def test_Anchoring(self):
#self.assertRaises(cs.ComplexCoordSysException, cs.RotAndTrans, numpy.array([0.,0.,0.,0.,0.,0.]))
# Generates a series of rotated molecular geometries and views them.
a = cs.RotAndTrans(numpy.array([1., 0., 0., 1., 1., 1.]))
z = cs.ZMatrix(file2str("butane1.zmt"), anchor=a)
print z.get_internals()
atoms1 = z.atoms.copy()
alphas = numpy.arange(0., 1., 0.01) * 2 * numpy.pi
vs = numpy.arange(0., 1., 0.01)
geoms_list = []
for alpha, v in zip(alphas, vs):
vec = common.normalise([1, v, -v])
vec = numpy.sin(alpha / 2) * vec
q = numpy.hstack([vec])
v = numpy.array([1., 1., 1.])
a.set(numpy.hstack([q, v]))
geoms_list.append(z.atoms.copy())
if visual:
ase.view(geoms_list)
def test_var_mask_big_water_opt(self):
print "Running optimisation tests with masking of variables:"
print " Lots of water molecules with internal and rotational coordinates frozen."
ccs, var_types = self.form_ccs_waters(16)
def gen_mask(c):
if c == 'i':
return False
elif c == 'r':
return True
elif c == 'p':
return True
else:
raise False
mask = map(gen_mask, var_types)
ccs.set_var_mask(mask)
ccs.set_calculator(test_calc())
opt = ase.LBFGS(ccs)
list = []
for i in range(8):
opt.run(steps=1, fmax=0.0)
list.append(ccs.atoms.copy())
if visual:
ase.view(list)
def test_ComplexCoordSys(self):
x = cs.XYZ(file2str("H2.xyz"))
a_h2o1 = cs.RotAndTrans(numpy.array([1., 0., 0., 3., 1., 1.]),
parent=x)
a_h2o2 = cs.RotAndTrans(numpy.array([1., 0., 0., 1., 1., 1.]),
parent=x)
a_ch4 = cs.RotAndTrans(numpy.array([1., 0., 0., 1., -1., 1.]),
parent=x)
h2o1 = cs.ZMatrix(file2str("H2O.zmt"), anchor=a_h2o1)
h2o2 = cs.ZMatrix(file2str("H2O.zmt"), anchor=a_h2o2)
ch4 = cs.ZMatrix(file2str("CH4.zmt"), anchor=a_ch4)
parts = [x, h2o1, h2o2, ch4]
ccs = cs.ComplexCoordSys(parts)
ccs.set_calculator(test_calc())
dyn = ase.LBFGS(ccs)
list = []
for i in range(8):
list.append(ccs.atoms.copy())
dyn.run(steps=1, fmax=0.01)
list.append(ccs.atoms.copy())
if visual:
ase.view(list)
def test_var_mask_big_water_opt(self):
print "Running optimisation tests with masking of variables:"
print " Lots of water molecules with internal and rotational coordinates frozen."
ccs, var_types = self.form_ccs_waters(16)
def gen_mask(c):
if c == 'i':
return False
elif c == 'r':
return True
elif c == 'p':
return True
else:
raise False
mask = map(gen_mask, var_types)
ccs.set_var_mask(mask)
ccs.set_calculator(test_calc())
opt = ase.LBFGS(ccs)
list = []
for i in range(8):
opt.run(steps=1,fmax=0.0)
list.append(ccs.atoms.copy())
if visual:
ase.view(list)
def test_ComplexCoordSys(self):
x = cs.XYZ(file2str("H2.xyz"))
a_h2o1 = cs.RotAndTrans(numpy.array([1.,0.,0.,3.,1.,1.]), parent=x)
a_h2o2 = cs.RotAndTrans(numpy.array([1.,0.,0.,1.,1.,1.]), parent=x)
a_ch4 = cs.RotAndTrans(numpy.array([1.,0.,0.,1.,-1.,1.]), parent=x)
h2o1 = cs.ZMatrix(file2str("H2O.zmt"), anchor=a_h2o1)
h2o2 = cs.ZMatrix(file2str("H2O.zmt"), anchor=a_h2o2)
ch4 = cs.ZMatrix(file2str("CH4.zmt"), anchor=a_ch4)
parts = [x, h2o1, h2o2, ch4]
ccs = cs.ComplexCoordSys(parts)
ccs.set_calculator(test_calc())
dyn = ase.LBFGS(ccs)
list = []
for i in range(8):
list.append(ccs.atoms.copy())
dyn.run(steps=1,fmax=0.01)
list.append(ccs.atoms.copy())
if visual:
ase.view(list)
def test_Anchoring(self):
#self.assertRaises(cs.ComplexCoordSysException, cs.RotAndTrans, numpy.array([0.,0.,0.,0.,0.,0.]))
# Generates a series of rotated molecular geometries and views them.
a = cs.RotAndTrans(numpy.array([1.,0.,0.,1.,1.,1.]))
z = cs.ZMatrix(file2str("butane1.zmt"), anchor=a)
print z.get_internals()
atoms1 = z.atoms.copy()
alphas = numpy.arange(0., 1., 0.01) * 2 * numpy.pi
vs = numpy.arange(0., 1., 0.01)
geoms_list = []
for alpha, v in zip(alphas, vs):
vec = common.normalise([1,v,-v])
vec = numpy.sin(alpha / 2) * vec
q = numpy.hstack([vec])
v = numpy.array([1.,1.,1.])
a.set(numpy.hstack([q,v]))
geoms_list.append(z.atoms.copy())
if visual:
ase.view(geoms_list)
def setUp(self):
UTDomainParallelSetup.setUp(self)
for virtvar in ['dtype']:
assert getattr(self,virtvar) is not None, 'Virtual "%s"!' % virtvar
# Create randomized atoms
self.atoms = create_random_atoms(self.gd, 5) # also tested: 10xNH3/BDA
# XXX DEBUG START
if False:
from ase import view
view(self.atoms*(1+2*self.gd.pbc_c))
# XXX DEBUG END
# Do we agree on the atomic positions?
pos_ac = self.atoms.get_positions()
pos_rac = np.empty((world.size,)+pos_ac.shape, pos_ac.dtype)
world.all_gather(pos_ac, pos_rac)
if (pos_rac-pos_rac[world.rank,...][np.newaxis,...]).any():
raise RuntimeError('Discrepancy in atomic positions detected.')
# Create setups for atoms
self.Z_a = self.atoms.get_atomic_numbers()
self.setups = Setups(self.Z_a, p.setups, p.basis,
p.lmax, xc)
# K-point descriptor
bzk_kc = np.array([[0, 0, 0]], dtype=float)
self.kd = KPointDescriptor(bzk_kc, 1)
self.kd.set_symmetry(self.atoms, self.setups, usesymm=True)
self.kd.set_communicator(self.kpt_comm)
# Create gamma-point dummy wavefunctions
self.wfs = FDWFS(self.gd, self.bd, self.kd, self.setups,
self.dtype)
spos_ac = self.atoms.get_scaled_positions() % 1.0
self.wfs.set_positions(spos_ac)
self.pt = self.wfs.pt # XXX shortcut
## Also create pseudo partial waveves
#from gpaw.lfc import LFC
#self.phit = LFC(self.gd, [setup.phit_j for setup in self.setups], \
# self.kpt_comm, dtype=self.dtype)
#self.phit.set_positions(spos_ac)
self.r_cG = None
self.buf_G = None
self.psit_nG = None
self.allocate()
def setUp(self):
UTDomainParallelSetup.setUp(self)
for virtvar in ['dtype']:
assert getattr(self,virtvar) is not None, 'Virtual "%s"!' % virtvar
# Create randomized atoms
self.atoms = create_random_atoms(self.gd, 5) # also tested: 10xNH3/BDA
# XXX DEBUG START
if False:
from ase import view
view(self.atoms*(1+2*self.gd.pbc_c))
# XXX DEBUG END
# Do we agree on the atomic positions?
pos_ac = self.atoms.get_positions()
pos_rac = np.empty((world.size,)+pos_ac.shape, pos_ac.dtype)
world.all_gather(pos_ac, pos_rac)
if (pos_rac-pos_rac[world.rank,...][np.newaxis,...]).any():
raise RuntimeError('Discrepancy in atomic positions detected.')
# Create setups for atoms
self.Z_a = self.atoms.get_atomic_numbers()
self.setups = Setups(self.Z_a, p.setups, p.basis,
p.lmax, xc)
# K-point descriptor
bzk_kc = np.array([[0, 0, 0]], dtype=float)
self.kd = KPointDescriptor(bzk_kc, 1)
self.kd.set_symmetry(self.atoms, self.setups)
self.kd.set_communicator(self.kpt_comm)
# Create gamma-point dummy wavefunctions
self.wfs = FDWFS(self.gd, self.bd, self.kd, self.setups,
self.block_comm, self.dtype)
spos_ac = self.atoms.get_scaled_positions() % 1.0
self.wfs.set_positions(spos_ac)
self.pt = self.wfs.pt # XXX shortcut
## Also create pseudo partial waveves
#from gpaw.lfc import LFC
#self.phit = LFC(self.gd, [setup.phit_j for setup in self.setups], \
# self.kpt_comm, dtype=self.dtype)
#self.phit.set_positions(spos_ac)
self.r_cG = None
self.buf_G = None
self.psit_nG = None
self.allocate()
def beadopt_calc(mi, params, indices):
"""Check that points with the specified indices are minima and minimise if necessary."""
for i in indices:
mol = mi.build_coord_sys(mi.reagent_coords[i])
opt = ase.LBFGS(mol)
s, l = 0, []
# FIXME: the final force norm printed by the optimiser is greater than the one specified here
maxit = params['maxit']
tol = params['tol']
while numpy.max(mol.get_forces()) > tol:
opt.run(steps=1)
s += 1
l.append(mol.atoms.copy())
if s >= maxit:
print "Max iterations exceeded."
break
ase.view(l)
def beadopt_calc(mi, params, indices):
"""Check that points with the specified indices are minima and minimise if necessary."""
for i in indices:
mol = mi.build_coord_sys(mi.reagent_coords[i])
opt = ase.LBFGS(mol)
s, l = 0, []
# FIXME: the final force norm printed by the optimiser is greater than the one specified here
maxit = params['maxit']
tol = params['tol']
while numpy.max(mol.get_forces()) > tol:
opt.run(steps=1)
s += 1
l.append(mol.atoms.copy())
if s >= maxit:
print "Max iterations exceeded."
break
ase.view(l)
def test_ComplexCoordSys_var_mask_opt(self):
print "Running tests with masking of variables"
#ch4 = cs.ZMatrix(file2str("CH4.zmt"))
ccs, x, h2o1, a_h2o1 = self.form_ccs1(
) #, h2o2, ch4, a_h2o2, a_ch4 = self.form_ccs()
ccs.set_calculator(test_calc())
#m = [True for i in range(0)] + [True for i in range(ccs.dims)]
parts = [x, h2o1, a_h2o1] #, h2o2, a_h2o2, ch4, a_ch4]
dims = [p._dims for p in parts]
print dims
torf = lambda d, f: [f for i in range(d)]
fs = [False, False, True] #, True, False, False, False]
m1 = [torf(d, f) for d, f in zip(dims, fs)]
print m1
m = [m_ for d, f in zip(dims, fs) for m_ in torf(d, f)]
print m
mask = numpy.array(m)
ccs.set_var_mask(mask)
self.assert_(sum(ccs._var_mask) == ccs.dims)
self.assertAlmostEqualVec(ccs._coords,
ccs._demask(ccs.get_internals()))
before = ccs._coords.copy()
#print ccs.int2cart(ccs.get_internals())
after = ccs._coords.copy()
self.assert_((before == after).all())
print "_coords", ccs._coords
if visual:
ase.view(ccs.atoms)
print "_coords", ccs._coords
print ccs.get_internals()
if visual:
ase.view(ccs.atoms)
dyn = ase.LBFGS(ccs)
list = []
for i in range(8):
list.append(ccs.atoms.copy())
dyn.run(steps=1, fmax=0.01)
list.append(ccs.atoms.copy())
#if visual:
ase.view(list)
def test_ComplexCoordSys2(self):
x = cs.XYZ(file2str("H2.xyz"))
a = cs.RotAndTrans(numpy.array([1., 0., 0., 3., 1., 1.]), parent=x)
z = cs.ZMatrix(file2str("butane1.zmt"), anchor=a)
parts = [x, z]
ccs = cs.ComplexCoordSys(parts)
ccs.set_calculator(test_calc())
print ccs.get_potential_energy()
print ccs.get_forces()
dyn = ase.LBFGS(ccs)
list = []
for i in range(8):
dyn.run(steps=1, fmax=0.01)
list.append(ccs.atoms.copy())
if visual:
ase.view(list)
def test_ComplexCoordSys2(self):
x = cs.XYZ(file2str("H2.xyz"))
a = cs.RotAndTrans(numpy.array([1.,0.,0.,3.,1.,1.]), parent=x)
z = cs.ZMatrix(file2str("butane1.zmt"), anchor=a)
parts = [x, z]
ccs = cs.ComplexCoordSys(parts)
ccs.set_calculator(test_calc())
print ccs.get_potential_energy()
print ccs.get_forces()
dyn = ase.LBFGS(ccs)
list = []
for i in range(8):
dyn.run(steps=1,fmax=0.01)
list.append(ccs.atoms.copy())
if visual:
ase.view(list)
def test_ComplexCoordSys_var_mask_opt(self):
print "Running tests with masking of variables"
#ch4 = cs.ZMatrix(file2str("CH4.zmt"))
ccs, x, h2o1, a_h2o1 = self.form_ccs1()#, h2o2, ch4, a_h2o2, a_ch4 = self.form_ccs()
ccs.set_calculator(test_calc())
#m = [True for i in range(0)] + [True for i in range(ccs.dims)]
parts = [x, h2o1, a_h2o1]#, h2o2, a_h2o2, ch4, a_ch4]
dims = [p._dims for p in parts]
print dims
torf = lambda d, f: [f for i in range(d)]
fs = [False, False, True]#, True, False, False, False]
m1 = [torf(d,f) for d,f in zip(dims, fs)]
print m1
m = [m_ for d,f in zip(dims, fs) for m_ in torf(d,f)]
print m
mask = numpy.array(m)
ccs.set_var_mask(mask)
self.assert_(sum(ccs._var_mask) == ccs.dims)
self.assertAlmostEqualVec(ccs._coords, ccs._demask(ccs.get_internals()))
before = ccs._coords.copy()
#print ccs.int2cart(ccs.get_internals())
after = ccs._coords.copy()
self.assert_((before == after).all())
print "_coords", ccs._coords
if visual:
ase.view(ccs.atoms)
print "_coords", ccs._coords
print ccs.get_internals()
if visual:
ase.view(ccs.atoms)
dyn = ase.LBFGS(ccs)
list = []
for i in range(8):
list.append(ccs.atoms.copy())
dyn.run(steps=1,fmax=0.01)
list.append(ccs.atoms.copy())
#if visual:
ase.view(list)
os.path.join(path, '2387', 'reactant.con'),
{1:{1:3.9,2:3.7},2:{1:3.7,2:3.3}})
chn2 = ChangingNeighbors(os.path.join(path, '0', 'reactant.con'),
os.path.join(path, '1635', 'reactant.con'),
{1:{1:3.9,2:3.7},2:{1:3.7,2:3.3}})
chn3 = ChangingNeighbors(os.path.join(path, '1635', 'reactant.con'),
os.path.join(path, '2387', 'reactant.con'),
{1:{1:3.9,2:3.7},2:{1:3.7,2:3.3}})
reac1 = chn1.neigh1.atoms
t1 = chn1.nrValues(chn1.lostNeighbors)
t2 = chn1.nrValues(chn2.lostNeighbors)
t3 = chn1.nrValues(chn3.lostNeighbors)
indx1 = (t1 > 0)
indx2 = (t2 > 0)
indx3 = (t3 > 0)
aseAtoms = cc.eon_2_ase(reac1)
aseAtoms = ca.color(aseAtoms,indexes=indx1,color='red', makeCopy=False)
aseAtoms = ca.color(aseAtoms,indexes=indx2,color='green', makeCopy=False)
aseAtoms = ca.color(aseAtoms,indexes=indx3,color='blue', makeCopy=False)
aseAtoms = ca.color(aseAtoms,indexes=np.logical_and(indx2,indx3),color='yellow', makeCopy=False)
view(aseAtoms)
def run(order_str, fn1, fn2, ixs):
""" Setup everything and run minimisation.
Based on ordering given in order_Str, geometries in fn1 and fn2, and the
indices ixs, rotate molecule in fn2 so that the atoms with indices ixs
coincide with those in fn1.
"""
# get re-ordering list
order = order_str.split()
order = array([int(o) for o in order])
tot = len(order)
assert tot % 2 == 0, "Atom ordering given has odd number of indices."
order = order.reshape(-1,2)
order1 = order[:,0].copy()
order2 = order[:,1].copy()
order1.sort(), order2.sort()
assert (order1 == order2).all(), "Atom ordering given has non-matching numbers."
a1 = ase.io.read(fn1)
a2 = ase.io.read(fn2)
assert len(a1) == len(a2), "Molecules specified don't have the same number of atoms."
n = len(a1)
assert len(order) == len(a1), "Number of atoms was %d but number of pairs given was %d." % (len(a1), len(order))
# get coords
geom1 = a1.get_positions().copy()
geom2 = a2.get_positions().copy()
# re-order coords so that they are both the same
g1 = []
g2 = []
chem_symbols = []
for o in order:
i,j = o
g1.append(geom1[i])
g2.append(geom2[j])
print i, j, a1.get_chemical_symbols()[i] + " = " + a2.get_chemical_symbols()[j]
assert a1.get_chemical_symbols()[i] == a2.get_chemical_symbols()[j], a1.get_chemical_symbols()[i] + " = " + a2.get_chemical_symbols()[j]
chem_symbols.append(a2.get_chemical_symbols()[j])
g1 = array(g1)
g2 = array(g2)
old_dist_sum1 = aaa_dist(g1)
old_dist_sum2 = aaa_dist(g2)
a1.set_positions(g1)
r = Rotate(g1.copy(), g2.copy(), ixs=ixs)
x, err, g2_new, _ = r.align()
print "Optimising vector:", x
print "Alignment error:", err
g2_new = r.trans(g2, x)
a1.set_chemical_symbols(chem_symbols)
a2.set_chemical_symbols(chem_symbols)
a1.set_positions(g1)
a2.set_positions(g2_new)
new_dist_sum1 = aaa_dist(g1)
new_dist_sum2 = aaa_dist(g2_new)
# Make sure the geometries haven't changes shape in any way by comparing
# the old/new interatom distance.
assert abs(old_dist_sum1 - new_dist_sum1) < 1e-6
assert abs(old_dist_sum2 - new_dist_sum2) < 1e-6
ase.view([a1,a2])
ase.io.write(fn1 + '.t', a1, format='xyz')
ase.io.write(fn2 + '.t', a2, format='xyz')
logo = """\
H HH HHH
H H H H
HHH H HH
H H H H
H H HH HHH"""
d = 0.8
atoms = Atoms()
for y, line in enumerate(logo.split('\n')):
for x, c in enumerate(line):
if c == 'H':
atoms.append(Atom('H', [d * x, -d * y, 0]))
atoms.center(vacuum=2.0)
view(atoms)
if 0:
calc = GPAW(nbands=30)
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('ase-logo.gpw')
else:
calc = GPAW('ase-logo.gpw', txt=None)
density = calc.get_pseudo_density()
image = density[..., density.shape[2] // 2]
if 1: # scale colors to wiki background / foreground
import numpy as np
background = np.array([[[19., 63., 82.]]]).T / 255 # 1c4e63 blueish
logo = """\
H HH HHH
H H H H
HHH H HH
H H H H
H H HH HHH"""
d = 0.8
atoms = Atoms()
for y, line in enumerate(logo.split('\n')):
for x, c in enumerate(line):
if c == 'H':
atoms.append(Atom('H', [d * x, -d * y, 0]))
atoms.center(vacuum=2.0)
view(atoms)
if 0:
calc = GPAW(nbands=30)
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write('ase-logo.gpw')
else:
calc = GPAW('ase-logo.gpw', txt=None)
density = calc.get_pseudo_density()
image = density[..., density.shape[2] // 2]
if 1: # scale colors to wiki background / foreground
import numpy as np
background = np.array([[[19., 63., 82.]]]).T / 255 # 1c4e63 blueish
