## Table of contents

- Table of contents
- Details
- Complex numbers
- Datasets with spin symmetry
- The INTS Group
- The SCF Group
- The RESP Group
- The RT 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)

##
`INTS`

Group

The 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) |

##
`SCF`

Group

The 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` |

##
`RESP`

Group

The 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}` |

###
`RESIDUE`

Group

The 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` |

###
`FDR`

Group

The 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}` |

##
`RT`

Group

The 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}` |