DMol

5       Methodology--Insight

This section is a general description of how to use the DMol module of the Insight program. The on-line help utility contains further details about what individual commands and parameters do, and Tutorial--The Insight Environment describes examples of their use. On-line help (accessed by clicking the help icon) also presents information about parameters and commands.

Commands provided in the DMol module are discussed in general terms in the order in which they are used in a typical calculation. Also included are hints about when certain parameter values should or should not be used.

Much of this information is background material for the DMol tutorial lessons described under Tutorial--The Insight Environment, so you should read this section before starting them.

Using DMol in the Insight environment

The commands in the DMol module can be grouped in four classes, roughly corresponding to the four basic steps of a DMol calculation:

• The Setup/System command is used to select the molecule and choose the type of calculation. The Symmetry/Find_Pt_Group command is used to find or set the point-group symmetry of the molecule.

• The Setup/Parameters command and the commands in the Optimize pulldown are used to define the molecule's electronic state, set up the calculation, and specify the desired optional properties to be calculated. The Pseudo_Atom pulldown (in the Builder module) is useful in defining constraints.

• The Background_Job and Run pulldowns are used to specify run conditions and start the DMol job.

• The Analyze pulldown (and other pulldowns and icons that are part of the Insight interface) aids in analyzing the results of the calculation.

Outline of basic steps of a DMol calculation

Next, the Symmetry/Find_Pt_Group command may be executed to determine the point-group symmetry of the system. Roughly symmetrical molecules can be geometrically adjusted to the exact symmetry required for DMol calculations by increasing the value of the Symmetry_Threshold parameter.

Step 2: Setting up the calculation parameters

You can read in parameters that were used in a previous calculation by toggling the Load_Input parameter in the Setup/System command to on. You should also set the Calculation_Type to the same type of calculation specified in the input file you load, since it will otherwise be overwritten by your new choice.

Step 3: Performing the DMol calculation

The Background_Job pulldown is used to set nondefault run conditions.

The Run/Run_DMol command writes out the necessary input files and specifies a name that is used as the root name for all output files.

The Run_DMol command also creates a shell script file (run_name.csh) that actually runs the DMol calculation. You can have the Insight program automatically submit this job to the background or just write it to disk, so you can submit it manually later.

Step 4: Analyzing the results

Setting up calculations with the commands in the DMol module

DMol uses a defaults file for setting up default values for the DMol interface in Insight. The Insight program looks in a cascading series of directories for a defaults file: first in current-working-directory, then in $HOME, and, if the file has still not been found, finally in $BIOSYM/data/dmol. You can customize the defaults file to tailor the parameter values to your liking. Site administrators may choose to update the file in $BIOSYM/data/dmol, and ordinary users will probably want to copy or modify a file in their home directory.

You can reload the DMol interface with data from a previous job. This can speed revisions when only a minor change is needed for another calculation. This is accomplished by toggling the Setup/System command's Load_Input parameter to on.

Defining the molecule and its point-group symmetry

To specify the system, enter a name in the Object Name parameter box by picking a molecule or assembly in the display area of the screen, choosing its name from the Assem/Mol Names value-aid, or typing it in the Object Name parameter box.

Select Energy to compute the electronic energy of your system. To compute energy and a single gradient without optimization, select Gradient. Select the Optimize parameter to optimize the geometry of your system. To compute harmonic frequencies at the specified geometry, select the Frequency parameter. The Optimize_Frequency parameter allows you to optimize the geometry before computing the harmonic frequencies

In addition, you can toggle the Load_Input parameter on to read in previously set parameter values from a command input file, by entering its name in the File Name parameter box. You also need to set the Calculation_Type to match that in the input file.

Finding and adjusting the point-group symmetry

Important

You must execute the Symmetry/Find_Pt_Group command in order to take advantage of any symmetry (other than C1) for DMol runs that are set up from the Insight interface.

Toggling the Snap_Symmetry parameter on means to attempt to change the relationship of the atoms to their ideal symmetry positions (the symmetry is adjusted when the command is executed). The symmetry label is displayed whether Snap_Symmetry is on or off.

Snap_Orientation can be toggled if Snap_Symmetry is on. Toggling the Snap_Orientation parameter on means to attempt to place the molecule in the standard orientation around the origin and symmetry axes. Note: this may significantly displace your molecule. If Snap_Orientation is off, the molecule orientation does not change.

If you want to execute the Symmetry/Find_Pt_Group command with Snap_Orientation toggled on, you must do so before using the Grid pulldown, to prevent a mismatch between the positions of the molecule and the grid.

If the Symmetry/Find_Pt_Group command is not executed with Snap_Symmetry and Snap_Orientation toggled on, C₁ symmetry is used in an optimization calculation (even if the Use_Symmetry parameter in the Optimize/Parameters command is toggled on).

The Find_Pt_Group command can be used in two different ways. First, you may want to use it to simply determine if there is essentially exact symmetry (other than C₁, which is no symmetry) at the current geometry. This is done by executing the command once with Symmetry_Threshold set to a small value (e.g., 10^-6) and the Snap parameters toggled on. The molecule is translated and/or rotated so that its center of mass resides at the origin of the Cartesian coordinate system, and any non-Abelian symmetry found is used during the subsequent DMol background job.

You should avoid setting Symmetry_Threshold to values 0.8-1.0 Bohr. If you find that you need to use threshold values this large, you should probably use the Builder tools to manually adjust the geometry.

Specifying parameters that control the calculation

Each of these commands contains a group of parameters that must be defined before performing a DMol calculation if you want values other than the defaults.

Using the Setup/Parameters command

The usual default appearance of DMol's Setup/Parameters parameter block is shown below. Additional parameters may become accessible as you set various options in this parameter block.

Choosing functionals

As described under NLSD functionals in DMol, DMol supports several commonly used functionals. By default, the VWN functional is selected. This is the most popular local spin density (LSD) functional. It can be used successfully to predict molecular structures in molecules with covalent bonds. For molecules with weak (e.g., hydrogen) bonds or the obtain quantitative thermochemical results, the gradient-corrected functionals should be used. DMol supports the Becke (1988) gradient-corrected exchange functional (B_88), together with local correlation (BVWN) and the gradient-corrected correlation functionals of Perdew and Wang (1992) (BPW) and Lee, Yang, and Parr (BLYP). The gradient-corrected functionals are computationally more expensive than the local functional, but they are necessary to obtain accurate results.

If any of the gradient-corrected functionals is selected, you can set the Non_Local_Type parameter to Perturbed_Energy or SCF_Potential as the type of calculation. The Perturbed_Energy type of calculation is computationally less expensive than the SCF_Potential type. Choosing Perturbed_Energy means that the local (VWN) functional is used in SCF iterations and the final LSD density is applied for NLSD calculations of both energy and gradients. Selecting SCF_Potential means that the chosen NLSD functional is used in SCF calculations as well as in the energy and gradient calculations. This is the most accurate type of method for obtaining the new NLSD density. Experience shows, however, that the difference between the LSD and NLSD densities is rather small; therefore, the Perturbed_Energy type is recommended as a good compromise between accuracy and computational expense.

DMol allows you to select Other_Functionals, both Local and Gradient-Corrected. You can, for example, select the HL_JMW local functional instead of the VWN functional. (The JMW function was the default in previous releases of DMol.) The Other_Functionals choice is recommended for comparison or validation purposes only. In particular, caution is needed if only a correlation-gradient functional is selected, but no B_88 exchange contribution is chosen.

Parameters controlling the basis set

To define the number and type of atomic orbitals used by DMol to expand the molecular orbitals, use the Atomic_Basis_Set parameter. Its value can be set to Minimal, Double_Numeric, DND, or DNP. The Minimal basis set uses one atomic orbital for each occupied orbital in the free atom. Minimal basis sets are generally inadequate for anything but qualitative results. The Double_Numeric basis set uses approximately two atomic orbitals for each occupied orbital in the free atom. The DNP basis set uses double-numerical basis functions together with polarization functions, i.e., functions with angular momentum one higher than that of the highest occupied orbital in the free atom. For example, the polarization function for H is 2p, for C is 3d, and for Fe is 4p. This basis set is comparable in quality to Gaussian 6-31G** sets. DNP basis functions usually yield the most reliable calculations. The DND basis set is identical to DNP except that no p functions are used for hydrogen. This basis set is comparable in size to Gaussian 6-31G* basis sets, but is of much better quality.

The input .basis file included with DMol contains at least a DNP basis set for each atom up to U. Triple-zeta basis sets and/or diffuse orbitals are also provided for some elements. Refer to the Basis set summary in Utilities for a complete list of the basis functions included for each element. Although the orbital data for all four basis sets is read from the .basis file, only the data for the basis set selected by this command are used in the DMol calculation. Atomic orbitals associated with the remaining basis sets are labeled eliminated in the output file for that run.

The Frozen_Orbitals parameter allows you to freeze specific orbitals (i.e., eliminate them from the calculation). The available parameter values are:

• None--No orbitals are frozen.

• Inner_Core--Freeze the 1s orbitals on atoms B to Ne, the 1s2s on Na-Ar, the 1s2s2p on K-Kr, and the 1s2s2p3s3p3d on Rd-Xe.

• All_Core--Freeze the 1s orbitals on atoms Li to Ne, the 1s2s2p on Na-Ar, the 1s2s2p3s3p on K-Kr, and the 1s2s2p3s3p3d 4s4p on Rd-Xe.

• Extra_Coarse--Fewest number of mesh points defined. Use only for debugging calculations, where the actual results are not really important, or when you are interested only in qualitative results. You may also use an extra-coarse grid when you are generating plot data, since the appearance of the plotted data (MOs, density, etc.) is not affected by the number of mesh points.

• Coarse--Uses slightly more mesh points than the extra-coarse option. Although the quantitative results are better than those produced with an extra-coarse mesh, they are still not precise enough for most applications.

• Medium--Selects the default number of mesh points. Provides a reasonable compromise between numerical precision and computational overhead.

• Fine--Uses slightly more mesh points than the medium option. Use it whenever you encounter problems such as discontinuous energies, i.e., bumpy potential energy surfaces.

• Extra_Fine--Uses the maximum number of mesh points, almost to the saturation point of the mesh grid. Use it only for reference calculations.

Although DMol automatically chooses appropriate occupations for a neutral or ionic system, you can define the total molecular charge for ionic systems using the Charge parameter. Alternatively, you can input user-specified occupations via a file called run_name.occup. These occupations remain fixed during the DMol run. Toggle User_Occupations on and input a filename for the Occup_File_Name parameter.

Toggle the Impose_Elec_Fld parameter on to impose a static electric field on the system. Setting the Impose_Elec_Fld parameter on activates the Stat_Electric_Fld parameter, which allows you to enter the X, Y, and Z coordinates, in atomic units, of the static electric field.

Set the Point_Charges parameter on to include point charges in the calculation. Setting the Point_Charges parameter on activates the Charges_File_Name parameter The Charges_File_Name parameter is filled in with the name of the point-charge file. Choose the desired file from the value-aid that appears when you click the Charges_File_Name parameter box.

To request calculations in a solvent using the COSMO model, toggle the Solvate parameter on and input the name of the cosmo_input file as the COSMO_File_Name parameter.

SCF parameters

Toggle the Restart_SCF parameter on to restart an interrupted or unconverged calculation from the .tpotl file, which contains the analytic representation of the Coulombic potential. Alternatively, using a previous .tpotl file at a different geometry can give the calculation a much better starting guess than the default, which is simply the density from the superposition of atomic densities. Setting the Restart_SCF parameter on makes the Restart_SCF_File parameter accessible, which allows you to select which .tpotl file to use.

Set the Direct_Procedure parameter on to store the SCF orbital values in memory instead of on disk. The DMol integration requires the evaluation of quantities of the form:

Eq. 130    

If disk space is a limiting factor, DMol can construct these quantities in memory as needed, rather than reading them from the disk, using what is referred to as the direct procedure. This technique has the advantage of eliminating the FWV file, thus significantly reducing disk requirements. However, there is some CPU overhead associated with this procedure. Typical calculations require 25-50% more time when you specify the direct method.

Set the Direct_Procedure parameter off to store the SCF orbital values on disk.

Toggle the SCF_Parameters parameter on to access the Iteration parameter, which allows you to specify the maximum number of iterations in the self-consistent solution for the LDF equations. Enter a larger number to achieve better convergence. However, each iteration increases the processing time. If the program exceeds this number of iterations before meeting the specified SCF convergence threshold, it automatically suspends the calculation.

Use the SCF_Dens parameter to specify the minimum degree of convergence for the SCF procedure. The degree of convergence is measured by the rms change in the density from one iteration to the next. The program automatically suspends calculation when convergence, as defined by this parameter, is reached.

The SCF procedure is terminated when the change in the total energy from one iteration to the next is less than the SCF_Ener threshold. SCF_Ener is zero (off) by default, which means that some other criterion for SCF convergence is applied. By default, the norm of the electron density matrix (SCF_Dens, see above) is used to monitor and stop the SCF process.

DIIS_Size invokes the DIIS algorithm of Pulay (Pulay, 1982). DIIS calculates the new fitted density as a linear combination of the current fitted density and densities from the previous SCF cycles. The total number of SCF cycles considered for DIIS interpolation is DIIS_Size. The default and recommended value is 4, the maximum is 10. It may be necessary to use a larger DIIS space (e.g., 8) for metallic clusters, together with small values of the Mix parameters and a non-zero value for Smearing (below).

The Mix_Alpha and Mix_Beta parameters restrict the maximum allowed change in the charge (or spin) density for each iteration of the self-consistent procedure. If _old is the charge density from the previous iteration and _curr is the density from the current iteration, then the new density is calculated as:

Eq. 131    

To prevent automatic reduction of the Mix parameters, specify negative values for them. (The absolute value of the parameters are actually used for the calculation.) Mix parameter values as small as 0.005 are not unusual for systems with a large number of low-lying excited states, such as metal clusters. The program also automatically reduces this parameter any time it detects an oscillatory pattern instead of convergence during the LDF self-consistent procedure.

The Bad_Steps parameter allows you to define the maximum number of consecutive bad (divergent) iterations allowed before DMol aborts an LDF calculation. Divergence may occur if the Mix parameters are too large. Since the LDF algorithm often makes a single divergent step and recovers in the next iteration, do not enter a value of 1. This option ensures that the CPU does not waste valuable time attempting to complete a divergent calculation.

The Smearing parameter allows electrons to be smeared out among all orbitals within a given E of the Fermi level. This procedure improves convergence of the SCF procedure by allowing orbital relaxation to take place more rapidly. The character of the resulting virtual orbitals can be more effectively mixed into the occupied space, since they are now fractionally occupied. It is important to confirm that, as the density converges to its self-consistent value, the amount of charge smearing also tends to zero, to ensure that the calculation converges to the ground state.

Large values of the Smearing parameter may prevent the calculation from converging. If this occurs, restart the calculation with the Restart_SCF option toggled on and reduce the Smearing parameter.

To smear charges within X Hartrees of the Fermi level, enter X as the Smearing parameter, where X is a floating-point number from 0.001 to 0.1. To ensure consistent results, the value of Smearing should be less than the Mix parameters by a factor of 2-10.

Properties and population analysis parameters

Electric moments

Toggle the Electric_Moments parameter on to calculate the dipole moment.

Electric field gradients

If Nuclear_EFG is toggled on, the electric field gradients at all nuclei are calculated. For a geometry optimization, the EFG calculation is performed only for the final, optimized geometry.

Technical notes for EFG

• There is no restriction as to the symmetry employed in the DMol calculation. However, calculations lower than the actual molecular point-group symmetry may lead to less accurate EFG tensors (especially as far as the asymmetry parameter is concerned).

• It is possible to run EFG calculations with frozen core basis sets when the COSMO solvation model (COSMO--solvation effects) is not used. However, no significant validation of this option has been performed.

• If point charges are supplied, these are automatically included in the EFG calculation.

• If a COSMO calculation (Specifying COSMO parameters) is performed, the molecular surface charges are automatically included in the EFG calculation.

• To calculate the EFG for a particular nucleus, the LMAX value at that nucleus has to be at least 2, since the EFG calculation shares information with the Poisson solver for the electrostatic potential.

Toggle the Partial_DOS parameter on to calculate partial density-of-states results.

Optical absorption spectra

The Optical Absorption and related parameters allow you to specify calculation of an optical absorption spectrum. Toggle the Optical Absorption option on to include optical absorption in your calculation. This also gives access to two additional parameters, which specify the energy range for which transitions are to be calculated. The energies are specified in units of wavenumbers. The default range extends between 10,000 and 250,000 cm^-1.

It is possible to run optical absorption calculations with frozen-core basis sets, and for both spin restricted and spin unrestricted models.

Mulliken population analysis

You can toggle the Mulliken_Charges parameter on to enable a simple Mulliken analysis. Here, the total effective number of electrons in each atomic orbital is included in the population analysis. Toggling Mulliken_Charges to on activates the Overlap_Matrix parameter. Toggle the Overlap_Matrix parameter on to also include the population-overlap matrix in the analysis. Toggling Overlap_Matrix to on activates the Reduced_Orbital parameter. Set the Reduced_Orbital parameter on to limit the Mulliken analysis of the overlap matrix to reduced or condensed orbitals.

Bond order

Toggling the Bond_Order parameter on allows you to calculate Mulliken and Mayer bond orders and Mayer valencies as defined under Mulliken and Mayer bond orders. If the model has an odd number of electrons, then the free valence is calculated as well.

Technical note for bond order

This option works only for models without symmetry.

Hirshfeld charges

Hirshfeld_Charges properties are determined by Atomic_Dipoles and Atomic_Quadrupoles. The Hirshfeld partitioned charges are defined relative to the deformation density. The deformation density is the difference between the molecular and the unrelaxed atomic charge densities and is given by:

Eq. 132    

where (r) is the molecular charge density and (r - R) is the density of the free atom at coordinates R. Using the deformation density, the effective atomic charges, dipoles, and quadrupoles on atom are defined as (Delley 1986):

Eq. 133    

Eq. 134    

Eq. 135    

The weight W(r) is defined as the fraction of the atomic density from atom at coordinate r:

Eq. 136    

ESP-fitted charges

After you toggle the ESP_Charges parameter on and submit the DMol job, the run_name.input file contains the line:

ESP_Charges  1

The ESP charges can be displayed by using the DMol module's Analyze/Charge_Display command, as described under Displaying charges.

COSMO--solvation effects

The Environment/COSMO command gives you access to parameters that are used to define the DMol/COSMO calculation and the input file. Each parameter in this command gives access an additional group of parameters that must be defined before performing a DMol/COSMO calculation if you want values other than the defaults.

After you select an appropriate parameter you may want to write COSMO input by toggling the Write_COSMO_Input parameter on. When this parameter is toggled on, a COSMO_Input_File parameter box appears with the default name of the input file, run_name.cosinp. You may change this name if you want. Select Execute to write the current COSMO parameter values to the COSMO_Input_File. You will then select this file in the Setup/Parameters command as described below (Specifying a COSMO calculation).

Each of the COSMO_Options is discussed separately here.

• Dielectric_Constant

The Dielectric_Constant parameter is used to specify the dielectric constant of the solvent. The default dielectric constant is 78.4, which corresponds to water at room temperature. You can also set COSMO_Values to Infinite for an "infinite" dielectric constant, which corresponds to a conductor. (In actuality, a value of 999.0 is used rather than infinity.) Setting COSMO_Values to By_Solvent displays a list of several common solvents. Choosing one of these solvents sets the Dielectric_Constant to the dielectric constant of that solvent. Selecting MAIN_OPTIONS returns you to the previous lists of parameters. You can enter your own value for the dielectric constant by setting COSMO_Values to User and entering a real number in the Dielectric_Constant parameter box.

• Surface_Definition

The Surface_Definition parameter allows for custom design of the cavity (i.e., the solvent-accessible) surface, which is constructed by the method of Klamt. The main parameters governing surface construction are the number of points in the basic grid, the number of segments on the surface, and the solvent probe radius.

Typically, you do not change the values of the surface parameters, but rather leave them at their default values. The values of the default parameters are displayed in the information area near the bottom of the main Insight window. If you set COSMO_Values to User, you may change the parameters that define the surface construction. After selecting User, the allowed values of some of the parameters (as you select them from the upper list in the parameter block) are displayed under COSMO_Values. For other parameters, suggested default values (which you can change) are displayed in a Parameter_Value parameter box if you in addition set COSMO_Values to User. (This is easier to understand if you select the Environment/COSMO command in the DMol module of the Insight program and try choosing the various parameters as you read.)

The following parameters can be specified from the Insight interface:

Basic_Grid_Size	Number of the points of the basic grid
Number_Of_Segments	Number of segments on the surface.
Solvent_Radius	Solvent probe radius.
A_Matrix_Cutoff	The interaction between surface segments is calculated approximately if the distance (in angstroms) between these segments is larger than A_Matrix_Cutoff.
Radius_Increment	Common increment to the van der Waals atomic radii. The default for Radius_Increment is 0.1 Å, which means that the actual atomic radius used in the calculation is increased with respect to the van der Waals radius by 0.1 Å.

We recommend that you not change the default values of surface definition parameters for typical DMol/COSMO runs.

• Non_Electrostatic

The Non_Electrostatic parameter controls two other parameters, A_Constant and B_Constant (accessible when you select Non_Electrostatic and then set COSMO_Values to User), which are used to approximate the nonelectrostatic contributions to the free solvation energy within the COSMO model. The two parameters define this contribution via Eq. 83, where the surface_area is the area of the cavity surface enclosing the molecule.

• Atomic_Radii

The Atomic_Radii parameter is used to define the atomic radii of the atoms present in the molecule. You can modify the value of an atomic radius by setting COSMO_Values to User and then selecting the element from the COSMO_Elements list (this list is empty if you did not previously specify a molecule with the Setup/System command). The VDW_Radius parameter shows the van der Waals radius of the chosen element. You can modify the VDW_Radius by entering a different value.

Caution

Be cautious in changing the Atomic_Radii or Radius_Increment parameters, since COSMO results depend strongly on the choice of the size of the cavity enclosing the molecule. The A_Constant and B_Constant that define the Non_Electrostatic term were optimized for the default values of the van der Waals radii, so that changing atomic radii without reoptimization of these constants will introduce an error.

Specifying a COSMO calculation

Once you have written a COSMO input file by executing (either in your current Insight session or previously) the Environment/COSMO command with the Write_COSMO_Input parameter toggled on, you can specify a COSMO calculation.

Select the Setup/Parameters command and toggle the Solvate parameter on. This makes a COSMO_File_Name parameter box become accessible. You can enter the name of the COSMO input file by choosing its name from a DMol_Files value-aid. All the input COSMO files (suffix = .cosinp) that reside in the current directory appear in this list. Once you specify the COSMO input file in the COSMO_File_Name parameter box, you can set other parameters and then select Execute and proceed as usual with DMol job submission. The output of the DMol/COSMO run and the results file run_name.cosmo are described in Files.

Vibrational parameters

The Finite_Differences parameter allows you to select the number of finite differences of gradients used during frequency evaluation, either Single_Point and Two_Point. Harmonic vibrational frequencies are computed by diagonalizing the mass-weighted second-derivative matrix F (Wilson et al. 1980). The elements of F are given by:

Eq. 137    

Since DMol does not calculate the second derivatives analytically, it calculates finite differences of the first derivatives instead. Gradients are computed at displaced geometries and the second derivatives are computed numerically.

• Select Single_Point to enable single-point differencing for this process, i.e., displacements are taken in only one direction:

Eq. 138    

The two terms represent the analytic derivatives at the equilibrium geometry and at a geometry with coordinate qj displaced by distance .

• Select Two_Point to enable two-point (or central) differencing to obtain the second derivatives:

Eq. 139    

Although two-point differencing reduces numerical rounding-off, it almost doubles the computation time.

The Restart_A parameter allows you to restart a frequency evaluation starting at a specific atom. DMol calculates the gradient for each atom perturbed in the x, y, and z directions and stores it in the .hess file. If a calculation is interrupted, you can restart it beginning with displacements on atom #n, thereby saving all previous calculations. A value of 0 or 1 restarts the calculation from the first atom. A restart value greater than the number of atoms causes the program to read in all the available data in HESS and evaluate the vibrational frequencies.

The Project_Matrix parameter allows you to project the translations and rotations from the force-constant matrix any time that the force-constant (i.e., second-derivative) matrix is not evaluated at the point of the zero gradient. Instead of the 6 normal modes with value zero, corresponding to 3 translational and 3 rotational degrees of freedom, this projection forces six 0 eigenvalues. This method has a slight effect on the remaining 3N - 6 vibrational frequencies.

Using OPTIMIZE in the Insight environment

1. Construct the molecule to be optimized using the Builder or read in the geometry from an existing .car file or appropriate database.

2. Specify any desired geometric constraints with the Optimize/Constraints command. This may include standard distance, angle, or dihedral constraints among any atoms in the system, as well as frozen Cartesian coordinates. Dummy atoms can be defined with the Pseudo_Atom pulldown (Builder module) to aid in defining constraints that are awkward or impossible to define with only real atoms.

3. Minimize the geometry interactively, using one of the molecular mechanics forcefields available as part of the Discover package (the default forcefield is adequate for most routine organic molecules). It is strongly recommended that you also calculate a Hessian matrix at this time. (Starting with even a relatively simple mechanics Hessian can dramatically reduce the number of cycles required to reach convergence, especially with Cartesian coordinates.) You should also make sure that the desired constraints are met, as much as possible, before starting the quantum optimization run.

4. Check the mechanics-converged geometry for symmetry using the Symmetry/Find_Pt_Group command. If no symmetry is found and you suspect that your molecule ought to have some, increase the symmetry tolerance and try again. If symmetry is still not found, try repeating Step 3 with a tighter gradient-convergence criterion.

5. Steps 1-4 can be repeated to build, say, the backbone of a molecule and ensure that it has the desired symmetry and/or constraints before adding side chains and additional functional groups. (Note, that if you do modify the molecule, you will need to recalculate the Hessian, using the same mechanics forcefield as in Step 3. Do this by invoking the Discover program again.)

6. When you are satisfied with your molecule's symmetry and constraints, only then should you set the remaining optimization parameters and prepare your job for submission.

Using a good starting Hessian is virtually mandatory in optimizations in Cartesian space, which perform very poorly otherwise, especially for larger systems with little or no symmetry (Table 1). Optimizations in natural internal coordinates are much less sensitive to the initial Hessian data--the (default) diagonal Hessian is, in general, just as good as a full mechanics-generated Hessian. Thus, if you are optimizing in natural internal coordinates, an input Hessian is not obligatory for good performance.

Table 1     . Efficiency of optimization under various conditions

Number of optimization cycles needed to reach convergence for minimization using Cartesian and internal coordinates, starting with a unit, a diagonal, or a molecular mechanics-derived Hessian. Calculations were done with Turbomole, but the same general results would be obtained in any DFT calculation.

molecule	number of atoms	symmetry group	number of variables	Cartesian coordinates		internal coordinates
				unit Hessian	mechanics Hessian	unit Hessian	diagonal Hessian	mechanics Hessian
water	3	C2v	2	5	5	7	5	6
ammonia	4	C3v	2	7	6	7	5	6
acetylene	4	Dh	2	7	6	5	7	6
benzene	12	D6h	2	6	4	5	3	4
ethane	8	D3d	3	7	4	6	4	5
propadiene	7	D2d	3	10	5	8	5	5
neopentane	17	Td	3	10	5	7	5	5
1,3,5-trifluoro- benzene	12	D3h	4	7	5	6	5	5
hydroxysulfane	4	C1	6	21	11	17	10	8
disilyl ether	9	C2v	7	27	10	13	8	8
acetone	10	C2v	8	22	7	7	6	6
furan	9	C2v	8	10	8	11	7	8
naphthalene	18	D2h	9	11	5	9	7	5
methylamine	7	Cs	10	10	5	7	5	6
1,3,5-trisilacyclo- hexane	18	C3v	11	36	8	14	8	8
1,3-difluoro- benzene	12	C2v	11	8	5	9	6	5
ethanol	9	Cs	13	18	6	8	6	6
difluoropyrazine	16	C2h	15	21	8	11	9	9
1,5-difluoro- naphthalene	18	C2h	17	16	6	11	7	6
benzidine	26	D2	18	26	10	25	12	9
benzaldehyde	14	Cs	25	17	6	9	6	6
4-methyl-3-pen- ten-2-one	17	Cs	28	38	7	9	8	7
2-amino-4-pteri- dinol	17	Cs	31	23	9	12	11	10
2-hydroxybi- cyclopentane	14	C1	36	45	15	23	13	15
caffeine	24	Cs	42	39	10	11	10	12
histidine	20	C1	54	102	30	44	23	19
dimethylpentane	23	C1	63	29	9	15	16	12
menthone	29	C1	81	100	14	26	16	13

However, under certain circumstances the topology of your molecule might be such that OPTIMIZE has difficulty generating a complete set of internal coordinates. If this occurs, the default procedure is to switch to Cartesian coordinates, where a starting Hessian is needed. Bear this in mind when deciding whether or not to generate a Discover Hessian for your ab initio optimization.

Optimization parameters are set within the Insight environment by selecting the Optimize/Opt_Parameters command. The commands in the Optimize pulldown in the DMol user interface appear greyed out if an OPTIMIZE calculation has not been selected (via the Setup/System command). This is intended to keep you from defining parameters that do not affect the calculation.

When the Optimize/Opt_Parameters command is first selected, the parameter block shown in Figure 2 appears. The parameters and their meanings are discussed below.

Figure 2. Default appearance of the Optimize/Opt_Parameters parameter block

This is the appearance of the Optimize/Opt_Parameters parameter block the first time this command is selected, if the parameters in the Session/Cmd_Display command have not been changed. (Please see the Insight documentation for information on the effects of the Session/Cmd_Display command.)  

Coordinate_System refers to the coordinates used to describe the molecule to be optimized. These can be Cartesian or Internal coordinates--the latter are generated automatically by OPTIMIZE, so no user input is required. The default is Auto, which means that OPTIMIZE attempts to generate a set of internal coordinates and use these, but if this fails, the program switches to Cartesian coordinates. Specifying Cartesian or Internal forces the coordinate choice. For successful optimization using Cartesian coordinates, a reliable starting Hessian (read from a file specified by Hessian_File after toggling Starting_Hessian to on) is recommended.

Use_Constraints is toggled on (indicated by highlighting and a pushed-in appearance) if you already set any geometric constraints for your molecule with the Optimize/Constraints command. Two algorithms are available for constrained optimization: Penalty functions and Lagrange multipliers. The former is more robust; the latter is more accurate and more efficient. The default is Lagrange_Penalty, which means that OPTIMIZE first tries the Lagrange multiplier algorithm and, if this fails, it then switches to penalty functions. The other option, Penalty_Lagrange, uses penalty functions and, at convergence, refines the final structure using Lagrange multipliers. Specifying Penalty or Lagrange forces a particular algorithm.

You may have convergence problems if you use angle constraints near 0° or 180°. It may be necessary to optimize using only penalty functions first and then use the Lagrange multiplier method in a separate run after the first has converged.

The current maximum number of specific distance or angle constraints that is allowed is 100. More "constraints" can be set by freezing atom positions: any number of atoms may be frozen. You may request other distance and angle constraints and frozen coordinates in the same job; however, take care that your constraints are not mutually exclusive.

Note that constrained transition-state searches can be done only with the Lagrange multiplier method--the penalty function algorithm cannot be used.

Use_Symmetry is on if you used the Symmetry/Find_Pt_Groups command to find the symmetry of your molecule. (Symmetry is not used in the optimization unless the Symmetry/Find_Pt_Groups command has been executed, even if Use_Symmetry is on.)

Locate_Trans_State should be toggled on if you want to optimize to a transition state. The Calc_Mode parameter becomes accessible when Locate_Trans_State is on and is used to indicate which Hessian mode to maximize--the default is to maximize along the lowest mode. Other modes can be requested by setting Calc_Mode accordingly; however, this is not recommended unless you know the Hessian structure in some detail. Without a reasonable starting Hessian, transition-state searches have limited chances of success.

GDIIS_Mode invokes the GDIIS algorithm of Pulay (Pulay 1982). This is available only for minimization. GDIIS calculates the new geometry as a linear combination of the current geometry and geometries from previous optimization steps; the total number of such geometries utilized is given by Max_DIIS, which becomes accessible when GDIIS_Mode is set to Manual. A suggested range for Max_DIIS is 2-10. Setting GDIIS_Mode to Automatic causes OPTIMIZE to estimate a suitable value for Max_DIIS based on the number of degrees of freedom.

Tolerances refers to the criteria that must be met for the geometry to be considered converged. The Grad_Conv criterion and either the Ener_Conv or Disp_Conv criteria (or both) must be satisfied for the optimization to be considered converged.

Grad_Conv is the convergence criterion for the maximum component of the gradient vector (in atomic units). The default is 0.0003, which should be more than sufficient for most purposes. To obtain accurate vibrational frequencies for very floppy molecules, this value should be reduced. For general optimizations using DMol, a value of 0.001 is more suitable, due to the heavy numerics involved in this code.

Ener_Conv is the convergence criterion for the energy change from the previous optimization step (in atomic units). The default is 0.000001 Hartree. For general optimizations using DMol, a value of 0.00005 is more suitable, due to the heavy numerics involved in this code.

Disp_Conv is the convergence criterion for the maximum predicted displacement, that is, the maximum component of the displacement vector for the next step (in atomic units). The default is 0.001, which should be more than sufficient for most purposes. For very floppy molecules this value can be increased without affecting the energetics. For general optimizations using DMol, a value of 0.001 is more suitable, due to the heavy numerics involved in this code.

Cycles is the maximum number of optimization cycles allowed for the job. The default is 50, which should be more than enough under most circumstances. If convergence is not achieved in Cycles steps, the job aborts.

Max_Disp is the maximum allowed step size, that is, the maximum permitted length of the displacement vector from one optimization cycle to the next (in atomic units). The default is 0.3. For awkward optimizations (e.g., to transition states or very shallow minima) with starting geometries known (or suspected) to be close to the final converged geometry, Max_Disp should be reduced.

All optimizations, especially those using Cartesian coordinates, should be initiated with a good starting Hessian. For standard minimizations, a good Hessian can be obtained from the Discover program; for transition-state searches, DMol should be instructed to calculate a Hessian before starting the optimization (by selecting the Setup/System and choosing the Frequency option).

Toggling Hessian_Update to on enables you to access the Hessian_Update_Mode parameter, which indicates the manner in which the starting Hessian is updated during the optimization procedure. Three update methods are supported: Powell, BFGS, and BFGS_Safe. Defaults are provided, depending on the settings of various other parameters in this parameter block. These defaults should not be changed.

• The Powell update is a general-purpose method that allows the Hessian eigenvalue structure to change. It is the default for a transition-state search.

• The BFGS update is the standard default method for minimization. This update tends to preserve positive definiteness, that is, if the Hessian on a particular cycle has all positive eigenvalues, this situation is likely to carry over to the next cycle, hence its suitability for minimization.

• The BFGS_Safe update is like the normal BFGS, except that additional safeguards ensure that a positive-definite Hessian always remains so. If this property is threatened, Hessian updating is skipped for that cycle. This is the default for an optimization using GDIIS.

Figure 3. Appearance of Optimize/Opt_Parameters parameter block after GDIIS_Mode is set to Manual

Here, the GDIIS_Mode parameter has been set to Manual, which makes the Max_DIIS parameter box available (compare Figure 2).  

When you have set all the parameters in this parameter block, select Execute to actually set the internal DMol parameters and to exit the parameter block.

Volumetric and print parameters

Densities

Set the Charge_Density parameter on to generate plot data to represent the total charge density. Set the Deformation_Dnsty parameter on to generate plot data for the deformation density (molecular charge density minus atomic charge densities). Set the Spin_Density parameter on to generate plot data for the spin density (alpha-spin minus beta-spin density).

Electrostatic potential

Set the Potential parameter on to generate plot data for the electrostatic potential.

Molecular orbitals

Set the HOMO parameter on to generate plot data for the highest occupied molecular orbital. Set the LUMO parameter on to generate plot data for the lowest unoccupied molecular orbital. Set the Other_MO parameter on so that you can enter numbers, separated by spaces, in the Molecular_Orbitals parameter box to specify which molecular orbitals to plot. List the lowest orbital energy first. (You cannot plot frozen-core orbitals.)

Optional output file contents

Set the MO_Coefficients parameter on to include molecular orbital coefficients in the output file. Set the Eigenvalues parameter on to include the eigenvalues in the output file.

Setup_Grid_Output command

The Grid_Style parameter allows you to select the method used to compute the grid boundaries. Setting Grid_Style to Enclosure automatically determines the upper and lower limits of the x, y, and z dimensions of the grid, based on the coordinates of the molecule and the value of the Border_Space parameter. The value of the Border_Space parameter (in angstroms) is added to the maximum value in each of the x, y, and z dimensions spanned by the molecule, and, similarly, subtracted from the minimum value in each dimension to define the 3D rectangular region of the grid.

You also need to specify the method for determining the positions of the grid points. With Grid_Style set to Enclosure, you specify the grid points with the Number_of_Steps parameter. The Number_of_Steps parameter allows you to choose the number of points per dimension of the 3D grid. These points are evenly spaced in each of the x, y, and z dimensions. This method provides a constant number of points in each dimension, but not a constant point density for any molecule or assembly. Note that the lower boundaries of the grid will be shifted so that the grid points fall exactly on the grid boundaries.

With Grid_Style set to Extents, you explicitly specify the upper and lower grid boundaries in each of the X, Y, and Z dimensions, using the Lower_Bounds and Upper_Bounds parameters.

By setting Grid_Style to Extents, you specify the positions of the grid points with the Grid_Step parameter. The Grid_Step parameter allows you to specify the distance, in angstroms, between points in each dimension of the 3D grid. This value must be greater than zero. This method provides a constant density of points in each dimension of any size grid.

Setting up the background job

When the Background_Job/Setup_Bkgd_Job command is used, the background job list shows only those background jobs that are run from the current module and can be run on a remote host. If the module contains only one job, the parameter is automatically filled in. The list of hosts shows only those hosts that are associated with that background job in the background_job_hosts file at your site. It is possible for you to specify a remote host that is unavailable (off line, for instance) or for which you have no login account.

Use the Background_Job/Control_Background_Job command to coordinate running background jobs by detaching selected jobs from or attaching them to Insight. In addition, you can use this command to specify the interval for invoking a task specific to a particular background job for processing its output.

Every background job submitted via the generic background utility is assigned a job number. This number is displayed in the information area when the job is submitted (e.g., Starting Module background job ... as job 1). You should note the job number when the job is submitted, since it can be used later to check on the job's completion status or kill the job.

The Setup_Bkgd_Job command does not actually run the command; it simply records your host and execution mode preferences. The default host is Local. Your selected host and Execution_Mode are used for any subsequent background jobs for the duration of the Insight session. When you start up a new session, all background job parameters are set to their default values.

The Execution_Mode parameter allows you to run a background job concurrently (Cont_Insight) or interactively (Wait_For_Job) or to simply create the necessary command files to submit the job, but not actually execute them (Cmd_File_Only).

The Send_Mail parameter allows you to have the system send you an electronic mail message upon completion of the background job. This parameter is not active if Execution_Mode is set to Wait_For_Job. You may find this option useful when running long jobs where you exit the Insight program before the job completes.

The Save_Cmd_Files parameter allows you to save the command file used to submit the background job (bkgd_job_run_name#.csh). Otherwise this file is deleted when the job completes. This parameter is not active when Execution_Mode is set to Cmd_File_Only.

All background jobs return a completion status. The completion status is an integer code that indicates success, failure, and/or reason for failure of the job. The status code is always displayed when you are notified that the job has completed.

If you consistently want to send background jobs to another host, you can modify your personal Insight startup file to invoke Setup_Bkgd_Job for each module/background job(s) that you want to automatically assign. Note that you must first change to the appropriate module in which the background job's interface is found before using Setup_Bkgd_Job to set a preference for that module's background jobs.

The Completion_Window parameter can be used to prevent the notification window from appearing when the background job completes. The default value is on.

Support for the network queuing system (NQS) is now available in the Background_Job/Setup_Bkgd_Job command.

For the user interface to present parameter defaults and a value-aid containing available queues, and to correctly formulate an NQS command, the user's NQS queue environment information must be provided to the Insight program. The Background_Job_Hosts file contains the NQS queue information, or you may enter the required information directly using the Background_Job/Setup_Bkgd_Job command.

Based on the parameter values provided in the Background_Job/Setup_Bkgd_Job command for Queued Submission_Mode, the Insight background job mechanism formulates a standard NQS command and starts a process to execute it. It is assumed that the NQS command constructed by the Insight program functions with your NQS configuration.

Starting the job

Monitoring a background job

The Report_Mode parameter is used to indicate what information you would like the command to return: status of one job, status of all jobs, or the meaning of a return status code from a particular job.

The Job_Number parameter becomes active when One_Job is selected. It is used to specify the background job that you want to monitor.

The Background_Job and Status parameters become active when Look_Up_Status is chosen. They are used to specify a status code that you want to look up.

The Kill_Bkgd_Job command is used to stop execution of a background job by killing its process and, optionally, deleting its output files.

The Job_Number parameter is used to specify which background job to kill. A value-aid containing a list of all currently running background jobs is provided.

If the Save_Output parameter is toggled on, then all output files generated by the background job are saved when the job is killed. The default value of this parameter is off, meaning that all output files are deleted.

Visual aids to analyzing results

You can use the Analyze/Orbital_Contour command to automatically contour both the plus and minus phases of a molecular orbital in one step (the Grid/Contour command requires two separate steps for contouring the plus and minus phases of an orbital; and the contour levels, contour colors, and contour name root parameters have no default values.) You can also use this command to recalculate an orbital contour, by toggling the Recalc_Contours parameter on.

The name of the grid that contains the relevant data is specified with the Scalar Grid Name parameter. A name is given to a grid during its creation with the Grid/Get command (the Grid pulldown is accessed from one of the icons along the side of the main Insight window).

The Contour Name parameter specifies the root name to be given to a created contour objects or the name of the contour pair that you want to recalculate. When calculating a new contour, you usually do not need to pay any attention to this parameter, since a unique default name is derived from the value of Grid Name parameter. When recalculating, both the positive and negative contours are recalculated.

The Orbital_Amplitude parameter is used to specify the value of the contour to create. For orbital amplitude contours, the default value of is usually appropriate.

The colors assigned to the plus and minus phases of the orbital contour are specified with the Plus Contour Color and Minus Contour Color parameters, respectively. The color can be specified as a character string such as red, as an RGB triplet of integers specifying the red, green, and blue contributions, or by choosing a standard or custom-mixed color from a color palette value-aid. Control of color is explained further in the Insight II User Guide.

Displaying charges

• The Display setting reads atomic charges from a summary file (see Files) and displays them as atom-centered CPKs. The radius of the CPK in angstroms equals the value of the atomic charge in electrostatic charge units, if a scale factor of 1.0 is applied.

• The UnDisplay setting clears the atomic charge display.

• The Load setting reads the atomic charges from the summary file and applies them to the model as its new partial charges.

The remaining choices of the Charge_Type are the types of atomic charges that are supplied by DMol, Turbomole, or Zindo.

The color of positive and negative charges is specified through the Charge_Plus_Color and the Charge_Minus_Color parameters, respectively. The charge spheres can be scaled using the Charge_Scale_Factor parameter, which defaults to 1.0 (no scaling).

Displaying optical absorption spectra

The initial state of this command (Spectrum_Action = Create, File Name = *.optabs) is to take the optical absorption calculation results from the .optabs file (see Optical absorption results) and create a bar graph in the display area of the Insight window.

The graph can then be modified by setting Spectrum_Action to Modify and applying line broadening. Two modes of line broadening are supported:

• Lorentzian

Functional form =

• Gaussian

Functional form =

E_Min defaults to zero if E_Min or E_Max is activated after changing the Sigma parameter. E_Max defaults to [(the highest transition energy) plus (three times Sigma)] if E_Max or E_Min is activated after changing the Sigma parameter.

Customizing the Spectrum_Display command

So that you can display the optical absorption spectrum with energy units different from the default units of wavenumbers (cm^-1) used throughout the DMol module in Insight, a mechanism is provided for customizing the energy units. The customization is based on the environment variable $SPECTRUM_UNITS. The Spectrum_Display command recognizes the following settings automatically:

SPECTRUM_UNITS              cm-1 (wavenumber units, default) 
SPECTRUM_UNITS              eV (electron Volt units) 
SPECTRUM_UNITS              Ry or Rydberg (Rydberg units) 
SPECTRUM_UNITS              Ry or Rydberg (Rydberg units) 
SPECTRUM_UNITS              a.u. (atomic units)

SPECTRUM_UNITS              Unit_Name Unit_Conversion_Factor 

This setup can be written as the following BCL Macro called OA_Units, which you can add to the Analyze pulldown:

Define_Macro OA_Units \
    Enumer              Energy_Unit \
    Short_Ident         Unit_Name \
    Short_Float         CnvFactor

Def_enum Energy_Unit "cm-1"
Def_enum Energy_Unit eV
Def_enum Energy_Unit Rydberg
Def_enum Energy_Unit "a.u."
Def_enum Energy_Unit Specified
Set_enum Energy_Unit "cm-1"

Param_Comment Energy_Unit "Optical Absorption" Center

Param_Comment Unit_Name "Unit Specification" Center

Lstring Scr

Condition Unit_Name Energy_Unit Specified off off
Condition CnvFactor Energy_Unit Specified off off

If ( $Energy_Unit != Specified )
Env_var SPECTRUM_UNITS Set $Energy_Unit
End
Else
Scr = $Unit_Name // " " // $CnvFactor
Env_var SPECTRUM_UNITS Set $Scr
End
Env_var SPECTRUM_UNITS Get

End_Macro

DMol
Add_To_Pulldown OA_Units Analyze

Specifying isotopes

The Isotope_Setup command provides basic capability for specifying particular atomic masses before performing a normal mode analysis (below). It also provides access to default isotopic masses for a wide range of nuclear isotopes. The information is taken from a separate data file and can therefore be customized.

The Isotope parameter defines the action to be taken. The Standard_Weight and Substitute_Isotope settings of the Isotope parameter define the atomic mass for all atoms specified with the Atom parameter. The Atom parameter's scope is limited to atoms of the same element type.

The Substitute_Isotope setting makes two additional parameters accessible: Isotope Name and Isotope Mass.

Isotope Name refers to the name of the isotope that is obtained by prefixing the number of nucleons to the element symbol. The information is read from the q_isotopes.dat data file (see Files). The isotopes for a given element are listed in the Isotope List value-aid. For example, for hydrogen you would find the entries H, 1H, 2H, and 3H. The entry with only the element symbol (H here) refers to the standard weight, which is an average of isotope masses according to their relative abundances. The Isotope Mass parameter is entered automatically, depending on what Isotope Name is selected, but it can be modified. The Isotope Name is resolved to the first element found if the Atom parameter contains a wildcard.

The List_Current setting activates two parameters that are related to visualizing the current atomic mass definitions: List_In_Table and Label_Atoms.

The List_In_Table parameter, if toggled on, writes all the atomic masses, along with the atom names, to a table in a separate window when the command is executed. Clicking a table cell in that table adds an atomic mass label to the atom picked. This has the side effect that once the molecule is moved, labels are redrawn with the value of the partial charges.

The Label_Atoms parameter, if toggled on, attaches labels in the form of textual user objects to all the atoms in a molecule specified by the Molecule Name parameter.

The labels' styles can be modified--the relevant parameter names in the Isotope_Setup parameter block are self-explanatory--as can its precision (through the Precision parameter in the Insight Viewer's Session/Environment command).

Displaying normal mode vibrations

The Isotope_Subst parameter appears if the harmonic frequencies are actually calculated from a Hessian matrix supplied with the File_Contains parameter set to Hessian_Matrix. If the Isotope_Subst parameter is toggled on, the values for the atomic masses specified through the Isotope_Setup command (above) are used in the normal mode computation.

The Analyze/Normal_Mode command allows you to specify a wavenumber or an energy range for which to plot the frequency spectrum. The spectrum can be broadened. Modes can be displayed as arrows, and a distort function allows you to displace the geometry in the direction of a particular mode. A table containing the normal mode frequencies is generated, which can be used for selecting modes for the various visual representations.

Statistical thermodynamics

The Analyze/Stat_Mech command operates on the basis of a frequency table supplied by the Analyze/Normal_Mode command. This frequency table is generated through a .hessian file supplied by either Discover or quantum codes such as DMol or Turbomole. The frequency table contains all the information required to perform the thermodynamic analysis, i.e., the values of all frequencies for the given system as a result of the normal mode analysis performed with the Normal_Mode command, as well as the atomic coordinates and masses needed for computing the translational and rotational contributions to the thermodynamic quantities. The atomic masses can be modified with the Analyze/Isotope_Setup command before performing the normal mode analysis.

Files needed and produced

When the Stat_Mech command is executed, it launches a background job named stat_mech, which uses one input file called stat_mech.input and produces two output files, stat_mech.output and stat_mech.tbl:

• The stat_mech.input file contains all the data extracted from the frequencies table, along with the atomic masses and coordinates and the particular calculation options specified from the Stat_Mech parameter block.

• The stat_mech.output file contains the complete output of the statistical mechanics calculation (see Files for details).

• The stat_mech.tbl file can be analyzed with the help of the generic Insight Graph commands.

Temperature range

The range of temperatures for which thermodynamic quantities are to be computed is specified through three parameters:

• T_Initial defines the initial temperature.

• T_Final defines the final temperature.

• T_Step defines the temperature step to be taken in the temperature scan.

Thermodynamic quantities

The thermodynamic quantities computed are:

• The enthalpy H.

• The entropy S.

• The free energy G.

• The heat capacity at constant pressure C_p.

Additional parameters control the printing of the zero-point vibrational energy (Report_ZPVE) and of the moments of inertia (Report_Rotor_Info) to the .output file. The Report_Symmetry parameter, if toggled on, both reports the symmetry number for the particular system and includes it in the rotational partition function.

Displaying density-of-states information

Once a converged electron density has been calculated, there are several ways to analyze the results, in particular the wavefunction. A convenient way of displaying the molecular orbital spectrum is by constructing and plotting the density of states. For molecular systems, this is commonly done by graphing the molecular orbitals as a function of the MO eigenvalues. The degeneracy of the orbitals is then indicated by the height of the functions. The theory is presented under Density of states analysis.

The DOS intensities can be convoluted with either a Gaussian or a Lorentzian broadening function, or you can use nonconvoluted delta functions. Display parameters like the broadening parameter NM_Sigma and the energy range Freq Min, Freq Max for the DOS graphs can be changed. The data from which the graphs are created are stored in a table. This table contains the eigenvalues, occupations and intensities, and the labels for the symmetry representations and can be used for further reference.

You can also display Loewdin or Mulliken partial density of states (PDOS) or the conventional PDOS, which is a straight projection of the atomic orbitals on the molecular wavefunctions. The advantage of Loewdin and Mulliken is that they are normalized and, for all atomic orbitals, add up to the occupation for each molecular orbital.

Displaying a summary of DMol output

For frequency calculations, the vibrations are included, and if properties were calculated, both Mulliken and Hirshfeld data, as well as the electrostatic moments, are summarized.

The run statistics (the computer and CPU used, total CPU time) are included at the end of the summary file. This command is also useful for polling running jobs to see how they are progressing.

Using other Insight pulldowns

Please see the Insight documentation for further information on using the Grid and other Insight pulldowns and icons.