├── .gitignore ├── AUTHORS ├── DFTB ├── Analyse │ ├── Cube.py │ ├── MolecularGraph.py │ ├── SymmetryAssignment.py │ ├── __init__.py │ ├── absorption_spectrum.py │ ├── add_columns.py │ ├── analyse_IVR.py │ ├── analyse_transition_densities.py │ ├── average_fragment_data.py │ ├── blender │ │ ├── __init__.py │ │ ├── animatecube.blend │ │ ├── animatecube.py │ │ ├── in2blender.py │ │ ├── in2blender.xyz │ │ ├── template.blend │ │ ├── visualize_dipoles.blend │ │ ├── visualize_xyz.blend │ │ ├── visualize_xyz.py │ │ └── xyz2blender.py │ ├── bond_indeces.py │ ├── extract_frame.py │ ├── fcclasses_input.py │ ├── hueckel_polyene.py │ ├── integrate_cube_Tn.py │ ├── linear_excitonic_chain.py │ ├── mayavi │ │ ├── CubeViewerWidget.py │ │ ├── GUI.py │ │ └── __init__.py │ ├── ph_correlation.py │ ├── plot_ph_charges_planar.py │ ├── porphene_wire_shifts.py │ └── vmd │ │ ├── __init__.py │ │ ├── vmd_cube_browser.py │ │ ├── vmd_plot_charges.tcl │ │ ├── vmd_plot_cubes.tcl │ │ └── vmd_plot_vectors.tcl ├── AtomicData.py ├── BasisSets.py ├── CPKS.py ├── Cavity.py ├── ChargeConstraint.py ├── ConvAcceleration.py ├── DFTB2.py ├── DensityFitting.py ├── DiskMemory.py ├── Dispersion.py ├── Dynamics │ ├── Analyse │ │ ├── Viewer │ │ │ ├── __init__.py │ │ │ ├── trajViewer.py │ │ │ ├── trajViewer2.py │ │ │ ├── window.ui │ │ │ └── window2.ui │ │ ├── __init__.py │ │ ├── classify_isomers.py │ │ ├── energy_trajectory.py │ │ ├── fragments.py │ │ ├── lambda2_average.py │ │ ├── plot_populations.py │ │ ├── populations.py │ │ └── vmd │ │ │ ├── make_movie.sh │ │ │ ├── pyrene_crystal_trajectories.tcl │ │ │ ├── show_trajectories.tcl │ │ │ └── vmd_input.py │ ├── GaussianWavepacket.py │ ├── HarmonicApproximation.py │ ├── SurfaceHopping.py │ ├── __init__.py │ ├── check_initial_distribution.py │ ├── dftbaby.sh │ ├── dftbaby_handler.py │ ├── initial_conditions.py │ └── random_velocities.py ├── ExcGradients.py ├── ForceField │ ├── PeriodicForceField.py │ ├── __init__.py │ ├── assign_atom_types.py │ ├── copy_atom_types.py │ ├── copy_transition_charges.py │ ├── enlarge_unitcell.py │ ├── examples │ │ ├── 10_TIP5P.ff │ │ ├── C60.ff │ │ ├── benzene.ff │ │ ├── butadiene.ff │ │ ├── cyclohexane.ff │ │ ├── ethane.ff │ │ ├── ethanoic_acid.ff │ │ ├── ethene.ff │ │ ├── ethene_twisted.ff │ │ ├── exciton_spectrum.dat │ │ ├── h2.ff │ │ ├── h2_opt.xyz │ │ ├── pyrene.ff │ │ ├── pyrene_crystal.ff │ │ ├── tyrosine.ff │ │ └── water_dimer.ff │ ├── ff_optimize.py │ ├── ff_spectra.py │ ├── fit_electric_charges.py │ ├── fit_magnetic_dipoles.py │ └── src │ │ ├── Makefile │ │ ├── atoms.h │ │ ├── dreiding.h │ │ ├── ff.c │ │ ├── ff.h │ │ ├── ff_pythonmodule.c │ │ ├── input.c │ │ ├── input.h │ │ ├── linked_list.c │ │ ├── linked_list.h │ │ └── setup.py ├── Formats │ ├── DynamicsOut.py │ ├── Gaussian2py │ │ ├── Checkpoint.py │ │ ├── Gaussian.py │ │ ├── GaussianWavepacket.py │ │ ├── WignerEnsemble.py │ │ ├── __init__.py │ │ ├── extract_geometries_g09.py │ │ ├── optimize_am1.sh │ │ └── test_hessian │ │ │ ├── benzene_opt.com │ │ │ ├── benzene_opt.out │ │ │ ├── cs2_opt.com │ │ │ └── cs2_opt.out │ ├── MyCheckpoint.py │ ├── Tinker.py │ ├── Turbomole.py │ ├── __init__.py │ ├── pc_t2x.py │ ├── sample_trajectory.py │ ├── xyz2gen.py │ └── xyz2gjf.sh ├── GammaApproximation.py ├── ImplicitSolvent.py ├── LR_TDDFTB.py ├── LongRangeCT.py ├── Mathematica_scripts │ ├── ApB_AmB_CC.nb │ ├── RotationMatrix2EulerAngles.nb │ ├── SlaterKosterDipoles.nb │ ├── SlaterKosterDipoles_v2.nb │ ├── SlaterKosterDipoles_v3.nb │ ├── SlaterKosterDipoles_v4.nb │ ├── SlaterKosterDipoles_v5.nb │ ├── SlaterKosterDipoles_v5_batch.m │ ├── SlaterKosterDipoles_v5_py_f90.nb │ ├── SlaterKosterDipoles_v6_py_f90.nb │ ├── SlaterKosterDipoles_v6_py_f90_batch.m │ ├── SlaterKosterDipoles_v7_py_f90_batch_lmax1.m │ ├── SlaterKosterDipoles_v7_py_f90_batch_lmax2.m │ ├── SlaterKosterTransformation.nb │ ├── SlaterKosterTransformation_py_f90.nb │ ├── Tomonaga.nb │ ├── approx_0p1.dat │ ├── approx_0p2.dat │ ├── approx_0p333.dat │ ├── compare_gamma_lr_exact_approx.py │ ├── compare_switching_functions.py │ ├── comparison_gamma_lr_exact_approx.png │ ├── coulomb_function_overlap.nb │ ├── equations_of_motion_RPA.py │ ├── exact_0p1.dat │ ├── exact_0p2.dat │ ├── exact_0p333.dat │ ├── force_field_gradients.nb │ ├── gamma_functions.nb │ ├── gamma_lr_integral_approximation.nb │ ├── homogeneous_spheres_coulomb.nb │ ├── hydrogen_molecular_ion.nb │ ├── long_range_switching_erf_fermi.nb │ ├── math.out │ ├── mathematica.out │ ├── prolate_spheroidal_coordiantes.nb │ ├── rotated_Yreal.nb │ ├── sktransflistxyz.expr │ ├── sktransflistxyz_lmax1.expr │ ├── sktransflistxyz_lmax2.expr │ ├── sktransflistxyz_lmax2.expr.save │ ├── sktransflistxyz_multipoles.expr │ ├── sktransflistxyz_multipoles_lmax1.expr │ ├── slako_transformations_dipole_lmax1.f90 │ ├── slako_transformations_grad_lmax1.f90 │ ├── slako_transformations_grad_lmax2.f90 │ ├── slako_transformations_lmax1.py │ ├── slako_transformations_lmax2.f90 │ ├── slako_transformations_lmax2.py │ ├── slako_transformations_lmaxlmax.py │ ├── transformations_dipole.py │ ├── uniform_sphere_TWeizsacker.nb │ └── vlongrange_erfgau.nb ├── MetaDynamics │ ├── __init__.py │ ├── cvcustom.py │ ├── cvfunctions.py │ ├── meta-config.py │ ├── meta.py │ ├── mulliken.py │ └── reconstruct.py ├── Modeling │ ├── BondOrders.py │ ├── CarbonNanotubes.py │ ├── MinimalEnclosingBox.py │ ├── MolecularCoords.py │ ├── OrbitalRotations.py │ ├── Puckering.py │ ├── __init__.py │ ├── analyse_pyrene_dimer.py │ ├── assign_partial_charges.py │ ├── average_pyrene_displacements.py │ ├── build_cnts.py │ ├── build_polyfluorene.py │ ├── build_water_cluster.py │ ├── convert_xyz.py │ ├── cut_sphere.py │ ├── dupliverts.py │ ├── filter_fragments.py │ ├── interpolate_linearly.py │ ├── modify_internal.py │ ├── nanotube_builder.py │ ├── polyomino_random_growth.py │ ├── polyominos_reactivity.py │ ├── porphyrin_flakes.py │ ├── porphyrin_opt_b3lyp.xyz │ ├── pprint_xyz.py │ ├── show_molcoords.py │ ├── split_xyz.py │ ├── test_hydrogen_labels.py │ ├── thomson.py │ ├── thomson2.py │ ├── water_dimer.xyz │ └── water_monomer.xyz ├── Molden.py ├── MolecularIntegrals │ ├── BasissetFreeDFT.py │ ├── ContinuumLCAO.py │ ├── ContinuumLCAO_ee.py │ ├── ERIs.py │ ├── FVVM.py │ ├── FiniteDifferences.py │ ├── Ints1e.py │ ├── LebedevQuadrature.py │ ├── MulticenterIntegration.py │ ├── NACs.py │ ├── NumericalGammaApproximation.py │ ├── OnSiteIntegrals.py │ ├── SphericalCoords.py │ ├── __init__.py │ ├── associatedLegendrePolynomials.py │ ├── becke_dft.py │ ├── chebyshev.py │ ├── fchkfile.py │ ├── gtobasis.py │ ├── hmi_continuum.py │ ├── hmi_variational_kohn.py │ ├── integrals.py │ ├── lebedev_quad_points.py │ ├── lithium_cation_continuum.py │ ├── settings.py │ ├── stuff │ │ └── FiniteDifferences.py │ └── test │ │ ├── h2_pbe_aug-cc-pV5Z.gjf │ │ ├── h2_pbe_aug-cc-pV5Z.out │ │ ├── h2o_hf_sv.fchk │ │ ├── h2o_hf_sv.gjf │ │ ├── h2o_pbe_aug-cc-pV5Z.fchk │ │ ├── h2o_pbe_aug-cc-pV5Z.gjf │ │ ├── pyscf_dft_h2.py │ │ ├── test_asymptotic_vxc.py │ │ ├── test_leeuwen_baerends_exchange.py │ │ └── test_settings.py ├── Mulliken.py ├── MultipleScattering │ ├── MoldenFile.py │ ├── MuffinTin.py │ ├── PAD.py │ ├── Wavefunctions.py │ ├── __init__.py │ ├── electroSka.py │ └── src │ │ ├── COUL90.FOR │ │ ├── Makefile │ │ ├── Wigner3j.f95 │ │ ├── Wigner3j.pyf │ │ ├── cart2sph.f90 │ │ ├── cms.f90 │ │ ├── cms.pyf │ │ ├── coul90.pyf │ │ ├── coul90_wrapper.f90 │ │ ├── mod_bessel.f90 │ │ ├── mod_bessel.pyf │ │ ├── ms.f90 │ │ ├── ms.pyf │ │ ├── numerov.f90 │ │ ├── numerov.pyf │ │ ├── photo.f90 │ │ ├── photo.pyf │ │ ├── sphharm.f90 │ │ ├── sphharm.pyf │ │ ├── splder.f │ │ └── splines.f90 ├── NACsApprox.py ├── NACsMO.py ├── NEB.py ├── NTOs.py ├── NonHermitianSolver.py ├── Optimize │ ├── Constraints.py │ ├── GeometryOptimization.py │ ├── InternalCoords.py │ ├── Optimize.py │ └── __init__.py ├── OrbitalLocalization.py ├── PES.py ├── Parallization.py ├── Parameters.py ├── Periodic.py ├── Poisson │ ├── __init__.py │ ├── electrostatic_potential.py │ ├── poisson_pspfft.py │ ├── poisson_pspfft.x │ ├── poisson_test.py │ ├── src │ │ ├── Makefile │ │ ├── io_pspfft.f90 │ │ ├── poisson_iterative.f90 │ │ └── poisson_pspfft.f90 │ └── vector_potential.py ├── QMMM.py ├── RepulsivePotential │ ├── FitForces.py │ ├── FitReppots.py │ ├── Gaussian.py │ ├── RepulsivePotential.py │ ├── __init__.py │ ├── automatic_fitting_HCNO │ │ ├── FITTING │ │ │ ├── DFTB │ │ │ │ ├── acetic_acid_dislocated.energies.dat │ │ │ │ ├── acetic_acid_equilib_dislocated.energies.dat │ │ │ │ ├── acetone_dislocated.energies.dat │ │ │ │ ├── acetone_equilib_dislocated.energies.dat │ │ │ │ ├── acetonitrile_dislocated.energies.dat │ │ │ │ ├── acetonitrile_equilib_dislocated.energies.dat │ │ │ │ ├── ammonia_dislocated.energies.dat │ │ │ │ ├── ammonia_equilib_dislocated.energies.dat │ │ │ │ ├── anisole_dislocated.energies.dat │ │ │ │ ├── anisole_equilib_dislocated.energies.dat │ │ │ │ ├── azidobenzene_dislocated.energies.dat │ │ │ │ ├── azidobenzene_equilib_dislocated.energies.dat │ │ │ │ ├── benzene_dislocated.energies.dat │ │ │ │ ├── benzene_equilib_dislocated.energies.dat │ │ │ │ ├── carbon_dioxide_dislocated.energies.dat │ │ │ │ ├── carbon_dioxide_equilib_dislocated.energies.dat │ │ │ │ ├── carbonic_acid_dislocated.energies.dat │ │ │ │ ├── carbonic_acid_equilib_dislocated.energies.dat │ │ │ │ ├── dimethylamine_dislocated.energies.dat │ │ │ │ ├── dimethylamine_equilib_dislocated.energies.dat │ │ │ │ ├── dimethylether_dislocated.energies.dat │ │ │ │ ├── dimethylether_equilib_dislocated.energies.dat │ │ │ │ ├── dinitrogen_trioxide_dislocated.energies.dat │ │ │ │ ├── dinitrogen_trioxide_equilib_dislocated.energies.dat │ │ │ │ ├── dipeptide_dislocated.energies.dat │ │ │ │ ├── dipeptide_equilib_dislocated.energies.dat │ │ │ │ ├── ethane_CC_stretch.energies.dat │ │ │ │ ├── ethane_dislocated.energies.dat │ │ │ │ ├── ethane_equilib_dislocated.energies.dat │ │ │ │ ├── ethanimine_dislocated.energies.dat │ │ │ │ ├── ethanimine_equilib_dislocated.energies.dat │ │ │ │ ├── ethanol_dislocated.energies.dat │ │ │ │ ├── ethanol_equilib_dislocated.energies.dat │ │ │ │ ├── ethene_CC_stretch.energies.dat │ │ │ │ ├── ethene_dislocated.energies.dat │ │ │ │ ├── ethene_equilib_dislocated.energies.dat │ │ │ │ ├── ethenol_dislocated.energies.dat │ │ │ │ ├── ethenol_equilib_dislocated.energies.dat │ │ │ │ ├── ethine_CC_stretch.energies.dat │ │ │ │ ├── ethine_dislocated.energies.dat │ │ │ │ ├── ethine_equilib_dislocated.energies.dat │ │ │ │ ├── formaldehyde_dislocated.energies.dat │ │ │ │ ├── formaldehyde_equilib_dislocated.energies.dat │ │ │ │ ├── furan_dislocated.energies.dat │ │ │ │ ├── furan_equilib_dislocated.energies.dat │ │ │ │ ├── glycine_dislocated.energies.dat │ │ │ │ ├── glycine_equilib_dislocated.energies.dat │ │ │ │ ├── h2.energies.dat │ │ │ │ ├── h2_scaled.energies.dat │ │ │ │ ├── h2_stretch.energies.dat │ │ │ │ ├── hydrazine_dislocated.energies.dat │ │ │ │ ├── hydrazine_equilib_dislocated.energies.dat │ │ │ │ ├── hydrogen_peroxide_dislocated.energies.dat │ │ │ │ ├── hydrogen_peroxide_equilib_dislocated.energies.dat │ │ │ │ ├── methane_dislocated.energies.dat │ │ │ │ ├── methane_equilib_dislocated.energies.dat │ │ │ │ ├── methanol_dislocated.energies.dat │ │ │ │ ├── methanol_equilib_dislocated.energies.dat │ │ │ │ ├── methylamine_dislocated.energies.dat │ │ │ │ ├── methylamine_equilib_dislocated.energies.dat │ │ │ │ ├── n2_stretch.energies.dat │ │ │ │ ├── nitrate_dislocated.energies.dat │ │ │ │ ├── nitrate_equilib_dislocated.energies.dat │ │ │ │ ├── nitrite_dislocated.energies.dat │ │ │ │ ├── nitrobenzene_dislocated.energies.dat │ │ │ │ ├── nitrobenzene_equilib_dislocated.energies.dat │ │ │ │ ├── nitrous_acid_dislocated.energies.dat │ │ │ │ ├── nitrous_acid_equilib_dislocated.energies.dat │ │ │ │ ├── piperidine_dislocated.energies.dat │ │ │ │ ├── piperidine_equilib_dislocated.energies.dat │ │ │ │ ├── propan-2-imine_dislocated.energies.dat │ │ │ │ ├── propan-2-imine_equilib_dislocated.energies.dat │ │ │ │ ├── pyridine_dislocated.energies.dat │ │ │ │ ├── pyridine_equilib_dislocated.energies.dat │ │ │ │ ├── pyrimidine_dislocated.energies.dat │ │ │ │ ├── pyrimidine_equilib_dislocated.energies.dat │ │ │ │ ├── pyrrole_dislocated.energies.dat │ │ │ │ ├── pyrrole_equilib_dislocated.energies.dat │ │ │ │ ├── trimethylamine_dislocated.energies.dat │ │ │ │ ├── trimethylamine_equilib_dislocated.energies.dat │ │ │ │ ├── water_dislocated.energies.dat │ │ │ │ ├── water_equilib_dislocated.energies.dat │ │ │ │ ├── zundel_cation_dislocated.energies.dat │ │ │ │ └── zundel_cation_equilib_dislocated.energies.dat │ │ │ ├── FIT_PATHS │ │ │ │ ├── acetic_acid_dislocated.xyz │ │ │ │ ├── acetic_acid_equilib_dislocated.xyz │ │ │ │ ├── acetone_dislocated.xyz │ │ │ │ ├── acetone_equilib_dislocated.xyz │ │ │ │ ├── acetonitrile_dislocated.xyz │ │ │ │ ├── acetonitrile_equilib_dislocated.xyz │ │ │ │ ├── ammonia_dislocated.xyz │ │ │ │ ├── ammonia_equilib_dislocated.xyz │ │ │ │ ├── anisole_dislocated.xyz │ │ │ │ ├── anisole_equilib_dislocated.xyz │ │ │ │ ├── azidobenzene_dislocated.xyz │ │ │ │ ├── azidobenzene_equilib_dislocated.xyz │ │ │ │ ├── benzene_dislocated.xyz │ │ │ │ ├── benzene_equilib_dislocated.xyz │ │ │ │ ├── carbon_dioxide_dislocated.xyz │ │ │ │ ├── carbon_dioxide_equilib_dislocated.xyz │ │ │ │ ├── carbonic_acid_dislocated.xyz │ │ │ │ ├── carbonic_acid_equilib_dislocated.xyz │ │ │ │ ├── dimethylamine_dislocated.xyz │ │ │ │ ├── dimethylamine_equilib_dislocated.xyz │ │ │ │ ├── dimethylether_dislocated.xyz │ │ │ │ ├── dimethylether_equilib_dislocated.xyz │ │ │ │ ├── dinitrogen_trioxide_dislocated.xyz │ │ │ │ ├── dinitrogen_trioxide_equilib_dislocated.xyz │ │ │ │ ├── dipeptide_dislocated.xyz │ │ │ │ ├── dipeptide_equilib_dislocated.xyz │ │ │ │ ├── ethane_CC_stretch.xyz │ │ │ │ ├── ethane_dislocated.xyz │ │ │ │ ├── ethane_equilib_dislocated.xyz │ │ │ │ ├── ethanimine_dislocated.xyz │ │ │ │ ├── ethanimine_equilib_dislocated.xyz │ │ │ │ ├── ethanol_dislocated.xyz │ │ │ │ ├── ethanol_equilib_dislocated.xyz │ │ │ │ ├── ethene_CC_stretch.xyz │ │ │ │ ├── ethene_dislocated.xyz │ │ │ │ ├── ethene_equilib_dislocated.xyz │ │ │ │ ├── ethenol_dislocated.xyz │ │ │ │ ├── ethenol_equilib_dislocated.xyz │ │ │ │ ├── ethine_CC_stretch.xyz │ │ │ │ ├── ethine_dislocated.xyz │ │ │ │ ├── ethine_equilib_dislocated.xyz │ │ │ │ ├── formaldehyde_dislocated.xyz │ │ │ │ ├── formaldehyde_equilib_dislocated.xyz │ │ │ │ ├── furan_dislocated.xyz │ │ │ │ ├── furan_equilib_dislocated.xyz │ │ │ │ ├── glycine_dislocated.xyz │ │ │ │ ├── glycine_equilib_dislocated.xyz │ │ │ │ ├── h2_stretch.xyz │ │ │ │ ├── hydrazine_dislocated.xyz │ │ │ │ ├── hydrazine_equilib_dislocated.xyz │ │ │ │ ├── hydrogen_peroxide_dislocated.xyz │ │ │ │ ├── hydrogen_peroxide_equilib_dislocated.xyz │ │ │ │ ├── methane_dislocated.xyz │ │ │ │ ├── methane_equilib_dislocated.xyz │ │ │ │ ├── methanol_dislocated.xyz │ │ │ │ ├── methanol_equilib_dislocated.xyz │ │ │ │ ├── methylamine_dislocated.xyz │ │ │ │ ├── methylamine_equilib_dislocated.xyz │ │ │ │ ├── n2_stretch.xyz │ │ │ │ ├── nitrate_equilib_dislocated.xyz │ │ │ │ ├── nitrobenzene_dislocated.xyz │ │ │ │ ├── nitrobenzene_equilib_dislocated.xyz │ │ │ │ ├── nitrous_acid_dislocated.xyz │ │ │ │ ├── nitrous_acid_equilib_dislocated.xyz │ │ │ │ ├── piperidine_dislocated.xyz │ │ │ │ ├── piperidine_equilib_dislocated.xyz │ │ │ │ ├── propan-2-imine_dislocated.xyz │ │ │ │ ├── propan-2-imine_equilib_dislocated.xyz │ │ │ │ ├── pyridine_dislocated.xyz │ │ │ │ ├── pyridine_equilib_dislocated.xyz │ │ │ │ ├── pyrimidine_dislocated.xyz │ │ │ │ ├── pyrimidine_equilib_dislocated.xyz │ │ │ │ ├── pyrrole_dislocated.xyz │ │ │ │ ├── pyrrole_equilib_dislocated.xyz │ │ │ │ ├── trimethylamine_dislocated.xyz │ │ │ │ ├── trimethylamine_equilib_dislocated.xyz │ │ │ │ ├── water_dislocated.xyz │ │ │ │ ├── water_equilib_dislocated.xyz │ │ │ │ ├── zundel_cation_dislocated.xyz │ │ │ │ └── zundel_cation_equilib_dislocated.xyz │ │ │ ├── README.txt │ │ │ ├── REFERENCE │ │ │ │ ├── acetic_acid_dislocated.energies.dat │ │ │ │ ├── acetic_acid_equilib_dislocated.energies.dat │ │ │ │ ├── acetone_dislocated.energies.dat │ │ │ │ ├── acetone_equilib_dislocated.energies.dat │ │ │ │ ├── acetonitrile_dislocated.energies.dat │ │ │ │ ├── acetonitrile_equilib_dislocated.energies.dat │ │ │ │ ├── ammonia_dislocated.energies.dat │ │ │ │ ├── ammonia_equilib_dislocated.energies.dat │ │ │ │ ├── anisole_dislocated.energies.dat │ │ │ │ ├── anisole_equilib_dislocated.energies.dat │ │ │ │ ├── azidobenzene_dislocated.energies.dat │ │ │ │ ├── azidobenzene_equilib_dislocated.energies.dat │ │ │ │ ├── benzene_dislocated.energies.dat │ │ │ │ ├── benzene_equilib_dislocated.energies.dat │ │ │ │ ├── carbon_dioxide_dislocated.energies.dat │ │ │ │ ├── carbon_dioxide_equilib_dislocated.energies.dat │ │ │ │ ├── carbonic_acid_dislocated.energies.dat │ │ │ │ ├── carbonic_acid_equilib_dislocated.energies.dat │ │ │ │ ├── dimethylamine_dislocated.energies.dat │ │ │ │ ├── dimethylamine_equilib_dislocated.energies.dat │ │ │ │ ├── dimethylether_dislocated.energies.dat │ │ │ │ ├── dimethylether_equilib_dislocated.energies.dat │ │ │ │ ├── dinitrogen_trioxide_dislocated.energies.dat │ │ │ │ ├── dinitrogen_trioxide_equilib_dislocated.energies.dat │ │ │ │ ├── dipeptide_dislocated.energies.dat │ │ │ │ ├── dipeptide_equilib_dislocated.energies.dat │ │ │ │ ├── ethane_CC_stretch.energies.dat │ │ │ │ ├── ethane_dislocated.energies.dat │ │ │ │ ├── ethane_equilib_dislocated.energies.dat │ │ │ │ ├── ethanimine_dislocated.energies.dat │ │ │ │ ├── ethanimine_equilib_dislocated.energies.dat │ │ │ │ ├── ethanol_dislocated.energies.dat │ │ │ │ ├── ethanol_equilib_dislocated.energies.dat │ │ │ │ ├── ethene_CC_stretch.energies.dat │ │ │ │ ├── ethene_dislocated.energies.dat │ │ │ │ ├── ethene_equilib_dislocated.energies.dat │ │ │ │ ├── ethenol_dislocated.energies.dat │ │ │ │ ├── ethenol_equilib_dislocated.energies.dat │ │ │ │ ├── ethine_CC_stretch.energies.dat │ │ │ │ ├── ethine_dislocated.energies.dat │ │ │ │ ├── ethine_equilib_dislocated.energies.dat │ │ │ │ ├── formaldehyde_dislocated.energies.dat │ │ │ │ ├── formaldehyde_equilib_dislocated.energies.dat │ │ │ │ ├── furan_dislocated.energies.dat │ │ │ │ ├── furan_equilib_dislocated.energies.dat │ │ │ │ ├── glycine_dislocated.energies.dat │ │ │ │ ├── glycine_equilib_dislocated.energies.dat │ │ │ │ ├── h2.energies.dat │ │ │ │ ├── h2_scaled.energies.dat │ │ │ │ ├── h2_stretch.energies.dat │ │ │ │ ├── hydrazine_dislocated.energies.dat │ │ │ │ ├── hydrazine_equilib_dislocated.energies.dat │ │ │ │ ├── hydrogen_peroxide_dislocated.energies.dat │ │ │ │ ├── hydrogen_peroxide_equilib_dislocated.energies.dat │ │ │ │ ├── methane_dislocated.energies.dat │ │ │ │ ├── methane_equilib_dislocated.energies.dat │ │ │ │ ├── methanol_dislocated.energies.dat │ │ │ │ ├── methanol_equilib_dislocated.energies.dat │ │ │ │ ├── methylamine_dislocated.energies.dat │ │ │ │ ├── methylamine_equilib_dislocated.energies.dat │ │ │ │ ├── n2_stretch.energies.dat │ │ │ │ ├── nitrate_equilib_dislocated.energies.dat │ │ │ │ ├── nitrobenzene_dislocated.energies.dat │ │ │ │ ├── nitrobenzene_equilib_dislocated.energies.dat │ │ │ │ ├── nitrous_acid_dislocated.energies.dat │ │ │ │ ├── nitrous_acid_equilib_dislocated.energies.dat │ │ │ │ ├── piperidine_dislocated.energies.dat │ │ │ │ ├── piperidine_equilib_dislocated.energies.dat │ │ │ │ ├── propan-2-imine_dislocated.energies.dat │ │ │ │ ├── propan-2-imine_equilib_dislocated.energies.dat │ │ │ │ ├── pyridine_dislocated.energies.dat │ │ │ │ ├── pyridine_equilib_dislocated.energies.dat │ │ │ │ ├── pyrimidine_dislocated.energies.dat │ │ │ │ ├── pyrimidine_equilib_dislocated.energies.dat │ │ │ │ ├── pyrrole_dislocated.energies.dat │ │ │ │ ├── pyrrole_equilib_dislocated.energies.dat │ │ │ │ ├── trimethylamine_dislocated.energies.dat │ │ │ │ ├── trimethylamine_equilib_dislocated.energies.dat │ │ │ │ ├── water_dislocated.energies.dat │ │ │ │ ├── water_equilib_dislocated.energies.dat │ │ │ │ ├── zundel_cation_dislocated.energies.dat │ │ │ │ └── zundel_cation_equilib_dislocated.energies.dat │ │ │ ├── REPPOT_TABLES │ │ │ │ ├── __init__.py │ │ │ │ ├── c_c.py │ │ │ │ ├── c_n.py │ │ │ │ ├── c_o.py │ │ │ │ ├── dummy.py │ │ │ │ ├── h_c.py │ │ │ │ ├── h_cl.py │ │ │ │ ├── h_h.py │ │ │ │ ├── h_n.py │ │ │ │ ├── h_o.py │ │ │ │ ├── n_n.py │ │ │ │ ├── n_o.py │ │ │ │ └── o_o.py │ │ │ ├── STRUCTURES │ │ │ │ ├── acetic_acid.xyz │ │ │ │ ├── acetone.xyz │ │ │ │ ├── acetonitrile.xyz │ │ │ │ ├── ammonia.xyz │ │ │ │ ├── anisole.xyz │ │ │ │ ├── azidobenzene.xyz │ │ │ │ ├── benzene.xyz │ │ │ │ ├── carbon_dioxide.xyz │ │ │ │ ├── carbonic_acid.xyz │ │ │ │ ├── dimethylamine.xyz │ │ │ │ ├── dimethylether.xyz │ │ │ │ ├── dinitrogen_trioxide.xyz │ │ │ │ ├── dipeptide.xyz │ │ │ │ ├── ethane.xyz │ │ │ │ ├── ethanimine.xyz │ │ │ │ ├── ethanol.xyz │ │ │ │ ├── ethene.xyz │ │ │ │ ├── ethenol.xyz │ │ │ │ ├── ethine.xyz │ │ │ │ ├── formaldehyde.xyz │ │ │ │ ├── furan.xyz │ │ │ │ ├── glycine.xyz │ │ │ │ ├── h2.xyz │ │ │ │ ├── hydrazine.xyz │ │ │ │ ├── hydrogen_peroxide.xyz │ │ │ │ ├── methane.xyz │ │ │ │ ├── methanol.xyz │ │ │ │ ├── methylamine.xyz │ │ │ │ ├── n2.xyz │ │ │ │ ├── nitrate.xyz │ │ │ │ ├── nitrite.xyz │ │ │ │ ├── nitrobenzene.xyz │ │ │ │ ├── nitrous_acid.xyz │ │ │ │ ├── piperidine.xyz │ │ │ │ ├── propan-2-imine.xyz │ │ │ │ ├── pyridine.xyz │ │ │ │ ├── pyrimidine.xyz │ │ │ │ ├── pyrrole.xyz │ │ │ │ ├── trimethylamine.xyz │ │ │ │ ├── water.xyz │ │ │ │ └── zundel_cation.xyz │ │ │ ├── calc_fitpaths.sh │ │ │ ├── dftbaby.cfg │ │ │ └── make_fitpaths.sh │ │ └── VALIDATION │ │ │ ├── DFTB │ │ │ ├── acetic_acid.xyz │ │ │ ├── acetonitrile.xyz │ │ │ ├── ammonia.xyz │ │ │ ├── benzene.xyz │ │ │ ├── dimethylamine.xyz │ │ │ ├── dimethylether.xyz │ │ │ ├── dipeptide.xyz │ │ │ ├── ethane.xyz │ │ │ ├── ethanimine.xyz │ │ │ ├── ethene.xyz │ │ │ ├── ethine.xyz │ │ │ ├── formaldehyde.xyz │ │ │ ├── furan.xyz │ │ │ ├── h2.xyz │ │ │ ├── methane.xyz │ │ │ ├── methanol.xyz │ │ │ ├── nitrobenzene.xyz │ │ │ └── water.xyz │ │ │ ├── REFERENCE │ │ │ ├── acetic_acid.xyz │ │ │ ├── acetonitrile.xyz │ │ │ ├── ammonia.xyz │ │ │ ├── benzene.xyz │ │ │ ├── dimethylamine.xyz │ │ │ ├── dimethylether.xyz │ │ │ ├── dipeptide.xyz │ │ │ ├── ethane.xyz │ │ │ ├── ethanimine.xyz │ │ │ ├── ethene.xyz │ │ │ ├── ethine.xyz │ │ │ ├── formaldehyde.xyz │ │ │ ├── furan.xyz │ │ │ ├── h2.xyz │ │ │ ├── methane.xyz │ │ │ ├── methanol.xyz │ │ │ ├── nitrobenzene.xyz │ │ │ └── water.xyz │ │ │ ├── STRUCTURES │ │ │ ├── acetic_acid.xyz │ │ │ ├── acetonitrile.xyz │ │ │ ├── ammonia.xyz │ │ │ ├── benzene.xyz │ │ │ ├── dimethylamine.xyz │ │ │ ├── dimethylether.xyz │ │ │ ├── dipeptide.xyz │ │ │ ├── ethane.xyz │ │ │ ├── ethanimine.xyz │ │ │ ├── ethene.xyz │ │ │ ├── ethine.xyz │ │ │ ├── formaldehyde.xyz │ │ │ ├── furan.xyz │ │ │ ├── h2.xyz │ │ │ ├── methane.xyz │ │ │ ├── methanol.xyz │ │ │ ├── nitrobenzene.xyz │ │ │ └── water.xyz │ │ │ ├── compare_reaction_energies.sh │ │ │ ├── compare_structures.sh │ │ │ ├── dftbaby.cfg │ │ │ ├── opt_template.gjf │ │ │ ├── optimize_dftb.sh │ │ │ ├── optimize_reference.sh │ │ │ ├── reaction_energies.txt │ │ │ ├── reaction_energy.py │ │ │ └── structure_comparison.txt │ ├── convert_reppotfile.py │ ├── create_dimer_trajectory.py │ ├── dftb_forces_trajectory.py │ ├── fit_reppot_dimer.sh │ ├── force_trajectory.py │ ├── gaussian_forces_trajectory.py │ ├── generate_repulsive_potentials.py │ ├── perturb_geometry.py │ ├── plot_reppotfile.py │ ├── reppot_tables │ └── scale_geometry.py ├── SKMatrixElements.py ├── STO3G_valence.py ├── ScalarCoupling.py ├── SlaterKoster │ ├── PolarTwoCenterGrid.py │ ├── PseudoAtomDFT.py │ ├── RadialIntegrator.py │ ├── RadialPotential.py │ ├── SKIntegrals.py │ ├── XCFunctionals.py │ ├── __init__.py │ ├── confined_pseudo_atoms │ │ ├── README.txt │ │ ├── __init__.py │ │ ├── c.py │ │ ├── gamma_integrals.py │ │ ├── h.py │ │ ├── n.py │ │ ├── o.py │ │ ├── onsite_electron_integrals.py │ │ └── zn.py │ ├── density_spline.py │ ├── fit_densities.py │ ├── free_pseudo_atoms │ │ ├── __init__.py │ │ ├── c.py │ │ ├── gamma_integrals.py │ │ ├── h.py │ │ ├── n.py │ │ ├── o.py │ │ ├── onsite_electron_integrals.py │ │ └── zn.py │ ├── generate_confined_pseudoatoms.py │ ├── generate_free_pseudoatoms.py │ ├── generate_gamma_integrals.py │ ├── generate_onsite_integrals.py │ ├── generate_ptcgrid.py │ ├── generate_slakotables.py │ ├── hotbit_format.py │ ├── plot_gamma_integrals.py │ ├── plot_pseudoatoms.py │ ├── plot_slakofile.py │ ├── pylibxc │ │ ├── Makefile │ │ ├── __init__.py │ │ ├── pylibxc.cpp │ │ ├── pylibxc.py │ │ └── setup.py │ ├── slako_tables │ │ ├── README.txt │ │ ├── __init__.py │ │ ├── c_c.py │ │ ├── c_n.py │ │ ├── c_o.py │ │ ├── c_zn.py │ │ ├── h_c.py │ │ ├── h_h.py │ │ ├── h_n.py │ │ ├── h_o.py │ │ ├── h_zn.py │ │ ├── n_n.py │ │ ├── n_o.py │ │ ├── n_zn.py │ │ ├── o_o.py │ │ ├── o_zn.py │ │ └── zn_zn.py │ ├── slako_transformations.py │ ├── slako_transformations_dipole.py │ ├── slako_transformations_dipole_lmax1.py │ └── slako_transformations_dipole_lmax2.py ├── Solver.py ├── SphericalHarmonics.py ├── StabilityAnalysis.py ├── Symmetry.py ├── Thermochemistry.py ├── Timer.py ├── XYZ.py ├── __init__.py ├── dftbaby.cfg ├── extensions │ ├── Makefile │ ├── __init__.py │ ├── cosmo.f90 │ ├── grad.f90 │ ├── mulliken.f90 │ ├── slako.f90 │ ├── slako_transformations_dipole_lmax1.f90 │ ├── slako_transformations_dipole_lmax1.f90.old │ ├── slako_transformations_dipole_lmax2.f90 │ ├── slako_transformations_grad_lmax2.f90 │ ├── slako_transformations_lmax2.f90 │ ├── splder.f │ ├── splines.f90 │ ├── tddftb.f90 │ └── thomson.f90 ├── optimize.py ├── optimize_meci.py ├── optimize_neb.py ├── optimize_neb_g09.py ├── optparse.py ├── scan.py └── utils.py ├── LICENSE ├── MANIFEST.in ├── README.txt ├── VERSION ├── dftbaby.modulefile ├── dftbaby_env.sh ├── doc ├── Makefile ├── make.bat ├── source │ ├── Ag6_twosided_pyramid.png │ ├── ag-ag_repforce.png │ ├── ag-ag_repforce_fit.png │ ├── ag-ag_reppot_fit.png │ ├── ag6_reppot_chemical_environment.png │ ├── c_confined_pseudo_atom.png │ ├── conf.py │ ├── excited_states.rst │ ├── gradient_and_hessian.rst │ ├── ground_state.rst │ ├── h2_dimer_repulsive_gradient.png │ ├── h_h_repulsive_gradient_fit.png │ ├── h_h_repulsive_gradient_scatter.png │ ├── h_h_repulsive_potential_compare.png │ ├── h_h_repulsive_potential_fit.png │ ├── index.rst │ ├── introduction.rst │ ├── parametrization.rst │ ├── slakofile_c_c_H.png │ └── slakofile_c_c_S.png └── wiki-markdown │ ├── main_page.md │ ├── options.md │ ├── parametrization.md │ ├── screenshot_excited_states.png │ ├── screenshot_ground_state.png │ ├── screenshot_save_movie.png │ ├── screenshot_trajviewer2.png │ ├── screenshot_trajviewer2_superpositions.png │ ├── scripts.md │ ├── slakofile_c_c_H.png │ └── slakofile_c_c_S.png ├── examples ├── CHELPG │ ├── Makefile │ ├── README.txt │ ├── ethene.gjf │ └── multiwfn.inp ├── CPKS │ ├── README.txt │ ├── charge_gradients.py │ └── water.xyz ├── EXCITON │ ├── README.txt │ ├── monomer.chromo │ ├── monomer.ff │ ├── monomer.gjf │ ├── show_transition_charges.tcl │ ├── show_unit_cell.tcl │ ├── tube_unit_cell.chromo │ ├── tube_unit_cell.ff │ └── tube_unit_cell_ROTDIP.chromo ├── META │ ├── F2_rotated.xyz │ ├── README.txt │ ├── dftbaby.cfg │ ├── dynamics.in │ ├── meta-config.py │ └── vg_2500-g.png ├── NAMD │ ├── F1_C2v.xyz │ ├── README.txt │ ├── dftbaby.cfg │ └── dynamics.in ├── NEB │ ├── README.txt │ ├── dftbaby.cfg │ └── water_flip.xyz ├── ORB_LOC │ ├── README.txt │ ├── dftbaby.cfg │ ├── dynamics.in │ ├── ethene_dimer.xyz │ └── localized_orbitals.molden ├── QMMM │ ├── README.txt │ ├── dftbaby.cfg │ ├── pyrene_crystal.ff │ └── pyrene_crystal.xyz ├── RELAXED_SCAN │ ├── README.txt │ ├── dftbaby.cfg │ └── phenylbenzene.xyz └── SKA │ ├── README.txt │ ├── furan_dyson.json │ ├── furan_dyson.molden │ └── water.json └── setup.py /.gitignore: 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