Binary Reference

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	$`1`$