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  • Binary Reference

Last edited by Xiaolin Liu Nov 30, 2020
Page history

Binary Reference

Table of contents

  • Table of contents
  • Details
  • Complex numbers
  • Datasets with spin symmetry
  • The INTS Group
  • The SCF Group
  • The RESP Group
    • The RESIDUE Group
    • The FDR Group
  • The RT Group
  • The CC Group

Details

The ChronusQ binary file is a standard HDF5 file. As such, it can be inspected using the HDF5 tools, (e.g. h5ls, h5dump, etc.) or it can be opened in any program that can interface with HDF5 files. Commonly, the C/C++ HDF5 libraries and API or the h5py Python package are used to interface with the binary file. It is organized as a hierarchy with each dataset within a group based on whether it is a raw integral or the type of calculation in which it is involved.

Complex numbers

HDF5 does not have native support for complex numbers. ChronusQ uses the following compound datatype for complex numbers:

DATATYPE  H5T_COMPOUND {
  H5T_IEEE_F64LE "r";
  H5T_IEEE_F64LE "i";
}

Datasets with spin symmetry

For all datasets with a _<SPIN> suffix, SPIN is one of (SCALAR, MZ, MY, MX). SCALAR datasets are available in all calculations; MZ datasets are available for all calculations aside from those with restricted symmetry; MY and MX are available only for two component calculations. (generalized spin or relativistic calculations)

The INTS Group

The following datasets are available in the INTS group. This section is populated in all ChronusQ calculations. All operators are a two dimensional dataset with size \mathrm{NB}, \mathrm{NB} where \mathrm{NB} is the number of basis functions.

Dataset Name Description
OVERLAP Overlap between basis functions
KINETIC Kinetic energy
POTENTIAL Nuclear attraction potential
CORE_HAMILTONIAN_SCALAR Core Hamiltonian (Kinetic & Nuclear Attraction)
ELEC_DIPOLE_LEN_<DIR> Electric dipole element in the length gauge. DIR is one of (X, Y, Z)
ELEC_DIPOLE_VEL_<DIR> Electric dipole element in the velocity gauge. DIR is one of (X, Y, Z)
ELEC_QUADRUPOLE_LEN_<DIR> Electric quadrupole element in the length gauge. DIR is one of (XX, XY, XZ, YY, YZ, ZZ)
ELEC_QUADRUPOLE_VEL_<DIR> Electric quadrupole element in the velocity gauge. DIR is one of (XX, XY, XZ, YY, YZ, ZZ)
ELEC_OCTUPOLE_LEN_<DIR> Electric octupole element in the length gauge. DIR is one of (XXX, XXY, XXZ, XYY, XYZ, XZZ, YYY, YYZ, YZZ, ZZZ)
ELEC_OCTUPOLE_VEL_<DIR> Electric octupole element in the velocity gauge. DIR is one of (XXX, XXY, XXZ, XYY, XYZ, XZZ, YYY, YYZ, YZZ, ZZZ)
MAG_DIPOLE_<DIR> Magnetic dipole element. DIR is one of (X, Y, Z)
MAG_QUADRUPOLE_<DIR> Magnetic quadrupole element. DIR is one of (XX, XY, XZ, YY, YZ, ZZ)

The SCF Group

The following datasets are available in the SCF group. They are created during the course of self-consistent wavefunction optimization. This group is populated in all ChronusQ calculations.

Dataset Name Description Dimension
1PDM_<SPIN> Spin component of the one particle density matrix in the AO basis \mathrm{NB},\mathrm{NB}
1PDM_ORTHO_<SPIN> Spin component of the one particle density matrix in the orthonormalized AO basis \mathrm{NB},\mathrm{NB}
FOCK_<SPIN> Spin component of the Fock matrix in the AO basis \mathrm{NB}, \mathrm{NB}
FOCK_ORTHO_<SPIN> Spin component of the Fock matrix in the orthonormalized AO basis \mathrm{NB}, \mathrm{NB}
MO1 Molecular orbital coefficents between the AO and MO basis \mathrm{NB}, \mathrm{NB}
MO2 Beta molecular orbital coefficents between the AO and MO basis. Only present in calculations with unrestricted spin symmetry \mathrm{NB}, \mathrm{NB}
ONE_BODY_ENERGY Energy of all the one-body operators contributing to the Fock matrix 1
MANY_BODY_ENERGY Energy of all the multi-body operators contributing to the Fock matrix 1
TOTAL_ENERGY Energy of the total molecular system 1

The following datasets are also available in the SCF group, but they are only meaningful at the end of a successful optimization.

Dataset Name Description Dimension
S_EXPECT Expectation value of the spin operator in each direction (X, Y, Z) 3
S_SQUARED Expectation value of the spin squared operator 1
LEN_ELECTRIC_DIPOLE Expectation value of the dipole operator in the length gauge 3
LEN_ELECTRIC_QUADRUPOLE Expectation value of the quadrupole operator in the length gauge 3,3
LEN_ELECTRIC_OCTUPOLE Expectation value of the octupole operator in the length gauge 3,3,3

The RESP Group

The following datasets are available in the RESP group. They are created during the course of self-consistent wavefunction optimization. This group is populated in ChronusQ RESP calculations. In the dimensions below, \mathrm{FD} stands for the full dimension of one of the sides of the propagator matrix and \mathrm{NR} stands for the number of roots to be solved for.

Dataset Name Description Dimension
DOFULL Whether to do the full matrix 1
FULLMATRIX Full propagator matrix \mathrm{FD},\mathrm{FD}

The RESIDUE Group

Dataset Name Description Dimension
DEMIN Minimum energy of eigenvalues 1
GPLHR_M Subspace expansion parameter 1
GPLHR_SIGMA Harmonic shift 1
EIGENVALUES Eigenvalues of the response problem (e.g. transition energies) \mathrm{NR}
EIGENVECTORS Eigenvectors of the response problem (e.g. transition densities) \mathrm{NR},\mathrm{FD}
OSC_STRENGTH Oscillator strength of each transition \mathrm{NR}
ROT_STRENGTH_LEN_EDA Rotary strength of each transition within the length gauge and electric dipole approximation \mathrm{NR}
TRANSITION_ELECTRIC_DIPOLE_LENGTH Transition dipole in the length gauge \mathrm{NR},3
TRANSITION_ELECTRIC_DIPOLE_VELOCITY Transition dipole in the velocity gauge \mathrm{NR},3
TRANSITION_ELECTRIC_QUADRUPOLE_LENGTH Transition quadrupole in the length gauge \mathrm{NR},6
TRANSITION_ELECTRIC_QUADRUPOLE_VELOCITY Transition quadrupole in the velocity gauge \mathrm{NR},6
TRANSITION_ELECTRIC_OCTUPOLE_LENGTH Transition octupole in the length gauge \mathrm{NR},10
TRANSITION_ELECTRIC_OCTUPOLE_VELOCITY Transition octupole in the velocity gauge \mathrm{NR},10
TRANSITION_MAGNETIC_DIPOLE Transition magnetic dipole \mathrm{NR},3
TRANSITION_MAGNETIC_QUADRUPOLE Transition magnetic quadrupole \mathrm{NR},10

The FDR Group

In this section, \mathrm{NF} stands for the number of frequencies

Dataset Name Description Dimension
DAMP Damping parameter 1
OMEGA Frequencies at which to calculate \mathrm{NF}
ED_ED_POLARIZABILITY_LENGTH Electric dipole/electric dipole polarizability in the length gauge \mathrm{NF},3,3
EQ_ED_POLARIZABILITY_LENGTH Electric quadrupole/electric dipole polarizability in the length gauge \mathrm{NF},3,6
MD_ED_POLARIZABILITY_LENGTH Magnetic dipole/electric dipole polarizability in the length gauge \mathrm{NF},3,3
OPA_CROSS_SECTION_EDA One photon absorption cross section in the electric dipole approximation \mathrm{NF}

The RT Group

The following datasets are available in the RT group. They are created during the course of self-consistent wavefunction optimization. This group is populated in all ChronusQ calculations. In this section, \mathrm{NS} stands for the number of steps.

Dataset Name Description Dimension
TIME Time at each step \mathrm{NS}
ENERGY Energy at each step \mathrm{NS}
LEN_ELEC_DIPOLE Electric dipole in the length gauge at each step \mathrm{NS},3
LEN_ELEC_DIPOLE_FIELD External electric dipole field in the length gauge at each step \mathrm{NS},3
TD_1PDM_<SPIN> Spin component of the time-dependent one particle density matrix in the AO basis at the last saved step \mathrm{NB},\mathrm{NB}
TD_1PDM_ORTHO_<SPIN> Spin component of the time-dependent one particle density matrix in the orthonormalized AO basis at the last saved step \mathrm{NB},\mathrm{NB}

The CC Group

The following datasets are available in the CC group. They are created during the course of Coupled-cluster calculations. This group is populated in ChronusQ CC calculations.

Dataset Name Description Dimension
CORRELATION_ENERGY The CC correlation energy 1
T_NORM The norm of CC amplitudes $1$
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Overview and Features

Getting ChronusQ

Running ChronusQ

Input sections

     Overview
     QM and PROTQM
     Molecule
     Basis and DFBasis
     Ints
     DFTInts
     SCF
     RT
     Response
     CC
     MCSCF
     Misc

FAQ

Examples

     HF energy
     Relativistic DFT Energy
     Linear Response TDDFT
     Frequency dependent TDHF
     Model Order Reduction of TDDFT
     Electron dynamics

Keyword Reference

Binary Reference