One of the most powerful functions of ab initio calculations is geometry predictions. The minimum energy structure of a molecule for a given method and basis set is instructive especially when experiment is unable to determined the actual geometry. The MOLCAS program module STRUCTURE performs a geometry optimization at the SCF or RASSCF level of calculation.
The STRUCTURE module is actually a script which will call the correct MOLCAS program modules to optimize a molecular structure. It does allow, however, the user to use a similar input format as the other program modules. This is not necessary but MOLCAS defaults to performing a SCF calculation using the current input file. We will perform the calculation using the input file given in Figure 3.22.
Figure 3.22. Sample input requesting the STRUCTURE module to perform a SCF optimization using the input files listed.
&STRUCTURE &END Method SCF Input seward $InputDir/seward.input Input scf $InputDir/scf.input Input rasscf $InputDir/rasscf.input Input alaska $InputDir/alaska.input Input slapaf $InputDir/slapaf.input End of Input
The Method keyword is used to specify the method used to optimize the geometry. The default is the SCF method. STRUCTURE will control the calling of SEWARD, SCF, RASSCF if necessary and two other program modules, ALASKA and SLAPAF. The input information for each of these modules can be included in the same file as the STRUCTURE input information or in separate files and listed in the STRUCTURE input using the Input keyword. When using the Input option each module must be listed.
Sample inputs are given for the ALASKA and SLAPAF program modules in Figures 3.22 and 3.22 respectively. Very little is needed for the ALASKA input information. ALASKA computes the integral derivatives which are used by the SLAPAF module to iterate to the lowest energy geometry. The SLAPAF module input can vary greatly. If there is no keyword specified, the current version generates the nonredundant internal coordinates required for the optimization in the symmetry of the chosen wave function. It is possible to restrict the geometry to a higher symmetry using SLAPAF keywords and define the required internal coordinates (see section 4.2).
Figure 3.22. Sample input requesting the ALASKA module to compute
the gradients for water in C
symmetry.
&ALASKA &END End of Input
Figure 3.22. Sample input requesting the SLAPAF module to compute the optimized geometry using nonredundant internal coordinates.
&SLAPAF &END Iterations 20 End of Input
Figure 3.22. Sample input requesting the SLAPAF module to compute a numerical hessian for a subsequent transition state search.
&SLAPAF &END Numerical TS Iterations 0 End of Input
Keyword TS request the program to perform a transition state search. Keyword NUMErical request the program to perform a numerical Hessian calculation. If both keywords are used simultaneously STRUCTURE will perform first a hessian and a transition state search immediately after using as many iterations as the default value or keyword ITERations have. If just a hessian is going to be computed ITERations must be set to zero. If the hessian is going to be used in a following transition state searching is recommended to include simultaneously the three keywords: NUMErical, TS, and ITERations, setting the last one to zero. In absence of TS the final hessian will be transformed specifically for a stationary point situation. In section slapaf (in users guide) of the user's guide and sections 4.2 and 4.5.2 the reader will find more detailed information about the use and possibilities of the SLAPAF program.
The script file to optimize a molecular geometry differs from the other scripts in that only the STRUCTURE module is run using the molcas run command which then itself calls the required MOLCAS modules. Modules run after the STRUCTURE module will use the optimized geometry.
STRUCTURE writes the energy, energy change and estimated final energy for each optimization step to the output file (See Figure 3.22). The maximum value of the gradient and coordinate step are listed along with the internal coordinate for each. In this case, the both coordinate elements, lnm001 and lnm002 (named after linear normal modes), have the largest gradient and step size for an iteration. When the geometry is optimized the output from each of the MOLCAS program modules called in the last iteration is printed to the output file. The SLAPAF section of the output repeats the information in Figure 3.22 in more detail and has the final optimized geometry and energy of the system at the end of the output.
Figure 3.22. The STRUCTURE output during geometry iterations truncated after the predicted final energy.
Energy Grad Grad Step Estimated ..
Iter Energy Change Norm Max Element Max Element Final Energy ..
1 -75.92824657 .00000000 .055884 .051771 lnm001 .292643 lnm001 -75.93601039 ..
2 -75.93564460 -.00739804 .028015 -.028008 lnm002 -.028318 lnm002 -75.93604175 ..
3 -75.93614295 -.00049835 .007000 -.006966 lnm002 -.009266 lnm002 -75.93617726 ..
4 -75.93617804 -.00003509 .000198 .000178 lnm001 .001007 lnm001 -75.93617814 ..
Each iteration of the optimization using the new geometry computed by the SLAPAF module and stored in the COMFILE. This geometry is used by subsequent MOLCAS modules. The COMFILE, in our case called water.ComFile, can be saved and used in subsequent calculations within need to reoptimize the geometry. To do that a specific link has to be added before starting the STRUCTURE calculation, because the $Project.ComFile file is deleted at the end of the calculation. Otherwise any subsequent SEWARD run would ignore the coordinates of the input. Alternatively of using the COMFILE file, the cartesian coordinates can be updated in the seward input section.
Other useful tool of the STRUCTURE program is the possibility to restart geometry optimizations and numerical hessian calculations if some of the codes has failed due to a reason that can be corrected. For a description of the restart procedure in STRUCTURE the reader is referred to section structure (in users guide) of the user's guide. It is also possible to execute any UNIX command before the run starts simply by writing the command on the STRUCTURE namelist preceded by an exclamation mark (!).