Output From a Standard HF Calculation
The contents of a Jaguar output file vary according to the calculation and output selections made. This section describes the output file for a standard, default, single point, closed shell Hartree-Fock calculation. Output File Content for Various Jaguar Calculation Types describes the variations in the output file for the calculation options described in Jaguar Capabilities.
All output files begin with a line listing the job name, the machine upon which the job ran, and the time the job was started, followed by the general copyright information for the version of Jaguar that was used for the run. The rest of this section describes output from each individual Jaguar program run for a default calculation.
The output from the program pre begins with a description of the calculation to be performed: the job name, the directory containing the executables used to run the job, the directory for temporary files, comments from the input file (if any), and the names and paths of any non-default data files used for the calculation (see General Description of the Jaguar Input File and Other Jaguar Files).
Next, the basis set used for the calculation, the molecule’s net charge and multiplicity, and the number of basis functions used for the calculation are specified. This information is followed by the molecular geometry input, which gives the atom label and coordinates for each atom. (If the atom labels provided in the geometry are not unique—for instance, if two hydrogens are each called “h”—this information is preceded by a list of original atom labels and new atom labels assigned by the program.)
The molecule’s symmetry is analyzed, a process which may involve translating and rotating the molecule. These procedures are noted in the output file, along with the point group used for the calculation, the nuclear repulsion energy, and the symmetrized geometry, which is used for the rest of the calculation.
One-electron integrals are calculated by the onee program, which prints the smallest eigenvalue of the overlap matrix S and the number of canonical orbitals used for the calculation. Canonical orbital eigenvectors with very small eigenvalues (less than 5.0 x 10−4) are removed and thus are not counted. The eigenvalue cutoff can be controlled by setting the keyword cut20 to the desired value in the gen section of the input file. The number of canonical orbitals can also be controlled by setting the keyword ncanorb in the gen section of the input file.
The program hfig constructs a starting wave function (initial guess) for a Hartree-Fock calculation. The output from the program hfig for a default calculation begins with the line, “initial wave function generated automatically from atomic wave functions.” Next, a table lists the number of orbitals, and of occupied orbitals in each shell, having each irreducible representation for the appropriate point group. Finally, the orbital occupation for each shell is listed; an occupation of “1.000” indicates a closed shell. An example, for a calculation of water using a 6‑31G** basis set, follows:
start of program hfig initial wave function generated automatically from atomic wave functions Irreducible Total no No of occupied orbitals representation orbitals Shell_1 Shell_2 ... A1 12 3 A2 2 0 B1 4 1 B2 7 1 ------------------------ Orbital occupation/shell 1.000 end of program hfig
If the molecule contains a transition metal atom, there may be several ways of occupying the d orbitals. In this case, hfig prints a list of the possible states, and continues with the first of these. It is possible, however, that a different initial occupation of the metal d orbitals would lead to a lower energy wave function. To see whether this is the case, you should run an SCF calculation for each of the possible degenerate states, by selecting the state with the istate keyword. An example for the FeH4 molecule follows.
Low energy states below 0.005000 hartree:
State Rel. Energy MOs: 9 10 11 12 13
metal d occupations
1 0.00000000 2 1 1 0 0
2 0.00000224 1 2 1 0 0
3 0.00062053 2 1 0 1 0
4 0.00062276 1 2 0 1 0
5 0.00071513 2 1 0 0 1
6 0.00071737 1 2 0 0 1
WARNING: The lowest energy configurations are
degenerate. The MO numbers with occupied metal
d orbitals are given in the table above. Jaguar
will use the first configuration, but you can
select a different state configuration number
from the table above with the istate keyword.
Using state configuration 1: 2 1 1 0 0
In this example, Jaguar has found six possible occupations of the five metal d orbitals that have essentially the same energy. The table shows which MO numbers correspond to the metal d orbitals (9-13 in this example), the occupation numbers (0, 1 or 2 electrons per orbital), and the relative energy, in hartrees. The lowest energy is the reference energy and is always 0.0.
The probe program, which follows hfig and ensures orthogonalization, has no significant output.
The output for the grid generation done by the program grid lists the number of grid points for each atom, as well as the total number of grid points, for each grid used in the application of the pseudospectral method. If you would like more information about these grids, see The Grid File for Jaguar Calculations. The rwr program, which generates the Q operators needed for the pseudospectral method, runs next, but has no significant output.
An example of the output from the next program, scf, again for a water molecule, is given here and is explained below.
start of program scf
number of electrons.......... 10
number of alpha electrons.... 5
number of beta electrons..... 5
number of orbitals, total.... 25
number of core orbitals...... 5
number of open shell orbs.... 0
number of occupied orbitals.. 5
number of virtual orbitals... 20
number of hamiltonians....... 1
number of shells............. 1
SCF type: HF
i u d i g
t p i c r RMS maximum
e d i u i energy density DIIS
r t s t d total energy change change error
etot 1 N N 5 M -75.61350567257 1.6E-02 3.3E-01
etot 2 Y Y 6 M -75.99456008691 3.8E-01 6.2E-03 6.9E-02
etot 3 Y Y 6 M -76.01904109359 2.4E-02 1.7E-03 2.9E-02
etot 4 N Y 2 U -76.02333233097 4.3E-03 7.6E-04 4.7E-03
etot 5 Y Y 6 M -76.02361760760 2.9E-04 1.7E-04 1.5E-03
etot 6 Y N 6 M -76.02364072535 2.3E-05 0.0E+00 0.0E-00
Energy components, in hartrees:
(A) Nuclear repulsion............ 9.33000672144
(E) Total one-electron terms..... -123.34165776264
(I) Total two-electron terms..... 37.98801031585
(L) Electronic energy............ -85.35364744679 (E+I)
(N) Total energy................. -76.02364072535 (A+L)
SCFE: SCF energy: HF -76.02364072535 hartrees iterations: 6
HOMO energy: -0.49745
LUMO energy: 0.21516
Orbital energies/symmetry label:
-20.55693 A1 -1.34635 A1 -0.71380 B2 -0.56828 A1
-0.49745 B1 0.21516 A1 0.30862 B2 1.01720 B2
1.09266 A1 1.13459 A1 1.16904 B1 1.29575 B2
1.41126 A1 1.80256 A2 1.82999 A1
end of program scf
The output from the program scf begins with a list of information detailing various numbers of electrons, orbitals, Hamiltonians used for the calculation, shells, and the calculation type.
Next, the energy output from the SCF iterations is shown in table form. Some of the text for the column headings should be read down rather than across. The number of the iteration is provided first in each row, followed by a “Y” or “N” indicating whether the Fock matrix was updated or not. When the Fock matrix is updated, the changes are made using a difference density matrix whose elements reflect the changes in the density matrix elements from the previous iteration to the current one.
The next entry indicates whether the DIIS convergence scheme was used for that iteration. As above, “Y” or “N” indicate yes or no. The DIIS method produces a new estimate of the Fock matrix as a linear combination of previous Fock matrices, including the one calculated during that iteration. DIIS, which is enabled by default, usually starts on the second iteration, and is not used on the final iteration. If the entry in this column reads “A,” it indicates that DIIS was not used for that iteration, but the density matrix was averaged.
The cutoff set for each iteration is indicated under the “icut” heading. Cutoff sets are explained in the cutoff file description in The Cutoff File for Jaguar Calculations.
The grid column lists the grid used for that iteration, which must be one of the grid types coarse (signified by a C), medium (M), fine (F), or ultrafine (U). See Grid and Dealiasing Function Keywords in the Jaguar Input File and The Grid File for Jaguar Calculations if you want more information on grids and grid types.
The total energy for the molecule in Hartrees appears in the next column, followed by the energy change from the previous iteration to the current one.
The RMS density change column provides the root mean square of the change in density matrix elements from the previous iteration to the current one.
In the last column, the maximum DIIS errors listed provide a measure of convergence by listing the maximum element of the DIIS error vector. For HF and DFT closed shell calculations, the DIIS error vector is given by FDS − SDF in atomic orbital space, where F, D, and S are the Fock, density, and overlap matrices, respectively. For open shell cases, the definition of the error vector is given in reference [11].
After the energy information for each SCF iteration, a summary of the components of the final, converged energy is given. Each of these energies is labeled with a letter (for example, “A” for the nuclear repulsion), and information to the right of some of the energies describes the relations between the components in terms of these letters. A line below the table summarizes the calculation type and energy, as well as the number of SCF iterations.
If the input system’s spin multiplicity is not singlet, the summary of the SCF output also includes a breakdown of the two-electron contribution to the energy into Coulomb and exchange parts. For each of these parts, the contribution from each Hamiltonian is listed.
The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies are listed next. Finally, the energies for each occupied orbital and for the ten lowest-energy virtual orbitals are provided, with each orbital identified by a symmetry label. Virtual orbitals and eigenvalues are determined in the same manner as in ref. [185]. The virtual orbitals are obtained by diagonalizing 
, where f is the occupation of each orbital (1 for a closed shell). For closed shell Hartree-Fock calculations, this definition yields the standard orbitals and eigenvalues.
Finally, the CPU time for the job, the machine upon which the job ran, and its time of completion are noted at the end of the output file.