Jaguar - Rigid Coordinate Scan Panel

The Jaguar - Rigid Coordinate Scan panel allows you to generate data for potential energy surfaces, from QM calculations performed over the ranges of one or more coordinates ("scans"), with all other coordinates held fixed.

For more information, see Jaguar Geometry Scans.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Structure Analysis → QM Rigid
  • Click the Tasks button and browse to Quantum Mechanics → Rigid
  • Click the Tasks button and browse to Jaguar → Rigid Coordinate Scan
  • Click the Tasks button and browse to Materials → Quantum Mechanics → Molecular Quantum Mechanics → More Molecular QM Tasks → Rigid

Jaguar jobs can also be run from the command line. To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see jaguar Command Help. See the Jaguar Command Reference Manual for further information, including a description of the input file.

  • Overview
  • Using
  • Features
  • Additional Resources
  • Examples

Coordinate Scan Overview

Jaguar has the capability of performing coordinate scans for up to five coordinates. This maximum number of coordinates can be scanned if the scan is run sequentially, but is limited to two coordinates if the scan is distributed over multiple processors.

In a scan, you specify the values of the coordinates, and Jaguar performs calculations on the molecule at those coordinate values. In a rigid scan, the calculation is an energy calculation. In a relaxed scan, the calculation is a geometry optimization in which all coordinates but the scan coordinates are optimized.

The coordinates that are scanned can be Cartesian coordinates or internal coordinates (distances, angles, dihedrals), but you cannot mix both types in the same scan. If you want to scan internal coordinates, the distances, angles, or dihedrals do not need to correspond to any bonding patterns in the molecule.

When you set up a scan in Maestro, the points in each coordinate are evenly spaced. If you want to perform scans with arbitrary points, you must include the relevant keywords in the zvar section of the input file. See The zvar, zvar2, and zvar3 Sections of the Jaguar Input File for details.

Setting Up and Running Coordinate Scans

After you have made settings in the other tabs (such as optimization parameters for a relaxed scan), you can set up the coordinates and their values in the Scan tab.

The geometry must be in the appropriate form for the coordinate type: Cartesian for Cartesian coordinates, and Z-matrix for distances, angles, and dihedrals. If it is not, you must change it before defining coordinates. To do so, click Edit, then in the Edit Job dialog box, select Structure and choose the appropriate conversion option from the Structure menu.

To set up a coordinate, first choose a coordinate type from the Type option menu in the Add New Coordinate section, then select Pick and choose an object from the Pick option menu. You can pick Atom for Cartesian coordinates, and Atom and Bond for all other types of coordinates. If you pick atoms for a distance, angle, or dihedral, they need not be bonded to each other. The atoms are marked in the Workspace as you pick them, and each coordinate is marked in the Workspace and entered in the Defined coordinates table as it is completed.

To set the values for the coordinate, select the row for the coordinate in the table, then enter the starting value, the final value, and the increment in the Selected Coordinate section. The Current value and Number of steps text boxes are noneditable. The number of steps is calculated from the values you provide.

The starting geometry for each scan point in a relaxed coordinate scan can be generated from the initial geometry or from the previous scan point, by selecting one of the Generate starting geometry from options. If you select previous optimized geometry, the scan points must be run sequentially, but the starting geometry for the optimization of the coordinates that are not being scanned is likely to be a lot better than if you select initial geometry without relaxation. The starting geometry for rigid scans is always generated from the initial geometry, as there is no relaxation to take into account.

Once you have defined all the coordinates and their values, you can start the job. If the starting geometry for the scan points is generated from the initial geometry, you can distribute the scan points over multiple processors, by selecting a host and specifying the number of processors in the Job Settings Dialog Box. The job generates a .grd file so you can plot the results of a 1D or 2D scan.

If a job for a data point fails, the result is marked by 'skip' in the output .grd file instead of a numeric value, and the failure is noted in the job log. When you plot the results (for 1D and 2D scans), there is a break in the curve or contour lines at the skipped plot point. If all jobs fail, no .grd file is generated.

The results of the scan are returned in a single Maestro file and incorporated into the project. Each scan coordinate is added as a property to the Project Table.

If you have run a one- or two-coordinate scan, you can display the results in Maestro in the Plot Coordinate Scan Results Panel. To open this panel click the Tasks button and browse to Structure Analysis → Plot Coordinate Scan, or use the Workflow Action Menu for the entry group of the scan job.

If you perform a scan using excited state methods, .grd files are generated for the ground state (jobname.grd) and each excited state specified (jobname_<state>.grd). See Excited state controls in the Theory tab for information on how to specify excited states. The .grd file corresponding to the ground state is opened by default when you use the Workflow Action Menu .

Jaguar - Rigid Coordinate Scan Panel Features

  • Input
  • Theory
  • SCF
  • Scan
  • Properties
  • Solvation
  • Output

Input Tab Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

Defaults tools

These tools allow you to specify the default basis set and the default level of theory.

Theory text box and button

Click the button to select the level of theory. A small pane opens with controls for selecting the level of theory. The pane consists of a search text box, a filter button, and a list of available theoretical models. Typing in the text box narrows the list to items that contain the text. Clicking the filter button allows you to set options to restrict the list to certain models, e.g. range-corrected DFT. When you choose an item from the list, the pane closes and the text box (which is noneditable) shows the level of theory you chose.

Making a choice of functional sets the dftname keyword in the gen section of the input file.

See DFT Keywords in the Jaguar Input File for information on the density functionals.

Basis set text box and button

Click the button to select the basis set. A small pane opens with controls for selecting the basis set. The pane consists of a search text box, a filter button, and a list of basis sets. Typing in the text box narrows the list to basis set names that contain the text. Clicking the filter button allows you to set options to restrict the list to basis sets with certain features: ECP, diffuse functions, pseudospectral, relativistic, RI-MP2 compatible. When you choose a basis set from the list, the pane closes and the text box (which is noneditable) shows the basis set you chose.

If the basis set is not available for any of the structures in the Structures table, the cell in the Basis Set column for that structure is colored red. If a composite method is chosen in the Theory text box, the corresponding pre-defined basis set is automatically selected, and the Basis set text box cannot be modified.

See Basis Sets for information on the basis sets available.

Structures table

This table lists the entries in the Project Table that are used as the input structures for the job, according to the choice from the Use structures from option menu. To change the structures used for the calculation, you can change the selected structures or included structures in the Project Table panel or the Entry List panel. You can double-click in a cell to edit the values (ID, In, and Entry Title columns are not editable). The columns of the table may be different depending on the calculation type, and include:

  • ID—The entry ID of the structure.
  • In—Use this column to display the structures in the Workspace, just as in the Project Table panel or the Entry List panel. If you chose Workspace as the source of structures, excluding structures from the Workspace (clearing the In box) removes them from the table.
  • Entry Title—The entry title of the structure.
  • Charge—Specify the charge (molchg in the gen section). Default is 0 and is displayed in italics. The value is stored as a Maestro property.
  • Spin Mult.—Specify the spin multiplicity (multip in the gen section). Default is 1 (singlet) and is displayed in italics. If you use the spin-orbit ZORA Hamiltonian, spin is no longer conserved, and the multiplicity is only related to the number of electrons (1 for even, 2 for odd). The value is stored as a Maestro property.
  • Theory—Specify the level of theory (dftname in the gen section) for each structure. Double-click in a cell to edit the level of theory. A small window is displayed with controls for selecting the functional. These controls are the same as for setting the default theory (see above), except that functionals that are not available for the molecule are dimmed.
  • Basis set—Specify the basis set (basis in the gen section) for each structure. Double-click in a cell to edit the basis set. A small window is displayed with controls for selecting the basis set. These controls are the same as for setting the default basis set (see above), except that basis sets that are not available for the molecule are dimmed. The tooltip for the cell shows the basis set and the number of basis functions for the structure. If a composite method is chosen in the Theory column, the corresponding pre-defined basis set is used and the cell becomes noneditable.

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

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

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 Eh.

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).

Scan Tab Features

In this tab, you set up the coordinates for a relaxed or a rigid coordinate scan. The coordinates are added to a zvar section in the input file.

Add New Coordinate section

Add a new scan coordinate by picking atoms in the Workspace. The order of picking of the coordinates determines which atoms are moved in the scan: the last atom picked is the moving atom, and the first atom picked remains stationary.

Type option menu

Choose the type of coordinate to scan. The type determines the number of atoms to pick. The Z-matrix must be in the appropriate form for the coordinate type: Cartesian for Cartesian coordinates, and Z-matrix for distances, angles, and dihedrals. The coordinate types are:

Cartesian-X   X coordinate of an atom. Pick one atom.
Cartesian-Y   Y coordinate of an atom. Pick one atom.
Cartesian-Z   Z coordinate of an atom. Pick one atom.
Distance   Distance between two atoms. Pick two atoms or one bond. If you pick atoms, they need not be bonded to each other.
Angle   Angle between three atoms. Pick three atoms or two bonds. If you pick atoms, they need not be bonded to each other.
Dihedral   Dihedral angle between four atoms. Pick four atoms or three bonds. If you pick atoms, they need not be bonded to each other.
Pick option menu

Choose a structure type from this option menu, then pick atoms or bonds in the Workspace to define the coordinate. When you choose from this menu, the Pick option is automatically selected. The available structure types are Atom for Cartesian coordinates, and Atom and Bond for all other types of coordinates. The first atom picked remains stationary; the last atom picked is the moving atom. The atoms are marked in the Workspace as you pick them, and each coordinate is marked in the Workspace and entered in the Defined coordinates table as it is completed.

Defined Coordinates table

Displays information on the scan coordinates. You can select a single row to define the range and point spacing for the coordinate in the Selected Coordinate section. The columns are:

Coordinate   Labels of the atoms that define the coordinate.
Type   Coordinate type, from the Type option menu.
Steps   Number of steps to take in the given coordinate. Calculated from the initial and final values and the increment.
Fixed Value   If this option is selected, the coordinate is treated as a static constraint. Otherwise, the scan coordinate is treated as a dynamic constraint. Specifying dynamic constraints in scans allows you to scan over coordinates contained in rings.

The total number of structures to be calculated is reported below the table, and is the product of the numbers in the Steps column.

Selected Coordinate section

Set the range of the scan and the spacing of the points along the scan coordinate for the coordinate that is selected in the table. These values are used to calculate the number of steps and the coordinate value at each step. The text boxes are described below.

Current value   Current value of the coordinate in the input structure. Noneditable.
Starting value   Initial value of the coordinate for the scan.
Final value   Final value of the coordinate for the scan.
Step size   Amount by which the coordinate is changed at each scan step.
Delete button
Delete the selected row in the Defined Coordinates table.
Generate starting geometries from options

Select an option for generating the starting geometries for each point in the scan. These options are only present for a relaxed scan.

  • previous optimized geometry—Use the most recent optimized geometry to generate a guess for the current geometry. If you select this option, the scan points are run sequentially, and any parallel processing is only used for individual points.

  • initial geometry without relaxation—Use the initial geometry to generate geometries for all scan points, without relaxation of other coordinates. If you select this option, the optimizations for each scan point can be distributed over multiple processors, as the initial geometries are generated before the scan starts and are thus independent.

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

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 Cv 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

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

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.

Estimated total time text and View details link

Displays an estimate of the total clock-time for the job. Click on the View details link to open the Estimated Total Time Details Dialog Box. For more information, see Timings for Typical Jaguar Jobs.

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 Rigid Coordinate Scan - 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.

Related Topics

Coordinate Scan Examples

Example input file (scan-rigid-0001.in):

&gen
basis=6-31G*
dftname=B3LYP-D3
&
&zmat
O1      0.0000000000000   0.0000000000000   0.0000000000000
H2      0.8433914458129   0.5372996083468   0.0000000000000
H3     -0.8433914458129   0.5372996083468   0.0000000000000
&
&zvar
a = 95 to 135 in 5
&
&coord
 H3 O1 H2 # a
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=scan_rigid_0001 scan-rigid-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: scan-rigid-0001.in
Output files

Example input file (scan-rigid-0002.in):

&gen
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
O1     -0.6791109812330  -0.2086276018900  -0.1786617245197
O2      0.6194421815655   0.2950564853165   0.2566520350204
H3     -0.5999103884802  -1.1465423448357  -0.0660695206196
H4      1.0772607858205   0.4551112774238  -0.5578529633853
&
&zvar
d = 100.66 to 460.66 in 13
&
&coord
 H4 O2 O1 H3 # d
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=scan_rigid_0002 scan-rigid-0002.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: scan-rigid-0002.in
Output files