DMol

3       General Methodology

This chapter explains the general methodology for performing DMol calculations, whether you are using DMol in the Insight environment or the standalone mode. Specific instructions for using DMol in either of these modes are contained in Chapters 5 and 8, respectively.

A thorough understanding of the DFT method is necessary for an appreciation of many of the input options for DMol. Chapter 2, Theory and Implementation, presents a brief overview of the DFT method as implemented in DMol and relates aspects of DFT theory to some of the input options. An understanding of the computational aspects of DFT theory enables you to use the DMol program more effectively.

If you are using the Insight program, you can still run DMol in the standalone mode, so you can, for example, set up a run with the Insight interface, run the calculation in standalone mode, and then analyze some of the results back in the Insight interface. The input and output files are all compatible between both modes. You could, for example, use the Insight modeling facilities to construct a molecule and the DMol module to determine the symmetry, set some constraints, and write out the command input file. You could then exit the Insight environment to modify the input file with a text editor or through the dmol_master interface and then submit the DMol job directly. After the run finishes, you can read the output back into the Insight program to, for example, examine the orbital density-of-states or animate the normal modes of vibration.

Choosing a job type

1. Energy calculation.

2. Geometry optimization.

3. Calculation of frequency and thermodynamic properties.

• Atomic and bond population analysis.

• Dipole moments.

• Static polarizabilities.

• ESP-fitted charges

• Electric field gradients (EFG) at nuclei.

• Optical absorption spectra.

• Solvation effects via the COSMO model.

• Two- and three-dimensional plotting of charge density, deformation density, spin density, electrostatic potential, and molecular orbitals.

Energy calculation

• Energy.

• Dipole moments.

• Static optical polarizabilities.

• Charges.

• Charge density, electrostatic potential, MOs.

• ESP-fitted charges

• EFG at nuclei.

• Optical absorption spectra.

• Bond orders.

• Solvation effects via the COSMO model.

You can, optionally, calculate the other properties listed above. How to do this is discussed in detail in the online help and Appendix E (Commands--Standalone Mode). Dipole moments, charges, and the properties to be graphed are each selected by setting a single parameter or keyword, either indirectly from within the Insight program or directly if you are using DMol in the standalone mode. However, calculating the optical polarizability requires four separate calculations with electric fields imposed on the molecule.

Geometry optimization

• How many times to update the geometry before stopping.

• The maximum gradient allowed before the minimization is terminated. A gradient of zero would be ideal, but this is not computationally realistic.

• How close in energy two geometries may be to be considered identical. If the minimizer chooses a new geometry whose energy is close enough to that of the previous geometry, minimization is terminated.

• Whether to use the Powell or BFGS minimizer. (For an overview of minimization techniques see Press et al. 1986 or Geometry optimization -- The OPTIMIZE suite of algorithms.)

After the geometry is successfully minimized, the program then computes any other properties requested.

DMol may exhibit slow SCF convergence when there is a small HOMO-LUMO gap. Using smearing and/or decreasing the mixing parameters are recommended for solving this problem.

The DIIS option should always be used, to improve SCF convergence.

Optimal strategy

The optimal strategy for geometry optimization may be as follows:

1. Perform an LSD calculation using a Medium grid and relaxed SCF and geometry optimization criteria.

For example, use SCF_Density_Convergence = 0.001; Opt_Energy_Convergence = 0.0001; Gradient_Convergence = 0.01 when running DMol in standalone mode (Appendix E). The equivalent parameter names for the DMol module in Insight are SCF_Dens, Ener_Conv, and Grad_Conv (Chapter 5).

1. After the first calculation is finished, run the calculation again with much better convergence criteria.

Start from the geometry obtained at the end of the first run and increase the grid to Fine.

Some molecules that have a flat potential energy surface may require an Xfine grid in order to meet the default convergence criteria.

• Use 1-point or 2-point differencing. The finite differencing proceeds from atom to atom. On a single atom, the displacements are done in the x, the y, and the z directions. If 2-point differencing is used, then the displacements are in the order +x, -x, +y, -y, +z, -z.

• The step size used during finite differencing.

• Whether to project out the 6 frequencies corresponding to translation and rotation of the molecule. (Note, however, that these frequencies are not necessarily zero if the molecular geometry was not sufficiently optimized.)

• Automatically restart an interrupted frequency calculation. The program reads the .hess file and restarts the frequency calculation with the next finite displacement.

To perform any calculation, you must specify at least the geometry of the molecule. You can also specify the following input parameters, to restrict or refine your calculations:

• Atomic basis functions.

• Local or nonlocal DFT functionals.

• Frozen core orbitals.

• Orbital occupation.

• Spin-restricted or unrestricted wavefunctions.

• Numerical integration parameters.

• Point-group symmetry.

• Convergence criteria for the DFT-SCF and optimization procedure.

Using the frozen core option together with symmetry and the minimal basis set is not recommended.

Symmetry can be used together with the Point_Charges option. However, you must be sure to check whether the input symmetry is a subgroup of both the molecule and the point-charge system.

Molecule size and hardware requirements

Outline of basic steps for a DMol calculation

1. Create and modify the input molecule.

2. Set up calculation parameters.

3. Run the calculation.

4. Analyze the results.

You need not remain in one mode as you proceed through all four steps. For example, you could (1) set up a molecular system using one or more modules within the Insight program; (2) set up the calculation parameters with the DMol module of the Insight program, then perhaps refine the input files after quitting the Insight environment, by editing them with a text editor; (3) start the run from the Insight interface or from the operating system, whichever is more convenient or appropriate; and finally (4) read the results into the Insight program for analysis in the Analysis, DMol, and other modules. Alternatively, you could perform Steps 1 and 2 both with the dialog interface to the standalone mode of DMol, start the run from the operating system using dmol_master, and use the Insight interface only for some analysis of the results.

For additional information on constructing and modifying molecules, you can refer to the documentation for the Insight program. Several computational products are available that you may want to use to refine a molecule before submitting it to a DMol run, including several packaged as modules or pulldowns within the Insight program, as well as separately licensed products such as the Discover and Search_Compare programs.