def test_ComplexCoordSys_pickling(self):
calc = test_calc()
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(calc)
forces0 = ccs.get_forces()
ccs_pickled = pickle.loads(pickle.dumps(ccs))
ccs_pickled.set_calculator(calc)
forces_pickled0 = ccs.get_forces()
dyn = ase.LBFGS(ccs_pickled)
dyn.run(steps=3)
forces_pickled1 = ccs_pickled.get_forces()
dyn = ase.LBFGS(ccs)
dyn.run(steps=3)
forces1 = ccs.get_forces()
self.assert_((forces0 == forces_pickled0).all())
self.assert_((forces1 == forces_pickled1).all())
self.assert_((forces0 != forces1).any())
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_opts(self):
z = cs.ZMatrix(file2str("butane1.zmt"))
new_coords = z.get_internals() * 1.15
z.set_internals(new_coords)
string_rep = z.xyz_str()
z.set_calculator(test_calc())
dyn = ase.LBFGS(z)
print "Running z-matrix optimisation"
dyn.run(steps=5)
e1 = z.get_potential_energy()
xyz = cs.XYZ(string_rep)
xyz.set_calculator(test_calc())
dyn = ase.LBFGS(xyz)
print "Running cartesian optimisation"
dyn.run(steps=5)
e2 = xyz.get_potential_energy()
self.assert_(e1 < e2)
def test_gaussian_chkpointing(self):
print """Testing that for a tricky wavefunction, the gaussian driver
will read in a guess and achieve speedier convergence the second time around."""
print "This test will take around 20 seconds..."
start = time.time()
g = pts.gaussian.Gaussian(mult=2)
b = cs.XYZ(file2str("benzyl.xyz"))
b.set_calculator(g)
b.get_potential_energy()
t0 = time.time() - start
coords = b.get_internals()
coords *= 1.05
start = time.time()
b.set_internals(coords)
b.get_potential_energy()
t1 = time.time() - start
print "Times for first calc and second calculations:", t0, t1
print "Ratio of times", (t1 / t0)
low, high = 0.3, 0.6
print "Must be between %f and %f" % (low, high)
self.assert_(low < t1 / t0 < high)
def form_ccs1(self):
"""Forms a complex coordinate system object from a few bits and pieces."""
x = cs.XYZ(file2str("H2.xyz"))
a_h2o1 = cs.RotAndTrans(numpy.array([1., 0., 0., 0., 1., 1.]),
parent=x)
# a_h2o2 = cs.RotAndTrans(numpy.array([1.,0.,0.,0.,1.,1.,1.]), parent=x)
# a_ch4 = cs.RotAndTrans(numpy.array([1.,0.,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)
return ccs, x, h2o1, a_h2o1 #, h2o2, ch4, a_h2o2, a_ch4
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_gaussian_benzyl(self):
g = pts.gaussian.Gaussian(charge=0, mult=2)
b = cs.XYZ(file2str("benzyl.xyz"))
b.set_calculator(g)
print b.get_forces()
import sys
import pts
import pts.coord_sys as csys
file = sys.argv[1]
s = aof.common.file2str(file)
if csys.ZMatrix2.matches(s):
mol = csys.ZMatrix2(s)
elif csys.XYZ.matches(s):
mol = csys.XYZ(s)
elif csys.ComplexCoordSys.matches(s):
mol = csys.ComplexCoordSys(s)
else:
raise MolInterfaceException("Unrecognised geometry string:\n" + s)
print "Mol has type:", type(mol)
print "mask:", mol._var_mask
print "dims:", mol.dims