def test_VCI4(inpdata):
if inpdata is None:
return 'VCI quadruples'
VSCF = vib.VSCF2D(inpdata.v1, inpdata.v2)
VSCF.solve_singles()
VCI = vib.VCI(VSCF.get_groundstate_wfn(), inpdata.v1, inpdata.v2)
VCI.generate_states(4)
VCI.solve()
d = np.abs(VCI.energies - inpdata.vci4).mean()
return d < 1
def test_VCI4_int(inpdata):
if inpdata is None:
return 'VCI quadruples intensities'
VSCF = vib.VSCF2D(inpdata.v1, inpdata.v2)
VSCF.solve_singles()
VCI = vib.VCI(VSCF.get_groundstate_wfn(), inpdata.v1, inpdata.v2)
VCI.generate_states(4)
VCI.solve()
VCI.calculate_intensities(inpdata.dm1, inpdata.dm2)
d = np.abs(VCI.intensities - inpdata.vci4_int).mean()
return d < 1
def test_VSCF_singles(inpdata):
if inpdata is None:
return 'VSCF gs + singles'
VSCF = vib.VSCF2D(inpdata.v1, inpdata.v2)
VSCF.solve_singles()
# diffrerence between the reference VSCF energies (ground state and singles)
# and currect energies
d = np.abs(np.array(VSCF.energies) - inpdata.vscf_singles_energies).mean()
# test passed if the mean absolute error is below 1cm-1
return d < 1
def test_diagonal_VSCF(inpdata):
if inpdata is None:
return 'Diagonal VSCF'
dVSCF = vib.VSCFDiag(inpdata.v1)
dVSCF.solve()
dVSCF.print_results()
# difference between the reference and current eigenvalues
d = (np.abs(dVSCF.eigv - inpdata.diagonal_eigv)).mean()
# test passed if the mean absolute error is below 1e-6 a.u.
return d < 1e-6
def test_diagonal_VSCF_harmonic(inpdata):
if inpdata is None:
return 'Diagonal VSCF with harmonic potential'
dVSCF = vib.VSCFDiag(inpdata.v1_harm)
dVSCF.solve()
dVSCF.print_results()
results = np.zeros(dVSCF.nmodes)
for i in range(dVSCF.nmodes):
results[i] = (dVSCF.eigv[i][1] - dVSCF.eigv[i][0]) / vib.Misc.cm_in_au
d = np.abs(results - inpdata.freqs).mean()
return d < 1
import os
res = VibTools.SNFResults(outname='snf_h2o/snf.out',
restartname='snf_h2o/restart',
coordfile='snf_h2o/coord')
res.read()
# use the normal modes in the following (no localization)
modes = res.modes
# Define the grid
ngrid = 16
amp = 14
grid = vib.Grid(res.mol, modes)
grid.generate_grids(ngrid, amp)
# Read in anharmonic 1-mode potentials
v1 = vib.Potential(grid, order=1)
v1.read_np(os.path.join('potentials', 'V1_g16.npy'))
# Read in anharmonic 1-mode dipole moments
dm1 = vib.Dipole(grid)
dm1.read_np(os.path.join('potentials', 'Dm1_g16.npy'))
# Read in anharmonic 2-mode potentials
v2 = vib.Potential(grid, order=2)
import Vibrations as vib
print vib.Misc.fancy_box('Example 1:')
print 'Use of existing grids and potentials.'
print
print ' Data taken from: http://pes-database.theochem.uni-stuttgart.de/surfaces/index.php'
print ' By Guntram Rauhut and co-workers'
# Create an empty grid
grid = vib.Grid()
# Read in an existing grid
grid.read_np('grids.npy')
# Create 1-mode potentials
v1 = vib.Potential(grid, order=1)
# Read in 1-mode potentials
v1.read_np('1D.npy')
v2 = vib.Potential(grid, order=2)
v2.read_np('2D.npy')
# Perform VSCF with 2-mode potentials
VSCF = vib.VSCF2D(v1, v2)
VSCF.solve_singles()
# VCI part
# Initialize a VCI object with the VSCF groundstate wavefunction and the
# potentials
VCI = vib.VCI(VSCF.get_groundstate_wfn(), v1, v2)
def __init__(self, dirname):
f = open(dirname + '/grid_params')
lines = f.readlines()
f.close()
whichmodes = None
localized = None
if os.path.isfile(dirname + '/whichmodes'):
whichmodes = []
f = open(dirname + '/whichmodes')
lines2 = f.readlines()
f.close
for l in lines2:
for el in l.split():
whichmodes.append(int(el))
grid_params = lines[0].split()
self.ngrid = int(grid_params[0])
self.amp = int(grid_params[1])
res = VibTools.SNFResults(outname=dirname + '/snf.out',
restartname=dirname + '/restart',
coordfile=dirname + '/coord')
res.read()
self.freqs = res.modes.freqs
self.ints = res.get_ir_intensity()
modes = res.modes
if whichmodes is not None:
self.freqs = res.modes.freqs[whichmodes]
self.ints = res.get_ir_intensity(
modes=res.modes.get_subset(whichmodes))
modes = res.modes.get_subset(whichmodes)
self.grid = vib.Grid(res.mol, modes)
self.grid.generate_grids(self.ngrid, self.amp)
self.v1 = vib.Potential(self.grid, 1)
self.v1.read_np(dirname + '/v1.npy')
self.v1_harm = vib.Potential(self.grid, 1)
self.v1_harm.generate_harmonic()
self.dm1_harm = vib.Dipole(self.grid, 1)
self.dm1_harm.generate_harmonic(res)
self.v2 = vib.Potential(self.grid, 2)
self.v2.read_np(dirname + '/v2.npy')
self.dm1 = vib.Dipole(self.grid, 1)
self.dm1.read_np(dirname + '/dm1.npy')
self.dm2 = vib.Dipole(self.grid, 2)
self.dm2.read_np(dirname + '/dm2.npy')
self.diagonal_eigv = np.load(dirname + '/diagonal_eigv.npy')
self.vscf_singles_energies = np.load(dirname + '/vscf_singles.npy')
self.vci1 = np.load(dirname + '/vci1.npy')
self.vci2 = np.load(dirname + '/vci2.npy')
self.vci3 = np.load(dirname + '/vci3.npy')
self.vci4 = np.load(dirname + '/vci4.npy')
self.vci1_int = np.load(dirname + '/vci1_int.npy')
import os
res = VibTools.SNFResults(outname='snf_h2o/snf.out',
restartname='snf_h2o/restart',
coordfile='snf_h2o/coord')
res.read()
# use the normal modes in the following (no localization)
modes = res.modes
# Define the grid
ngrid = 16
amp = 14
grid = vib.Grid(res.mol, modes)
grid.generate_grids(ngrid, amp)
dir_grid = 'grid'
if not os.path.exists(dir_grid):
os.makedirs(dir_grid)
# write xyz file for equilibrium structure
res.mol.write(os.path.join(dir_grid, 'grid_E0.dat'))
# generate xyz-files for 1-Mode Potentials
for i in range(modes.nmodes):
for j in range(ngrid):
print ' *** Writing Mode: ', i, ', Point: ', j