
assert output[0] == 2
assert output[1] == 0
# Third
output = np.zeros(2, float)
for exclude in np.array([[1, 0], [0, 1]]), np.array([[1, 0], [0, 0]]):
try:
cell.compute_distances(output, pos0, pos1, pairs=exclude)
assert False
except ValueError:
pass
def test_cell_distances2_exclude_b():
cell = Cell(np.zeros((0,3),float))
pos0 = np.array([
[0.0, 0.0, 0.0],
[0.0, 0.0, 1.0],
])
pos1 = np.array([
[0.0, 0.0, 1.0],
[0.0, 0.0, 2.0],
])
# Zeroth
output = np.zeros(4, float)
cell.compute_distances(output, pos0, pos1)
assert output[0] == 1
assert output[1] == 2
assert output[2] == 0
assert output[3] == 1
# First
output = np.zeros(3, float)
exclude = np.array([[0,0]])
cell.compute_distances(output, pos0, pos1, pairs=exclude)
assert output[0] == 2
assert output[1] == 0
assert output[2] == 1
# Second
output = np.zeros(2, float)
exclude = np.array([[0,0],[1,1]])
cell.compute_distances(output, pos0, pos1, pairs=exclude)
assert output[0] == 2
assert output[1] == 0
# Third
output = np.zeros(2, float)
for exclude in np.array([[1,0],[0,1]]), np.array([[1,0],[0,0]]):
try:
cell.compute_distances(output, pos0, pos1, pairs=exclude)
assert False
except ValueError:
pass
def test_cell_water32():
cell = get_system_water32().cell
assert (cell.rspacings == 9.865*angstrom).all()
assert (cell.gspacings == 1/(9.865*angstrom)).all()
assert abs(cell.volume - abs(np.linalg.det(cell.rvecs))) < 1e-10
assert abs(np.dot(cell.gvecs, cell.rvecs.transpose()) - np.identity(3)).max() < 1e-5
assert abs(np.dot(cell.gvecs.transpose(), cell.rvecs) - np.identity(3)).max() < 1e-5
vec1 = np.array([10.0, 0.0, 5.0])*angstrom
cell.mic(vec1)
assert abs(vec1 - np.array([0.135, 0.0, -4.865])*angstrom).max() < 1e-10
vec2 = np.array([10.0, 0.0, 5.0])*angstrom
cell.add_vec(vec2, cell.to_center(vec2))
assert abs(vec1 - vec2).max() < 1e-10
cell.add_vec(vec1, np.array([1,2,3]))
assert abs(vec1 - np.array([10.0, 19.73, 24.73])*angstrom).max() < 1e-10
cell2 = Cell(-cell.rvecs)
assert abs(cell2.volume - abs(np.linalg.det(cell.rvecs))) < 1e-10
def test_align_cell_quartz():
system = get_system_quartz()
system.cell = Cell(system.cell.rvecs[::-1].copy())
lcs = np.array([
[1, 1, 0],
[0, 0, 1],
])
system.align_cell(lcs)
# c should be aligned with z axis
rvecs = system.cell.rvecs
assert abs(rvecs[2][0]) < 1e-10
assert abs(rvecs[2][1]) < 1e-10
# sum of a and b should be aligned with x axis
assert abs(rvecs[0][1] + rvecs[1][1]) < 1e-10
assert abs(rvecs[0][2] + rvecs[1][2]) < 1e-10
# difference of a and b should be aligned with y axis
assert abs(rvecs[0][0] - rvecs[1][0]) < 1e-4
assert abs(rvecs[0][2] - rvecs[1][2]) < 1e-10
# check if the bonds are the same in the rotated structure
check_detect_bonds(system)
def main():
options, fns = parse()
#define logger
if options.silent:
log.set_level('silent')
else:
if options.very_verbose:
log.set_level('highest')
elif options.verbose:
log.set_level('high')
if options.logfile is not None and isinstance(options.logfile, str):
log.write_to_file(options.logfile)
with log.section('QFF', 1, timer='Initializing'):
log.dump('Initializing system')
#read system and ab initio reference
system = None
energy = 0.0
grad = None
hess = None
rvecs = None
for fn in fns:
if fn.endswith('.fchk') or fn.endswith('.xml'):
numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(
fn)
if system is None:
system = System(numbers,
coords,
rvecs=rvecs,
charges=None,
radii=None,
masses=masses)
else:
system.pos = coords.copy()
system.cell = Cell(rvecs)
system.numbers = numbers.copy()
if masses is not None: system.masses = masses.copy()
system._init_derived()
elif fn.endswith('.chk'):
sample = load_chk(fn)
if 'energy' in sample.keys(): energy = sample['energy']
if 'grad' in sample.keys(): grad = sample['grad']
elif 'gradient' in sample.keys(): grad = sample['gradient']
if 'hess' in sample.keys(): hess = sample['hess']
elif 'hessian' in sample.keys(): hess = sample['hessian']
if system is None:
system = System.from_file(fn)
else:
if 'pos' in sample.keys(): system.pos = sample['pos']
elif 'coords' in sample.keys():
system.pos = sample['coords']
if 'rvecs' in sample.keys():
system.cell = Cell(sample['rvecs'])
elif 'cell' in sample.keys():
system.cell = Cell(sample['cell'])
if 'bonds' in sample.keys(): system.bonds = sample['bonds']
if 'ffatypes' in sample.keys():
system.ffatypes = sample['ffatypes']
if 'ffatype_ids' in sample.keys():
system.ffatype_ids = sample['ffatype_ids']
system._init_derived()
else:
raise NotImplementedError('File format for %s not supported' %
fn)
assert system is not None, 'No system could be defined from input'
assert grad is not None, 'No ab initio gradient found in input'
assert hess is not None, 'No ab initio hessian found in input'
#complete the system information
if system.bonds is None: system.detect_bonds()
if system.masses is None: system.set_standard_masses()
if system.ffatypes is None:
if options.ffatypes in ['low', 'medium', 'high', 'highest']:
guess_ffatypes(system, options.ffatypes)
elif options.ffatypes is not None:
raise NotImplementedError(
'Guessing atom types from %s not implemented' %
options.ffatypes)
else:
raise AssertionError('No atom types defined')
#construct ab initio reference
ai = SecondOrderTaylor('ai',
coords=system.pos.copy(),
energy=energy,
grad=grad,
hess=hess,
pbc=pbc)
#detect a priori defined contributions to the force field
refs = []
if options.ei is not None:
if rvecs is None:
ff = ForceField.generate(system,
options.ei,
rcut=50 * angstrom)
else:
ff = ForceField.generate(system,
options.ei,
rcut=20 * angstrom,
alpha_scale=3.2,
gcut_scale=1.5,
smooth_ei=True)
refs.append(YaffForceField('EI', ff))
if options.vdw is not None:
ff = ForceField.generate(system, options.vdw, rcut=20 * angstrom)
refs.append(YaffForceField('vdW', ff))
if options.covres is not None:
ff = ForceField.generate(system, options.covres)
refs.append(YaffForceField('Cov res', ff))
#define quickff program
assert options.program_mode in allowed_programs, \
'Given program mode %s not allowed. Choose one of %s' %(
options.program_mode,
', '.join([prog for prog in allowed_programs if not prog=='BaseProgram'])
)
mode = program_modes[options.program_mode]
only_traj = 'PT_ALL'
if options.only_traj is not None: only_traj = options.only_traj.split(',')
program = mode(system,
ai,
ffrefs=refs,
fn_traj=options.fn_traj,
only_traj=only_traj,
plot_traj=options.ener_traj,
xyz_traj=options.xyz_traj,
suffix=options.suffix)
#run program
program.run()
def qff(args=None):
if args is None:
args = qff_parse_args()
else:
args = qff_parse_args(args)
#define logger
verbosity = None
if args.silent:
verbosity = 'silent'
else:
if args.very_verbose:
verbosity = 'highest'
elif args.verbose:
verbosity = 'high'
#get settings
kwargs = {
'fn_traj': args.fn_traj,
'only_traj': args.only_traj,
'program_mode': args.program_mode,
'plot_traj': args.plot_traj,
'xyz_traj': args.xyz_traj,
'suffix': args.suffix,
'log_level': verbosity,
'log_file': args.logfile,
'ffatypes': args.ffatypes,
'ei': args.ei,
'ei_rcut': args.ei_rcut,
'vdw': args.vdw,
'vdw_rcut': args.vdw_rcut,
'covres': args.covres,
}
settings = Settings(fn=args.config_file, **kwargs)
with log.section('INIT', 1, timer='Initializing'):
log.dump('Initializing system')
#read system and ab initio reference
system = None
energy = 0.0
grad = None
hess = None
pbc = None
rvecs = None
for fn in args.fn:
if fn.endswith('.fchk') or fn.endswith('.xml'):
numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(
fn)
if system is None:
system = System(numbers,
coords,
rvecs=rvecs,
charges=None,
radii=None,
masses=masses)
else:
system.pos = coords.copy()
system.cell = Cell(rvecs)
system.numbers = numbers.copy()
if masses is not None: system.masses = masses.copy()
system._init_derived()
elif fn.endswith('.chk'):
sample = load_chk(fn)
if 'energy' in list(sample.keys()): energy = sample['energy']
if 'grad' in list(sample.keys()): grad = sample['grad']
elif 'gradient' in list(sample.keys()):
grad = sample['gradient']
if 'hess' in list(sample.keys()): hess = sample['hess']
elif 'hessian' in list(sample.keys()): hess = sample['hessian']
if 'rvecs' in list(sample.keys()): pbc = [1, 1, 1]
else: pbc = [0, 0, 0]
if system is None:
system = System.from_file(fn)
else:
if 'pos' in list(sample.keys()): system.pos = sample['pos']
elif 'coords' in list(sample.keys()):
system.pos = sample['coords']
if 'rvecs' in list(sample.keys()):
system.cell = Cell(sample['rvecs'])
elif 'cell' in list(sample.keys()):
system.cell = Cell(sample['cell'])
if 'bonds' in list(sample.keys()):
system.bonds = sample['bonds']
if 'ffatypes' in list(sample.keys()):
system.ffatypes = sample['ffatypes']
if 'ffatype_ids' in list(sample.keys()):
system.ffatype_ids = sample['ffatype_ids']
system._init_derived()
else:
raise NotImplementedError('File format for %s not supported' %
fn)
assert system is not None, 'No system could be defined from input'
assert grad is not None, 'No ab initio gradient found in input'
assert hess is not None, 'No ab initio hessian found in input'
#complete the system information
if system.bonds is None: system.detect_bonds()
if system.masses is None: system.set_standard_masses()
if system.ffatypes is None:
if settings.ffatypes is not None:
set_ffatypes(system, settings.ffatypes)
else:
raise AssertionError('No atom types defined')
if settings.do_hess_negfreq_proj:
log.dump(
'Projecting negative frequencies out of the mass-weighted hessian.'
)
with log.section('SYS', 3, 'Initializing'):
hess = project_negative_freqs(hess, system.masses)
#construct ab initio reference
ai = SecondOrderTaylor('ai',
coords=system.pos.copy(),
energy=energy,
grad=grad,
hess=hess,
pbc=pbc)
#detect a priori defined contributions to the force field
refs = []
if settings.ei is not None:
if rvecs is None:
if settings.ei_rcut is None:
rcut = 50 * angstrom
else:
rcut = settings.ei_rcut
ff = ForceField.generate(system, settings.ei, rcut=rcut)
else:
if settings.ei_rcut is None:
rcut = 20 * angstrom
else:
rcut = settings.ei_rcut
ff = ForceField.generate(system,
settings.ei,
rcut=rcut,
alpha_scale=3.2,
gcut_scale=1.5,
smooth_ei=True)
refs.append(YaffForceField('EI', ff))
if settings.vdw is not None:
ff = ForceField.generate(system,
settings.vdw,
rcut=settings.vdw_rcut)
refs.append(YaffForceField('vdW', ff))
if settings.covres is not None:
ff = ForceField.generate(system, settings.covres)
refs.append(YaffForceField('Cov res', ff))
#define quickff program
assert settings.program_mode in allowed_programs, \
'Given program mode %s not allowed. Choose one of %s' %(
settings.program_mode,
', '.join([prog for prog in allowed_programs if not prog=='BaseProgram'])
)
mode = program_modes[settings.program_mode]
program = mode(system, ai, settings, ffrefs=refs)
#run program
program.run()
return program