3. API Documentation

This part of the documentation is generated from the docstrings in the source code.

• 3.1. horton – The main HORTON Package
  • 3.1.1. horton.cache – Avoid recomputation of earlier results and reallocation of existing arrays
  • 3.1.2. horton.cext – C++ extensions
  • 3.1.3. horton.constants – Physicochemical constants in atomic units
  • 3.1.4. horton.context – The context in which HORTON is used
  • 3.1.5. horton.exceptions – Definition of all excpetions in HORTON
  • 3.1.6. horton.log – Screen logging, timing and citation management
  • 3.1.7. horton.moments – Auxiliary routines related to multipole moments
  • 3.1.8. horton.orbital_utils – Utility functions for orbital modifications
  • 3.1.9. horton.periodic – Periodic table of elements
  • 3.1.10. horton.quadprog – A light-weight quadratic programming solver
  • 3.1.11. horton.symmetry – Geometric symmetries
  • 3.1.12. horton.units – Conversion from and to atomic units
  • 3.1.13. horton.utils – Utility functions
  • 3.1.14. horton/cell.h – Unit cell code to specify periodic boundary conditions
  • 3.1.15. horton/moments.h – Efficient evaluation of various of polynomials
  • 3.1.16. horton/nucpot.h – Low-level implementation of nuclear potential on a grid
• 3.2. horton.espfit – Electrostatic potential fitting
  • 3.2.1. horton.espfit.cext – C++ extensions
  • 3.2.2. horton.espfit.cost – ESP cost functions for estimating and testing charges
  • 3.2.3. horton/espfit/electrostatics.h – Computation of ESP cost functions
  • 3.2.4. horton/espfit/mask.h – Computation of weights for ESP cost functions
• 3.3. horton.gbasis – Gaussian basis sets
  • 3.3.1. horton.gbasis.cext – C++ extensions
  • 3.3.2. horton.gbasis.gobasis – Gaussian orbital basis set module.
  • 3.3.3. horton.gbasis.iobas – Input/Output routines for gaussian basis sets
  • 3.3.4. horton/gbasis/boys.h – The Boys function
  • 3.3.5. horton/gbasis/calc.h – Base class for any integral/evaluation of Gaussian functions
  • 3.3.6. horton/gbasis/cartpure.h – Conversion of Cartesian to Pure Gaussian functions
  • 3.3.7. horton/gbasis/cholesky.h – Cholesky decomposition of (any) four-center integrals
  • 3.3.8. horton/gbasis/common.h – Auxiliary functions
  • 3.3.9. horton/gbasis/fns.h – Evaluate functions on grids and derive Fock matrices from potentials on grids.
  • 3.3.10. horton/gbasis/gbasis.h – Gaussian basis set classes
  • 3.3.11. horton/gbasis/gbw.h – A four-center integral wrapper for the Cholesky code
  • 3.3.12. horton/gbasis/ints.h – Evaluation of integrals of Gaussian basis functions
  • 3.3.13. horton/gbasis/iter_gb.h – Iterators over Gaussian basis functions
  • 3.3.14. horton/gbasis/iter_pow.h – Iterators over Cartesian polynomials in one shell
• 3.4. horton.grid – Numerical integration grids
  • 3.4.1. horton.grid.atgrid – Atomic grids
  • 3.4.2. horton.grid.base – Base classes for 3D integration grids
  • 3.4.3. horton.grid.cext – C++ extensions
  • 3.4.4. horton.grid.int1d – 1D integration algorithms
  • 3.4.5. horton.grid.molgrid – Molecular integration grids
  • 3.4.6. horton.grid.ode2 – Finite-element second-order ODE solver
  • 3.4.7. horton.grid.poisson – Becke-style numerical Poisson solver
  • 3.4.8. horton.grid.radial – 1D Radial integration grid
  • 3.4.9. horton.grid.utils – Auxiliaries for numerical integrals
  • 3.4.10. horton.grid.visual – Grids suitable for visualization
  • 3.4.11. horton/grid/becke.h – Becke partitioning weight function
  • 3.4.12. horton/grid/cubic_spline.h – One-dimensional cubic splines (on uniform grids)
  • 3.4.13. horton/grid/evaluate.h – Evaluation of splines on grids
  • 3.4.14. horton/grid/lebedev_laikov.h – Grids for quadrature on a sphere
  • 3.4.15. horton/grid/ode2.h – Second-order finite-element ODE solver using Hermite polynomials
  • 3.4.16. horton/grid/rtransform.h – Transformation from uniform 1D to non-uniform 1D grids
  • 3.4.17. horton/grid/uniform.h – Uniform 3D grids
  • 3.4.18. horton/grid/utils.h – Auxiliary functions
• 3.5. horton.io – Input and output routines
  • 3.5.1. horton.io.cif – Crystalographic Information File format
  • 3.5.2. horton.io.cp2k – CP2K atomic wavefunctions
  • 3.5.3. horton.io.cube – Gaussian cube file format
  • 3.5.4. horton.io.gaussian – Gaussian LOG and FCHK file fromats
  • 3.5.5. horton.io.internal – HORTON internal file format
  • 3.5.6. horton.io.iodata – Input/output dispatcher for different file formats
  • 3.5.7. horton.io.lockedh5 – H5 file with lock
  • 3.5.8. horton.io.molden – Molden wavefunction input file format
  • 3.5.9. horton.io.molekel – Molekel wavefunction input file format
  • 3.5.10. horton.io.molpro – Molpro 2012 FCIDUMP format.
  • 3.5.11. horton.io.vasp – VASP POSCAR, CHGCAR and POTCAR file formats
  • 3.5.12. horton.io.wfn – WFN File format (Gaussian and GAMESS)
  • 3.5.13. horton.io.xyz – XYZ file format
• 3.6. horton.matrix – One-, two-, three- and four-dimensional matrix implementations
  • 3.6.1. horton.matrix.base – Base classes
  • 3.6.2. horton.matrix.cext – C++ extensions for matrix package
  • 3.6.3. horton.matrix.cholesky – Cholesky decomposition of four-index objects
  • 3.6.4. horton.matrix.dense – Dense matrix implementations
  • 3.6.5. horton/matrix/slicing.h – Low-level routines for CholeskyLinalgFactory
• 3.7. horton.meanfield – Mean-field electronic structure code
  • 3.7.1. horton.meanfield.bond_order – Generic implementation of bond orders for mean-field wavefunctions
  • 3.7.2. horton.meanfield.builtin – Built-in energy terms
  • 3.7.3. horton.meanfield.cext – C++ extensions
  • 3.7.4. horton.meanfield.convergence – Evaluation of convergence criteria
  • 3.7.5. horton.meanfield.gridgroup – Container for observables involving numerical integration
  • 3.7.6. horton.meanfield.guess – Initial guesses for wavefunctions
  • 3.7.7. horton.meanfield.hamiltonian – Mean-field DFT/HF Hamiltonian data structures
  • 3.7.8. horton.meanfield.libxc – Interface to LDA, GGA and hybrid functionals from LibXC
  • 3.7.9. horton.meanfield.observable – Base classes for energy terms and other observables of the wavefunction
  • 3.7.10. horton.meanfield.occ – Occupation number models
  • 3.7.11. horton.meanfield.project – Projection of 1-electron orbitals to a new basis set
  • 3.7.12. horton.meanfield.response – Evaluation of response functions
  • 3.7.13. horton.meanfield.rotate – Rotation of orbitals
  • 3.7.14. horton.meanfield.scf – Basic Self-Consistent Field (SCF) algorithm.
  • 3.7.15. horton.meanfield.scf_cdiis – Commutator DIIS SCF algorithm
  • 3.7.16. horton.meanfield.scf_diis – Abstract DIIS code used by the different DIIS implementations
  • 3.7.17. horton.meanfield.scf_ediis – Energy DIIS SCF algorithm
  • 3.7.18. horton.meanfield.scf_ediis2 – EDIIS+DIIS SCF algorithm
  • 3.7.19. horton.meanfield.scf_oda – Optimal Damping SCF algorithm
  • 3.7.20. horton.meanfield.utils – Utility functions
• 3.8. horton.modelhamiltonians – Model Hamiltonians
  • 3.8.1. horton.modelhamiltonians.physmodham – Physical Model Hamiltonian
• 3.9. horton.part – Density-based partitioning (fuzzy atoms-in-molecules) package
  • 3.9.1. horton.part.base – Base classes for (atoms-in-molecules) partitioning algorithms
  • 3.9.2. horton.part.becke – Becke partitioning
  • 3.9.3. horton.part.hirshfeld – Hirshfeld partitioning
  • 3.9.4. horton.part.hirshfeld_i – Iterative Hirshfeld (HI) partitioning
  • 3.9.5. horton.part.iterstock – Iterative Stockholder Analysis (ISA) partitioning
  • 3.9.6. horton.part.mbis – Minimal Basis Iterative Stockholder (MBIS) partitioning
  • 3.9.7. horton.part.mulliken – Mulliken partitioning
  • 3.9.8. horton.part.proatomdb – Pro-atom databases
  • 3.9.9. horton.part.stockholder – Base classes for all stockholder partitioning schemes
  • 3.9.10. horton.part.symmetry – Symmetry analysis of atoms-in-molecules results
• 3.10. horton.scripts – Code (solely) used by HORTON’s command line scripts
  • 3.10.1. horton.scripts.atomdb – Code used by horton-atomdb.py
  • 3.10.2. horton.scripts.common – Code shared by several scripts
  • 3.10.3. horton.scripts.espfit – Code used by ESP fitting scripts
  • 3.10.4. horton.scripts.hdf2csv – Code used by horton-hdf2csv.py
  • 3.10.5. horton.scripts.wpart – Utility functions for the horton-wpart.py script