Jaguar - IRC Panel

Jaguar - IRC Panel Features

• IRC tab
• Theory tab
• SCF tab
• Optimization tab
• Properties tab
• Solvation tab
• Output tab
• Keywords text box
• Job toolbar
• Status bar

• IRC
• Theory
• SCF
• Optimization
• Properties
• Solvation
• Output

IRC Tab Features

In this tab you specify the reactant, product, and transition state for the IRC (intrinsic reaction coordinate) scan, and set parameters for the scan. You also make settings for the symmetry and molecular state, and choose a basis set.

• Direction option menu
• Structures section
  • Inclusion button
  • Entry name text box
  • Choose button
• IRC scan controls
  • Number of IRC points text box
  • IRC step size text box
  • Maximum optimization steps per point text box
  • Use mass-weighted coordinates option
• Symmetry option menu
• Molecular state options
• Basis set section

Direction option menu

Choose the direction in which the scan proceeds from the transition state. menu. Sets ircmode in the gen section. All options except Downhill require an initial Hessian. Forward means toward the product; reverse means toward the reactant. If you do not supply the reactant and product structures, Jaguar defines the forward direction using the rules described in Intrinsic Reaction Coordinate (IRC) Keywords in the Jaguar Input File.

Forward/Reverse

Calculate points in both forward and reverse directions. This is the default. Sets ircmode to both.

Forward

Calculate points in the forward direction. Sets ircmode to forward.

Reverse

Calculate points in the reverse direction. Sets ircmode to reverse.

Downhill

Calculate points in the downhill direction from the provided non-transition-state structure (specified in the Structures section as if it was a transition state). Sets ircmode to downhill.

For downhill calculations, you do not need an initial guess of the Hessian. The scan follows the gradient from the initial point. Downhill mode is set automatically in the restart file for IRC jobs.

Structures section

Select the transition state, reactant, and product geometries in this section. The selections in this section add zmat2 and zmat3 sections to the input file. The controls in this section are the same as for the Transition State Tab. If you already specified structures in that tab, they are specified here by default. The same rules for atom numbering in the reactant and product structures apply as for transition state searches.

You must choose entries from the Project Table for these structures. If the atom numbering or labeling scheme is incompatible, a warning is displayed.

Inclusion button

When you have chosen a structure for a given structure type, this button becomes available. You can click it to display the structure in the Workspace, and click again to remove the structure from the Workspace. These buttons do not behave like the In column of the Project Table: they only affect the inclusion state of the corresponding entry. The inclusion state is reflected in the Project Table.

Entry name text box

Displays the entry name for the structure type. You can enter an entry name in this text box to select it for the structure type.

Choose button

Click this button to open an entry chooser, in which you can choose an entry for the structure type.

IRC scan controls

Set the parameters that control the scan.

Number of IRC points text box

Set the number of IRC points to be located in each direction. Sets ircmax in the gen section.

IRC step size text box

Set the size of the step along the reaction coordinate to be taken for each point. Sets ircstep in the gen section.

Maximum optimization steps per point text box

Set the maximum number of steps in the optimization of the geometry perpendicular to the reaction path. Sets ircmxcyc in the gen section. This value overrides any value set in the Optimization tab.

Use mass-weighted coordinates option

Use mass-weighted coordinates for the reaction path. Selected by default. Sets irc=2 in the gen section. Use of mass-weighted coordinates defines an IRC path. If you deselect this option (sets irc=1), the path is a minimum energy path (MEP).

Symmetry option menu

This menu allows you to control how symmetry is handled in the calculation. Sets isymm and idoabe in the gen section.

• Use if present—Use the full symmetry of the molecule (isymm=8). The symmetry is determined from the molecular geometry to a prescribed tolerance.
• Off—Run the calculation without symmetry (isymm=0).
• Abelian—Use D_2h and subgroups for the symmetry (idoabe=1).

For information on how to make sure the symmetry of your input structure is treated as you expect, see Symmetrizing a Molecule.

Molecular state options

In this section you specify the charge and the spin multiplicity (2S+1) of the molecule. Sets molchg and multip in the gen section.

Use charge and multiplicity from Project Table option

Select this option to use the molecular charge and multiplicity that are specified as properties in the Project Table.

Create Properties button

Create Charge and Multiplicity properties in the Project Table for all entries. If the properties don't exist, add them; if they do exist, update values for entries for which the properties don't have values.

Use these values option and text boxes

Select this option to enter the charge and the multiplicity in the Molecular charge and Spin multiplicity (2S+1) text boxes.

Keep multiplicity consistent with charge option

When changes are made in the Workspace, keep the spin multiplicity consistent with the charge (actually, with the number of electrons). If the multiplicity becomes inconsistent with the charge as a consequence of Workspace changes, it is set to 1 for molecules with an even number of electrons, and 2 for molecules with an odd number of electrons. If you change the charge in the Spin multiplicity text box to a value that is consistent with the number of electrons (for example, from 1 to 3), it is not adjusted.

Basis set section

In this section you select the basis set. Sets basis in the gen section. The number of basis functions and other details of the basis set are reported below the controls. You should ensure that you choose the same basis set for the reactants and the products for a reaction, otherwise the results will not be meaningful. See Basis Sets for information on the available basis sets.

Basis set option menu

Select the basis from this option menu. All the available basis sets are listed for the molecule in the Workspace. Basis sets in regular type are available for this molecule with the pseudospectral method. Basis sets in italic type are only available for this molecule in a nonpseudospectral calculation. Dimmed basis sets are not available for this molecule.

Polarization option menu

If the basis set has polarization functions, you can include them by selecting * or ** from this option menu.

Diffuse option menu

If the basis set has diffuse functions, you can include them by selecting + or ++ from this option menu.

Theory Tab Features

In this tab, you select options for the level of theory used in the calculation—SCF, DFT, LMP2. The controls displayed in this tab depend on the level of theory selected.

• Theory settings for option menu
• SCF Spin treatment options
• Excited state controls
• Grid density option menu
• Use 3-body dispersion correction with all applicable dispersion-corrected functionals option
• Core localization method option menu
• Valence localization method option menu
• Resonance option menu
• LMP2 Pairs options
• Hamiltonian option menu

Theory settings for option menu

Select an option from this menu to make settings for the three types of theoretical methods used: Hartree-Fock (HF), density functional theory (DFT), and local second-order Møller-Plesset perturbation theory (LMP2). The controls in the rest of the tab depend on the choice you make from this menu.

SCF and DFT options

Set options for SCF and DFT calculations.

SCF Spin treatment options

The treatment of spin restriction in the SCF process can be controlled by three options.

• Automatic—run a spin-unrestricted calculation for open-shell systems (multip>1) and a spin-restricted calculation for closed-shell systems (multip=1). Sets iuhf=2 in the gen section.

• Unrestricted—run a spin-unrestricted (UHF or UDFT) calculation for both closed-shell and open-shell systems. For closed-shell systems this may give the same result as a restricted calculation, but can deviate from it where a single determinant is no longer a good description of the wave function. Sets iuhf=1 in the gen section.

• Restricted—run a spin-restricted (ROHF or RODFT) calculation for open-shell systems (sets iuhf=0 in the gen section).

These options are only displayed if you choose HF (Hartree-Fock) or DFT (Density functional theory) from the Level of theory option menu. The default is Automatic: unrestricted for open-shell HF or DFT calculations, restricted for closed-shell calculations.

When using the spin-orbit ZORA Hamiltonian, the spin is no longer conserved. Time-reversal symmetry takes the place of spin symmetry, and Kramers restriction takes the place of spin restriction. So choosing Restricted runs a Kramers-restricted SCF calculation (where time-reversal symmetry is imposed), and Unrestricted runs a Kramers-unrestricted SCF calculation.

Excited state controls

Select the Excited state option to perform an excited state calculation using either the time-dependent density-functional method (TDDFT), if the level of theory is DFT, or the time-dependent Hartree-Fock (TDHF) method, if the level of theory is HF. (Note that the option label includes (TDHF) or (TDDFT) to distinguish the two levels of theory.) This option sets itddft=1 in the gen section. For a geometry optimization, this option is labeled Optimize first excited state to indicate that only the lowest excited state is optimized.

The full linear response method is used by default. If you want to use the Tamm-Dancoff approximation, you can choose it from the option menu (itda=1 in the gen section). For TDHF, this corresponds to a configuration interaction singles (CIS) calculation.

The excited states are excitations from a reference state. If the reference state is a closed shell, you can choose whether to generate singlet or triplet excited states, or both, from the Excited state type option menu. (These choices set rsinglet=1 and rtriplet=1 in the gen section). This option menu is not available if you are doing a geometry optimization. If the reference state is a spin-unrestricted open-shell state, all possible spin states that are accessible as single excitations are calculated, but there is no classification of these states by spin. The value of S² is reported for all states, so you can identify the spin state.

You can calculate excited states with both the scalar ZORA and the spin-orbit ZORA Hamiltonians (see the Hamiltonian option menu). For the scalar ZORA Hamiltonian, all the options are available. The spin-orbit ZORA Hamiltonian generates states of mixed spin, so the Excited state type option menu is not available when you choose this Hamiltonian. You can only use the spin-orbit ZORA Hamiltonian with a closed-shell reference state. This Hamiltonian is useful if you are interested in singlet-to-triplet transitions and phosphorescence lifetimes.

Several settings can be made for the excited state methods, which are only available when you select the Excited state option.

Number of excited states text box

Specify the number of excited states (sets nroot). Note that for a geometry optimization, only the lowest singlet excited state is optimized, regardless of the value in this text box.

You should select more excited states than you are actually interested in, for two reasons. The first is that the initial guess might not accurately reflect the final states, and the second is to ensure that near-degeneracies are accounted for.

Maximum TDHF iterations text box

Maximum TDDFT iterations text box

Specify the maximum number of iterations of the diagonalization procedure (sets mitertd).

Energy convergence threshold text box

Specify the threshold used to determine when the energies of the excited states have converged (sets econtd).

Residual convergence threshold text box

Specify the threshold used to determine when the norm of the residual vector for the excited states has converged (sets rcontd).

The excited state controls are only displayed if you choose HF (Hartree-Fock) or DFT (Density Functional Theory) from the Level of theory option menu.

Grid density option menu

Choose the grid density for the DFT calculation, from Medium, Fine, or Maximum. If you read an input file that contained some other grid density, the grid density is set to Other, otherwise this option is unavailable. If you choose a grid density from this menu, the previous grid density specification is replaced. By default, DFT calculations use grids with a medium point density.

This option menu is only displayed if for DFT methods.

Use 3-body dispersion correction with all applicable dispersion-corrected functionals option

Select this option to include an additional correction for three-body effects for any D3 dispersion-corrected functionals. Only present if you choose DFT (Density Functional Theory) from the Level of theory option menu.

LMP2 Options

Set options for LMP2 calculations. See Local MP2 Settings for more information on the method and its settings.

Core localization method option menu

Choose the localization method for the core orbitals from this option menu.Sets loclmp2c in the gen section. This menu is only displayed if you choose LMP2 (Local MP2) from the Level of theory option menu. The options are:

• None—Do not localize core orbitals (loclmp2c=0). This is the default.
• Pipek-Mezey—Perform Pipek-Mezey localization, maximizing Mulliken atomic populations (loclmp2c=2).
• Boys—Perform Boys localization (loclmp2c=1).
• Pipek-Mezey (alt)—Perform Pipek-Mezey localization, maximizing Mulliken basis function populations (loclmp2c=3).

Valence localization method option menu

Choose the localization method for the valence orbitals from this option menu. Sets loclmp2v in the gen section. This menu is only displayed if you choose LMP2 (Local MP2) from the Level of theory option menu. The options are

• Pipek-Mezey—Perform Pipek-Mezey localization, maximizing Mulliken atomic populations (loclmp2v=2). This is the default.
• Boys—Perform Boys localization (loclmp2v=1).
• Pipek-Mezey (alt)—Perform Pipek-Mezey localization, maximizing Mulliken basis function populations (loclmp2v=3).

Resonance option menu

Choose the handling of resonance structures for aromatic molecules and molecules with conjugated double bonds. Sets ireson in the gen section. This menu is only displayed if you choose LMP2 (Local MP2) or from the Level of theory option menu. The options are:

• None—Do not delocalize LMP2 pairs over other atoms (ireson=0).
• Partial delocalization—Delocalize LMP2 pairs over neighboring atoms in aromatic rings (ireson=1).
• Full delocalization—Delocalize LMP2 pairs over all atoms in aromatic rings (ireson=2).

LMP2 Pairs options

Select the types of LMP2 pairs to include in the calculation. Sets iheter in the gen section. This menu is only displayed if you choose LMP2 (Local MP2) from the Level of theory option menu. The options are:

• All atom pairs—Treat all atom pairs with LMP2 (iheter=0). This is the default.
• Hetero atom pairs—Treat atom pairs in which the two atoms are different (except CH pairs) with LMP2 (iheter=1).

RI-MP2 Options

Set options for RI-MP2 calculations. See RI-MP2 Calculations for more information on the method and its settings.

Freeze core option

Select this option to freeze core molecular orbitals (n_frozen_core = -1). The number of orbitals Jaguar freezes by default for each atom is listed here. If this option is not checked, all core molecular orbitals are included in the correlation.

Hamiltonian option menu

For heavy elements, it is necessary to include relativistic effects in the Hamiltonian. In Jaguar there are two ways of doing this: using ECPs, and with an explicit relativistic Hamiltonian. ECPs are handled via the basis set selection. The Hamiltonian option menu allows you to choose the Hamiltonian. The default is Nonrelativistic, which is the usual Schrödinger Hamiltonian. The other choices are for relativistic Hamiltonians, and include (relativistic) in the menu item, to indicate that they include relativistic effects.

• Nonrelativistic—Use the (nonrelativistic) Schrödinger Hamiltonian. This is the default, and should be used with ECPs. If you choose LMP2 for the level of theory, this Hamiltonian is selected, as LMP2 cannot currently be used with ZORA.

• Scalar ZORA—Use the scalar ZORA Hamiltonian (relham=zora-scalar or zora-1c in the gen section). This option is only available for single-point HF and DFT calculations. If you choose this option for LMP2, the Level of theory is reset to DFT.

• Spin-orbit ZORA—Use the spin-orbit ZORA Hamiltonian (relham=zora-so or zora-2c in the gen section). The Hamiltonian includes spin-orbit coupling, which mixes states of different spin and spatial symmetry. Properties are not available with this Hamiltonian. This option is only available for single-point HF and DFT calculations. If you choose this option for LMP2, the Level of theory is reset to DFT.

Both of the ZORA Hamiltonians use a one-center approximation for the ZORA integrals, with the potential taken from the atomic initial guess (potential=local in the relativity section). By default the ZORA integrals are only evaluated for elements with Z > 18; lighter atoms are treated nonrelativistically. You can override this by including a relatom keyword in the relativity section, set to a space- or comma-separated list of elements, e.g. relatom=C N O F.

For ZORA calculations, it is recommended that you choose a heavy-atom basis set that is contracted specifically for ZORA. These basis sets have zora in the name. The dyall-v2z_zora-j-pt-gen basis set is a double-zeta polarized basis set similar to cc-pvdz; the dyall-2zcvp_zora-j-pt-gen basis set adds outer core polarization. Both basis sets are generally contracted, and cover elements up to Rn. There are semi-segmented versions of these basis sets that run faster without loss of accuracy, dyall-v2z_zora-j-pt-seg and dyall-2zcvp_zora-j-pt-seg. The sarc-zora basis set is also of double-zeta quality, and is a segmented contraction, covering elements from La to Rn. For a higher quality, you can use the dyall-3zvp_zora-j-pt-seg and dyall-3zcvp_zora-j-pt-seg basis sets, which are triple-zeta basis sets.

SCF Tab Features

In this tab you set the parameters that control the SCF convergence. Keywords for the gen section of the input file that correspond to the controls in this tab are given in parentheses.

• Accuracy level option menu
• Initial guess option menu
• Convergence criteria section
  • Maximum iterations text box
  • Energy convergence text box
  • RMS density matrix change text box
• Convergence methods section
  • SCF level shift text box
  • Thermal smearing option menu
  • Initial temperature text box
  • Convergence scheme option menu
  • Force convergence option
  • Compute wave function stability option
• Orbitals section
  • Fixed symmetry populations option
  • Use consistent orbital sets when all input structures are isomers option
  • Final localization option menu

Accuracy level option menu

Set the accuracy for pseudospectral calculations, or turn off the pseudospectral method.

• Quick— Use mixed pseudospectral grids with loose cutoffs (Sets iacc=3).
• Accurate— Use mixed pseudospectral grids with accurate cutoffs (Sets iacc=2).
• Ultrafine— Use ultrafine pseudospectral grids with tight cutoffs (Sets iacc=1).
• Fully analytic— Perform a fully analytic calculation: turn off the pseudospectral method (Sets nops=1). Can be run in parallel with OpenMP threads—see Running a Multithreaded Jaguar Job with OpenMP.

For more information on grids and cutoffs, see The Grid File for Jaguar Calculations and The Cutoff File for Jaguar Calculations.

Initial guess option menu

Choose the method for generating an initial guess for the molecular orbitals.

• Atomic overlap—Construct a guess for the molecular orbitals from atomic orbitals (iguess=10). The core orbitals are set to the atomic core orbitals. The overlap matrix is diagonalized in the space of the valence atomic orbitals, and the eigenvectors with the largest eigenvalues are taken for the valence orbitals. The entire set is orthogonalized core first, then valence. This is the default.

• Atomic density—Construct a guess from a superposition of atomic densities (iguess=11). The density is projected onto the AO basis. The resulting matrix is diagonalized to give natural orbitals, which are used as the initial guess orbitals.

• Core Hamiltonian—Generate an initial guess by diagonalizing the one-electron Hamiltonian matrix (iguess=0). This is rarely a good guess, as the orbitals are usually too tight.

• Ligand field theory—For transition metal complexes, use ligand field theory to construct an initial guess for the metal d orbitals. (iguess=25) An effective Hamiltonian is diagonalized, taking into account the assigned formal charges on the metal and the ligand and the occupation of the ligand orbitals, to determine the d-orbitals and the orbital ordering. The core and ligand orbitals are determined from the atomic orbitals using the atomic overlap.

• Ligand field theory with d-d repulsion—For transition metal complexes, use ligand field theory including d-d repulsion to construct an initial guess (iguess=30). The procedure is the same as above, except that repulsion between the d electrons on the metals is included to determine the orbital ordering and hence the occupation of the d orbitals and the spin state.

Convergence criteria section

In this section you set the criteria for convergence of the SCF process.

Maximum iterations text box

Specify the maximum number of SCF iterations in this text box (maxit). The default value is 48. The absolute maximum allowed is 5000.

Energy convergence text box

Specify the SCF energy convergence threshold in this text box (econv). The default value is 5.0x10^-5 E_h.

RMS density matrix change text box

Specify the SCF density convergence threshold in this text box. This value is the maximum change in the RMS density difference between iterations. (dconv). The default value is 5.0x10^-6.

Convergence methods section

In this section you choose the methods used to enhance or control convergence.

SCF level shift text box

Specify the level shift for the virtual orbitals (vshift). The default value is 0.0 for non-metallic systems and Hartree-Fock calculations. For DFT calculations on metallic systems the default is 0.2 for hybrid functionals, 0.3 for pure functionals.

Thermal smearing option menu

Select the thermal smearing method for convergence control (ifdtherm). The menu options are:

• None— Do not use thermal smearing (ifdtherm=0).
• FON— Fractional occupation number method (ifdtherm=1).
• pFON— Pseudo-fractional occupation number method (ifdtherm=2).

See the Jaguar User Manual for details of this method.

Initial temperature text box

Set the initial temperature for thermal smearing. (fdtemp in the gen section of the input file). The initial temperature text box is only available if you choose an item other than None from the Thermal smearing option menu.

Convergence scheme option menu

Choose the SCF convergence acceleration scheme (iconv).

• DIIS— Use the DIIS convergence scheme (iconv=1).
• OCBSE— Use the OCBSE convergence scheme (iconv=3).
• GVB-DIIS— Use the GVB-DIIS convergence scheme (iconv=4).
• Other— Selected if the input file uses another convergence scheme, otherwise unavailable.

For more information on these convergence schemes, see the Jaguar User Manual.

Force convergence option

Attempt to force convergence by adding level shift and decreasing it during iterations, fixing the number of canonical orbitals, and running at ultrafine accuracy (vshift, iacscf=1).

Compute wave function stability option

Perform wave function stability analysis (wf_stability = 1). Eigenvalues of the diagonalized molecular orbital Hessian are reported.

Orbitals section

Set options relating to the orbital occupations, canonicalization, and localization.

Fixed symmetry populations option

Fix the number of electrons in each irreducible representation (ipopsym=1).

Use consistent orbital sets when all input structures are isomers option

When performing calculations on a set of isomers, taken either from the project table or from a file, select this option to ensure that all calculations use the same number of canonical orbitals. This ensures consistency of the calculations and enables the results to be validly compared.

This option is not present in the Jaguar - Reaction panel, as the structures are not isomeric.

Final localization option menu

Choose the localization method for the valence orbitals from this option menu (locpostv).

• None— Do not localize final valence orbitals (locpostv=0). This is the default.
• Pipek-Mezey— Perform Pipek-Mezey localization, maximizing Mulliken atomic populations (loclpostv=2).
• Boys— Perform Boys localization (loclmp2c=1).
• Pipek-Mezey (alt) Perform Pipek-Mezey localization, maximizing Mulliken basis function populations (locpostv=3).

Optimization Tab Features

In this tab you set parameters that control the optimization of geometries, and set constraints on geometric parameters in the optimization.

• Maximum steps text box
• Switch to analytic integrals near convergence option
• Convergence criteria option menu
• Initial Hessian option menu
• Coordinates option menu
• Save intermediate geometries to output structure file option
• Add New Constraint section
  • Type option menu
  • Pick option and menu
  • Add object button
• Constraints table

Maximum steps text box

Enter the maximum number of geometry steps to be taken in the optimization. (Sets maxitg.)

Many molecules will meet the convergence criteria after ten or fewer geometry iterations. Input containing very floppy molecules, transition metal complexes, poor initial geometries, or poor initial Hessians may require many cycles to converge.

Switch to analytic integrals near convergence option

When the optimization approaches convergence, switch to using analytic integrals rather than the pseudospectral method. This option is useful for cases where tight convergence is required, as the pseudospectral method may not provide sufficient accuracy. The switch is made when the quantities used to assess convergence are within a factor of 10 of the relevant convergence threshold (sets nops_opt_switch=10; this can be changed in the Edit Job Dialog Box).

Convergence criteria option menu

Set the convergence criteria for geometry optimizations. See Geometry Optimization and Transition-State Keywords in the Jaguar Input File for details of the criteria.

• Loose—These thresholds are five times larger than the default thresholds. (Sets iaccg=3.)
• Normal— Set the convergence criteria to the defaults. (iaccg is not set and different defaults are used depending on the system.)
• Accurate—Set the convergence criteria to the defaults, given in Table 7 in Geometry Optimization and Transition-State Keywords in the Jaguar Input File. (Sets iaccg=2.)
• Tight—These thresholds are ten times smaller than the default thresholds. (Sets iaccg=5.)
• Custom—The Energy change, Gradient RMS, and Maximal displacement RMS text boxes are displayed, so you can enter the values you want to use for these criteria.

For optimizations in solution, the default criteria are multiplied by a factor of three, and a higher priority is given to the energy convergence criterion.

Initial Hessian option menu

Choose an initial guess for the Hessian. Sets inhess in the gen section. The choices are:

• Fischer-Almlof—Use the Fischer-Almlof initial guess. Sets inhess=-1.

• Schlegel—Use the Schlegel initial guess (the default). Sets inhess=0.

• Unit Hessian—Use the unit matrix for the initial Hessian. Sets inhess=1.

• Quantum mechanical—Calculate the Hessian with the given basis set. This is the most expensive but most accurate option, recommended for floppy molecules and other molecules that are difficult to optimize. Sets inhess=4.

• Other—Read the Hessian from the input file hess section if it exists (see The hess Section of the Jaguar Input File). Otherwise use the default. Automatically selected if the input file has a Hessian, which is the case for restarting a geometry optimization. Sets inhess=2.

Coordinates option menu

Choose a coordinate representation to define the optimization parameters. Sets intopt in the gen section. The ideal set of coordinates is one in which the energy change along each coordinate is maximized, and the coupling between coordinates is minimized. The choices are:

• Redundant internal—Use internally-generated redundant internal coordinates for the optimization parameters. Sets intopt=1. This is the default, and the most efficient choice in most cases. New coordinates are chosen automatically if a group of atoms becomes collinear.

• Cartesian—Use Cartesian coordinates for the optimization parameters. Sets intopt=0. Avoids the problems of collinear coordinate sets, but is likely to take longer than for redundant internal coordinates.

• Z-matrix—Use the Z-matrix from the input file for the optimization parameters. Sets intopt=2. If the geometry input is in Cartesian format or contains a second bond angle rather than a torsional angle for any atom intopt is set to 1. This item is unavailable if you are doing an IRC calculation.

Save intermediate geometries to output structure file option

Save the geometry at each step of the optimization to the output structure file. The structures at each geometry step are imported into Maestro as an entry group. If the geometry optimization fails, you can select one of these structures in Maestro to restart the optimization. Sets ip472=2 in the gen section. You do not need to set this option to inspect the energy convergence, which you can do in the QM Monitor Panel.

Add New Constraint section

Choose a constraint type and pick atoms in the Workspace to define the constraint. When you have picked the required number of atoms for the constraint type, the constraint is listed in the Constraints table. Cartesian constraints are marked with an asterisk in the zmat section; distance, angle, and dihedral constraints are added to the coord section, which is created if it does not exist. You can also choose to add all constraints of a particular type.

Type option menu

Choose the type of constraint. Choices are Cartesian X, Cartesian Y, Cartesian Z, Cartesian XYZ, Distance, Angle, and Dihedral. The Cartesian constraints constrain movement in the specified direction (X, Y, Z, or all three).

Pick option and menu

Choose an object from this option menu, then pick atoms in the Workspace to define the constraint. When you choose from this menu, the Pick option is automatically selected. The available objects are Atoms for Cartesian constraints, and Atoms and Bonds for all other types of constraint. The atoms are marked in the Workspace as you pick them, and each constraint is marked in the Workspace and entered in the Constraints table as it is completed.

Add object button

This button adds all of the specified object type to the constraints table. It is mainly useful when you want to optimize only a small part of a molecule, which you can do by constraining the whole system, then deleting those constraints that you don't want. The button's label and function depend on the choice you make from the Type option menu:

• Add Selected Atoms—Add the atoms that are selected in the Workspace as constraints. Only available for Cartesian constraints. You can select atoms in the Workspace then click this button to add them to the constraints table.

• Add All Atom Pairs—Add all atom pairs in the molecule as constraints, whether bonded or not. This choice completely constrains all free parameters, so it is only useful as a first step to removing constraints on the atoms you want to move. Only available for distance constraints.

• Add All Bond Angles—Add all bond angles in the molecule, i.e. all angles in which the atom at the apex of the angle is bonded to the two other atoms. Only available for angle constraints.

• Add All Torsions—Add all bonded torsions in the molecule, i.e. all dihedrals defined by three contiguous bonds. Only available for dihedral constraints.

Constraints table

Displays the constraints with their type, and also the target value, if it is a dynamic constraint. You can select one row at at time in the table. The constraint for the selected row is highlighted in the Workspace. You can make a constraint dynamic by entering the desired value in the Target Value column.

You can delete a constraint by selecting it in the table and clicking Delete. To remove all constraints, click Delete All.

Properties Tab Features

In this tab, you select the properties you want to calculate and set any relevant options.

The tab consists of a table listing all the available properties, and controls for each of the properties that are displayed in the lower portion of the tab when you select the row for the property in the table.

• Properties table
• Vibrational frequencies controls
  • Use available Hessian option
  • IR intensities option
  • Atomic masses option menu
  • Scaling option menu
  • Thermochemistry controls
• Surfaces controls
  • Electrostatic potential option
  • Average local ionization energy option
  • Energy units option menu
  • Noncovalent interactions option
  • Noncovalent grid density text box
  • Electron densities options
  • Spin density option
  • Molecular orbitals option
  • NTO for excited states option
  • Box size adjustment text box
  • Grid density text box
• Atomic electrostatic potential charges controls
  • Fit ESP to option menu
  • Constraints option menu
  • Grid type options
• Mulliken populations controls
• NBO analysis controls
• Multipole moments controls
• Polarizability/Hyperpolarizability controls
  • Static option
    • Property / Method option menu
    • Finite field text box
  • Dynamic alpha, beta option
    • Type options
    • Frequency text box
• NMR shielding constants controls
• Atomic Fukui indices controls
• Stockholder charges controls
• Vibrational circular dichroism controls
• Electronic circular dichroism controls
• Raman spectroscopy controls
• Mössbauer controls
  • Atomic number text box
  • Nuclear quadrupole moment text box

Properties Table

The properties table lists all the properties that can be selected for calculation. Properties that are not available with the chosen level of theory are grayed out in the table.

To set options for a property, click the row containing the property. The controls for the property are displayed in the lower portion of the panel. If the property is not available for the chosen level of theory, the controls are displayed but are not available.

To select a property for calculation, click the check box in the Calculate column for the property.

Vibrational Frequencies Controls

Set options for vibrational frequency and thermochemistry calculations. See Jaguar Vibrational Frequencies for details.

Use available Hessian option

Select this option if there is a Hessian available in the input file and you want to use it to calculate the frequencies. Sets ifreq = −1 in the gen section. Otherwise, the Hessian is calculated. The Hessian from a geometry optimization is not usually accurate enough for frequency calculations.

IR intensities option

Calculate infrared and Raman intensities. Only available for closed-shell wave functions. Sets irder = 1 in the gen section. See Infrared and Raman Intensities for more information.

Atomic masses option menu

Select the option for the atomic masses used in the frequency calculations. Sets massav in the gen section. The choices are:

Most abundant isotopes

Use the mass of the most abundant isotopes (massav = 0). This is the default.

Average isotopic masses

Use the average atomic mass (massav = 1).

For information on setting isotopic mass numbers for individual elements, see Changing Atom and Residue Properties.

Scaling controls

Select options for the scaling of the frequencies. The keywords set in the gen section are given for each option. See Scaling of Jaguar Frequencies for more information.

None

Do not scale frequencies. This is the default. (isqm = 0)

Pulay SQM

Scale frequencies with the Pulay SQM method and use scaled frequencies in thermochemistry calculations (isqm = 1). Only available for B3LYP/6-31G calculations (with or without polarization).

Automatic

Scale frequencies using predetermined factors for the basis set and method chosen (auto_scale = 1). Optimized factors are available for a wide range of basis sets and methods.

Custom

Scale frequencies using the factor given in the text box, which is displayed when you choose this item (scalfr).

Thermochemistry controls

Set options and values for thermochemical properties (enthalpy, Gibbs energy, entropy, heat capacity, and so on). You can calculate thermochemical properties at a range of temperatures for the given pressure. Along with the total internal energy, total entropy, and total free energy (in hartrees) at the given (or initial) temperature, the thermochemical property values as a function of temperature and pressure are added to the output Maestro file as Maestro properties. They can be plotted in the Thermochemistry Viewer Panel.

Pressure

Enter the pressure in atmospheres. The default is 1.0 atm. Sets press in the gen section.

Start temperature

Enter the initial temperature in K. The default is 298.15 K. Sets tmpini in the gen section.

Increment

Enter the temperature step in K. Sets tmpstp in the gen section.

Number of steps

Enter the number of temperature steps. Sets ntemp in the gen section.

Output units

Select an option for output in kcal/mol or kJ/mol. The default is kcal/mol (for H and G) and cal/mol K (for C_v and S). Sets eunit in the gen section.

Surfaces Controls

Set options for generating plot data on a 3D grid (a "volume") that is used in Maestro to display surfaces. Plot data is written to a .vis file.

Electrostatic potential option

Calculate the electrostatic potential (ESP) on the grid (sets iplotesp=1 in the gen section). Also performs an analysis of the ESP on an isodensity surface and reports the results in the output file and as entry and atom properties in the Maestro file.

Average local ionization energy option

Calculate the average local ionization energy (ALIE) on the grid (sets iplotalie=1 in the gen section). Also performs an analysis of the ALIE on an isodensity surface and reports the results in the output file and as entry and atom properties in the Maestro file.

Energy units option menu

Select the units used to represent the ESP and the ALIE (sets espunit in the gen section).

Noncovalent interactions option

Calculate reduced density gradient and interaction strength for visualization of noncovalent interactions (sets iplotnoncov=1 in the gen section). See the topic Noncovalent Interactions Overview for an explanation.

Noncovalent grid density text box

Set the grid density for the reduced density gradient and interaction strength points for noncovalent interactions (sets plotresnoncov in the gen section). The default is 20 points per angstrom. A high grid density is needed for good visualization.

Electron densities options

Calculate the electron density and optionally the electron density difference on a grid. The two options are:

• Density only—Calculate only the electron density for the final converged wave function (sets iplotden=1 in the gen section).

• Density and density difference—Calculate the final converged electron density function and the electron density difference between the final converged density and the initial guess density (sets iplotden=2 in the gen section). The interpretation of this density difference depends on the initial guess. For example, if the initial guess density is the superposition of atomic densities, then the difference density is the density change on molecule formation. If it is derived from another geometry, it represents the relaxation of the density due to the geometry change.

Spin density option

Calculate the electron spin density on the grid (sets iplotden=1 in the gen section). Only available for UHF and UDFT wave functions.

Molecular orbitals option

Calculate the specified molecular orbitals on the grid. Not available for MP2 calculations. Localized orbitals are calculated if the localization was performed.

Choose the references for the molecular orbital indices from the option menus and enter the relative index in the text box.

HOMO -:  Count down from the HOMO, inclusive.
LUMO +:  Count up from the LUMO, inclusive.

Thus, From: HOMO - 0 To: LUMO + 0 includes both the HOMO and the LUMO. These controls set iorb1a and iorb2a in the gen section. The controls for beta orbitals are only available for UHF and UDFT wave functions, and set iorb1b and iorb2b in the gen section.

NTO for excited states option

Calculate natural transition orbitals (NTOs) for each excited state in a TDDFT calculation, and write out the surfaces for each particle and hole NTO with an eigenvalue (occupation) greater than 0.1. Sets tddft_nto to 1 in the gen section.

Box size adjustment text box

Enter a value to adjust the size of the box used to calculate the grid. The default box size encompasses the van der Waals radii of all atoms in the molecule. Sets xadj, yadj and zadj in the gen section.

Grid density text box

Enter the number of grid points per angstrom. Sets plotres in the gen section.

Atomic Electrostatic Potential Charges Controls

Set options for charge fitting to the electrostatic potential. The atomic charges are written to the output Maestro (.mae) file and are available in Maestro as the partial charge. By default, the values at the nuclei are also added as atom properties to the output Maestro file.

For electrostatic potential fitting of an LMP2 wave function, you should also compute a dipole moment for more accurate results, since the charge fitting will then include a coupled perturbed Hartree-Fock (CPHF) term as well. You might also want to constrain the charge fitting to reproduce the dipole moment, as described below. Because the CPHF term is computationally expensive, it is not included in LMP2 charge fitting by default.

Fit ESP to option menu

Choose option for fitting electrostatic potential. Sets icfit in the gen section.

Atomic centers

Fit to atomic centers only (icfit=1).

Atom + bond midpoints

Fit to atomic centers and bond midpoints (icfit=2).

Constraints option menu

Choose the level of charge and multipole moment constraints applied to the fit. Sets incdip in the gen section. The option All of the above applies each level sequentially (incdip=-1) .For LMP2 wave functions, only dipole moments are available.

Note that the more constraints you apply to electrostatic potential fitting, the less accurately the charge fitting will describe the Coulomb field around the molecule. The dipole moment from fitting only the charges is generally very close to the quantum mechanical dipole moment as calculated from the wave function. Constraining the charge fitting to reproduce the dipole moment is generally not a problem, but you might obtain poor results if you constrain the fitting to reproduce higher multipole moments. However, this option is useful for cases such as molecules with no net charge or dipole moment.

If multipole moment calculations are performed, the moments are also computed from the fitted charges for purposes of comparison.

Grid type options

Select the grid type for calculating the electrostatic potential. For either grid type, points within the molecular van der Waals surface are discarded. The van der Waals surface used for this purpose is constructed using DREIDING [108] van der Waals radii for hydrogen and for carbon through argon, and universal force field [105] van der Waals radii for all other elements. These radii are listed in Table 2 in Keywords in the Jaguar Input File That Specify Physical Properties. The radius settings can be altered by making vdw settings in the atomic section of an input file, as described in The atomic Section of the Jaguar Input File.

• Spherical—Use a spherical grid on each atom, like those used for pseudospectral or DFT calculations. Sets gcharge = −1 in the gen section.
• Rectangular—Use a rectangular grid [107]. Sets gcharge = −2 in the gen section. The grid spacing in bohr is specified in the text box (sets wispc in the gen section).

Mulliken Population Analysis Controls

This section provides three method options for the Mulliken population analysis. Sets mulken in the gen section. See Mulliken Population Analysis for more information.

• By atom—Calculate Mulliken populations by atom (mulken=1).
• By atom and basis function—Calculate Mulliken populations by atom and by basis function (mulken=2).
• Bond populations—Calculate Mulliken bond populations (mulken=3).

NBO Analysis Controls

There are no specific controls for NBO analysis [110, 111]. The default NBO analysis is performed. Adds an empty nbo section to the input file. See Natural Bond Orbital (NBO) Analysis for more information.

Multipole Moments Controls

There are no specific controls for multipole moments. Dipole, quadrupole, octupole and hexadecupole moments are calculated. Sets ldips=5 in the gen section. See Multipole Moments from Jaguar Calculations for more information.

Polarizability/Hyperpolarizability Controls

These controls allow you to specify which polarizabilities are calculated (static or dynamic; alpha, beta, gamma) and which method is used. The polarizabilities are reported in atomic units.

Static option

Calculate the specified static polarizabilities with the chosen method. The trace of the polarizability tensor (alpha) is reported as an entry property, Polarizability.

Property / Method option menu

Select the combination of property and method. Alpha, beta, and gamma are available with the analytic method, and alpha and beta with the finite field method. Sets ipolar in the gen section.

Finite field text box

For finite field methods, enter the field strength in atomic units. Sets efield in the gen section.

Dynamic alpha, beta option

Calculate dynamic (frequency-dependent) polarizabilities at a given frequency.

Type options

Specify the type of frequency-dependent calculation to perform.

• Second Harmonic Generation (SHG)—calculate polarizabilities for second harmonic generation, or frequency doubling; the frequencies are of the same sign and magnitude.

• Optical Rectification—calculate polarizabilities for optical rectification where the frequencies are of the opposite sign but the same magnitude.

Frequency text box

Specify the frequency of the photon, given in terms of an energy gap in eV.

NMR Shieldings Controls

There are no specific controls for NMR shielding calculations. The values reported for this property are the shieldings, in ppm; the shifts must be calculated from the shieldings and a reference value. Shifts for ¹H and ¹³C are calculated based on a linear fit to experimental data. Sets nmr=1 in the gen section. For Boltzmann-averaged chemical shifts, see spectroscopy.py: Calculation of Boltzmann-Averaged Properties. For more information, see NMR Shielding Constants.

Atomic Fukui Indices Controls

There are no specific controls for Fukui indices. Sets fukui=1 in the gen section. See Atomic Fukui Indices for more information.

Stockholder Charges Controls

There are no specific controls for stockholder (Hirshfeld partitioning) charges. Sets stockholder_q=1 in the gen section. See Stockholder Charges for more information.

Vibrational Circular Dichroism Controls

There are no specific controls for calculation of vibrational circular dichroism (VCD) spectra. Sets ivcd=1 in the gen section. See Vibrational and Electronic Circular Dichroism for more information.

You can run VCD calculations in parallel, by selecting multiple processors for the job. (It is actually only the most time-consuming part, the frequency calculation, that is run in parallel.) For a complete workflow including a conformational search, use the Jaguar Spectroscopy Panel.

The spectra can be plotted in the Spectrum Plot Panel.

Electronic Circular Dichroism Controls

There are no specific controls for calculation of electronic circular dichroism (ECD) spectra. Sets ecd=1 in the gen section. ECD is only available for calculation if you have set up a singlet TDDFT calculation in the Tamm-Dancoff approximation (itddft = 1, itda = 1, rsinglet = 1 in the gen section). See Vibrational and Electronic Circular Dichroism for more information.

You can run ECD calculations in parallel, by selecting multiple processors for the job. (It is actually only the most time-consuming part, the frequency calculation, that is run in parallel.) For a complete workflow including a conformational search, use the Jaguar Spectroscopy Panel.

The spectra can be plotted in the Spectrum Plot Panel.

Raman Spectroscopy Controls

There are no specific controls for Raman spectroscopy. Selecting this property generates Raman intensities. Sets ifreq=1 and iraman=1 in the gen section. The spectrum can be plotted in the Spectrum Plot Panel.

Mössbauer Controls

These controls allow you to specify the atom for which Mössbauer properties are calculated and its nuclear quadrupole moment. The properties generated are Nuclear Density, in au, and Quadrupole Splitting, in mm/s. The properties are added as atom-level properties, as they apply to specific atoms. Sets mossbauer=1 in the gen section.

Atomic number text box

Specify the atomic number of the element for which Mössbauer properties are calculated. These properties are calculated only for this element; if the element is not present in a molecule, no calculation is done. Sets moss_atnum in the gen section.

Nuclear quadrupole moment text box

Specify the nuclear quadrupole moment to use for the specified element. A default quadrupole moment is provided for Z = 26, 28, 50, 51, and 53 (Fe, Ni, Sn, Sb, I). Sets moss_nuc_quadrupole in the gen section.

Solvation Tab Features

• Solvent model option menu
• PCM model option menu
• PCM radii option menu
• PBF single-point energy at convergence option
• Solvent text box and button
• Optimize in gas phase (needed for solvation energy) option

Solvent model option menu

Choose the solvent model from this option menu. The choices are

• None—do not include solvation, run a gas phase calculation only.
• PBF—use the standard Poisson-Boltzmann continuum solvation model. This model generally produces better energies than the PCM models.
• PCM—use one of several polarizable continuum models for solvation. The PCM models generally produce smoother convergence in geometry optimizations than the PBF model. See PCM Model for more information on these models. Options for selection of the model and its parameters are displayed when you choose this option.
• SM6—use the Minnesota solvent model SM6 [231]. This model can only be used with water as the solvent. Only available for single-point and rigid scan calculations.
• SM8—use the Minnesota solvent model SM8) [223]. This model can be used with all available solvents. Only available for single-point and rigid scan calculations.
• SMD—use the Minnesota solvation model SMD [321]. This model can be used with all available solvents. Available for single-point, geometry optimization, and frequency calculations.

Apart from the Solvent option menu, the remaining controls in the tab are unavailable for the SM6 and SM8 models.

PCM model option menu

Choose a specific polarizable continuum model. See PCM Model for more information on these models. Only available when you choose PCM from the Solvent model option menu.

• CPCM—use the C-PCM model [234].
• COSMO—use the COSMO model [232].
• SS(v)PE—use the SS(v)PE model (surface simulation of volume polarization for electrostatics [235]).

PCM radii option menu

Choose the atomic radii to use with the polarizable continuum model. See PCM Model for more information on these parameters. Only available when you choose PCM from the Solvent model option menu.

• Bondi—use Bondi radii [241].
• UFF—use radii from the Universal Force Field [105].
• Klamt—use Klamt radii [242]

PBF single-point energy at convergence option

Run a single-point calculation with the PBF solvation model when the optimization with the PCM model has converged. PBF generally produces better energies than the PCM models. Only available when you choose PCM from the Solvent model option menu, and the Jaguar task involves an optimization.

Solvent text box and button

Click the button to select the solvent. A small pane opens with controls for selecting the solvent. The pane consists of a search text box, a filter button, and a list of available solvents. Typing in the text box narrows the list to solvent names that contain the text. Clicking the filter button allows you to set options to restrict the list to solvents with certain features: common, halogenated, aromatic, hydrocarbon, carbonyl, polar, and non-polar solvents. When you choose a solvent from the list, the pane closes and the text box (which is noneditable) shows the solvent you chose. For pKa calculations, the only solvent choices are Water, and DMSO. Water is the default for all except CH and NH acids, whose default is DMSO.

See Solvation Keywords in the Jaguar Input File for a list of available solvents.

Optimize in gas phase (needed for solvation energy) option

Optimize the geometry in the gas phase first, and use this energy as the gas-phase reference energy used to calculate the solvation energy. Sets nogas=0 in the gen section. Not present for single-point and rigid scan calculations.

Output Tab Features

In this tab, you can specify options for information to be included in the output file, and select other file formats for which input files are to be written.

• Write input files in the selected formats
• Extra detail to be written to output file
• Orbital coefficients to be written to output file
  • Calculation stage list
  • Orbitals option menu
  • Format option menu

Write input files in the selected formats

Select items from this list to write input files for the job in the given format. You can choose multiple formats using shift-click and control-click. Each choice sets the corresponding ipn option in the gen section.

Extra detail to be written to output file

Select items from this list to write extra information to the output file. You can choose multiple items using shift-click and control-click. Each choice sets the corresponding ipn option in the gen section.

Orbital coefficients to be written to output file

In this section you can select the stage at which orbital coefficients are written to the output file, select the orbitals to write and the format in which they are written. To write orbital coefficients for a given stage, select the stage in the list, then choose items from the Orbitals and Format option menus. Sets the appropriate ipn keyword (in the range n=100-107) in the gen section to the value for the chosen format.

Calculation stage list

Select a calculation stage from the list. You can only select one stage at a time. When you have selected a stage, you can choose items from the Orbitals and Format option menus to set the writing of the orbital coefficients. The choice determines which ipn keyword is set.

Orbitals option menu

Choose the orbitals to print. Choices are None (the default), Occupied, or All. Used to determine the value of the ipn keyword.

Format option menu

Choose the format to use in printing. Used to determine the value of the ipn keyword.

Keywords text box

Enter keywords and macros for the gen section. These keywords and macros override settings made elsewhere in the panel. They do not appear in the input file when you edit it with the Edit Job Dialog Box, but are added to the gen section when the file is written out on clicking Run. For more information on the keywords you can use, see The gen Section of the Jaguar Input File.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the IRC - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.