def main():
'''Main driver routine.'''
# coordinates of H2O, in atomic units
coords = np.array([
[0.000000000000000E+00, -0.188972598857892E+01, 0.000000000000000E+00],
[0.000000000000000E+00, 0.000000000000000E+00, 0.147977639152057E+01],
[0.000000000000000E+00, 0.000000000000000E+00, -0.147977639152057E+01]
])
# the values of extpot and extpotgrad used here were
# taken from file: test/api/mm/testers/test_extpot.f90
extpot = np.array(
[-0.025850198503435, -0.005996294763958, -0.022919371690684])
extpotgrad = np.array(
[[0.035702717378527, 0.011677956375860, 0.009766745155626],
[0.023243271928971, -0.000046945156575, 0.004850533043745],
[0.016384005706180, 0.004608295375551, 0.005401080774962]])
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.hsd',
logfile='log.log')
# set geometry
cdftb.set_geometry(coords, latvecs=None)
# set external potential and its gradients
cdftb.set_external_potential(extpot, extpotgrad=extpotgrad)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, forces and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschgs = cdftb.get_gross_charges()
# finalize DFTB+ and clean up
cdftb.close()
# print obtained nr. of atoms
print('(H2O) Obtained nr. of atoms: {:d}'.format(natoms))
# print obtained mermin free energy
print('(H2O) Obtained Mermin-energy: {:15.10f}'.format(merminen))
# print obtained gradients
print('(H2O) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[0]))
print('(H2O) Obtained gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[1]))
print('(H2O) Obtained gradient of atom 3: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[2]))
# print obtained Gross charges
print(
'(H2O) Obtained Gross charges: {:15.10f} {:15.10f}'.format(*grosschgs))
def main():
'''Main driver routine.'''
# coordinates of H2O, in atomic units
qmcoords = np.array(
[[0.0000000000000000, -1.8897259885789233, 0.0000000000000000],
[0.0000000000000000, 0.0000000000000000, 1.4797763915205659],
[0.0000000000000000, 0.0000000000000000, -1.4797763915205659]])
# coordinates of MM-charges, in atomic units
mmcoords = np.array(
[[-0.944863438887178, -9.44863438887178, 1.70075418999692],
[4.34637181888102, -5.85815332110050, 2.64561762888410]])
# MM-charges, in atomic units
mmcharges = np.array([2.5, -1.9])
potcalc = PotentialCalculator(qmcoords, mmcoords, mmcharges)
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.hsd',
logfile='log.log')
# set geometry
cdftb.set_geometry(qmcoords, latvecs=None)
cdftb.register_ext_pot_generator(potcalc, get_extpot, get_extpotgrad)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, forces and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschgs = cdftb.get_gross_charges()
# finalize DFTB+ and clean up
cdftb.close()
# print obtained nr. of atoms
print('(H2O) Obtained nr. of atoms: {:d}'.format(natoms))
# print obtained mermin free energy
print('(H2O) Obtained Mermin-energy: {:15.10f}'.format(merminen))
# print obtained gradients
print('(H2O) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[0]))
print('(H2O) Obtained gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[1]))
print('(H2O) Obtained gradient of atom 3: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[2]))
# print obtained Gross charges
print(
'(H2O) Obtained Gross charges: {:15.10f} {:15.10f}'.format(*grosschgs))
def main():
'''Main driver routine.'''
# coordinates of TiO2, in atomic units
coords = np.array([
[-0.016726922839251, 0.016725329441158, -0.000003204152532],
[-0.016726505918979, 1.920201169305565, -7.297102897292027],
[ 0.017412997824265, -0.024318617967798, 2.005339137853385],
[ 1.920770753428742, -0.024319922392223, -4.437737763954652],
[ 0.024319174400169, -0.017404302527510, -2.005347277168561],
[ 0.024317270342179, 1.886164739806594, -5.291732430733527]])
coords *= AA__BOHR
# lattice vectors of TiO2, in atomic units
latvecs = np.array([
[-1.903471721000000, 1.903471721000000, 4.864738245000000],
[ 1.903471721000000, -1.903471721000000, 4.864738245000000],
[ 1.903471721000000, 1.903471721000000, -4.864738245000000]])
latvecs *= AA__BOHR
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.hsd',
logfile='TiO2.log')
# set geometry
cdftb.set_geometry(coords, latvecs=latvecs)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, gradients and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschgs = cdftb.get_gross_charges()
# finalize DFTB+ and clean up
cdftb.close()
# print obtained nr. of atoms
print('(TiO2) Obtained nr. of atoms: {:d}'.format(natoms))
# print obtained mermin free energy
print('(TiO2) Obtained Mermin-energy: {:15.10f}'.format(merminen))
# print obtained gradients
print('(TiO2) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[0]))
# print obtained Gross charges
print('''(TiO2) Obtained Gross charges: {:15.10f} {:15.10f}
{:15.10f} {:15.10f} {:15.10f} {:15.10f}'''.format(*grosschgs))
def main():
'''Main driver routine.'''
# coordinates of H2O, in atomic units
coords = np.array([
[0.000000000000000E+00, -0.188972598857892E+01, 0.000000000000000E+00],
[0.000000000000000E+00, 0.000000000000000E+00, 0.147977639152057E+01],
[0.000000000000000E+00, 0.000000000000000E+00, -0.147977639152057E+01]
])
# the values of extpot and extpotgrad used here were
# taken from file: test/api/mm/testers/test_extpot.f90
extpot = np.array(
[-0.025850198503435, -0.005996294763958, -0.022919371690684])
extpotgrad = np.array(
[[0.035702717378527, 0.011677956375860, 0.009766745155626],
[0.023243271928971, -0.000046945156575, 0.004850533043745],
[0.016384005706180, 0.004608295375551, 0.005401080774962]])
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.hsd',
logfile='log.log')
# set geometry
cdftb.set_geometry(coords, latvecs=None)
# set external potential and its gradients
cdftb.set_external_potential(extpot, extpotgrad=extpotgrad)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, forces and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschg = cdftb.get_gross_charges()
dipole_mu = np.zeros(3)
#zstar = np.zeros((3, natoms, 3))
#qdot = np.zeros((3, natoms))
for icart in range(3):
energyRaw = np.zeros(2)
#gradientsRaw = np.zeros((2, natoms, 3))
#grosschgsRaw = np.zeros((2, natoms))
for istep in range(2):
efield = np.zeros(3)
delta_field = float(2 * istep - 1) * DELTA
efield[icart] = delta_field
extpot = np.dot(efield, coords.T)
extpotgrad = np.zeros((natoms, 3))
extpotgrad[:, icart] = delta_field
# set external potential
cdftb.set_external_potential(extpot, extpotgrad=extpotgrad)
# calculate energy, forces and gross (Mulliken) charges
energyRaw[istep] = cdftb.get_energy()
#gradientsRaw[istep] = cdftb.get_gradients()
#grosschgsRaw[istep] = cdftb.get_gross_charges()
dipole_mu[icart] = (energyRaw[0] - energyRaw[1]) / (2.0 * DELTA)
#zstar[icart] = (gradientsRaw[0] - gradientsRaw[1]) / (2.0 * DELTA)
#qdot[icart] = (grosschgsRaw[0] - grosschgsRaw[1]) / (2.0 * DELTA)
# finalize DFTB+ and clean up
cdftb.close()
# check whether calculator was initialized with correct nr. of atoms
print('(H2O) Obtained nr. of atoms: {:d}'.format(natoms))
print('(H2O) Expected nr. of atoms: {:d}\n'.format(NATOM0))
# evaluate mermin free energy
print('(H2O) Obtained Mermin-energy: {:15.10f}'.format(merminen))
print('(H2O) Expected Mermin-energy: {:15.10f}\n'.format(-3.9854803392))
# evaluate gradients
print('(H2O) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[0]))
print('(H2O) Expected gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'.
format(0.0176513638, -0.1831376018, 0.0031982515))
print('(H2O) Obtained gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[1]))
print('(H2O) Expected gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'.
format(-0.0061402266, 0.0955090293, 0.0394035230))
print('(H2O) Obtained gradient of atom 3: {:15.10f} {:15.10f} {:15.10f}'.
format(*gradients[2]))
print('(H2O) Expected gradient of atom 3: {:15.10f} {:15.10f} {:15.10f}\n'.
format(-0.0037720260, 0.0923535862, -0.0402979580))
# evaluate Gross charges
print(
'(H2O) Obtained Gross charges: {:15.10f} {:15.10f}'.format(*grosschg))
print('(H2O) Expected Gross charges: {:15.10f} {:15.10f}'.format(
-0.4943983279, 0.2641722128))
# evaluated dipole moment
print('(H2O) Obtained num. dipole moment: {:15.10f} {:15.10f} {:15.10f}'.
format(*dipole_mu))
print('(H2O) Expected dipole moment: {:15.10f} {:15.10f} {:15.10f}'.format(
0.0, 0.8759859216, 0.0))
#print('Born charges')
#for iat in range(natoms):
# print("atom %i" % (iat+1))
# for icart in range(3):
# print(zstar[icart][iat][:])
#print('Atom polarisability', qdot.T)
# --------------------------WRITE AUTOTEST.TAG------------------------------
# write autotest.tag file of water molecule calculation
write_autotest_tag('autotest.tag',
freeEgy=merminen,
forceTot=-gradients,
qOutAtGross=grosschg,
mu=dipole_mu)
def main():
'''Main driver routine.'''
# initial coordinates of Si2, in atomic units
initialcoords = np.array([
[0.0000000000000000, 0.0000000000000000, 0.0000000000000000],
[2.5639291987021915, 2.5639291987021915, 2.5639291987021915]])
# small displacement in the coordinates
coords = np.copy(initialcoords)
coords[0, 0] = initialcoords[0, 0] + 0.2 * AA__BOHR
# initial lattice vectors of Si2, in atomic units
initiallatvecs = np.array([
[5.1278583974043830, 5.1278583974043830, 0.0000000000000000],
[0.0000000000000000, 5.1278583974043830, 5.1278583974043830],
[5.1278583974043830, 0.0000000000000000, 5.1278583974043830]])
# small displacement in the lattice vectors
latvecs = np.copy(initiallatvecs)
latvecs[0, 0] = initiallatvecs[0, 0] + 0.1 * AA__BOHR
# ------------------CALCULATION OF INITIAL GEOMETRY-------------------------
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.hsd',
logfile='log.log')
# set initial geometry
cdftb.set_geometry(initialcoords, latvecs=initiallatvecs)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, forces and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschg = cdftb.get_gross_charges()
# check whether calculator was initialized with correct nr. of atoms
print('(Si2) Obtained nr. of atoms: {:d}'.format(natoms))
print('(Si2) Expected nr. of atoms: {:d}\n'.format(NATOM0))
# evaluate mermin free energy
print('(Si2) Obtained Mermin-energy: {:15.10f}'.format(merminen))
print('(Si2) Expected Mermin-energy: {:15.10f}\n'.format(-2.5933460731))
# evaluate gradients
print('(Si2) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[0]))
print('(Si2) Expected gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
.format(-0.0103215090, -0.0103215090, -0.0103215090))
print('(Si2) Obtained gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[1]))
print('(Si2) Expected gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}\n'
.format(0.0103215090, 0.0103215090, 0.0103215090))
# evaluate Gross charges
print('(Si2) Obtained Gross charges: {:15.10f} {:15.10f}'
.format(*grosschg))
print('(Si2) Expected Gross charges: {:15.10f} {:15.10f}\n\n'
.format(0.0, 0.0))
# ------------------CALCULATION OF DISPLACED GEOMETRY-----------------------
# set displaced geometry
cdftb.set_geometry(coords, latvecs=latvecs)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, forces and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschg = cdftb.get_gross_charges()
# check whether calculator was initialized with correct nr. of atoms
print('(Si2) Obtained nr. of atoms: {:d}'.format(natoms))
print('(Si2) Expected nr. of atoms: {:d}\n'.format(NATOM0))
# evaluate mermin free energy
print('(Si2) Obtained Mermin-energy: {:15.10f}'.format(merminen))
print('(Si2) Expected Mermin-energy: {:15.10f}\n'.format(-2.5854559427))
# evaluate gradients
print('(Si2) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[0]))
print('(Si2) Expected gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
.format(0.0442660049, -0.0147463633, -0.0193148538))
print('(Si2) Obtained gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[1]))
print('(Si2) Expected gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}\n'
.format(-0.0442660049, 0.0147463633, 0.0193148538))
# evaluate Gross charges
print('(Si2) Obtained Gross charges: {:15.10f} {:15.10f}'
.format(*grosschg))
print('(Si2) Expected Gross charges: {:15.10f} {:15.10f}'
.format(0.0, 0.0))
# finalize DFTB+ and clean up
cdftb.close()
# --------------------------WRITE AUTOTEST.TAG------------------------------
# write autotest.tag file of water molecule calculation
write_autotest_tag('autotest.tag', freeEgy=merminen,
forceTot=-gradients, qOutAtGross=grosschg)
def main():
'''Main driver routine.'''
# coordinates of Si2, in atomic units
coords_si2 = np.array(
[[0.0000000000000000, 0.0000000000000000, 0.0000000000000000],
[2.2639291987021915, 2.4639291987021915, 2.5639291987021915]])
# lattice vectors of Si2, in atomic units
latvecs_si2 = np.array(
[[5.2278583974043830, 5.1278583974043830, 0.0000000000000000],
[0.0000000000000000, 5.3278583974043830, 5.1278583974043830],
[5.1278583974043830, 0.0000000000000000, 5.4278583974043830]])
# coordinates of H2O, in atomic units
coords_h2o = np.array(
[[0.00000000000E+00, -0.10000000000E+01, 0.00000000000E+00],
[0.00000000000E+00, 0.00000000000E+00, 0.88306400000E+00],
[0.00000000000E+00, 0.00000000000E+00, -0.78306400000E+00]])
# initialize collective variables
merminentot, gradientstot, grosschgstot = init_collective_variables()
# dummy loop to test subsequent initializations/
# finalizations of the DFTB+ object
for iteration in range(0, NITER):
tsi2 = not bool(iteration % 2)
# use input for Si2 and H2O alternatingly, starting with Si2
if tsi2:
# set expected number of atoms
natom0 = NATOM_SI
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.Si2.hsd',
logfile='log.Si2.log')
# set geometry
cdftb.set_geometry(coords_si2, latvecs=latvecs_si2)
else:
# set expected number of atoms
natom0 = NATOM_H2O
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.H2O.hsd',
logfile='log.H2O.log')
# set geometry
cdftb.set_geometry(coords_h2o, latvecs=None)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, forces and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschgs = cdftb.get_gross_charges()
# finalize DFTB+ and clean up
cdftb.close()
if tsi2:
dummygrads = np.zeros(3)
dummychgs = 0
merminentot, gradientstot, grosschgstot = \
update_collective_variables(merminen,
np.vstack((gradients, dummygrads)),
np.hstack((grosschgs, dummychgs)),
merminentot, gradientstot, grosschgstot)
else:
merminentot, gradientstot, grosschgstot = \
update_collective_variables(merminen, gradients, grosschgs,
merminentot, gradientstot, grosschgstot)
if tsi2:
# check whether calculator was initialized with correct nr. of atoms
print('(Si2) Obtained nr. of atoms: {:d}'.format(natoms))
print('(Si2) Expected nr. of atoms: {:d}\n'.format(natom0))
# evaluate mermin free energy
print('(Si2) Obtained Mermin-energy: ' + \
'{:15.10f}'.format(merminen))
print('(Si2) Expected Mermin-energy: ' + \
'{:15.10f}\n'.format(-2.5897497363))
# evaluate gradients
print('(Si2) Obtained gradient of atom 1: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[0]))
print('(Si2) Expected gradient of atom 1: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(0.0306186399, 0.0026710677, -0.0007231241))
print('(Si2) Obtained gradient of atom 2: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[1]))
print('(Si2) Expected gradient of atom 2: ' + \
'{:15.10f} {:15.10f} {:15.10f}\n'
.format(-0.0306186399, -0.0026710677, 0.0007231241))
# evaluate Gross charges
print('(Si2) Obtained Gross charges: {:15.10f} {:15.10f}'.format(
*grosschgs))
print(
'(Si2) Expected Gross charges: {:15.10f} {:15.10f}\n\n'.format(
0.0, 0.0))
else:
# check whether calculator was initialized with correct nr. of atoms
print('(H2O) Obtained nr. of atoms: {:d}'.format(natoms))
print('(H2O) Expected nr. of atoms: {:d}\n'.format(natom0))
# evaluate mermin free energy
print('(H2O) Obtained Mermin-energy: ' + \
'{:15.10f}'.format(merminen))
print('(H2O) Expected Mermin-energy: ' + \
'{:15.10f}\n'.format(-3.7534584715))
# evaluate gradients
print('(H2O) Obtained gradient of atom 1: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[0]))
print('(H2O) Expected gradient of atom 1: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(0.0178274222, 1.1052225107, -0.0835776976))
print('(H2O) Obtained gradient of atom 2: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[1]))
print('(H2O) Expected gradient of atom 2: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(-0.0073820765, -0.4646991011, -0.5429357096))
print('(H2O) Obtained gradient of atom 3: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[2]))
print('(H2O) Expected gradient of atom 3: ' + \
'{:15.10f} {:15.10f} {:15.10f}\n'
.format(-0.0058552790, -0.6382027486, 0.6279471931))
# evaluate Gross charges
print('(H2O) Obtained Gross charges: ' + \
'{:15.10f} {:15.10f} {:15.10f}'
.format(*grosschgs))
print('(H2O) Expected Gross charges: ' + \
'{:15.10f} {:15.10f} {:15.10f}\n\n'
.format(-0.6519945363, 0.3314953102, 0.3204992261))
# --------------------------WRITE AUTOTEST.TAG------------------------------
# write autotest.tag file, containing the collective variables
write_autotest_tag('autotest.tag',
freeEgy=merminentot,
forceTot=-gradientstot,
qOutAtGross=grosschgstot)
def main():
'''Main driver routine.'''
# coordinates of H2O, in atomic units
qmcoords = np.array(
[[0.0000000000000000, -1.8897259885789233, 0.0000000000000000],
[0.0000000000000000, 0.0000000000000000, 1.4797763915205659],
[0.0000000000000000, 0.0000000000000000, -1.4797763915205659]])
# coordinates of MM-charges, in atomic units
mmcoords = np.array(
[[-0.944863438887178, -9.44863438887178, 1.70075418999692],
[4.34637181888102, -5.85815332110050, 2.64561762888410]])
# MM-charges, in atomic units
mmcharges = np.array([2.5, -1.9])
potcalc = PotentialCalculator(qmcoords, mmcoords, mmcharges)
# ----------------------------MAIN-CALCULATION------------------------------
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.hsd',
logfile='log.log')
# set geometry
cdftb.set_geometry(qmcoords, latvecs=None)
cdftb.register_ext_pot_generator(potcalc, get_extpot, get_extpotgrad)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, forces and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschgs = cdftb.get_gross_charges()
# check whether calculator was initialized with correct nr. of atoms
print('(H2O) Obtained nr. of atoms: {:d}'.format(natoms))
print('(H2O) Expected nr. of atoms: {:d}\n'.format(NATOM))
# evaluate mermin free energy
print('(H2O) Obtained Mermin-energy: ' + '{:15.10f}'.format(merminen))
print('(H2O) Expected Mermin-energy: ' +
'{:15.10f}\n'.format(-3.9854803392))
# evaluate gradients
print('(H2O) Obtained gradient of atom 1: ' +
'{:15.10f} {:15.10f} {:15.10f}'.format(*gradients[0]))
print('(H2O) Expected gradient of atom 1: ' +
'{:15.10f} {:15.10f} {:15.10f}'.format(0.0176513638, -0.1831376018,
0.0031982515))
print('(H2O) Obtained gradient of atom 2: ' +
'{:15.10f} {:15.10f} {:15.10f}'.format(*gradients[1]))
print('(H2O) Expected gradient of atom 2: ' +
'{:15.10f} {:15.10f} {:15.10f}'.format(-0.0061402266, 0.0955090293,
0.0394035230))
print('(H2O) Obtained gradient of atom 3: ' +
'{:15.10f} {:15.10f} {:15.10f}'.format(*gradients[2]))
print('(H2O) Expected gradient of atom 3: ' +
'{:15.10f} {:15.10f} {:15.10f}\n'.format(-0.0037720260, 0.0923535862,
-0.0402979580))
# evaluate Gross charges
print('(H2O) Obtained Gross charges: ' +
'{:15.10f} {:15.10f} {:15.10f}'.format(*grosschgs))
print('(H2O) Expected Gross charges: ' +
'{:15.10f} {:15.10f} {:15.10f}\n\n'.format(
-0.4943983279, 0.2641722128, 0.2302261151))
# finalize DFTB+ and clean up
cdftb.close()
# --------------------------WRITE AUTOTEST.TAG------------------------------
# write autotest.tag file of water molecule calculation
write_autotest_tag('autotest.tag',
freeEgy=merminen,
forceTot=-gradients,
qOutAtGross=grosschgs)
def main():
'''Main driver routine.'''
# coordinates of H2O, in atomic units
coords = np.array([
[0.000000000000000E+00, -0.188972598857892E+01, 0.000000000000000E+00],
[0.000000000000000E+00, 0.000000000000000E+00, 0.147977639152057E+01],
[0.000000000000000E+00, 0.000000000000000E+00, -0.147977639152057E+01]])
# the values of extpot and extpotgrad used here were
# taken from file: test/api/mm/testers/test_extpot.f90
extpot = np.array([-0.025850198503435,
-0.005996294763958,
-0.022919371690684])
extpotgrad = np.array([
[0.035702717378527, 0.011677956375860, 0.009766745155626],
[0.023243271928971, -0.000046945156575, 0.004850533043745],
[0.016384005706180, 0.004608295375551, 0.005401080774962]])
cdftb = dftbplus.DftbPlus(libpath=LIB_PATH,
hsdpath='dftb_in.hsd',
logfile='log.log')
# set geometry
cdftb.set_geometry(coords, latvecs=None)
# set external potential and its gradients
cdftb.set_external_potential(extpot, extpotgrad=extpotgrad)
# get number of atoms
natoms = cdftb.get_nr_atoms()
# calculate energy, forces and Gross charges
merminen = cdftb.get_energy()
gradients = cdftb.get_gradients()
grosschg = cdftb.get_gross_charges()
# finalize DFTB+ and clean up
cdftb.close()
# check whether calculator was initialized with correct nr. of atoms
print('(H2O) Obtained nr. of atoms: {:d}'.format(natoms))
print('(H2O) Expected nr. of atoms: {:d}\n'.format(NATOM0))
# evaluate mermin free energy
print('(H2O) Obtained Mermin-energy: {:15.10f}'.format(merminen))
print('(H2O) Expected Mermin-energy: {:15.10f}\n'.format(-3.9854803392))
# evaluate gradients
print('(H2O) Obtained gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[0]))
print('(H2O) Expected gradient of atom 1: {:15.10f} {:15.10f} {:15.10f}'
.format(0.0176513638, -0.1831376018, 0.0031982515))
print('(H2O) Obtained gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[1]))
print('(H2O) Expected gradient of atom 2: {:15.10f} {:15.10f} {:15.10f}'
.format(-0.0061402266, 0.0955090293, 0.0394035230))
print('(H2O) Obtained gradient of atom 3: {:15.10f} {:15.10f} {:15.10f}'
.format(*gradients[2]))
print('(H2O) Expected gradient of atom 3: {:15.10f} {:15.10f} {:15.10f}\n'
.format(-0.0037720260, 0.0923535862, -0.0402979580))
# evaluate Gross charges
print('(H2O) Obtained Gross charges: {:15.10f} {:15.10f}'
.format(*grosschg))
print('(H2O) Expected Gross charges: {:15.10f} {:15.10f}'
.format(-0.4943983279, 0.2641722128))
# --------------------------WRITE AUTOTEST.TAG------------------------------
# write autotest.tag file of water molecule calculation
write_autotest_tag('autotest.tag', freeEgy=merminen,
forceTot=-gradients, qOutAtGross=grosschg)
def __init__(self,
restart=None,
ignore_bad_restart_file=False,
label='',
atoms=None,
kpts=None,
slako_dir=None,
**kwargs):
"""
All keywords for the dftb_in.hsd input file (see the DFTB+ manual)
can be set by ASE. Consider the following input file block:
Hamiltonian = DFTB {
SCC = Yes
SCCTolerance = 1e-8
MaxAngularMomentum = {
H = s
O = p
}
}
This can be generated by the DFTB+ calculator by using the
following settings:
calc = Dftb(Hamiltonian_='DFTB', # line is included by default
Hamiltonian_SCC='Yes',
Hamiltonian_SCCTolerance=1e-8,
Hamiltonian_MaxAngularMomentum_='',
Hamiltonian_MaxAngularMomentum_H='s',
Hamiltonian_MaxAngularMomentum_O='p')
In addition to keywords specific to DFTB+, also the following keywords
arguments can be used:
restart: str
Prefix for restart file. May contain a directory.
Default is None: don't restart.
ignore_bad_restart_file: bool
Ignore broken or missing restart file. By default, it is an
error if the restart file is missing or broken.
label: str (default 'dftb')
Prefix used for the main output file (<label>.out).
atoms: Atoms object (default None)
Optional Atoms object to which the calculator will be
attached. When restarting, atoms will get its positions and
unit-cell updated from file.
kpts: (default None)
Brillouin zone sampling:
* ``(1,1,1)`` or ``None``: Gamma-point only
* ``(n1,n2,n3)``: Monkhorst-Pack grid
* ``dict``: Interpreted as a path in the Brillouin zone if
it contains the 'path_' keyword. Otherwise it is converted
into a Monkhorst-Pack grid using
``ase.calculators.calculator.kpts2sizeandoffsets``
* ``[(k11,k12,k13),(k21,k22,k23),...]``: Explicit (Nkpts x 3)
array of k-points in units of the reciprocal lattice vectors
(each with equal weight)
Additional attribute to be set by the embed() method:
pcpot: PointCharge object
An external point charge potential (for QM/MM calculations)
"""
if slako_dir is None:
slako_dir = os.environ.get('DFTB_PREFIX', './')
if not slako_dir.endswith('/'):
slako_dir += '/'
self.slako_dir = slako_dir
self.lib = os.environ.get('DFTB_LIB', './')
self.default_parameters = dict(
Hamiltonian_='DFTB',
Hamiltonian_SlaterKosterFiles_='Type2FileNames',
Hamiltonian_SlaterKosterFiles_Prefix=self.slako_dir,
Hamiltonian_SlaterKosterFiles_Separator='"-"',
Hamiltonian_SlaterKosterFiles_Suffix='".skf"',
Hamiltonian_MaxAngularMomentum_='',
Options_='',
Options_WriteResultsTag='Yes')
self.pcpot = None
self.lines = None
self.atoms = atoms
self.temp_atoms = atoms
self.atoms_input = None
self.do_forces = True
self.root = str(label)
label = str(label) + 'dftb'
Calculator.__init__(self, restart, ignore_bad_restart_file, label,
atoms, **kwargs)
self.outfilename = str(self.root) + 'dftb.out'
self.write_dftb_in(str(self.root) + 'dftb_in.hsd')
self.calc = dftbplus.DftbPlus(libpath=self.lib,
hsdpath=str(self.root) + 'dftb_in.hsd')
self.BOHR__AA = 0.529177249
self.AA__BOHR = 1 / self.BOHR__AA