def calc_gradients(xyzfile, optionfile):
"""calculates DFTB energies and gradients for a molecule in the xyz_file
with the options given in the optionfile"""
outputfile = open("output_dftb.txt", "a") # redirect output to file
sys.stdout = outputfile
try:
options = read_options(optionfile) # read options
atomlist = XYZ.read_xyz(xyzfile)[0] # read structure
init_options = extract_options(options, TD_INIT_OPTIONLIST)
td_options = extract_options(options, TD_OPTIONLIST)
grad_options = extract_options(options, GRAD_OPTIONS)
kwds = XYZ.extract_keywords_xyz(xyzfile)
tddftb = LR_TDDFTB(atomlist, **init_options) # create object
tddftb.setGeometry(atomlist, charge=kwds.get("charge", 0.0))
tddftb.getEnergies(**td_options) # calculate energies
grad = Gradients(tddftb) # calculate gradients
grad.getGradients(**grad_options)
energies = list(tddftb.dftb2.getEnergies()) # get partial energies
if tddftb.dftb2.long_range_correction == 1: # add long range correction to partial energies
energies.append(tddftb.dftb2.E_HF_x)
return str(energies)
except:
print sys.exc_info()
return "error"
def test_dftb_eigenvector_derivative():
"""compare analytical and numerical gradients of MO coefficients and orbital energies"""
from DFTB.XYZ import read_xyz, extract_keywords_xyz
from DFTB.DFTB2 import DFTB2
from DFTB.Analyse.Cube import CubeExporterEx
from DFTB.Molden import MoldenExporter
from DFTB import utils
from DFTB.LR_TDDFTB import LR_TDDFTB
from DFTB.ExcGradients import Gradients
import sys
import os
usage = "Usage: %s <xyz-file>\n" % sys.argv[0]
usage += " --help option will give more information\n"
parser = utils.OptionParserFuncWrapper([\
DFTB2.__init__, DFTB2.runSCC, \
LR_TDDFTB.getEnergies, LR_TDDFTB.saveAbsorptionSpectrum, LR_TDDFTB.analyseParticleHole, \
LR_TDDFTB.graphical_analysis, \
CubeExporterEx.exportCubes, MoldenExporter.export, \
Gradients.getGradients], \
usage)
(options, args) = parser.parse_args(DFTB2.__init__)
if len(args) < 1:
print(usage)
exit(-1)
xyz_file = args[0]
atomlist = read_xyz(xyz_file)[0]
kwds = extract_keywords_xyz(xyz_file)
tddftb = LR_TDDFTB(atomlist, **options)
(options, args) = parser.parse_args(tddftb.getEnergies)
(scf_options, args) = parser.parse_args(tddftb.dftb2.runSCC)
options.update(scf_options)
tddftb.setGeometry(atomlist, charge=kwds.get("charge", 0.0))
tddftb.getEnergies(**options)
grad = Gradients(tddftb)
grad.gradient(I=0, save_intermediates_CPKS=1)
dE_an, dX_an = grad.getMOgradients()
dftb2 = tddftb.dftb2
E = dftb2.getKSEnergies()
X = dftb2.getKSCoefficients()
dE_num, dX_num = dftb_numerical_mo_gradients(dftb2, atomlist)
print("eigenvalues")
print(E)
print("numerical eigenvalue gradients")
print(dE_num)
print("analytical eigenvalue gradients")
print(dE_an)
err_dE = la.norm(dE_num - dE_an)
err_dX = la.norm(dX_num - dX_an)
assert err_dE < 1.0e-3, "err(dE) = %s" % err_dE
def __init__(self, atomlist, Nst=2, **kwds):
"""
The DFTB module has many parameters which can be set from the command
line using options, e.g. --scf_conv=1.0e-10.
During the initialization
- the command line arguments are parsed for options
- Slater-Koster tables and repulsive potentials
are loaded for the atom pair present in the molecule
Parameters:
===========
atomlist: list of tuples (Zi,[xi,yi,zi]) for each atom in the molecule
Nst: number of electronic states (including ground state)
"""
usage = "Type --help to show all options for DFTB"
parser = optparse.OptionParserFuncWrapper([
DFTB2.__init__, DFTB2.runSCC, SolventCavity.__init__,
LR_TDDFTB.getEnergies
],
usage,
section_headers=["DFTBaby"],
unknown_options="ignore")
options, args = parser.parse_args(DFTB2.__init__)
self.atomlist = atomlist
self.tddftb = LR_TDDFTB(atomlist, **options)
solvent_options, args = parser.parse_args(SolventCavity.__init__)
solvent_cavity = SolventCavity(**solvent_options)
self.tddftb.dftb2.setSolventCavity(solvent_cavity)
self.grads = Gradients(self.tddftb)
self.tddftb.setGeometry(atomlist, charge=kwds.get("charge", 0.0))
self.options, args = parser.parse_args(self.tddftb.getEnergies)
self.scf_options, args = parser.parse_args(self.tddftb.dftb2.runSCC)
self.options.update(self.scf_options)
self.Nst = Nst
# # always use iterative diagonalizer for lowest Nst-1 excited states
self.options["nstates"] = Nst - 1
# save geometry, orbitals and TD-DFT coefficients from
# last calculation
self.last_calculation = None
# save transition dipoles from last calculation
self.tdip_old = None
def __init__(self, atomlist, options, Nst=2, **kwds):
usage = "Type --help to show all options for DFTB"
parser = utils.OptionParserFuncWrapper(
[DFTB2.__init__, DFTB2.runSCC, LR_TDDFTB.getEnergies], usage)
self.options = options
td_init_options = extract_options(self.options, TD_INIT_OPTIONLIST)
self.atomlist = atomlist
self.tddftb = LR_TDDFTB(atomlist, **td_init_options)
self.grads = Gradients(self.tddftb)
self.tddftb.setGeometry(atomlist, charge=kwds.get("charge", 0.0))
self.scf_options = extract_options(self.options, SCF_OPTIONLIST)
self.options = copy(self.scf_options)
self.Nst = Nst
# # always use iterative diagonalizer for lowest Nst-1 excited states
self.options["nstates"] = Nst - 1
# save geometry, orbitals and TD-DFT coefficients from
# last calculation
self.last_calculation = None
# save transition dipoles from last calculation
self.tdip_old = None
def test_dftb_charge_derivative():
"""compare analytical and numerical gradients of Mulliken charges"""
from DFTB.XYZ import read_xyz, extract_keywords_xyz
from DFTB.DFTB2 import DFTB2
from DFTB.Analyse.Cube import CubeExporterEx
from DFTB.Molden import MoldenExporter
from DFTB import utils
from DFTB.LR_TDDFTB import LR_TDDFTB
from DFTB.ExcGradients import Gradients
import sys
import os
usage = "Usage: %s <xyz-file>\n" % sys.argv[0]
usage += " --help option will give more information\n"
parser = utils.OptionParserFuncWrapper([\
DFTB2.__init__, DFTB2.runSCC, \
LR_TDDFTB.getEnergies, LR_TDDFTB.saveAbsorptionSpectrum, LR_TDDFTB.analyseParticleHole, \
LR_TDDFTB.graphical_analysis, \
CubeExporterEx.exportCubes, MoldenExporter.export, \
Gradients.getGradients], \
usage)
(options, args) = parser.parse_args(DFTB2.__init__)
if len(args) < 1:
print usage
exit(-1)
xyz_file = args[0]
atomlist = read_xyz(xyz_file)[0]
kwds = extract_keywords_xyz(xyz_file)
tddftb = LR_TDDFTB(atomlist, **options)
(options, args) = parser.parse_args(tddftb.getEnergies)
(scf_options, args) = parser.parse_args(tddftb.dftb2.runSCC)
options.update(scf_options)
tddftb.setGeometry(atomlist, charge=kwds.get("charge", 0.0))
tddftb.getEnergies(**options)
grad = Gradients(tddftb)
grad.gradient(I=0, save_intermediates_CPKS=1)
dQdp_ana = grad.getChargeGradients()
dftb2 = tddftb.dftb2
dQdp_num = dftb_numerical_charge_gradients(dftb2, atomlist)
print "partial Mulliken charges"
print dftb2.getPartialCharges()
print "numerical charge gradients"
print dQdp_num
print "analytical charge gradients"
print dQdp_ana
print "difference"
print dQdp_num - dQdp_ana
err_dQ = la.norm(dQdp_num - dQdp_ana)
print "err(dQdp) = %s" % err_dQ
#assert err_dQ < 1.0e-4, "err(dQdp) = %s" % err_dQ
# show timings
print T
class PotentialEnergySurfaces(object):
def __init__(self, atomlist, Nst=2, **kwds):
"""
The DFTB module has many parameters which can be set from the command
line using options, e.g. --scf_conv=1.0e-10.
During the initialization
- the command line arguments are parsed for options
- Slater-Koster tables and repulsive potentials
are loaded for the atom pair present in the molecule
Parameters:
===========
atomlist: list of tuples (Zi,[xi,yi,zi]) for each atom in the molecule
Nst: number of electronic states (including ground state)
"""
usage = "Type --help to show all options for DFTB"
parser = optparse.OptionParserFuncWrapper([
DFTB2.__init__, DFTB2.runSCC, SolventCavity.__init__,
LR_TDDFTB.getEnergies
],
usage,
section_headers=["DFTBaby"],
unknown_options="ignore")
options, args = parser.parse_args(DFTB2.__init__)
self.atomlist = atomlist
self.tddftb = LR_TDDFTB(atomlist, **options)
solvent_options, args = parser.parse_args(SolventCavity.__init__)
solvent_cavity = SolventCavity(**solvent_options)
self.tddftb.dftb2.setSolventCavity(solvent_cavity)
self.grads = Gradients(self.tddftb)
self.tddftb.setGeometry(atomlist, charge=kwds.get("charge", 0.0))
self.options, args = parser.parse_args(self.tddftb.getEnergies)
self.scf_options, args = parser.parse_args(self.tddftb.dftb2.runSCC)
self.options.update(self.scf_options)
self.Nst = Nst
# # always use iterative diagonalizer for lowest Nst-1 excited states
self.options["nstates"] = Nst - 1
# save geometry, orbitals and TD-DFT coefficients from
# last calculation
self.last_calculation = None
# save transition dipoles from last calculation
self.tdip_old = None
def getEnergies(self, x):
"""
This functions computes the adiabatic energies ONLY. It should
not be used during a dynamics simulation
"""
self.atomlist = XYZ.vector2atomlist(x, self.atomlist)
self.tddftb.setGeometry(self.atomlist,
keep_charge=True,
update_symmetry=False)
self.tddftb.getEnergies(**self.options)
# total ground state energy
E0 = self.tddftb.dftb2.E_tot
# excitation energies
Exc = self.tddftb.getExcEnergies()
# total energies of ground and excited states
energies = np.hstack(([E0], E0 + Exc))
return energies[:self.Nst]
def getEnergy_S0(self, x):
"""
This function compute the ground state energy ONLY.
"""
self.atomlist = XYZ.vector2atomlist(x, self.atomlist)
self.tddftb.setGeometry(self.atomlist,
keep_charge=True,
update_symmetry=False)
E0 = self.tddftb.dftb2.getEnergy(**self.scf_options)
energies = np.array([E0]) # only ground state energy
return energies
@T.timer
def getEnergiesAndGradient(self, x, gradient_state):
"""
This function computes the adiabatic electronic energies
for the nuclear geometry contained in 'x' and the gradient
of the total energy of state 'gradient_state'.
Parameters:
===========
x: a numpy array with the nuclear coordinates,
x[3*i:3*(i+1)] should contain the cartesian coordinates of atom i
gradient_state: index of the electronic state, whose gradient should
be calculated. 0 stands for the ground state, 1 for the 1st excited
state, etc.
Returns:
========
energies: numpy array with total energies (in Hartree) for all electronic
states
gradTot: total gradient of the selected state,
gradTot[3*i:3*(i+1)] contains the energy derivative w/r/t the 3 cartesian
coordinates of atom i.
"""
self.atomlist = XYZ.vector2atomlist(x, self.atomlist)
self.tddftb.setGeometry(self.atomlist,
keep_charge=True,
update_symmetry=False)
self.tddftb.getEnergies(**self.options)
# total ground state energy
E0 = self.tddftb.dftb2.E_tot
# excitation energies
Exc = self.tddftb.getExcEnergies()
# total energies of ground and excited states
energies = np.hstack(([E0], E0 + Exc))
gradVrep, gradE0, gradExc = self.grads.gradient(
I=gradient_state, save_intermediates_CPKS=1)
gradTot = gradVrep + gradE0 + gradExc
# QM/MM
if self.tddftb.dftb2.qmmm != None:
# expand gradient to the full system
gradTot = self.tddftb.dftb2.qmmm.getGradientFull(gradTot)
# confining cavity
if self.tddftb.dftb2.cavity != None:
if self.tddftb.dftb2.qmmm != None:
atomlist = self.tddftb.dftb2.qmmm.getGeometryFull()
else:
atomlist = self.atomlist
gradTot += self.tddftb.dftb2.cavity.getGradient(atomlist)
return energies, gradTot
def getEnergyAndGradient_S0(self, x, has_scf=False):
"""
obtain the ground state energy and gradient while skipping an excited state calculation.
This function should be called with has_scf=True directly after a failed TD-DFTB calculation. Then the scf calculation is skipped as well, assuming that the converged ground state orbitals are available.
Returns:
========
E0: ground state energy
gradTot: gradient on ground state
"""
# ground state energy
if has_scf == True:
# SCF calculation has been done already
E0 = self.tddftb.dftb2.E_tot
else:
self.atomlist = XYZ.vector2atomlist(x, self.atomlist)
self.tddftb.setGeometry(self.atomlist,
keep_charge=True,
update_symmetry=False)
# SCF calculation
E0 = self.tddftb.dftb2.getEnergy(**self.scf_options)
# try to compute gradient on ground state
gradVrep, gradE0, gradExc = self.grads.gradient(
I=0, save_intermediates_CPKS=1)
gradTot = gradVrep + gradE0 + gradExc
# QM/MM
if self.tddftb.dftb2.qmmm != None:
# expand gradient to the full system
gradTot = self.tddftb.dftb2.qmmm.getGradientFull(gradTot)
# confining cavity
if self.tddftb.dftb2.cavity != None:
if self.tddftb.dftb2.qmmm != None:
atomlist = self.tddftb.dftb2.qmmm.getGeometryFull()
else:
atomlist = self.atomlist
gradTot += self.tddftb.dftb2.cavity.getGradient(atomlist)
return E0, gradTot
def resetXY(self):
# reset excitation vectors, so that in the next iteration
# we start with a clean guess
self.tddftb.XmY = None
self.tddftb.XpY = None
def resetSCF(self):
# set Mulliken partial charges to zero and density matrix P to
# reference density matrix P0, so that in the next iteration
# we start with a clean guess
self.tddftb.dftb2.dq *= 0.0
self.tddftb.dftb2.P = self.tddftb.dftb2.density_matrix_ref()
def getScalarCouplings(self, threshold=0.01):
"""
Parameters:
===========
threshold: smaller excitation coefficients are neglected in the calculation
of overlaps
Returns:
========
coupl: antisymmetric matrix with scalar non-adiabatic coupling
coupl[A,B] ~ <Psi_A|d/dt Psi_B>*dt
The coupling matrix has to be divided by the nuclear time step dt
It is important that this function is called
exactly once after calling 'getEnergiesAndGradient'
"""
atomlist2 = self.atomlist
orbs2 = self.tddftb.dftb2.orbs
C2 = self.tddftb.Cij[:self.Nst -
1, :, :] # only save the states of interest
# off-diagonal elements of electronic hamiltonian
SC = ScalarCoupling(self.tddftb)
# retrieve last calculation
if self.last_calculation == None:
# This is the first calculation, so use the same data
atomlist1, orbs1, C1 = atomlist2, orbs2, C2
else:
atomlist1, orbs1, C1 = self.last_calculation
Sci = SC.ci_overlap(atomlist1,
orbs1,
C1,
atomlist2,
orbs2,
C2,
self.Nst,
threshold=threshold)
# align phases
# The eigenvalue solver produces vectors with arbitrary global phases
# (+1 or -1). The orbitals of the ground state can also change their signs.
# Eigen states from neighbouring geometries should change continuously.
signs = np.sign(np.diag(Sci))
self.P = np.diag(signs)
# align C2 with C1
C2 = np.tensordot(self.P[1:, :][:, 1:], C2, axes=(0, 0))
# align overlap matrix
Sci = np.dot(Sci, self.P)
# The relative signs for the overlap between the ground and excited states at different geometries
# cannot be deduced from the diagonal elements of Sci. The phases are chosen such that the coupling
# between S0 and S1-SN changes smoothly for most of the states.
if hasattr(self, "last_coupl"):
s = np.sign(self.last_coupl[0, 1:] / Sci[0, 1:])
w = np.abs(Sci[0, 1:] - self.last_coupl[0, 1:])
mean_sign = np.sign(np.sum(w * s) / np.sum(w))
sign0I = mean_sign
for I in range(1, self.Nst):
Sci[0, I] *= sign0I
Sci[I, 0] *= sign0I
#
state_labels = [("S%d" % I) for I in range(0, self.Nst)]
if self.tddftb.dftb2.verbose > 0:
print "Overlap <Psi(t)|Psi(t+dt)>"
print "=========================="
print utils.annotated_matrix(Sci, state_labels, state_labels)
# overlap between wavefunctions at different time steps
olap = np.copy(Sci)
coupl = Sci
# coupl[A,B] = <Psi_A(t)|Psi_B(t+dt)> - delta_AB
# ~ <Psi_A(t)|d/dR Psi_B(t)>*dR/dt dt
# TEST
# The scalar coupling matrix should be more or less anti-symmetric
# provided the time-step is small enough
# set diagonal elements of coupl to zero
coupl[np.diag_indices_from(coupl)] = 0.0
err = np.sum(abs(coupl + coupl.transpose()))
if err > 1.0e-1:
print "WARNING: Scalar coupling matrix is not antisymmetric, error = %s" % err
#
# Because of the finite time-step it will not be completely antisymmetric,
# so antisymmetrize it
coupl = 0.5 * (coupl - coupl.transpose())
# save coupling for establishing relative phases
self.last_coupl = coupl
state_labels = [("S%d" % I) for I in range(0, self.Nst)]
if self.tddftb.dftb2.verbose > 0:
print "Scalar Coupling"
print "==============="
print utils.annotated_matrix(coupl, state_labels, state_labels)
# save last calculation
self.last_calculation = (atomlist2, orbs2, C2)
return coupl, olap
def saveLastCalculation(self):
"""
save geometry, MO coefficients and TD-DFTB coefficients of last calculation.
This data is needed to align the phases between neighbouring steps.
"""
atomlist = self.atomlist
orbs = self.tddftb.dftb2.orbs
# only save the states of interest
C = self.tddftb.Cij[:self.Nst - 1, :, :]
# save last calculation
self.last_calculation = (atomlist, orbs, C)
def alignCoefficients(self, c):
"""
align phases of coefficients of adiabatic states
"""
if hasattr(self, "P"):
c = np.dot(self.P[1:, :][:, 1:], c)
return c
def getTransitionDipoles(self):
"""
computes and aligns transition dipoles between all Nst states
This function should be called only once directly after getScalarCouplings!
"""
tdip = self.tddftb.getTransitionDipolesExc(self.Nst)
# eigenvectors can have arbitrary phases
# align transition dipoles with old ones
tdip_old = self.tdip_old
if type(tdip_old) == type(None):
tdip_old = tdip
for A in range(0, self.Nst):
for B in range(0, self.Nst):
sign = np.dot(tdip_old[A, B, :], tdip[A, B, :])
if sign < 0.0:
tdip[A, B, :] *= -1.0
self.tdip_old = tdip
if self.tddftb.dftb2.verbose > 0:
state_labels = [("S%d" % I) for I in range(0, self.Nst)]
print "Transition Dipoles"
print "=================="
print "X-Component"
print utils.annotated_matrix(tdip[:, :, 0], state_labels,
state_labels)
print "Y-Component"
print utils.annotated_matrix(tdip[:, :, 1], state_labels,
state_labels)
print "Z-Component"
print utils.annotated_matrix(tdip[:, :, 2], state_labels,
state_labels)
#
return tdip
def calculate_charge_derivative():
"""compute analytical gradients of Mulliken charges"""
#
# This long prologue serves for reading all options
# from the command line or the dftbaby.cfg file.
# The command-line option
#
# --cpks_solver='direct' or 'iterative'
#
# determines whether the full CPKS matrix should be constructed ('direct')
# or whether the system of linear equations should be solved iteratively using the Krylov
# subspace method.
#
from DFTB.XYZ import read_xyz, extract_keywords_xyz
from DFTB.DFTB2 import DFTB2
from DFTB import utils
from DFTB.LR_TDDFTB import LR_TDDFTB
from DFTB.ExcGradients import Gradients
import sys
import os
usage = "Usage: %s <xyz-file>\n" % sys.argv[0]
usage += " --help option will give more information\n"
parser = utils.OptionParserFuncWrapper([\
DFTB2.__init__, DFTB2.runSCC, \
LR_TDDFTB.getEnergies, LR_TDDFTB.saveAbsorptionSpectrum, LR_TDDFTB.analyseParticleHole, \
Gradients.getGradients], \
usage)
(options, args) = parser.parse_args(DFTB2.__init__)
if len(args) < 1:
print usage
exit(-1)
xyz_file = args[0]
atomlist = read_xyz(xyz_file)[0]
# number of atoms
Nat = len(atomlist)
kwds = extract_keywords_xyz(xyz_file)
tddftb = LR_TDDFTB(atomlist, **options)
(options, args) = parser.parse_args(tddftb.getEnergies)
(scf_options, args) = parser.parse_args(tddftb.dftb2.runSCC)
options.update(scf_options)
tddftb.setGeometry(atomlist, charge=kwds.get("charge", 0.0))
tddftb.getEnergies(**options)
#
# The important part starts here.
#
grad = Gradients(tddftb)
# A CPKS calculation has to be preceeded by a gradient calculation.
# The option `save_intermediates_CPKS=1` tells the program to save intermediate
# variables that are needed later during the CPKS calculation.
grad.gradient(I=0, save_intermediates_CPKS=1)
# This runs a CPKS calculation and computes the gradients of the charges
dQdp = grad.getChargeGradients()
# The gradient of the charge on atom B w/r/t the position of atom A is
# d(Q_B)/dR_A = dQdp[3*A:3*(A+1), B]
A = 0 # first atom
B = Nat - 1 # last atom
print "Gradient of Mulliken charge on atom A=%d w/r/t nucleus B=%d d(Q_B)/dR_A = %s" \
% (A, B, dQdp[3*A:3*(A+1), B])