4.4 The General Options Menu

After you specified all data concerning the molecule you want to examine, you are on your way to the last of the four main menus. Before reaching it, you will perhaps get a message like the following:

define has scanned your input file for this session and found some data groups which might have become obsolete. If they are still acceptable depends on the changes you made during your present define session. They are obviously incorrect if you changed the molecule under consideration; but any change in the basis sets or the occupation numbers will make them dangerous, too, because you might not know some day if they really refer to the basis set which is defined in this control file. As a rough guide, delete them whenever you have made changes in one of the first three main menus during your define session.

After that you will reach the last main menu of define which helps you to control the actions of all TURBOMOLE programs. The meanings of the various options are explained in more detail in the description of the individual programs, therefore only a short explanation will be given here.

Now have a look at the menu:

This menu serves very different purposes. The next subsection deals with commands required to activate and/or specify specific methods of calculation. The subsequent subsection describes commands used to select non-default options. Standard SCF calculations do not require special action, just leave the menu. The final subsection describes the settings for property calculations.

4.4.1 Important commands

DFT calculations

Command dft leads you to the menu:

To activate DFT input on and then specify the grid for the quadrature of exchange-correlation terms. TURBOMOLE offers grids 1 (coarse) to 7 (finest), and the multiple grids m3 to m5 [4]. The latter employ a coarser grid during SCF iterations, and grid 3 to grid 5 in the final SCF iteration and the gradient evaluation. Default is grid m3, for clusters with more than 50 atoms use m4.

The functionals supported are obtained with the command func:

The programs dscf and grad are used to carry out conventional DFT treatments, i.e. J and K are evaluated without approximations.

RI-J calculations

For non-hybrid functionals we strongly recommend the RI-J procedure, which speeds up calculations by a factor 10 at least (as compared to conventional treatments) without sacrificing accuracy. Command ri gives:

Activate RI-J with on, and choose with m the memory you can dedicate to store three-center integrals (Keyword: $ricore), default is 200MB. The more memory, the faster the calculation.

A rough guide: put $ricore to about 2∕3 of the memory of the computer. Use OS specific commands (top on most UNIX systems), during an ridft run to find the actual memory usage and then adjust $ricore, the keyword in control specifying memory.

If the option jbas is selected, define enters a submenu which allows the assignment of auxiliary basis sets (for an explanation of the menu items see Section 4.2). Where available, the program will select by default the auxiliary basis sets optimized for the orbital basis used. Please note that treatment of systems with diffuse wavefunctions may also require an extension of the auxiliary basis. For this cases enlarge the sets of s- and p-functions with diffuse functions.

The RI-J option is only supported by programs ridft and rdgrad, if you use jobex to optimize molecular geometry, put: nohup jobex -ri ...

MARI-J option

RI-J calculations can be done even more efficiently with the Multipole Accelerated RI-J (MARI-J) option, especially for larger molecules where almost linear scaling is achieved [32].

Just rely on the defaults.

Multiple auxiliary basis sets

With the command trunc you can switch on this option. Effect: a reduced auxiliary (or fitting) basis to represent the electron density is employed during SCF iterations, the final SCF iteration and the gradient are computed with the full auxiliary basis.

Note: trunc is presently not compatible with marij!

RI in SCF calculations

Considerable savings in CPU times are achieved with the RI technique for both Coulomb J and exchange K terms in SCF calculations, the RI-JK method [33], provided large basis sets are employed, e.g. TZVPP, cc-pVTZ, or cc-pVQZ. With rijk you get:

For an explanation of the menu items see Section 4.4.1. RI-JK calculations can be carried out with the program ridft.

Optimization to minima and transition structures using STATPT

Structure optimizations can be carried out by the program statpt. For minimizations no additional keywords are required. The default values are assumed, which work in most of the cases. Structure optimization is performed in internal coordinates if they have been set. Otherwise, Cartesian coordinates are used. One can switch the optimization in internal coordinates on or off, respectively in internal redundant or cartesian coordinates. For transition structure optimizations the index of transition vector has to be set to an integer value > 0 (0 means structure minimization). The value of the index specifies transition vector to follow during the saddle point search. Note, that Hessian eigenpairs are stored in ascending order of the eigenvalues, i.e. the eigenpair with the smallest eigenvector has the index 1.

The command stp gives:

Excited states, frequency-dependent properties, and stability analysis

Excited state calculations with RPA or CIS (based on HF-SCF) and TDDFT procedures as well as stability analyses (SCF or DFT) are carried out by the program escf.

You will need a well converged HF-SCF or DFT calculation that were converged to at least $scfconv=7, see Section 4.4.2.

Details of calculations are specified with the command ex:

If you have selected an option, e.g. rpas, and quit this menu, you will get another menu:

This should be self-evident.

MP2, MP2-F12, RI-MP2, and PNO-MP2

We recommend to use MP2 for standard applications together with the RI technique using the ricc2 program. The mpgrad program is supplied for special benchmark application where the RI approximation needs to be avoided. The pnoccsd program is meant only for very large (> 100 atoms and > 3000 basis functions) MP2 and MP2-F12 single point energy calculations. This is more efficient and supports the frozen core option in the gradient calculation.

The entry mp2 leads to a submenu which allows to set some keywords for MP2 and RI-MP2 calculations, e.g. defining frozen orbitals, maximum memory usage, or assign auxiliary basis sets for RI-MP2 calculations, etc. If you want to use ricc2, you have to use the entry cc and the submenu ricc2 in order to assign MP2 as wavefunction model. For the pnoccsd program you have to use the entry pnocc and the submenu pnoccsd to assign the wavefunction model.

Conventional MP2 calculations with mpgrad require a number of additional settings for which it is recommended to invoke the interactive tool mp2prep. For geometry optimizations with jobex use nohup jobex -level mp2 -ri ...

CC2 and CCSD calculations

The entry cc leads to a submenu which allows to set a number of keywords essential for calculations with the programs ricc2 and ccsdf12. In particular it allows the assignment of the wavefunction method(s), selection of auxiliary basis sets, the specification of frozen orbitals, and the definition of a scratch directory and of the maximum core memory usage.

The ricc2 program must be used for excitation energies and response properties with second-order methods (MP2, CIS(D), ADC(2), CC2, etc. and their spin-scaled variants), while the ccsdf12 program must be used for third- and higher-order methods (MP3, CCSD, CCSD(T), etc.).

2nd analytical derivatives for SCF and DFT

The program aoforce computes force constants and IR and Raman Spectra on SCF and DFT level. Analytical second derivative calculations can directly be started from converged SCF or DFT calculations. Note, that the basis is restricted to d-functions, and ROHF as well as broken occupation numbers are not allowed. For better efficiency, in case of larger systems, use the keyword $maxcor as described in Chapter 14 to reduce computational cost. RI will be used if the RI option for DFT has been specified.

4.4.2 Special adjustments

Adjustments described by the following menus are often better done directly in the control file; have a look at the keywords in Chapter 20. For common calculations just start with the defaults, and change keywords directly in control if you encounter problems with your calculation.

SCF options

By the command $fermi you can switch on smearing of occupation numbers, and thus automatically optimize occupations and spin.

Menu drv

The most important of the derivative menus is the first one which tells the programs which derivatives to calculate. This is only necessary for special purposes and you should better not change default options.

The handling of these options is very simple. With the exception of tol, all are logical switches which are either true (or on, active) or false (or off, inactive). You can switch between the two states if you enter, for example, crt (to switch calculation of Cartesian first derivatives on) or -crt (to switch it off). The options crt, sec and bas should provide no problems. glb refers to a global scaling factor for all basis set exponents. Imagine that you would like to replace your basis set, which contains basis functions

by another basis set which contains basis functions

where α is the same for all primitive basis functions χ_μ. With command glb you are able to calculate analytical derivatives of the total energy with respect to α and can thus easily determine the optimum α.

dip enables you to calculate the first derivatives of the electric dipole moment with respect to nuclear displacements which gives you infrared intensities. pol allows you to calculate the contribution of the nuclear rearrangement on the electric polarizability. fa finally performs only a frequency analysis which means that aoforce will read the force constant matrix ($hessian or $hessian (projected)), diagonalize it and give you the frequencies and normal modes. tol is not a logical switch as the other options in this menu, but a cutoff threshold for the derivative integrals, i.e. integrals below this threshold will be neglected in the derivative calculations.

Entering * will bring you to the second derivative submenu.

Debug Options for the Derivative Programs

The following menu deals only with some debug options for grad. Use them with caution, each of them can produce lots of useless output:

4.4.3 Relax Options

Program relax has a huge variety of options to control its actions which in program define are grouped together in eight consecutive menus. These are only briefly described in the following sections; for a more detailed discussion of the underlying algorithms refer to the documentation of program relax (see Section 5.3). Only experts should try to change default settings.

Optimization Methods

The first of the relax subgenus deals with the type of optimization to be performed:

Coordinate Updates

The next submenu deals with the way relax updates the old coordinates. You may choose a maximum change for the coordinates or you can allow coordinate updates by means of extrapolation:

Interconversion Between Internal and Cartesian Coordinates

The interconversion between internal and Cartesian coordinates is not possible directly (in this direction). Instead it is performed iteratively. The following options control this conversion:

Updating the Hessian

relax provides a variety of methods to generate an updated Hessian every cycle. This includes the well known methods such as BFGS, DFP, or MS update methods as well as some less common procedures:

General Boundary Conditions for Update

The force constant matrix will only be updated if least mingeo cycles exist. The maximum number of cycles used for the update is specified by the parameter maxgeo. Normally the default values provided by define need not be changed.

Special Boundary Conditions for Ahlrichs and Pulay Updates

For the default update method ahlrichs some additional control parameters are available which can be defined in this menu:

For detailed description consult Section 5.3.

Initialization of the Hessian

Finally there are some options to control the choice of the initial Hessian during your geometry optimization:

4.4.4 Definition of External Electrostatic Fields

This submenu allows you to calculate first and second numerical derivatives of the energy with respect to an external electric field. The first three options should be clear; 1st and 2nd are logical switches which are turned on and off the usual way (1st or -1st) and delta is the increment for the numerical differentiation, that is, the finite value of the external field, which replaces the (ideally) differential field:

Take Care, due to some inconsistencies in define it is always necessary to switch on the field calculations manually. Therefore edit the control file after having finished your define session and enter on after the entries of fields and geofield.

4.4.5 Properties

The program moloch used for this purpose is currently being revamped, and will then be much simpler to use. The subsequent description for an older version may not work in all cases—sorry for that.

If you enter prop in the general menu, define first will check whether the data group $properties does already exist in your control file or in a file referenced therein. If this is not the case you will be asked to specify the file on which $properties shall be written:

Option trace

trace will calculate the trace of density times overlap matrix:

If the orbitals are orthonormal, N should yield the total number of electrons in your molecule. If this is not true, your MO-vector will most probably be erroneous. For example, the vector might belong to another geometry or basis set. As this is a very sensitive test for errors like these and the calculation requires almost no time, you should always switch on this option.

Option moments

This option leads you to the following submenu:

Option potential

This option collects all possible quantities related to the electrostatic field created by the molecular charge distribution. This includes the following suboptions:

Option cowan-griffin

This option activates the computation of the first order relativistic correction to the energy as given by the expectation value of the Cowan–Griffin operator.

Option localization

Specifying option localization will switch on a Boys localization of molecular orbitals. define by default chooses a set of MOs to be localized according to a certain threshold for the orbital energy. Information about these are displayed like this:

all

selects all occupied orbitals

thr

selects all occupied orbitals with orbital energy larger than a certain threshold

man

enables you to select the MOs manually later in this section

If the selection method thr is specified you then will be asked for the threshold to be applied for the selection. Afterwards you have the possibility to change some other topics concerning the localization:

• specify other localization directions
• switch on utilization of localized orbitals for population analysis and/or preparation of plot data within the same moloch run
• set the maximum number of sweeps in the localization procedure
• specify a file where localized orbitals shall be written to

Option population analyses

When activating this option you first have to specify whether the population analysis (PA) should be performed in the CAO (default) or AO basis. Afterwards define will ask you whether you want to perform a Mulliken population analysis. In this case, the following submenu will be displayed:

After having left the Mulliken PA section you will be asked whether a population analysis based on occupation numbers (a modified Roby–Davidson PA) should be performed by moloch. When typing y you will see the following submenu, where you can switch on several special options for the PA in the same manner as described above.

Option plot

This option allows you to prepare the data needed for contour plots of orbital amplitudes or total electron densities. We do not recommend to prepare plotting data this way; an easier method—with an easier syntax—is to generate these data directly by the programs, where densities (also MP2 or excited ones) and Molecular orbitals are calculated. This is described in Chapter 18. If you nevertheless want to prepare the input for plotting data as needed by moloch using define, on activating plot you get the following menu:

In case you do not want to add a new data group as described above but to change an existing one, you will be asked which one of the specifications you want to modify.