Jaguar - Reaction Panel

Jaguar - Reaction Panel Features

• Reaction tab
• Molecules tab
• Theory tab
• SCF tab
• Properties tab
• Solvation tab
• Output tab
• Keywords text box
• Job toolbar
• Status bar

• Reaction
• Molecules
• Theory
• SCF
• Properties
• Solvation
• Output

Reaction Tab Features

In this tab you select the structures for the reactants and products of a single reaction. These structures must be present as entries in the project or a file (which is imported into the project).

• Tile in Workspace button
• Reactants section
• Products section

 

Tile in Workspace button

Show the reactant and product structures in the Workspace in separate sections of the Workspace ("tiles"). See the Tiling the Workspace topic for more information on tiling. The tiles show the Title property and the Jaguar Reaction ID property, which stores the label used in the product display.

Reactants section

In this section you specify the reactants, which are shown in separate boxes.

Add button

Add a reactant structure to the reaction. A new display box is added for the new reactant, and it is labeled with a numerical index.

Reactant display

For each reactant molecule there is a display box that shows the 2D structure, labeled using a numerical index as Reactant n. This label is displayed on the structure option menu in the Molecules tab, so you can set the charge and spin multiplicity for the molecule. It is also displayed in the Workspace when you show the structure in the Workspace.

Initially the display box is empty. To add a structure, right-click and choose the structure source from the shortcut menu. You can choose a structure from the Project Table or from a file. If the file has multiple structures, only the first is imported. If you choose the wrong structure, you can simply repeat the process to choose the correct structure.

Click in the display box to show the structure in the Workspace.

If you decide you don't want to include a reactant, you can right click it and choose Delete from the shortcut menu to delete the reactant with its display box. If there was only one reactant, a new blank display box is added.

Products section

In this section you specify the products, which are shown in separate boxes.

Add button

Add a product structure to the reaction. A new display box is added for the new product, and it is labeled with a numerical index.

Product display

For each product molecule there is a display box that shows the 2D structure, labeled using a numerical index as Product n. This label is displayed on the structure option menu in the Molecules tab, so you can set the charge and spin multiplicity for the molecule.

Initially the display box is empty. To add a structure, right-click and choose the structure source from the shortcut menu. You can choose a structure from the Project Table or from a file. If the file has multiple structures, only the first is imported. If you choose the wrong structure, you can simply repeat the process to choose the correct structure.

Click in the display box to show the structure in the Workspace.

If you decide you don't want to include a product, you can right click it and choose Delete from the shortcut menu to delete the product with its display box. If there was only one product, a new blank display box is added.

Molecules Tab Features

In this tab, you select the symmetry treatment, set the charge and multiplicity, and select a basis set for the structures.

• Structure option menu
• Symmetry option menu
• Molecular state options
• Basis set section

Structure option menu

Select the structure in the Reactions tab whose state you want to define, from this option menu. The structures are listed as Reactantn and Productn.

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).

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).

Properties Tab Features

In this tab, you can select the thermodynamic properties you want to calculate.

• Calculate options

Calculate options

There are two options controlling the calculations.

• ΔH, ΔG—Calculate the enthalpy and free energy changes for the reaction. This involves performing frequency calculations for the reactants and products.

• Pre-optimize geometry—Before calculating the frequencies for the thermodynamic properties, optimize the geometries of the reactants and the products. This should be done if the input structures are not at their equilibrium geometries.

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 Reaction - 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.