def test_harmonic(self):
a = 20.0
hb = HarmonicBasis(20, a)
x = np.arange(0.0, a, 0.1)
v = 0.5*(x-a/2)**2
#v = 5*(1+np.cos(2*np.pi*x/a))**2
v_coeffs = hb.fit_fn(x, v, 20, even=True, v_threshold=0.1)
energies, orbitals = hb.solve(1, v_coeffs, evecs=True)
expected = np.arange(10) + 0.5
self.assertAlmostEqual(energies[0], 0.5, 1)
self.assertAlmostEqual(energies[1], 1.5, 1)
self.assertAlmostEqual(energies[2], 2.5, 1)
self.assertAlmostEqual(energies[3], 3.5, 1)
self.assertAlmostEqual(energies[4], 4.5, 1)
self.assertAlmostEqual(energies[5], 5.5, 1)
self.assertAlmostEqual(energies[6], 6.5, 1)
import matplotlib.pyplot as pt
x = np.arange(0.0, a, 0.001)
pt.clf()
for i in xrange(10):
f = hb.eval_fn(x, orbitals[:,i])
pt.plot(x, f)
with tmpdir(__name__, 'test_harmonic1') as dn:
pt.savefig(os.path.join(dn, "harmonic_wavefunctions.png"))
pt.clf()
v = hb.eval_fn(x, v_coeffs)
pt.plot(x, v)
for energy in energies[:10]:
pt.axhline(energy)
pt.xlim(0,a)
with tmpdir(__name__, 'test_harmonic2') as dn:
pt.savefig(os.path.join(dn, "harmonic_levels.png"))
def test_harmonic(self):
a = 20.0
hb = HarmonicBasis(20, a)
x = np.arange(0.0, a, 0.1)
v = 0.5 * (x - a / 2)**2
#v = 5*(1+np.cos(2*np.pi*x/a))**2
v_coeffs = hb.fit_fn(x, v, 20, even=True, v_threshold=0.1)
energies, orbitals = hb.solve(1, v_coeffs, evecs=True)
expected = np.arange(10) + 0.5
self.assertAlmostEqual(energies[0], 0.5, 1)
self.assertAlmostEqual(energies[1], 1.5, 1)
self.assertAlmostEqual(energies[2], 2.5, 1)
self.assertAlmostEqual(energies[3], 3.5, 1)
self.assertAlmostEqual(energies[4], 4.5, 1)
self.assertAlmostEqual(energies[5], 5.5, 1)
self.assertAlmostEqual(energies[6], 6.5, 1)
import matplotlib.pyplot as pt
x = np.arange(0.0, a, 0.001)
pt.clf()
for i in range(10):
f = hb.eval_fn(x, orbitals[:, i])
pt.plot(x, f)
with tmpdir(__name__, 'test_harmonic1') as dn:
pt.savefig(os.path.join(dn, "harmonic_wavefunctions.png"))
pt.clf()
v = hb.eval_fn(x, v_coeffs)
pt.plot(x, v)
for energy in energies[:10]:
pt.axhline(energy)
pt.xlim(0, a)
with tmpdir(__name__, 'test_harmonic2') as dn:
pt.savefig(os.path.join(dn, "harmonic_levels.png"))
def test_checkpoint(self):
molecule = load_molecule_cp2k(
pkg_resources.resource_filename("tamkin", "data/test/cp2k/pentane/sp.out"),
pkg_resources.resource_filename("tamkin", "data/test/cp2k/pentane/freq.out"))
nma1 = NMA(molecule)
with tmpdir(__name__, 'test_checkpoint') as dn:
fn_out = os.path.join(dn, 'test.chk')
nma1.write_to_file(fn_out)
nma2 = NMA.read_from_file(fn_out)
self.assertEqual(nma1.freqs.shape, nma2.freqs.shape)
self.assertEqual(nma1.modes.shape, nma2.modes.shape)
self.assertEqual(nma1.masses.shape, nma2.masses.shape)
self.assertEqual(nma1.numbers.shape, nma2.numbers.shape)
self.assertEqual(nma1.coordinates.shape, nma2.coordinates.shape)
self.assertEqual(nma1.inertia_tensor.shape, nma2.inertia_tensor.shape)
assert abs(nma1.freqs - nma2.freqs).max()/abs(nma1.freqs).max() < 1e-15
assert abs(nma1.modes - nma2.modes).max()/abs(nma1.modes).max() < 1e-15
assert abs(nma1.masses - nma2.masses).max()/abs(nma1.masses).max() < 1e-15
assert abs(nma1.coordinates - nma2.coordinates).max()/abs(nma1.coordinates).max() < 1e-15
assert abs(nma1.inertia_tensor - nma2.inertia_tensor).max()/abs(nma1.inertia_tensor).max() < 1e-15
assert (nma1.numbers==nma2.numbers).all()
self.assertAlmostEqual(nma1.mass, nma2.mass)
self.assertAlmostEqual(nma1.energy, nma2.energy)
self.assertEqual(nma1.multiplicity, nma2.multiplicity)
self.assertEqual(nma1.symmetry_number, nma2.symmetry_number)
def test_checkpoint(self):
molecule = load_molecule_cp2k(
pkg_resources.resource_filename(__name__, "../data/test/cp2k/pentane/sp.out"),
pkg_resources.resource_filename(__name__, "../data/test/cp2k/pentane/freq.out"))
nma1 = NMA(molecule)
with tmpdir(__name__, 'test_checkpoint') as dn:
fn_out = os.path.join(dn, 'test.chk')
nma1.write_to_file(fn_out)
nma2 = NMA.read_from_file(fn_out)
self.assertEqual(nma1.freqs.shape, nma2.freqs.shape)
self.assertEqual(nma1.modes.shape, nma2.modes.shape)
self.assertEqual(nma1.masses.shape, nma2.masses.shape)
self.assertEqual(nma1.numbers.shape, nma2.numbers.shape)
self.assertEqual(nma1.coordinates.shape, nma2.coordinates.shape)
self.assertEqual(nma1.inertia_tensor.shape, nma2.inertia_tensor.shape)
self.assert_(abs(nma1.freqs - nma2.freqs).max()/abs(nma1.freqs).max() < 1e-15)
self.assert_(abs(nma1.modes - nma2.modes).max()/abs(nma1.modes).max() < 1e-15)
self.assert_(abs(nma1.masses - nma2.masses).max()/abs(nma1.masses).max() < 1e-15)
self.assert_(abs(nma1.coordinates - nma2.coordinates).max()/abs(nma1.coordinates).max() < 1e-15)
self.assert_(abs(nma1.inertia_tensor - nma2.inertia_tensor).max()/abs(nma1.inertia_tensor).max() < 1e-15)
self.assert_((nma1.numbers==nma2.numbers).all())
self.assertAlmostEqual(nma1.mass, nma2.mass)
self.assertAlmostEqual(nma1.energy, nma2.energy)
self.assertEqual(nma1.multiplicity, nma2.multiplicity)
self.assertEqual(nma1.symmetry_number, nma2.symmetry_number)
def test_ethane_hindered(self):
molecule = load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/ethane/gaussian.fchk"))
nma = NMA(molecule)
rot_scan = load_rotscan_g03log(
pkg_resources.resource_filename(__name__, "../data/test/rotor/gaussian.log"))
rotor = Rotor(rot_scan, molecule, rotsym=3, even=True, cancel_freq='scan')
pf = PartFun(nma, [ExtTrans(), ExtRot(6), rotor])
self.assertAlmostEqual(rotor.cancel_freq/lightspeed*centimeter, 298, 0)
rotor = Rotor(rot_scan, molecule, rotsym=3, even=True)
self.assertAlmostEqual(rotor.cancel_freq/lightspeed*centimeter, 314, 0)
pf = PartFun(nma, [ExtTrans(), ExtRot(6), rotor])
self.assertArraysAlmostEqual(
rotor.hb.eval_fn(rot_scan.potential[0], rotor.v_coeffs),
rot_scan.potential[1] - rot_scan.potential[1].min(), 1e-4
)
# reference data from legacy code (Veronique & co)
self.assertAlmostEqual(rotor.moment/amu, 11.092362911176032, 2)
self.assertAlmostEqual(rotor.reduced_moment/amu, 5.5461814555880098, 2)
self.assertAlmostEqual(np.exp(rotor.log_terms(100.0)[1]), 0.12208E+00, 1)
self.assertAlmostEqual(rotor.heat_capacity_terms(100.0)[1]/(joule/mol/kelvin), 2.567, 0)
self.assertAlmostEqual(rotor.entropy_terms(100.0)[1]/(joule/mol), 0.766, 0)
self.assertAlmostEqual(np.exp(rotor.log_terms(800.0)[1]), 0.21108E+01, 1)
self.assertAlmostEqual(rotor.heat_capacity_terms(800.0)[1]/(joule/mol/kelvin), 6.346, 1)
self.assertAlmostEqual(rotor.entropy_terms(800.0)[1]/(joule/mol), 14.824, 1)
with tmpdir(__name__, 'test_ethane_hindered') as dn:
rotor.plot_levels(os.path.join(dn, "ethane_hindered_levels.png"), 300)
pf.write_to_file(os.path.join(dn, "ethane_hindered.txt"))
ta = ThermoAnalysis(pf, [200,300,400,500,600,700,800,900])
ta.write_to_file(os.path.join(dn, "ethane_hindered_thermo.csv"))
def test_legacy1(self):
a = 2*np.pi
mass = 5.5*amu
hb = HarmonicBasis(100, a)
v_coeffs = np.zeros(hb.size, float)
v_coeffs[0] = 0.5*11.5*kjmol*np.sqrt(a)
v_coeffs[5] = 0.5*11.5*kjmol*np.sqrt(a/2)
self.assertArraysAlmostEqual(
hb.eval_fn(np.array([0, a/6]), v_coeffs),
np.array([11.5*kjmol, 0.0]),
)
energies, orbitals = hb.solve(mass, v_coeffs, evecs=True)
import matplotlib.pyplot as pt
x = np.arange(0.0, a, 0.001)
pt.clf()
for i in xrange(10):
f = hb.eval_fn(x, orbitals[:,i])
pt.plot(x, f+i)
with tmpdir(__name__, 'test_legacy1') as dn:
pt.savefig(os.path.join(dn, "legacy_wavefunctions.png"))
# check energy levels
expected = np.array([
1.7635118, 1.76361979, 5.11795465, 8.04553104, 8.1095722,
10.3876796, 11.8999683, 12.9078395, 14.6739639, 16.7836847,
19.1722507,
1.76361979, 5.11795465, 5.12218335, 8.1095722, 10.3876796,
10.8661504, 12.9078395, 14.6739639, 16.7544718, 19.1722507,
])
expected.sort()
self.assertArraysAlmostEqual(energies[:10]/kjmol, expected[:10], 1e-3)
self.assertAlmostEqual(np.exp(-energies/(100*boltzmann)).sum()/3.0, 0.12208E+00, 5)
def compare_lammps_yaff_swap_noncovalent(name, thresh=1.0):
# Load the system
fn_system = pkg_resources.resource_filename(__name__, '../../data/test/system_%s.chk'%name)
system = System.from_file(fn_system)
# Generate the YAFF ForceField
fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_%s.txt'%name)
ff = ForceField.generate(system, fn_pars, alpha_scale=3.2, gcut_scale=1.5, rcut=15.0*angstrom, smooth_ei=True)
gpos_yaff, vtens_yaff = np.zeros(ff.system.pos.shape), np.zeros((3,3))
eyaff = ff.compute(gpos=gpos_yaff, vtens=vtens_yaff)
pyaff = np.trace(vtens_yaff)/3.0/ff.system.cell.volume
# Replace noncovalent contributions with LAMMPS table
with tmpdir(__name__, 'test_liblammps_swap') as dirname:
fn_system = os.path.join(dirname,'system.dat')
fn_table = os.path.join(dirname,'table.dat')
ff_lammps = swap_noncovalent_lammps(ff, fn_system=fn_system,
fn_table=fn_table)
gpos_lammps, vtens_lammps = np.zeros(ff.system.pos.shape), np.zeros((3,3))
elammps = ff_lammps.compute(gpos=gpos_lammps, vtens=vtens_lammps)
plammps = np.trace(vtens_lammps)/3.0/ff.system.cell.volume
rmsd_gpos = np.std(gpos_yaff-gpos_lammps)
rmsd_vtens = np.std(vtens_yaff-vtens_lammps)
print("E_YAFF = %12.4f E_LAMMPS = %12.4f E_DIFF = %12.4f kJ/mol"%(eyaff/kjmol,elammps/kjmol,(eyaff-elammps)/kjmol))
print("P_YAFF = %12.4f P_LAMMPS = %12.4f P_DIFF = %12.4f MPa"%(pyaff/mpa,plammps/mpa,(pyaff-plammps)/mpa))
print("RMSD GPOS = %12.8f kJ/mol/A"%(rmsd_gpos/kjmol*angstrom))
print("RMSD VTENS = %12.8f kJ/mol"%(rmsd_vtens/kjmol))
assert np.abs(eyaff-elammps)<1e-1*kjmol*thresh
assert np.abs(pyaff-plammps)<1*mpa*thresh
assert rmsd_gpos<1e-2*kjmol/angstrom*thresh
assert rmsd_vtens<0.5*kjmol*thresh
def compare_lammps_yaff_ff(ff, thresh=1.0, do_ei=True, do_vdw=True):
lammps_ffa, lammps_ffa_ids = get_lammps_ffatypes(ff)
gpos_yaff, vtens_yaff = np.zeros(ff.system.pos.shape), np.zeros((3,3))
eyaff = ff.compute(gpos=gpos_yaff, vtens=vtens_yaff)
with tmpdir(__name__, 'test_liblammps') as dirname:
# Write LAMMPS data file
fn_system = os.path.join(dirname,'system.dat')
write_lammps_system_data(ff.system, ff=ff,fn=fn_system)
# Write LAMMPS table file
fn_table = os.path.join(dirname,'table.dat')
write_lammps_table(ff,fn=fn_table)
# Construct the LAMMPS force-field contribution
fn_log = os.path.join(dirname,'lammps.log')
part_lammps = ForcePartLammps(ff,fn_log=fn_log,scalings_table=np.zeros(3),scalings_ei=np.zeros(3),
fn_system=fn_system,fn_table=fn_table,do_ei=do_ei, do_table=do_vdw)
gpos_lammps, vtens_lammps = np.zeros(ff.system.pos.shape), np.zeros((3,3))
elammps = part_lammps.compute(gpos=gpos_lammps, vtens=vtens_lammps)
rmsd_gpos = np.std(gpos_yaff-gpos_lammps)
rmsd_vtens = np.std(vtens_yaff-vtens_lammps)
# print("E_YAFF = %12.4f E_LAMMPS = %12.4f E_DIFF = %12.4f kJ/mol"%(eyaff/kjmol,elammps/kjmol,(eyaff-elammps)/kjmol))
# print("RMSD GPOS = %12.8f kJ/mol/A"%(rmsd_gpos/kjmol*angstrom))
# print("RMSD VTENS = %12.8f kJ/mol"%(rmsd_vtens/kjmol))
assert np.abs(eyaff-elammps)<1e-3*kjmol*thresh
assert rmsd_gpos<1e-4*kjmol/angstrom*thresh
assert rmsd_vtens<1e-2*kjmol*thresh
def test_molecule_checkpoint_full():
mol1 = load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/sterck/aa.fchk"))
mol1.set_default_graph()
mol1.unit_cell = UnitCell(np.identity(3, float)*25)
mol1.symbols = [periodic[n].symbol for n in mol1.numbers]
with tmpdir(__name__, 'test_molecule_checkpoint_full') as dn:
fn_out = os.path.join(dn, "molecule_checkpoint_full.chk")
mol1.write_to_file(fn_out)
mol2 = Molecule.read_from_file(fn_out)
assert mol1.numbers.shape == mol2.numbers.shape
assert abs(mol1.numbers - mol2.numbers).max() == 0
assert mol1.coordinates.shape == mol2.coordinates.shape
assert abs(mol1.coordinates - mol2.coordinates).max() < 1e-10
assert mol1.masses.shape == mol2.masses.shape
assert abs(mol1.masses - mol2.masses).max() < 1e-10
assert abs(mol1.energy - mol2.energy) < 1e-10
assert mol1.gradient.shape == mol2.gradient.shape
assert abs(mol1.gradient - mol2.gradient).max() < 1e-10
assert mol1.hessian.shape == mol2.hessian.shape
assert abs(mol1.hessian - mol2.hessian).max() < 1e-10
assert mol1.multiplicity == mol2.multiplicity
assert mol1.symmetry_number == mol2.symmetry_number
assert mol1.periodic == mol2.periodic
assert mol1.graph.edges == mol2.graph.edges
assert mol1.title == mol2.title
assert mol1.unit_cell.matrix.shape == mol2.unit_cell.matrix.shape
assert abs(mol1.unit_cell.matrix - mol2.unit_cell.matrix).max() < 1e-10
assert mol1.unit_cell.active.shape == mol2.unit_cell.active.shape
assert (mol1.unit_cell.active == mol2.unit_cell.active).all()
assert mol1.symbols == mol2.symbols
def test_consistency_io():
for fn_parameters in '../../data/test/parameters_bks.txt', '../../data/test/parameters_water.txt':
pf1 = Parameters.from_file(pkg_resources.resource_filename(__name__, fn_parameters))
with tmpdir(__name__, 'test_consistency_io') as dn:
pf1.write_to_file('%s/parameters_foo.txt' % dn)
pf2 = Parameters.from_file('%s/parameters_foo.txt' % dn)
check_consistent(pf1, pf2)
def test_plumed_md():
with tmpdir(__name__, 'test_plumed_md') as dirname:
ff = get_ff_water32()
kappa, V0 = 1.6 * kjmol / angstrom**6, ff.system.cell.volume
# PLUMED input commands
commands = "vol: VOLUME\n"
commands += "RESTRAINT ARG=vol AT=%.20f KAPPA=%.20f LABEL=restraint\n"%\
(V0/nanometer**3,kappa/kjmol*nanometer**6)
commands += "PRINT STRIDE=1 ARG=vol FILE=%s\n" % (os.path.join(
dirname, 'cv.log'))
commands += "FLUSH STRIDE=1\n"
# Write PLUMED commands to file
fn = os.path.join(dirname, 'plumed.dat')
with open(fn, 'w') as f:
f.write(commands)
# Setup Plumed
timestep = 1.0 * femtosecond
plumed = ForcePartPlumed(ff.system, timestep=timestep, fn=fn)
ff.add_part(plumed)
# Setup integrator with a barostat, so plumed has to compute forces
# more than once per timestep
tbc = TBCombination(MTKBarostat(ff, 300, 1 * bar), NHCThermostat(300))
verlet = VerletIntegrator(ff, timestep, hooks=[tbc, plumed])
# Run a short MD simulation, keeping track of the CV (volume in this case)
cvref = [ff.system.cell.volume]
for i in range(4):
verlet.run(1)
cvref.append(ff.system.cell.volume)
# Read the PLUMED output and compare with reference
cv = np.loadtxt(os.path.join(dirname, 'cv.log'))
assert cv.shape[0] == 5
assert np.allclose(cv[:, 0] * picosecond, np.arange(5) * timestep)
assert np.allclose(cv[:, 1] * nanometer**3, cvref)
def test_dump_modes_xyz(self):
molecule = load_molecule_charmm(
pkg_resources.resource_filename(__name__,
"../data/test/an/ethanol.cor"),
pkg_resources.resource_filename(
__name__, "../data/test/an/ethanol.hess.full"))
nma = NMA(molecule)
with tmpdir(__name__, 'test_dump_modes_xyz') as dn:
prefix = os.path.join(dn, 'mode')
dump_modes_xyz(nma, 6, prefix=prefix, amplitude=50.0)
with open(prefix + ".6.xyz") as f:
# 1st line
line = f.readline().strip()
self.assertEqual(line, "9")
# 2nd line
line = f.readline().strip()
self.assertEqual(line, "frame 0")
# 3rd line
line = f.readline()
words = line.split()
self.assertEqual(len(words), 4)
self.assertEqual(words[0], "C")
self.assertEqual(words[2], "0.081608346")
for i in range(9):
line = f.readline().strip()
self.assertEqual(line, "9")
def test_reaction_analysis_sterck(self):
pf_react1 = PartFun(
NMA(
load_molecule_g03fchk(
pkg_resources.resource_filename(
__name__, "../data/test/sterck/aa.fchk"))),
[ExtTrans(cp=False), ExtRot(1)])
pf_react2 = PartFun(
NMA(
load_molecule_g03fchk(
pkg_resources.resource_filename(
__name__, "../data/test/sterck/aarad.fchk"))),
[ExtTrans(cp=False), ExtRot(1)])
pf_ts = PartFun(
NMA(
load_molecule_g03fchk(
pkg_resources.resource_filename(
__name__, "../data/test/sterck/paats.fchk"))),
[ExtTrans(cp=False), ExtRot(1)])
km = KineticModel([pf_react1, pf_react2], pf_ts)
ra = ReactionAnalysis(km, 280, 360)
# not a very accurate check because the fit is carried out differently
# in the fancy excel file where these numbers come from.
self.assertAlmostEqual(ra.Ea / kjmol, 25.96, 1)
self.assertAlmostEqual(km.unit, meter**3 / mol / second)
self.assertEqual(km.unit_name, "m^3 mol^-1 s^-1")
self.assertAlmostEqual(np.log(ra.A / km.unit), np.log(2.29E+02), 1)
with tmpdir(__name__, 'test_reaction_analysis_sterck') as dn:
ra.plot_arrhenius(os.path.join(dn, "arrhenius_aa.png"))
ra.monte_carlo()
ra.write_to_file(os.path.join(dn, "reaction_aa.txt"))
ra.plot_parameters(os.path.join(dn, "parameters_aa.png"))
def test_plot_spectrum(self):
molecule = load_molecule_charmm(
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.cor"),
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.hess.full"))
nma = NMA(molecule)
invcm = lightspeed/centimeter
with tmpdir(__name__, 'test_plot_spectrum') as dn:
plot_spectrum_lines(
os.path.join(dn, "spectrum-lines.1.png"),
[nma.freqs, nma.freqs], title="standard settings")
plot_spectrum_lines(
os.path.join(dn, "spectrum-lines.2.png"),
[nma.freqs, nma.freqs], low=-10.0*invcm, high=500.0*invcm, title="zoom")
plot_spectrum_dos(
os.path.join(dn, "spectrum-dos.1.png"),
[nma.freqs], title="standard settings")
plot_spectrum_dos(
os.path.join(dn, "spectrum-dos.2.png"),
[nma.freqs], low=-10.0*invcm, high=1500.0*invcm, title="zoom")
plot_spectrum_dos(
os.path.join(dn, "spectrum-dos.3.png"),
[nma.freqs], low=-10.0*invcm, high=1500.0*invcm, width=50.0*invcm, title="width")
plot_spectrum_dos(
os.path.join(dn, "spectrum-dos.4.png"),
[nma.freqs], low=-10.0*invcm, high=1500.0*invcm, width=50.0*invcm, step=20.0*invcm, title="step size")
plot_spectrum_dos(
os.path.join(dn, "spectrum-dos.5.png"),
[nma.freqs, nma.freqs*1.1], title="two spectra")
plot_spectrum_dos(
os.path.join(dn, "spectrum-dos.6.png"),
[nma.freqs, nma.freqs*1.1], all_amps=[1.0,2.0], title="different amplitude")
def test_reaction_analysis_sterck(self):
pf_react1 = PartFun(NMA(load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/sterck/aa.fchk"))),
[ExtTrans(cp=False), ExtRot(1)])
pf_react2 = PartFun(NMA(load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/sterck/aarad.fchk"))),
[ExtTrans(cp=False), ExtRot(1)])
pf_ts = PartFun(NMA(load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/sterck/paats.fchk"))),
[ExtTrans(cp=False), ExtRot(1)])
km = KineticModel([pf_react1, pf_react2], pf_ts)
ra = ReactionAnalysis(km, 280, 360)
# not a very accurate check because the fit is carried out differently
# in the fancy excel file where these numbers come from.
self.assertAlmostEqual(ra.Ea/kjmol, 25.96, 1)
self.assertAlmostEqual(km.unit, meter**3/mol/second)
self.assertEqual(km.unit_name, "m^3 mol^-1 s^-1")
self.assertAlmostEqual(np.log(ra.A/km.unit), np.log(2.29E+02), 1)
with tmpdir(__name__, 'test_reaction_analysis_sterck') as dn:
ra.plot_arrhenius(os.path.join(dn, "arrhenius_aa.png"))
ra.monte_carlo()
ra.write_to_file(os.path.join(dn, "reaction_aa.txt"))
ra.plot_parameters(os.path.join(dn, "parameters_aa.png"))
def test_reaction_analysis_mat(self):
pf_react = PartFun(
NMA(
load_molecule_g03fchk(
pkg_resources.resource_filename(
__name__, "../data/test/mat5T/react.fchk"))), [])
pf_ts = PartFun(
NMA(
load_molecule_g03fchk(
pkg_resources.resource_filename(
__name__, "../data/test/mat5T/ts.fchk"))), [])
km = KineticModel([pf_react], pf_ts)
ra = ReactionAnalysis(km, 100, 1200, temp_step=50)
# not a very accurate check because the fit is carried out differently
# in the fancy excel file where these numbers come from.
self.assertAlmostEqual(ra.Ea / kjmol, 160.6, 0)
self.assertAlmostEqual(km.unit, 1.0 / second)
self.assertEqual(km.unit_name, "s^-1")
self.assertAlmostEqual(np.log(ra.A / km.unit), np.log(3.33e10), 0)
with tmpdir(__name__, 'test_reaction_analysis_mat1') as dn:
ra.plot_arrhenius(os.path.join(dn, "arrhenius_mat1.png"))
ra.monte_carlo()
ra.write_to_file(os.path.join(dn, "reaction_mat1.txt"))
ra.plot_parameters(os.path.join(dn, "parameters_mat1.png"))
wigner = Wigner(pf_ts) # Blind test of the wigner correction and
# the corrected reaction analysis.
km = KineticModel([pf_react], pf_ts, tunneling=wigner)
ra = ReactionAnalysis(km, 100, 1200, temp_step=50)
with tmpdir(__name__, 'test_reaction_analysis_mat2') as dn:
ra.plot_arrhenius(os.path.join(dn, "arrhenius_mat1w.png"))
ra.monte_carlo()
ra.write_to_file(os.path.join(dn, "reaction_mat1w.txt"))
ra.plot_parameters(os.path.join(dn, "parameters_mat1w.png"))
km = KineticModel([pf_react], pf_ts)
ra = ReactionAnalysis(km, 670, 770)
# not a very accurate check because the fit is carried out differently
# in the fancy excel file where these numbers come from.
self.assertAlmostEqual(ra.Ea / kjmol, 161.9, 1)
self.assertAlmostEqual(np.log(ra.A / km.unit), np.log(4.08e10), 0)
with tmpdir(__name__, 'test_reaction_analysis_mat3') as dn:
ra.plot_arrhenius(os.path.join(dn, "arrhenius_mat2.png"))
ra.monte_carlo()
ra.write_to_file(os.path.join(dn, "reaction_mat2.txt"))
ra.plot_parameters(os.path.join(dn, "parameters_mat2.png"))
def test_load_dump_indices1(self):
subs = range(10)
with tmpdir(__name__, 'test_load_dump_indices1') as dn:
dump_indices(os.path.join(dn, "subs-atoms.1.txt"), subs, shift=0)
dump_indices(os.path.join(dn, "subs-atoms.2.txt"), subs, shift=1)
dump_indices(os.path.join(dn, "subs-atoms.3.txt"), subs)
subs1 = load_indices(os.path.join(dn, "subs-atoms.1.txt"), shift=0)
subs2 = load_indices(os.path.join(dn, "subs-atoms.2.txt"),
shift=-1)
subs22 = load_indices(os.path.join(
dn, "subs-atoms.2.txt")) # should not matter
subs3 = load_indices(os.path.join(dn, "subs-atoms.3.txt"))
blocks = [range(10), range(10, 20)]
dump_indices(os.path.join(dn, "blocks.1.txt"), blocks, shift=0)
dump_indices(os.path.join(dn, "blocks.2.txt"), blocks, shift=1)
dump_indices(os.path.join(dn, "blocks.3.txt"), blocks)
blocks1 = load_indices(os.path.join(dn, "blocks.1.txt"),
shift=0,
groups=True)
blocks2 = load_indices(os.path.join(dn, "blocks.2.txt"),
shift=-1,
groups=True)
blocks22 = load_indices(os.path.join(dn, "blocks.2.txt"),
groups=True) # should not matter
blocks3 = load_indices(os.path.join(dn, "blocks.3.txt"),
groups=True)
self.assertEqual(len(subs), len(subs1))
for (i, j) in zip(subs, subs1):
self.assertEqual(i, j)
self.assertEqual(len(subs), len(subs2))
for i, j in zip(subs, subs2):
self.assertEqual(i, j)
self.assertEqual(len(subs), len(subs22))
for i, j in zip(subs, subs22):
self.assertEqual(i, j)
self.assertEqual(len(subs), len(subs3))
for i, j in zip(subs, subs3):
self.assertEqual(i, j)
self.assertEqual(len(blocks), len(blocks1))
for bl, bl1 in zip(blocks, blocks1):
for i, j in zip(bl, bl1):
self.assertEqual(i, j)
self.assertEqual(len(blocks), len(blocks2))
for bl, bl1 in zip(blocks, blocks2):
for i, j in zip(bl, bl1):
self.assertEqual(i, j)
self.assertEqual(len(blocks), len(blocks22))
for bl, bl1 in zip(blocks, blocks22):
for i, j in zip(bl, bl1):
self.assertEqual(i, j)
self.assertEqual(len(blocks), len(blocks3))
for bl, bl1 in zip(blocks, blocks3):
for i, j in zip(bl, bl1):
self.assertEqual(i, j)
def test_consistency_io():
for fn_parameters in '../../data/test/parameters_bks.txt', '../../data/test/parameters_water.txt':
pf1 = Parameters.from_file(
pkg_resources.resource_filename(__name__, fn_parameters))
with tmpdir(__name__, 'test_consistency_io') as dn:
pf1.write_to_file('%s/parameters_foo.txt' % dn)
pf2 = Parameters.from_file('%s/parameters_foo.txt' % dn)
check_consistent(pf1, pf2)
def test_thermo_analysis_mat(self):
# just a blind test to see test whether the code does not crash.
pf = PartFun(NMA(load_molecule_g03fchk(
pkg_resources.resource_filename("tamkin", "data/test/mat5T/react.fchk"))),
[ExtTrans(), ExtRot(1)])
ta = ThermoAnalysis(pf, [200,300,400,500,600,700,800,900])
with tmpdir(__name__, 'test_thermo_analysis_mat') as dn:
ta.write_to_file(os.path.join(dn, "thermo_mat2.csv"))
def test_thermo_analysis_mat(self):
# just a blind test to see test whether the code does not crash.
pf = PartFun(NMA(load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/mat5T/react.fchk"))),
[ExtTrans(), ExtRot(1)])
ta = ThermoAnalysis(pf, [200,300,400,500,600,700,800,900])
with tmpdir(__name__, 'test_thermo_analysis_mat') as dn:
ta.write_to_file(os.path.join(dn, "thermo_mat2.csv"))
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 test_mtd_alanine():
try:
from plumed import Plumed
except:
from nose.plugins.skip import SkipTest
raise SkipTest(
'Could not import PLUMED, skipping PLUMED related tests')
# MTD settings
sigma = 0.35 * rad
pace = 4
K = 1.2 * kjmol
# Construct metadynamics as a Yaff hook
ff = get_alaninedipeptide_amber99ff()
cv = CVInternalCoordinate(ff.system, DihedAngle(4, 6, 8, 14))
with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5',
driver='core',
backing_store=False) as f:
hdf5 = HDF5Writer(f)
mtd = MTDHook(ff,
cv,
sigma,
K,
f=f,
start=pace,
step=pace,
periodicities=2 * np.pi)
nvt = VerletIntegrator(ff, 1.0 * femtosecond, hooks=[mtd])
vel0 = nvt.vel.copy()
nvt.run(12)
# Check HDF5 output
assert 'hills' in f
assert np.all(f['hills/q0'][:] == mtd.hills.q0s)
assert np.all(f['hills/K'][:] == mtd.hills.Ks)
assert f['hills/sigma'].shape[0] == 1
assert f['hills/sigma'][0] == sigma
# Same simulation using PLUMED
with tmpdir(__name__, 'test_mtd_alanine') as dirname:
# PLUMED input commands
commands = "phi: TORSION ATOMS=5,7,9,15\n"
commands += "metad: METAD ARG=phi PACE=%d HEIGHT=%f SIGMA=%f FILE=%s\n"\
% (pace, K/kjmol, sigma/rad, os.path.join(dirname,'hills'))
commands += "FLUSH STRIDE=1"
# Write PLUMED commands to file
fn = os.path.join(dirname, 'plumed.dat')
with open(fn, 'w') as f:
f.write(commands)
# Setup Plumed
ff = get_alaninedipeptide_amber99ff()
plumed = ForcePartPlumed(ff.system, fn=fn)
ff.add_part(plumed)
nvt = VerletIntegrator(ff,
1.0 * femtosecond,
hooks=[plumed],
vel0=vel0)
nvt.run(12)
hills = np.loadtxt(os.path.join(dirname, 'hills'))
# Compare hill centers
assert np.all(np.abs(hills[:, 1] - mtd.hills.q0s[:, 0]) < 1e-10 * rad)
def test_xyz():
system0 = get_system_water32()
with tmpdir(__name__, 'test_xyz') as dirname:
system0.to_file('%s/tmp.xyz' % dirname)
system1 = System.from_file('%s/tmp.xyz' % dirname,
rvecs=system0.cell.rvecs,
ffatypes=system0.ffatypes,
ffatype_ids=system0.ffatype_ids)
compare_water32(system0, system1, 1e-10, xyz=True)
def test_dump_modes_gaussian(self):
molecule = load_molecule_charmm(
pkg_resources.resource_filename("tamkin", "data/test/an/ethanol.cor"),
pkg_resources.resource_filename("tamkin", "data/test/an/ethanol.hess.full"))
nma = NMA(molecule)
with tmpdir(__name__, 'test_dump_modes_gaussian') as dn:
# blind test, no double checking of the output file
fn_log = os.path.join(dn, 'modes_gaussian.log')
dump_modes_gaussian(fn_log, nma)
def test_dump_modes_gaussian(self):
molecule = load_molecule_charmm(
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.cor"),
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.hess.full"))
nma = NMA(molecule)
with tmpdir(__name__, 'test_dump_modes_gaussian') as dn:
# blind test, no double checking of the output file
fn_log = os.path.join(dn, 'modes_gaussian.log')
dump_modes_gaussian(fn_log, nma)
def test_hdf5():
system0 = get_system_water32()
with tmpdir(__name__, 'test_hdf5') as dirname:
fn = '%s/tmp.h5' % dirname
system0.to_file(fn)
with h5.File(fn) as f:
assert 'system' in f
system1 = System.from_file(fn)
compare_water32(system0, system1)
def test_lammps_system_data_water32():
system = get_system_water32()
with tmpdir(__name__, 'test_lammps_system_water32') as dirname:
fn = os.path.join(dirname, 'lammps.system')
write_lammps_system_data(system, fn=fn)
with open(fn, 'r') as f:
lines = f.readlines()
natom = int(lines[2].split()[0])
assert natom == system.natom
assert (system.natom + system.bonds.shape[0] + 23) == len(lines)
def test_lammps_ffconversion_mil53():
fn_system = pkg_resources.resource_filename(
__name__, '../../data/test/system_mil53.chk')
fn_pars = pkg_resources.resource_filename(
__name__, '../../data/test/parameters_mil53.txt')
system = System.from_file(fn_system)
with tmpdir(__name__, 'test_lammps_ffconversion_mil53') as dirname:
ff2lammps(system, fn_pars, dirname)
# No test for correctness, just check that output files are present
assert os.path.isfile(os.path.join(dirname, 'lammps.in'))
assert os.path.isfile(os.path.join(dirname, 'lammps.data'))
def test_hdf5_assign_ffatypes():
system0 = get_system_water32()
with tmpdir(__name__, 'test_hdf5_assign_ffatypes') as dirname:
system0.ffatypes = ['O', 'H']
system0.ffatype_ids = np.array([0, 1, 1] * 32)
fn = '%s/tmp.h5' % dirname
system0.to_file(fn)
with h5.File(fn) as f:
assert 'system' in f
system1 = System.from_file(fn)
compare_water32(system0, system1)
def test_blav():
# generate a time-correlated random signal
n = 50000
eps0 = 30.0/n
eps1 = 1.0
y = np.sin(np.random.normal(0, eps0, n).cumsum() + np.random.normal(0, eps1, n))
# create a temporary directory to write the plot to
with tmpdir(__name__, 'test_blav') as dn:
fn_png = '%s/blav.png' % dn
error, sinef = blav(y, 100, fn_png)
assert os.path.isfile(fn_png)
def test_reaction_analysis_mat(self):
pf_react = PartFun(NMA(load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/mat5T/react.fchk"))), [])
pf_ts = PartFun(NMA(load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/mat5T/ts.fchk"))), [])
km = KineticModel([pf_react], pf_ts)
ra = ReactionAnalysis(km, 100, 1200, temp_step=50)
# not a very accurate check because the fit is carried out differently
# in the fancy excel file where these numbers come from.
self.assertAlmostEqual(ra.Ea/kjmol, 160.6, 0)
self.assertAlmostEqual(km.unit, 1.0/second)
self.assertEqual(km.unit_name, "s^-1")
self.assertAlmostEqual(np.log(ra.A/km.unit), np.log(3.33e10), 0)
with tmpdir(__name__, 'test_reaction_analysis_mat1') as dn:
ra.plot_arrhenius(os.path.join(dn, "arrhenius_mat1.png"))
ra.monte_carlo()
ra.write_to_file(os.path.join(dn, "reaction_mat1.txt"))
ra.plot_parameters(os.path.join(dn, "parameters_mat1.png"))
wigner = Wigner(pf_ts) # Blind test of the wigner correction and
# the corrected reaction analysis.
km = KineticModel([pf_react], pf_ts, tunneling=wigner)
ra = ReactionAnalysis(km, 100, 1200, temp_step=50)
with tmpdir(__name__, 'test_reaction_analysis_mat2') as dn:
ra.plot_arrhenius(os.path.join(dn, "arrhenius_mat1w.png"))
ra.monte_carlo()
ra.write_to_file(os.path.join(dn, "reaction_mat1w.txt"))
ra.plot_parameters(os.path.join(dn, "parameters_mat1w.png"))
km = KineticModel([pf_react], pf_ts)
ra = ReactionAnalysis(km, 670, 770)
# not a very accurate check because the fit is carried out differently
# in the fancy excel file where these numbers come from.
self.assertAlmostEqual(ra.Ea/kjmol, 161.9, 1)
self.assertAlmostEqual(np.log(ra.A/km.unit), np.log(4.08e10), 0)
with tmpdir(__name__, 'test_reaction_analysis_mat3') as dn:
ra.plot_arrhenius(os.path.join(dn, "arrhenius_mat2.png"))
ra.monte_carlo()
ra.write_to_file(os.path.join(dn, "reaction_mat2.txt"))
ra.plot_parameters(os.path.join(dn, "parameters_mat2.png"))
def run_opt_water32(suffix, prefix):
# Work in a temporary directory
with tmpdir(suffix, prefix) as dn_tmp:
# Setup a test FF
ff = get_ff_water32()
# Run a test simulation
with h5.File('%s/output.h5' % dn_tmp) as f:
hdf5 = HDF5Writer(f)
opt = CGOptimizer(FullCellDOF(ff), hooks=hdf5)
opt.run(5)
assert opt.counter == 5
yield dn_tmp, opt, f
def run_opt_water32(suffix, prefix):
# Work in a temporary directory
with tmpdir(suffix, prefix) as dn_tmp:
# Setup a test FF
ff = get_ff_water32()
# Run a test simulation
with h5.File('%s/output.h5' % dn_tmp) as f:
hdf5 = HDF5Writer(f)
opt = CGOptimizer(FullCellDOF(ff), hooks=hdf5)
opt.run(5)
assert opt.counter == 5
yield dn_tmp, opt, f
def run_nve_water32(suffix, prefix):
# Work in a temporary directory
with tmpdir(suffix, prefix) as dn_tmp:
# Setup a test FF
ff = get_ff_water32()
# Run a test simulation
with h5.File('%s/output.h5' % dn_tmp) as f:
hdf5 = HDF5Writer(f)
nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5)
nve.run(5)
assert nve.counter == 5
yield dn_tmp, nve, f
def test_timer(self):
timer = Timer()
timer.sample("start")
for i in range(100000):
j = i**2
timer.sample("done")
self.assertEqual(timer.labels[0], "start")
self.assertEqual(timer.labels[1], "done")
#timer.dump() # to write logfile to screen
# just testing whether writing to file works
with tmpdir(__name__, 'test_timer') as dn:
timer.write_to_file(os.path.join(dn, "logfile-timings.txt"))
def test_xyz_select():
with tmpdir(__name__, 'test_xyz_select') as dn:
fn_xyz = os.path.join(dn, 'foobar.xyz')
xyz = XYZWriter(fn_xyz, select=[0,1,2])
nve = VerletIntegrator(get_ff_water32(), 1.0*femtosecond, hooks=[xyz])
nve.run(15)
assert os.path.isfile(fn_xyz)
assert nve.counter == 15
## Ugly hack to make tests pass on Windows. The root cause is that the SliceReader
## in molmod.io.common is poorly written.
xyz.xyz_writer._auto_close = False
xyz.xyz_writer._f.close()
def test_blav():
# generate a time-correlated random signal
n = 50000
eps0 = 30.0 / n
eps1 = 1.0
y = np.sin(
np.random.normal(0, eps0, n).cumsum() + np.random.normal(0, eps1, n))
# create a temporary directory to write the plot to
with tmpdir(__name__, 'test_blav') as dn:
fn_png = '%s/blav.png' % dn
error, sinef = blav(y, 100, fn_png)
assert os.path.isfile(fn_png)
def test_mbh(self):
molecule = load_molecule_charmm(
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.cor"),
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.hess.full"))
blocks = load_indices(
pkg_resources.resource_filename(__name__, "../data/test/an/fixed.07.txt"),
groups=True)
nma = NMA(molecule, MBH(blocks))
self.check_ortho(nma.modes)
with tmpdir(__name__, 'test_mbh') as dn:
dump_modes_molden(os.path.join(dn, "ethanol.mbh.molden.log"), nma)
self.check_ortho(nma.modes) # write_molden should not have changed this
def test_timer(self):
timer = Timer()
timer.sample("start")
for i in range(100000):
j = i**2
timer.sample("done")
self.assertEqual(timer.labels[0], "start")
self.assertEqual(timer.labels[1], "done")
#timer.dump() # to write logfile to screen
# just testing whether writing to file works
with tmpdir(__name__, 'test_timer') as dn:
timer.write_to_file(os.path.join(dn, "logfile-timings.txt"))
def test_constrain1(self):
molecule = load_molecule_charmm(
pkg_resources.resource_filename("tamkin", "data/test/an/ethanol.cor"),
pkg_resources.resource_filename("tamkin", "data/test/an/ethanol.hess.full"))
fixed = [[1,2]]
nma = NMA(molecule, Constrain(fixed))
#print nma.freqs/lightspeed*centimeter
self.check_ortho(nma.modes)
self.assertEqual(nma.modes.shape[0],27)
self.assertEqual(nma.modes.shape[1],26)
with tmpdir(__name__, 'test_constrain1') as dn:
dump_modes_molden(os.path.join(dn, "ethanol.constr.molden.log"), nma)
def test_constrain2(self):
molecule = load_molecule_charmm(
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.cor"),
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.hess.full"))
fixed = [[1,2], [0,4], [0,5],[2,8],[3,4],[4,5],[5,6],[6,7],[7,8],[7,1],[7,3]]
nma = NMA(molecule, Constrain(fixed))
#print nma.freqs/lightspeed*centimeter
self.check_ortho(nma.modes)
self.assertEqual(nma.modes.shape[0],27)
self.assertEqual(nma.modes.shape[1],16)
with tmpdir(__name__, 'test_constrain2') as dn:
dump_modes_molden(os.path.join(dn, "ethanol.constr.molden.log"), nma)
def run_nve_water32(suffix, prefix):
# Work in a temporary directory
with tmpdir(suffix, prefix) as dn_tmp:
# Setup a test FF
ff = get_ff_water32()
# Run a test simulation
with h5.File('%s/output.h5' % dn_tmp) as f:
hdf5 = HDF5Writer(f)
nve = VerletIntegrator(ff, 1.0 * femtosecond, hooks=hdf5)
nve.run(5)
assert nve.counter == 5
yield dn_tmp, nve, f
def run_nvt_water32(suffix, prefix):
# Work in a temporary directory
with tmpdir(suffix, prefix) as dn_tmp:
# Setup a test FF
ff = get_ff_water32()
# Run a test simulation
with h5.File('%s/output.h5' % dn_tmp) as f:
hdf5 = HDF5Writer(f)
thermostat = LangevinThermostat(temp=300)
nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[hdf5, thermostat])
nvt.run(5)
assert nvt.counter == 5
yield dn_tmp, nvt, f
def test_load_dump_indices1(self):
subs = range(10)
with tmpdir(__name__, 'test_load_dump_indices1') as dn:
dump_indices(os.path.join(dn, "subs-atoms.1.txt"), subs, shift=0)
dump_indices(os.path.join(dn, "subs-atoms.2.txt"), subs, shift=1)
dump_indices(os.path.join(dn, "subs-atoms.3.txt"), subs)
subs1 = load_indices(os.path.join(dn, "subs-atoms.1.txt"), shift=0)
subs2 = load_indices(os.path.join(dn, "subs-atoms.2.txt"), shift=-1)
subs22 = load_indices(os.path.join(dn, "subs-atoms.2.txt")) # should not matter
subs3 = load_indices(os.path.join(dn, "subs-atoms.3.txt"))
blocks = [range(10), range(10,20)]
dump_indices(os.path.join(dn, "blocks.1.txt"), blocks, shift=0)
dump_indices(os.path.join(dn, "blocks.2.txt"), blocks, shift=1)
dump_indices(os.path.join(dn, "blocks.3.txt"), blocks)
blocks1 = load_indices(os.path.join(dn, "blocks.1.txt"), shift=0, groups=True)
blocks2 = load_indices(os.path.join(dn, "blocks.2.txt"), shift=-1, groups=True)
blocks22 = load_indices(os.path.join(dn, "blocks.2.txt"), groups=True) # should not matter
blocks3 = load_indices(os.path.join(dn, "blocks.3.txt"), groups=True)
self.assertEqual(len(subs),len(subs1))
for (i,j) in zip(subs,subs1):
self.assertEqual(i,j)
self.assertEqual(len(subs),len(subs2))
for i,j in zip(subs,subs2):
self.assertEqual(i,j)
self.assertEqual(len(subs),len(subs22))
for i,j in zip(subs,subs22):
self.assertEqual(i,j)
self.assertEqual(len(subs),len(subs3))
for i,j in zip(subs,subs3):
self.assertEqual(i,j)
self.assertEqual(len(blocks),len(blocks1))
for bl,bl1 in zip(blocks,blocks1):
for i,j in zip(bl,bl1):
self.assertEqual(i,j)
self.assertEqual(len(blocks),len(blocks2))
for bl,bl1 in zip(blocks,blocks2):
for i,j in zip(bl,bl1):
self.assertEqual(i,j)
self.assertEqual(len(blocks),len(blocks22))
for bl,bl1 in zip(blocks,blocks22):
for i,j in zip(bl,bl1):
self.assertEqual(i,j)
self.assertEqual(len(blocks),len(blocks3))
for bl,bl1 in zip(blocks,blocks3):
for i,j in zip(bl,bl1):
self.assertEqual(i,j)
def test_pcm_correction(self):
mol = load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/sterck/aa_1h2o_a.fchk"))
pf0 = PartFun(NMA(mol), [])
pf1 = PartFun(NMA(mol), [PCMCorrection((-5*kjmol,300))])
pf2 = PartFun(NMA(mol), [PCMCorrection((-5*kjmol,300), (-10*kjmol,600))])
# real tests
self.assertAlmostEqual(pf0.free_energy(300)-5*kjmol, pf1.free_energy(300))
self.assertAlmostEqual(pf0.free_energy(300)-5*kjmol, pf2.free_energy(300))
self.assertAlmostEqual(pf0.free_energy(600)-5*kjmol, pf1.free_energy(600))
self.assertAlmostEqual(pf0.free_energy(600)-10*kjmol, pf2.free_energy(600))
# blind tests
pf2.heat_capacity(300)
with tmpdir(__name__, 'test_pcm_correction') as dn:
pf1.write_to_file(os.path.join(dn, "pcm_partf1.txt"))
pf2.write_to_file(os.path.join(dn, "pcm_partf2.txt"))
def test_flat(self):
a = 10.0
mass = 1.0
hb = HarmonicBasis(10, a)
energies, orbitals = hb.solve(mass, np.zeros(hb.size), evecs=True)
import matplotlib.pyplot as pt
x = np.arange(0.0, a, 0.001)
pt.clf()
for i in xrange(10):
f = hb.eval_fn(x, orbitals[:,i])
pt.plot(x, f+i)
with tmpdir(__name__, 'test_flat') as dn:
pt.savefig(os.path.join(dn, "flat_wavefunctions.png"))
indexes = np.array([0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10])
expected = 0.5/mass*(2*indexes*np.pi/a)**2
self.assertArraysAlmostEqual(energies, expected, 1e-4)
def test_ethyl_free(self):
molecule = load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/ethyl/gaussian.fchk"))
nma = NMA(molecule)
dihedral = [5, 1, 0, 2]
rot_scan = RotScan(dihedral, molecule)
rotor = Rotor(rot_scan, molecule, rotsym=6, even=True)
self.assertAlmostEqual(rotor.cancel_freq/lightspeed*centimeter, 141.2, 0)
pf = PartFun(nma, [ExtTrans(), ExtRot(1), rotor])
# reference data from legacy code (Veronique & co)
self.assertAlmostEqual(rotor.reduced_moment/amu, 4.007, 1)
self.assertAlmostEqual(np.exp(rotor.log_terms(100.0)[1]), 0.6386, 1)
self.assertAlmostEqual(np.exp(-rotor.log_terms(100.0)[0]), 0.4168, 1)
self.assertAlmostEqual(np.exp(rotor.log_terms(800.0)[1]), 1.8062, 1)
self.assertAlmostEqual(np.exp(-rotor.log_terms(800.0)[0]), 3.9273, 1)
with tmpdir(__name__, 'test_ethyl_free') as dn:
rotor.plot_levels(os.path.join(dn, "ethyl_free_levels.png"), 300)
pf.write_to_file(os.path.join(dn, "ethyl_free.txt"))
ta = ThermoAnalysis(pf, [200,300,400,500,600,700,800,900])
ta.write_to_file(os.path.join(dn, "ethyl_free_thermo.csv"))
def test_molecule_checkpoint_basic():
mol1 = load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/sterck/aa.fchk"))
with tmpdir(__name__, 'test_molecule_checkpoint_basic') as dn:
fn_out = os.path.join(dn, "molecule_checkpoint_basic.chk")
mol1.write_to_file(fn_out)
mol2 = Molecule.read_from_file(fn_out)
assert mol1.numbers.shape == mol2.numbers.shape
assert abs(mol1.numbers - mol2.numbers).max() == 0
assert mol1.coordinates.shape == mol2.coordinates.shape
assert abs(mol1.coordinates - mol2.coordinates).max() < 1e-10
assert mol1.masses.shape == mol2.masses.shape
assert abs(mol1.masses - mol2.masses).max() < 1e-10
assert abs(mol1.energy - mol2.energy) < 1e-5
assert mol1.gradient.shape == mol2.gradient.shape
assert abs(mol1.gradient - mol2.gradient).max() < 1e-10
assert mol1.hessian.shape == mol2.hessian.shape
assert abs(mol1.hessian - mol2.hessian).max() < 1e-10
assert mol1.multiplicity == mol2.multiplicity
assert mol1.symmetry_number == mol2.symmetry_number
assert mol1.periodic == mol2.periodic
def test_fit_fn_sym(self):
a = 9.0
hb = HarmonicBasis(90, a)
grid = np.arange(0.0, 1.501, 0.1)
f = np.exp(-(grid/2)**2)
f -= f.mean()
coeffs = hb.fit_fn(grid, f, 30, rotsym=3, even=True)
g = hb.eval_fn(grid, coeffs)
self.assertArraysAlmostEqual(f, g)
grid = np.arange(0.0, 9.001, 0.1)
g = hb.eval_fn(grid, coeffs)
self.assertArraysAlmostEqual(f, g[0:16])
self.assertArraysAlmostEqual(f, g[30:46])
self.assertArraysAlmostEqual(f, g[60:76])
self.assertArraysAlmostEqual(f[::-1], g[15:31])
self.assertArraysAlmostEqual(f[::-1], g[45:61])
self.assertArraysAlmostEqual(f[::-1], g[75:91])
import matplotlib.pyplot as pt
pt.clf()
pt.plot(grid, g, "k-", lw=2)
pt.plot(grid[:16], f, "rx", mew=2)
with tmpdir(__name__, 'test_fit_fn_sym') as dn:
pt.savefig(os.path.join(dn, "test_fit_fn_sym.png"))
def test_load_dump_indices2(self):
randint = np.random.randint
for counter in xrange(20):
for compact in True, False:
shift = randint(-5,5)
indices = []
for i in xrange(randint(10,20)):
l = list(set(randint(0,10,randint(20))))
if len(l) > 0:
indices.append(l)
indices_flat = sum(indices, [])
with tmpdir(__name__, '{}_{}'.format('test_load_dump_indices2', counter)) as dn:
dump_indices(os.path.join(dn, "indices_blocks.txt"), indices, compact=compact, shift=shift)
dump_indices(os.path.join(dn, "indices_flat.txt"), indices_flat, compact=compact, shift=shift)
check = load_indices(os.path.join(dn, "indices_blocks.txt"), shift=-shift, groups=True)
self.assertEqual(indices, check)
check = load_indices(os.path.join(dn, "indices_blocks.txt"), shift=-shift)
self.assertEqual(indices_flat, check)
check = load_indices(os.path.join(dn, "indices_flat.txt"), shift=-shift, groups=True)
self.assertEqual([indices_flat], check)
check = load_indices(os.path.join(dn, "indices_flat.txt"), shift=-shift)
self.assertEqual(indices_flat, check)
def test_dump_modes_xyz(self):
molecule = load_molecule_charmm(
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.cor"),
pkg_resources.resource_filename(__name__, "../data/test/an/ethanol.hess.full"))
nma = NMA(molecule)
with tmpdir(__name__, 'test_dump_modes_xyz') as dn:
prefix = os.path.join(dn, 'mode')
dump_modes_xyz(nma, 6, prefix=prefix, amplitude=50.0)
with open(prefix + ".6.xyz") as f:
# 1st line
line = f.readline().strip()
self.assertEqual(line,"9")
# 2nd line
line = f.readline().strip()
self.assertEqual(line,"frame 0")
# 3rd line
line = f.readline()
words = line.split()
self.assertEqual(len(words),4)
self.assertEqual(words[0],"C")
self.assertEqual(words[2],"0.081608346")
for i in range(9):
line = f.readline().strip()
self.assertEqual(line,"9")