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
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])