In simple calculations or just because the user is used to this way of working in other calculation packages it can be useful to have a procedure to run a complete calculation without preparing any shell-script at all. This is the task performed by the AUTOMOLCAS program. The shell AUTOMOLCAS will run the MOLCAS programs sequentially in the order they appear in the unique input file. The precautions to be aware of when AUTOMOLCAS is used are the same as in any other calculation, such as that the order of the inputs, and therefore the programs, is the correct one (see the flow graphs for each of the programs).
Some restrictions have been imposed when geometry optimizations or numerical hessians are run with AUTOMOLCAS. These restrictions, the normal way to run an AUTOMOLCAS calculation, and the supplementary tools are fully described in section automolcas (in users guide) of the user's guide. AUTOMOLCAS has no input. However, several keywords specific for AUTOMOLCAS can be included in the single input file between the different MOLCAS inputs. Especially useful are the keywords Skip Input and Exit Job. The first one prevents AUTOMOLCAS to run between two consecutive Skip Input entries and the second stops the job in that particular point. It is also possible to execute any UNIX command at any desired point of the run (between two MOLCAS programs, of course) simply by writing the command on the input file preceded by an exclamation mark (!).
One important precaution has to be taken into consideration when AUTOMOLCAS is used. There are certain default definitions in MOLCAS for linking files. For instance, if a program requires the INPORB file as starting orbitals and the user has not defined previously any link to INPORB, MOLCAS will search automatically in $WorkDir for any possible formated orbital file in the sequence: $Project.RasOrb, $Project.Pt2Orb, $Project.ScfOrb, etc. For a better control of the orbital files is therefore convenient to explicitly link as INPORB or JOBOLD files those the user consider the most appropriate ones just by including, for instance, !ln -fs Orb.file INPORB. This is important in cases when, for example, calculations with different basis sets are performed.
As an illustration for the use of AUTOMOLCAS we will include the procedure to perform the calculations showed in section 4.1.1 on the NiH molecule. The first task is to prepare the input file and compute the integrals and SCF wave functions running the SEWARD and SCF programs. It appears on figure 3.23.
Figure 3.23. Sample input for SEWARD and SCF programs in the AUTOMOLCAS format for NiH
!ln -fs /temp/$LOGNAME/$Project.OneInt ONEINT !ln -fs /temp/$LOGNAME/$Project.OrdInt ORDINT &SEWARD &END Title NiH G.S. Symmetry X Y Basis set Ni.ANO-L...5s4p3d1f. Ni 0.00000 0.00000 0.000000 Bohr End of basis Basis set H.ANO-L...3s2p. H 0.000000 0.000000 2.747000 Bohr End of basis End of Input !ln -fs /temp/$LOGNAME/$Project.ScfOrb SCFORB &SCF &END TITLE NiH G.S. OCCUPIED 8 3 3 1 OCCN 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0 End of input exit job
The goal of the links is to save the integral files and SCF orbitals in a directory different to WorkDir. They can be also defined in the script. Once the SCF orbitals have been checked and the CLEAnup and SUPSym designed for the RASSCF program we can continue with the input:
!ln -fs /temp/$LOGNAME/$Project.OneInt ONEINT !ln -fs /temp/$LOGNAME/$Project.OrdInt ORDINT skip input 1 &SEWARD &END Title NiH G.S. Symmetry X Y Basis set Ni.ANO-L...5s4p3d1f. Ni 0.00000 0.00000 0.000000 Bohr End of basis Basis set H.ANO-L...3s2p. H 0.000000 0.000000 2.747000 Bohr End of basis End of Input !ln -fs /temp/$LOGNAME/$Project.ScfOrb SCFORB &SCF &END TITLE NiH G.S. OCCUPIED 8 3 3 1 OCCN 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0 End of input skip input 1 !ln -fs /temp/$LOGNAME/$Project.ScfOrb INPORB !ln -fs /temp/$LOGNAME/$Project.State1.JobIph JOBIPH &RASSCF &END Title NiH 2Delta CAS s, s*, 3d, 3d'. Symmetry 4 Spin 2 Nactel 11 0 0 Inactive 5 2 2 0 Ras2 6 2 2 2 Thrs 1.0E-07,1.0E-05,1.0E-05 Cleanup 1 4 6 10 13 18 L 4 13 14 15 17 1 1 7 L 1 9 1 1 7 L 1 8 0 Supsym 1 4 6 10 13 18 1 1 7 1 1 7 0 Iter 50,25 LumOrb End of Input exit job
The 'skip input' option avoids running the SEWARD and SCF programs again. The SCFORB file is used as input for the RASSCF programs although we can substitute it later with a link to the file JOBOLD from one of the $Project.JobIph files from the RASSCF calculations. We can continue by linking and saving the JOBIPH file for other states because they will be needed in RASSI calculations.
Obviously all the links are unnecessary if one wants to run a simple job where no files should be stored for further use.