def main(file_name):
xyz_file = XYZFile(file_name)
frames = xyz_file.geometries
# titles = xyz_file.titles
# Unit cell, decide how to make this general
matrix = np.array([[
1.4731497044857509E+01, 3.2189795740722255E-02, 4.5577626559295564E-02
], [
4.2775481701113616E-02, 2.1087874593411915E+01, -2.8531114198383896E-02
], [
6.4054385616337750E-02, 1.3315840416191497E-02, 1.4683043045316882E+01
]])
matrix *= angstrom
cell = UnitCell(matrix)
frac = UnitCell.to_fractional(cell, frames)
xmin = np.min(frac[:, :, 0])
ymin = np.min(frac[:, :, 1])
zmin = np.min(frac[:, :, 2])
frac[:, :, 0] -= -0.5 # xmin
frac[:, :, 1] -= -0.5 # ymin
frac[:, :, 2] -= -0.5 # zmin
decimals = np.modf(frac)[0]
# decimals[:,:,0] += xmin
# decimals[:,:,1] += ymin
# decimals[:,:,2] += zmin
frac_wrapped = np.where(decimals < 0, 1 + decimals, decimals)
# frac_wrapped[:,:,0] += xmin
# frac_wrapped[:,:,1] += ymin
# frac_wrapped[:,:,2] += zmin
cart_wrapped = UnitCell.to_cartesian(cell, frac_wrapped)
xyz_file.geometries = cart_wrapped
xyz_file.write_to_file(file_name.rsplit(".", 1)[0] + "_wrapped.xyz")
def test_many_separate(self):
psf = PSFFile()
molecule = XYZFile("input/ethene.xyz").get_molecule()
psf.add_molecule(molecule)
psf.add_molecule(molecule)
molecule = XYZFile("input/tea.xyz").get_molecule()
psf.add_molecule(molecule)
psf.write_to_file("output/many_separate.psf")
def test_tetra(self):
molecule = XYZFile("input/tetra.xyz").get_molecule()
psf = PSFFile()
psf.add_molecule(molecule)
self.assert_(psf.bonds.shape[0] == 4)
self.assert_(psf.bends.shape[0] == 6)
psf.write_to_file("output/tetra.psf")
def test_distance_matrix(self):
molecule = XYZFile("input/tpa.xyz").get_molecule()
dm = 0
for i in 0,1,2:
dm += numpy.subtract.outer(molecule.coordinates[:,i],molecule.coordinates[:,i])**2
dm = numpy.sqrt(dm)
self.assert_((abs(molecule.distance_matrix - dm) < 1e-5).all(), "Wrong distance matrix")
def test_blind(self):
m = XYZFile("input/precursor.xyz").get_molecule()
def yield_positioned_objects():
for row, coordinate in enumerate(m.coordinates):
yield PositionedObject(row, coordinate)
sbo = SparseBinnedObjects(yield_positioned_objects(), 7.1)
environments = calculate_environments(sbo, 7)
def test_one(xyz_fn, checks, reorder=False):
mol = XYZFile(xyz_fn).get_molecule()
graph = MolecularGraph.from_geometry(mol)
zmat_gen = ZMatrixGenerator(graph)
if reorder is False:
self.assertArraysEqual(zmat_gen.new_index, numpy.arange(mol.size))
self.assertArraysEqual(zmat_gen.old_index, numpy.arange(mol.size))
zmat0 = zmat_gen.cart_to_zmat(mol.coordinates)
for field, index, value in checks:
self.assertAlmostEqual(zmat0[field][index], value, 2, "%s:%i %f!=%f" % (field,index,zmat0[field][index],value))
numbers0, coordinates0 = zmat_to_cart(zmat0)
mol0 = Molecule(numbers0, coordinates0)
mol0.write_to_file("output/zmat_%s" % os.path.basename(xyz_fn))
graph0 = MolecularGraph.from_geometry(mol0)
zmat_gen0 = ZMatrixGenerator(graph0)
self.assertArraysEqual(zmat_gen0.new_index, numpy.arange(mol.size))
self.assertArraysEqual(zmat_gen0.old_index, numpy.arange(mol.size))
zmat1 = zmat_gen0.cart_to_zmat(mol0.coordinates)
for field, index, value in checks:
self.assertAlmostEqual(zmat1[field][index], value, 2, "%s:%i %f!=%f" % (field,index,zmat1[field][index],value))
numbers1, coordinates1 = zmat_to_cart(zmat1)
self.assertArraysEqual(numbers0, numbers1)
self.assertArraysAlmostEqual(coordinates0, coordinates1, 1e-5)
def test_volume_dinitrogen(self):
mol = XYZFile("input/dinitrogen.xyz").get_molecule()
vdw_volume, sas_volume, ses_volume, error = estimate_volumes(mol)
self.assert_(ses_volume > vdw_volume)
self.assert_(sas_volume > ses_volume)
r = periodic["N"].vdw_radius
ses_upper_limit = 4.0 / 3.0 * numpy.pi * r**3 + numpy.pi * r**2 * numpy.linalg.norm(
mol.coordinates[0] - mol.coordinates[1])
self.assert_(vdw_volume < ses_upper_limit)
self.assert_(ses_volume < ses_upper_limit)
def main(file1_name, file2_name, start_step, end_step, trim, unitcell_name):
"""
Takes a xyz trajectory and can combine it with the ptcv trajectory, trim it
and add unit cell parameters in the title lines so that PLUMED can process it
if the unit cell is variable
"""
if os.path.isfile(file1_name):
xyz_file1 = XYZFile(file1_name)
xyz_file3 = xyz_file1
geo1 = xyz_file1.geometries[start_step:end_step]
if file2_name is not None:
if os.path.isfile(file2_name):
xyz_file2 = XYZFile(file2_name)
geo2 = xyz_file2.geometries[start_step:end_step]
xyz_file2.symbols = ('He', )
min_size = min(geo1.shape[0], geo2.shape[0])
xyz_file3.geometries = np.concatenate(
(geo1[:min_size:trim], geo2[:min_size:trim]), axis=1)
xyz_file3.symbols = np.concatenate(
(xyz_file1.symbols, xyz_file2.symbols), axis=0)
xyz_file3.write_to_file('coord-ptcv.xyz')
if unitcell_name is not None:
unitcellmerge(xyz_file3, start_step, end_step, trim,
unitcell_name)
else:
print('%s does not exist' % (file2_name))
else:
xyz_file3.geometries = geo1[::trim]
if unitcell_name is not None:
xyz_file3 = unitcellmerge(xyz_file3, start_step, end_step,
trim, unitcell_name)
xyz_file3.write_to_file('coord-processed.xyz')
else:
print('%s does not exist' % (file1_name))
def main(file_name, parameters, start_step, end_step, temp):
"""
Loads molecular geometries, generates file with time evolution
of given angles and bonds. Prints force parameters for a
harmonic oscillator that reproduces the behavior of
each bond/angle to use as input for biased simulations
"""
# Timestep in fs
timestep = 0.5
# Create output directory
out_dir = "output_txt/"
if not os.path.exists(out_dir):
os.makedirs(out_dir)
# Create trajectory object and store the geometries in numpy array
xyz_file = XYZFile(file_name)
geometries = xyz_file.geometries[start_step:end_step]
# Read atom list from input file (input is 1-based indexing)
with open(parameters, 'r') as f:
atoms_input = json.load(f)
atoms = [np.array(a) - 1 for a in atoms_input]
# Calculate bonds and angles
time = (np.arange(geometries.shape[0]) + 1) * timestep
bonds_angles = [get_bonds_angles(geometries, i) for i in atoms]
labels = [convert_label(i) for i in atoms_input]
# Compute histograms and saves results
for i, qty in enumerate(bonds_angles):
all_distr, coefficients = generate_histogram(qty, temp)
np.savetxt("{}{}-hist.dat".format(out_dir, labels[i]), all_distr)
np.savetxt("{}{}-time.dat".format(out_dir,
labels[i]), np.stack((time, qty)).transpose())
np.savetxt("{}{}-coeff.dat".format(out_dir,
labels[i]),
coefficients,
fmt='%1.3f',
header='x0, sigma, k, R2')
plot_all(all_distr, qty, coefficients, atoms_input[i], time)
# Store in a pandas dataframe for further analysis (to do)
all_data = pd.DataFrame(
data=np.stack(bonds_angles).transpose(),
index=time,
columns=labels)
all_data.to_csv("{}all_data.dat".format(out_dir), sep='\t')
def test_dihedral_ethene(self):
mol = XYZFile("input/ethene.xyz").get_molecule()
c = mol.coordinates.copy()
self.assertAlmostEqual(ic.dihed_cos(c[2], c[0], c[3], c[5])[0], 1.0)
self.assertAlmostEqual(ic.dihed_angle(c[2], c[0], c[3], c[5])[0], 0.0)
for i in xrange(1000):
angle = numpy.random.uniform(-numpy.pi, numpy.pi)
radius = numpy.random.uniform(0, 5*angstrom)
offset = numpy.random.uniform(0, 5*angstrom)
c[5] = [
offset,
-radius*numpy.cos(angle),
radius*numpy.sin(angle),
]
self.assertAlmostEqual(ic.dihed_cos(c[2], c[0], c[3], c[5])[0], numpy.cos(angle))
self.assertAlmostEqual(ic.dihed_angle(c[2], c[0], c[3], c[5])[0], angle)
def test_volume_error_water(self):
mol = XYZFile("input/water.xyz").get_molecule()
vdw_volumes = []
sas_volumes = []
ses_volumes = []
errors = []
for i in xrange(100):
vdw_volume, sas_volume, ses_volume, error = estimate_volumes(
mol, 2.0 * angstrom)
vdw_volumes.append(vdw_volume)
sas_volumes.append(sas_volume)
ses_volumes.append(ses_volume)
errors.append(error)
#print "vdw", numpy.mean(vdw_volumes), numpy.std(vdw_volumes), numpy.mean(errors)
#print "sas", numpy.mean(sas_volumes), numpy.std(sas_volumes), numpy.mean(errors)
#print "ses", numpy.mean(ses_volumes), numpy.std(ses_volumes), numpy.mean(errors)
self.assert_(numpy.std(vdw_volumes) < numpy.mean(errors) * 1.5)
self.assert_(numpy.std(sas_volumes) < numpy.mean(errors) * 1.5)
self.assert_(numpy.std(ses_volumes) < numpy.mean(errors) * 1.5)
def test_bigbox_dinitrogen(self):
mol = XYZFile("input/dinitrogen.xyz").get_molecule()
self.check_bigbox(mol)
def test_bigbox_water(self):
mol = XYZFile("input/water.xyz").get_molecule()
self.check_bigbox(mol)
def test_volume_order_dinitrogen(self):
mol = XYZFile("input/dinitrogen.xyz").get_molecule()
self.check_volume_order(mol)
def test_volume_order_water(self):
mol = XYZFile("input/water.xyz").get_molecule()
self.check_volume_order(mol)
def load_molecule(self, xyz_fn):
molecule = XYZFile(os.path.join("input", xyz_fn)).get_molecule()
molecule.graph = MolecularGraph.from_geometry(molecule)
return molecule
def test_volume_argon(self):
mol = XYZFile("input/argon.xyz").get_molecule()
vdw_volume, sas_volume, ses_volume, error = estimate_volumes(mol)
self.assertEqual(vdw_volume, ses_volume)
self.assert_(sas_volume > vdw_volume)
def test_volume_tpa(self):
mol = XYZFile("input/tpa.xyz").get_molecule()
vdw_volume, sas_volume, ses_volume, error = estimate_volumes(mol)
self.assert_(ses_volume > vdw_volume)
self.assert_(sas_volume > ses_volume)
def test_dump(self):
m = XYZFile("input/thf.xyz").get_molecule()
psf = PSFFile()
psf.add_molecule(m)
psf.write_to_file("output/thf.psf")
def yield_test_molecules(self):
for filename in ["tpa.xyz", "water.xyz", "thf_single.xyz"]:
molecule = XYZFile(os.path.join("input", filename)).get_molecule()
molecule.filename = filename
graph = MolecularGraph.from_geometry(molecule)
yield molecule, graph
CC30A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,6,6))
CC31A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,6,1))
CC32A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,1,1))
CC33A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,1,1,1))
atom_filters = {
"CC30A": CC30A,
"CC31A": CC31A,
"CC32A": CC32A,
"CC33A": CC33A,
"HCA1": CritAnd(HasAtomNumber(1), HasNeighbors(CC31A)),
"HCA2": CritAnd(HasAtomNumber(1), HasNeighbors(CC32A)),
"HCA3": CritAnd(HasAtomNumber(1), HasNeighbors(CC33A)),
}
def get_atom_type(index, graph):
for atom_type, atom_filter in atom_filters.items():
if atom_filter(index, graph):
return atom_type
raise ValueError("Unrecognized atom (index %i)." % index)
args = sys.argv[1:]
molecule = XYZFile(args[0]).get_molecule()
graph = MolecularGraph.from_geometry(molecule)
atom_types = [get_atom_type(index, graph) for index in range(molecule.size)]
psf = PSFFile()
psf.add_molecular_graph(graph, atom_types=atom_types)
psf.write_to_file(args[0].replace(".xyz", ".psf"))
def load_molecule(self, xyz_fn):
molecule = XYZFile(os.path.join("input", xyz_fn)).get_molecule()
molecule.graph = MolecularGraph.from_geometry(molecule)
return molecule
def test_bigbox_argon(self):
mol = XYZFile("input/argon.xyz").get_molecule()
self.check_bigbox(mol)
def test_bigbox_tpa(self):
mol = XYZFile("input/tpa.xyz").get_molecule()
self.check_bigbox(mol)
def yield_test_molecules(self):
for filename in ["tpa.xyz", "water.xyz", "thf_single.xyz"]:
molecule = XYZFile(os.path.join("input", filename)).get_molecule()
molecule.filename = filename
graph = MolecularGraph.from_geometry(molecule)
yield molecule, graph
def test_volume_water(self):
mol = XYZFile("input/water.xyz").get_molecule()
vdw_volume, sas_volume, ses_volume, error = estimate_volumes(mol, 1.0)
self.assert_(ses_volume > vdw_volume)
self.assert_(sas_volume > ses_volume)
def test_radius_water(self):
mol = XYZFile("input/water.xyz").get_molecule()
radius, error = estimate_radius(mol)
def get_molecules(self):
tpa = XYZFile("input/tpa.xyz").get_molecule()
tpa.title = "tpa"
tea = XYZFile("input/tea.xyz").get_molecule()
tea.title = "tea"
water = XYZFile("input/water.xyz").get_molecule()
water.title = "water"
cyclopentane = XYZFile("input/cyclopentane.xyz").get_molecule()
cyclopentane.title = "cyclopentane"
return [tpa, tea, water, cyclopentane]
def load_molecule(self, filename):
m = XYZFile("input/" + filename).get_molecule()
return m.coordinates, numpy.array(
[periodic[number].mass for number in m.numbers], float)