Native .fcc format
Since JOYCE3.0, [28]
the default format for the file containing the QM molecular information (e.g. geometry, energy, gradient and Hessian) is the .fcc state files, the native format used in
3, [19]
which has now been added to the formatted checkpoint file (), produced by the GAUSSIAN16 code and originally[1,21] read by JOYCE (see next subsection).
In this way, we can exploit the tools distributed from a public repository,[24] and developed to generate the state files from a plethora of different codes for electronic structure calculations.
Depending on the type of calculation, the file is organized into sections, which can appear in the file in any order.
Some of the most relevant sections for JOYCE are the following:
- GEOM (optionally specifying the units, i.e., (UNITS = ANGS))
This section includes the molecular geometry in XYZ format. Namely, the first line of the section indicates the number of atoms, followed by a line that generally contains a comment.
Then, the element name and x, y, z coordinates (in Å) are given for each atom in the structure.
- ENER (optionally specifying the units, i.e., (UNITS = AU))
This section contains the absolute energy in atomic units.
- GRAD (optionally specifying the units, i.e., (UNITS = AU))
This section includes the elemenets of the gradient, ordered by atom including the x,y,z components for each one. The number of elements by line is arbitrary, but it is usually limited by 5 per line.
- HESS (optionally specifying the units, i.e., (UNITS = AU))
This section contains the elements of the lower triangular part of the Hessian matrix, in atomic units.
In the following a sample state file in .fcc format for water is given.
note that not all sections are required in a run and can therefore be skipped.
INFO
State file generated from file: water.fchk (format: fchk)
GEOM UNITS=ANGS
3
Geometry from water.fchk in xyz format (with filter: all)
O 0.00000000 0.00000000 -0.06661080
H 0.00000000 -0.75914368 0.52858090
H -0.00000000 0.75914368 0.52858090
ENER UNITS=AU
-7.63256737E+01
GRAD UNITS=AU
7.81563942E-28 0.00000000E+00 -7.78708105E-06 1.29381262E-23 -4.22604034E-07
3.12721587E-07 -1.29389077E-23 4.22604034E-07 3.12721587E-07
HESS UNITS=AU
3.85407173E-06 0.00000000E+00 6.75100308E-01 0.00000000E+00 0.00000000E+00
4.68278502E-01 -1.92703587E-06 0.00000000E+00 0.00000000E+00 1.71308411E-06
0.00000000E+00 -3.37550154E-01 1.95839781E-01 0.00000000E+00 3.68859016E-01
0.00000000E+00 2.64651356E-01 -2.34139251E-01 0.00000000E+00 -2.30245568E-01
2.20815038E-01 -1.92703587E-06 0.00000000E+00 0.00000000E+00 2.13951761E-07
0.00000000E+00 0.00000000E+00 1.71308411E-06 0.00000000E+00 -3.37550154E-01
-1.95839781E-01 0.00000000E+00 -3.13088619E-02 -3.44057875E-02 0.00000000E+00
3.68859016E-01 0.00000000E+00 -2.64651356E-01 -2.34139251E-01 0.00000000E+00
3.44057875E-02 1.33242132E-02 0.00000000E+00 2.30245568E-01 2.20815038E-01
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