Properties Keywords in the Jaguar Input File

Overview
Examples

Keywords to request calculation of molecular properties, including multipole moments and charge fitting properties are listed in Table 1, most of which correspond to GUI options described in Molecular Properties from Jaguar Calculations. Only the values listed in the table are allowed. Notes on various properties are given below the table. Properties that are calculated per atom are returned in the output Maestro file as atom-level properties, as well as listed in the Jaguar output.

If you want to track properties such as charges, multipole moments, or Fukui indices during a geometry optimization, you can set props_each_step=1 in the gen section.

Table 1. Keywords for molecular property calculations
Keyword	Value	Description
icfit	0	Do not do electrostatic potential fitting
	1	Fit electrostatic potential to atomic centers (default for PBF solvation calculations)
	2	Fit electrostatic potential to atomic centers and bond midpoints
cfiterr	1.0×10⁻⁶	Allowed error in electrostatic potential charge fitting when fitting is constrained to reproduce multipole moments
wispc	0.75	Spacing in bohrs of rectangular grid for electrostatic potential fitting
incdip	0	Use only total charge as constraint in electrostatic potential fitting
	1	Use charge and dipole moment as constraints in electrostatic potential (ESP) fitting
	11	Use charge, dipole moment, and quadrupole moment as constraints in electrostatic potential (ESP) fitting
	111	Use charge, dipole moment, quadrupole moment, and octupole moment as constraints in electrostatic potential (ESP) fitting
	ijk	Compute ESP fitted charges using total charge as a constraint, also constraining to dipole moment if k=1, to quadrupole moment if j=1, and to octupole moment if i=1
	−1	Do all incdip options sequentially
ldips	1	Do not calculate any multipole moments
	2	Calculate dipole moments
	3	Calculate dipole and quadrupole moments
	4	Calculate dipole, quadrupole, and octupole moments
	5	Calculate dipole, quadrupole, octupole, and hexadecapole moments
ipolar	0	Do not calculate polarizabilities or hyperpolarizabilities
	−2	Use CPHF to calculate polarizabilities α and first and second hyperpolarizabilities β and γ
	−1	Use CPHF to calculate polarizabilities α and hyperpolarizabilities β
	1	Calculate α using 3-point finite field method
	2	Calculate α and β using 3-point finite field method
	5	Calculate α and β using 5-point finite field method
	7	Calculate α and β using 7-point finite field method
efield	0.024	Electric field for polarizability and hyperpolarizability calculations, in au (default is 0.006 for ipolar=1)
ifdpol	0	Do not calculate frequency-dependent polarizabilities or hyperpolarizabilities
	1	Calculate frequency-dependent polarizability α(ω)
	2	Calculate frequency-dependent polarizability and hyperpolarizability α(ω) and β(ω)
fdpol_freq1	1.78574	Frequency (energy) of the first photon for frequency-dependent polarizability and hyperpolarizability calculations, in eV. If used with the optrot keyword, fdpol_freq1 is the frequency (energy) for optical rotation calculations, in eV. The default value in this case is 2.10392318, which corresponds to the sodium D line (589.3 nm).
fdpol_freq2	1.78574	Frequency (energy) of the second photon for frequency-dependent hyperpolarizability (β) calculations, in eV. This should be the same as the first photon for second harmonic generation (SHG), the negative of the first for optical rectification (OR).
ldens	0	Do not calculate electron density
	1	Calculate electron density on grid (grid choice set by grid keyword geldens; ultrafine grid used by default)
denspc	0.75	Spacing in bohrs of rectangular grid for electron density calculation
mulken	0	Do not calculate Mulliken populations
	1	Calculate Mulliken populations by atom, returned as atom-level properties `r_j_Mulliken_Charges` and `r_j_Mulliken_Spin_Populations`.
	2	Calculate Mulliken populations by basis function and by atom, returned as atom-level properties `r_j_Mulliken_Charges` and `r_j_Mulliken_Spin_Populations`.
	3	Calculate Mulliken bond populations
lowdin	0	Do not calculate Löwdin populations
	1	Calculate Löwdin populations by atom, returned as atom-level properties `r_j_Lowdin_Charges` and `r_j_Lowdin_Spin_Populations`.
nmr	0	Do not calculate NMR shielding constants
	1	Calculate NMR shielding constants, in ppm, returned as property `r_j_NMR_Shielding`. NMR chemical shifts are also calculated with certain settings (isolv=0 for chemical shifts in chloroform, isolv=7 and solvent=dmso or water for chemical shifts in DMSO or water).
optrot	0	Do not perform an optical rotation calculation
	1	Perform an optical rotation calculation. Use fdpol_freq1 to set the frequency (energy) for optical rotation calculations, in eV. The molecule is moved to its center of mass to minimize numerical errors in the calculation of the optical rotation.
mossbauer	0	Do not calculate Mössbauer properties
	1	Calculate Mössbauer properties (densities at the nuclear positions and quadrupole splittings, isomer shifts for Fe)
moss_atnum	26	Specify the element (atomic number) for which to calculate Mössbauer properties. The calculations are performed for all atoms of this element in the input structures.
moss_nuc_quadrupole		Specify the quadrupole moment of the nucleus for which Mössbauer properties are to be calculated, in barns. Default values are supplied for ⁵⁷Fe, ⁶¹Ni, ¹¹⁹Sn, ¹²¹Sb, ¹²⁹I.
fukui	0	Do not calculate atomic Fukui indices.
	1	Calculate atomic Fukui indices [260, 261].
stockholder_q	0	Do not calculate stockholder charges by Hirshfeld partitioning.
	1	Calculate stockholder charges by Hirshfeld partitioning [259].
hirshfeld_basis	6-31G	Specify basis used for promolecule in Hirshfeld partitioning of electron density for stockholder charge calculation.
esp_analysis	0	Do not perform statistical analysis of the electrostatic potential
	1	Perform statistical analysis of the electrostatic potential on isodensity surface, including the electrostatic potential at the nuclei (sets iplotden=1 and iplotesp=1, also epn=1).
den_isoval	0.001	Isovalue, in electrons/bohr³, for creating the isodensity surface on which the ESP or the ALIE analysis is performed.
epn	0	Do not calculate the electrostatic potential at the nuclei.
	1	Calculate the electrostatic potential at the nuclei (EPN). This property is stored in the Maestro file as an atom property `r_j_EPN`. Values at ECP centers are erroneous due to the missing core density, and should be ignored.
ielec	0	Do not calculate the electrostatic potential and the electric field at a set of grid points.
	1	Calculate the electrostatic potential and the electric field at a set of grid points. The source of the grid must be specified with the negrid keyword. The values are written to the file jobname`.efld`.
negrid	−1	Read grid points for calculation of the electrostatic potential and the electric field from the egridpt section of the input file.
	−6	Read grid points for calculation of the electrostatic potential and the electric field from the file specified by `GPTSFILE`.
nbo	0	Do not run an NBO analysis at the end of the calculation.
	1	Run an NBO analysis [110, 111] at the end of the calculation, with NBO keyword `PRINT=3` set.

Polarizabilities

Analytic polarizabilities α and hyperpolarizabilities β and γ are available for HF, UHF, DFT, and UDFT methods. The definition of β is consistent with that used in Gaussian. The definitions of polarizabilities α, first hyperpolarizabilities β, and second hyperpolarizabilities γ, are:

If you want to calculate polarizabilities with the old definition, you must set iopt332=332 in the gen section, and you can only calculate α and β for closed-shell wave functions.

The finite field methods corresponding to ipolar > 0 differ in the data they use for numerical differentiation. The 3-point method uses the results from seven SCF calculations: one with no field, one with a field of E (whose input is described below) in the x direction, one with a field of −E in the x direction, and four others with fields of +E and −E in the y and z directions. The 5-point method uses the same data as the 3-point method, as well as data from SCF calculations using fields of +aE and −aE in the x, y, and z directions, where a is some constant. Similarly, the 7-point method uses the same data as the 3-point method, plus data obtained using fields of +aE, −aE, +bE, and −bE in the x, y, and z directions, where a and b are some constants. By default the magnitude of the electric field E is 0.024 au. If you want to use a different value, set the efield keyword to the desired value.

Jaguar prints polarizabilities and hyperpolarizabilities in atomic units. The atomic unit of polarizability is e²a₀²E_h⁻¹, where e is the charge on an electron, a₀ is the bohr radius, and E_h is the atomic unit of energy, or hartree. To convert to SI units, C²m²J⁻¹, multiply by 1.6488×10⁻⁴¹. The first-order hyperpolarizability β is in atomic units of e³a₀³E_h⁻², and the second-order hyperpolarizability γ is in atomic units of e⁴a₀⁴E_h⁻³. The conversion factors to SI units are 3.2064×10⁻⁵³ and 6.2354×10⁻⁶⁵, respectively. In addition to the molecular polarizability, the atomic polarizability is given for each atom in the molecule, calculated by contracting the density submatrix for each atom with the numerical derivative of the dipole moment with respect to the applied electric field, in the AO basis.

atomic polarizabilities

All polarizability methods are run with symmetry off: the keyword isymm is set to 0 automatically if ipolar ≠ 0. In all polarizability calculations, the keyword econv, which gives the energy convergence criterion, is set by default to 1.0×10⁻⁶ (although if the calculation first satisfies the criterion dictated by the keyword dconv, the energy convergence criterion is ignored).

Charge Fitting

When charge fitting is constrained to reproduce multipole moments (that is, when incdip>0), the keyword cfiterr determines whether the multipole moment constraint is too restrictive to produce adequate charges: if the error in the total resultant charges is more than cfiterr, the charge fitting is rerun with a lower multipole moment constraint. The keyword wispc is used to set the spacing of the rectangular grid for electrostatic potential fitting when the grid keyword gcharge=-2. Similarly, the keyword denspc is used to set the spacing of the electron density rectangular grid when ldens=1 and the grid keyword geldens=-3. The efield keyword allows you to specify an electric field for finite field polarizability and hyperpolarizability calculations. The default value shown in Table 1 applies when ipolar > 1. For ipolar=1 (3-point, polarizability-only calculations), the default value is 0.006 au.

If you want to fit atomic partial charges to the electrostatic potential at grid points that you specify, rather than the default grids, add the keyword settings gcharge=-6 along with icfit=1 to the gen section of your input file. The gcharge=-6 setting instructs Jaguar to use the grid points and weighting factors in a file whose name and location are specified by the GPTSFILE line in the input file (see General Description of the Jaguar Input File). The grid points you fit to must be outside the van der Waals surface of the molecule; any points inside this surface are discarded. If you add an ip172=2 setting, Jaguar writes out a file named jobname.resp containing the electrostatic potential data (see the text under Table 1). To fit a partial charge at the bond midpoints as well, use icfit=2.

Surface Electrostatic Potential and ALIE Analysis

If you set esp_analysis=1, a statistical analysis of the electrostatic potential on the molecular surface is performed [264]. This analysis is also automatically performed if you request a plot of the electrostatic potential (iplotesp=1, see Plotting Keywords in the Jaguar Input File). The molecular surface is represented by an isosurface of the electron density, which by default is created using an isovalue of 0.001 au, as in the original publication. You can change the isovalue using the den_isoval keyword. See ESP Analysis Output for information on the properties generated. The minimum, maximum, variances, balance property and local polarity property are written to the output Maestro file. In addition, the maximum and minimum ESP values for each atom are written to the output Maestro file and can be used to label the atoms in the Workspace. A similar analysis is automatically performed for average local ionization potential (ALIE) surfaces (iplotalie=1).

Electrostatic Potential and Electric Field

If you want to print out the electrostatic potential and the electric field at a specified set of grid points, set ielec=1 in the gen section. You then have to specify the source of the points, which can come from an external file or from the input file. To specify an external file, add a GPTSFILE line to the input file (see General Description of the Jaguar Input File) and set negrid=-6 in the gen section. To specify points in the input file, add an egridpt section and set negrid=-1 in the gen section. For both source types, the points must be specified as Cartesian coordinates in angstroms, space separated, with one point per line. (Any grid points that coincide with an atom are shifted by 0.001 bohr in each coordinate, to avoid infinities.) The output is written to a file named jobname.efld. The number of points is given on the first line, and the remaining lines contain the results. Each of these lines has the Cartesian coordinates first, followed by the electrostatic potential, and then the Cartesian electric field components. The electrostatic potential and the electric field are given in atomic units.

Electron Density

To print out the electron density at a specified set of grid points, set ldens=1 and geldens=-6 in the gen section, and add a GPTSFILE line to the input file that specifies the file containing the grid points. This file should list the Cartesian coordinates in angstroms and a weight factor, which should be zero, with one grid point per line. The output is in the file jobname.chdens.

NMR

Gas-phase NMR shielding constants in ppm are available for closed-shell and unrestricted open-shell wave functions. Chemical shifts are calculated for ¹³C and ¹H from the shieldings, using a linear fit to experiment for selected basis sets and density functionals (see NMR Shielding Constants). To calculate chemical shifts directly, you should calculate NMR shielding constants for the reference molecules for each element of interest, in the same basis set and with the same method as for the molecule of interest.

By default, shieldings are calculated for all atoms, including those with ECPs. Shielding constants for atoms whose core is represented by an ECP should be treated with caution, because the main contributions come from the core tail of the valence orbitals, which is largely absent at ECP centers. Chemical shifts derived from these shielding constants might display the correct trends, but are likely to have the wrong magnitude.

Mössbauer Properties

Mössbauer properties require an all-electron basis set on the atom for which the properties are calculated, and generally, a large, uncontracted basis set is used. Basis sets on other atoms can be standard sets. This means you will probably have to set up an atomic section to specify the basis set. You should run the calculation with UHF and nops=1. Two recommended basis sets for Fe are partridge-1 and wachters-f, for which fitting has been done for isomer shifts.

For Fe, the isomer shift is calculated for its oxidation states if you use the partridge-1 or wachters-f basis set on Fe and cc-pvdz on other atoms, in conjunction with any of the functionals B3LYP, BPW91, M06, M06-2X, OLYP, O3LYP, PBE, SVWN5 (see Ref. 295).