## Compiling Gaussion09 with the Intel compiler

Compiler and linker settings need to be done in several files in g09/bsd:

The compiliation procedure discussed in this blog has been followed.

** Note: **
In order to use Gaussian the user has to be ** member of the Gaussian user group.** Please, * contact* us for adding you to the user group.

## VSC-3: submission of Gaussian jobs

Sample submit script on VSC-3 for slurm, g09_job.sh:

#!/bin/bash # #SBATCH -J <JOBNAME> #SBATCH -N 1 #SBATCH --tasks-per-node=16 #SBATCH --ntasks-per-core=1 module load gaussian/RevD.01 g09 < INPUT > OUTPUT

Submit this script to slurm via:

$ sbatch g09_job.sh

### Benchmarks for Gaussian 09 on VSC-2

## Gaussian 09 Revision C.01 Release Notes

### Changes between Gaussian 09 Revisions B.01 and C.01:

- Changes to optimization algorithms and options: * The selection of modes to include when stepping down from a region of wrong curvature during an optimization has been improved. This can also now be controlled by route options: * Opt=NoDownHill ... don't try to go downhill, just take RFO-like step. * Opt=NGoDown=M ... Mix at most M eigenvectors in taking a downhill step. The default is 3. * Linear bends are handled more reliably, and included in internal coordinate more frequently, than before. This avoids many optimization problems involving nearly linear angles becoming exactly linear. c. The connectivities of reactant and product are now merged in generating the internal coordinates for the TS during QST2 and QST3 optimizations. d. The maximum number of steps allowed ever in an optimization (i.e., include later restarts) can be reduced. This is sometimes useful for very large systems in order to reduce memory and disk usage. e. The program now checks if the standard orientation of a molecule has flipped by 180 degrees during an optimization and avoids the flip. This avoids jumps when animating optimizations, IRCs, etc. in GaussView and improves SCF convergence. f. The memory allocation for generation of internal coordinates is now proportional to the amount of memory provided by %mem. This allows jobs with very large numbers of atoms or internal coordinates which previously failed to run if enough memory is provided. g. By default, internal coordinates for potential hydrogen bonds are not generated automatically. Bond coordinates are still added to connect otherwise disjoint fragments, so coordinates for hydrogen bonds which connect fragments will still be included. 2. Single-point BD calculations now default to frozen-core, with the core orbitals uncorrelated but updated using the BD Fock matrix. The previous default was to leave the core orbitals unchanged from the HF values, or from the orbitals read in with BD=Read. The new default produces energies which are independent of the choice of starting orbitals. Gradients with BD still require and defaults to full rather than frozen-core. The OldFCBD keyword requests the old-style frozen-core. 3 The memory required by very large ONIOM(MO:MM) and pure MM frequency calculations has been reduced. 4. On some machines fully direct integral transformation and fully direct MP2 are chosen if there is a large amount of memory, but the semidirect algorithms are faster. Tran=SemiDirect in the Default.Route file now forces the SemiDirect algorithm for MP2 as well as the transformation in higher level post-SCF calculations. (All method keywords such as MP2 are ignored in the Default.Route file, because otherwise they would force that model in all calculations.) 5. Output=Wfn and Output=WfX with post-SCF methods now defaults to Density=Current and Pop=NOAB, both of which are necessary for the post-SCF density to be stored in the .wfn/.wfx file. Problems with the orientation of the forces in these files and in generating them with ROHF wavefunctions and/or linearly dependent basis sets have also been fixed. Core densities are stored in the wfx file for calculations which use ECPs, so that AIM and other analysis can be done correctly for these cases. 6. Several customers have used the file generated for COSMORS as input to their local simulation programs, so this capability has been put back into G09. 7. Polar=Gamma has been added as more descriptive option for requesting second hyperpolarizabilities. It is synonym for Polar=(DCSHG,Cubic). 8. The definition of improper torsions in the Amber force field is dependent on the ordering of atoms in the molecule. Calculations in the Amber program on typical proteins are consistent because of the standard ordering of atoms withing residues and residues within a PDB file, but for general molecules produced with GaussView the results depend on the order of atoms in an arbitrary way. G09 has been changed to average over the 6 possible orders of atoms in an Amber improper torsion, making the results slightly different than the standard Amber force field, but making the energy independent of permuations of atoms in the molecule. 9. The RevTPSS exchange and correlation functionals have been added. 10. SDD now defaults to more recent basis sets for Actinides; OldSDD requests the previous default. 11. Printing during Pop=MK with IOp33 increased has been restored to include the data required for RESP charge fitting. However, G09 can now generate the data file for AnteChamber directly, by setting IOp(6/50=1) in the Pop=MK job, and this is the recommended method for generating input for RESP. 12. A bug in CIS frequencies with PCM solvation was fixed. 13. MaxDisk in a Default.Route file now applies to all steps of a compound job; previously, only the first step was defaulted properly. 14. A bug which prevented reading AlpB parameters for AM1 was fixed. 15. Convergence during SCVS calculations is now checked more carefully. Refer to the input files for tests 935-939 and 945 for examples of using SCVS. 16. TB and TW can now be used to specify memory and disk allocations in units of terabytes and terawords, respectively. 17. Pop=SaveBio in Stable=Opt jobs caused the stability calculation to be wrong or fail. This now works properly, saving the biorthogonal orbitals only after the wavefunction has been made stable. 18. External point charges now work with symmetry turned on. 19. A bug in TD-DFT gradients with frozen core was fixed. 20. Print statements for NMR shielding were fixed to work with more than 999 atoms. 21. A bug in DFTB using interpolated (not analytic) parameters with d functions was fixed. 22. A rare problem with uncompleted write statements on slow file systems was fixed. 23. Problems with some combinations of charge and multiplicity in fragments during Guess=Fragment calculations were fixed. 24. Printing of Coriolis terms during Freq=VibRot was restored. 25. Some memory allocation problems for PBC calculations with large unit cells were fixed. 26. Inconsistencies in how the geometry was modified in some cases by Symm=Loose were fixed. 27. A bug in the ROMP4 triples energy when NoSymm was specified was fixed. 28. A warning "The extrapolated energy is higher than the direct energy" is no long printed unnecessarily by the CBS extrapolation. 29. ONIOM(MO:MM) jobs which do microiterations and which fail to finish are now restartable. 30. A bug in reading ECPs with ONIOM when the same ECP was placed on multiple centers was fixed. 31. The combination of IRC and Freq, which did the frequency calculation at the last point of the IRC rather than the TS, is now rejected. 32. Several unsupported combinations of Douglas-Kroll-Hess with properties now generate an error message rather than incorrect answers. 33. A bug in generating the default (Harris) initial guess when using ECPs on charged species was fixed. The quality of the initial guess when using ECPs has also been improved. 34. Several defaults for whether to use FMM and other integral options have been updated for better performance on current models of CPU. 35. FormChk now writes -1 rather than ****** to the formatted checkpoint file if the value exceeds 10^13-1. This allows unfchk and other utilities to process the resulting fchk file. 36. A bug affecting geom=check after numerical frequencies when using ONIOM was fixed. 37. The Direct option is available for SAC-CI. This requests an integral-direct algorithm suitable for larger molecules. 38. A %oldchk link0 command has been added. The contents of the checkpoint file specified by %oldchk are copied to the checkpoint file of the current job step at the start of the job step. This allows data to be picked up from a previous calculation without destroying anything on the chk file from it. 39. The combination of BD or W1BD with SCRF, which does not work correctly, is now rejected by the route generator. 40. A new version of the ATLAS blas library is used on most platforms. This fixes several problems when using very large amounts of memory. In the event of such problems, IOp1=NoAssem can now be specified on the route line to turn off use of the ATLAS matrix multiplication routines. 41. A problem in reported transition moments between excited states computed in SAC-CI jobs was fixed. 42. Empirical dispersion with DFT and ghost atoms now runs. Empirical dispersion and PBC now produces an error message, since it is not implemented. 43. "Opt Freq" with ROHF/RODFT now works correctly, doing Freq=Numer with the restricted open-shell wavefunction in the second job step. 44. Franck-Condon calculations now function correctly for forbidden transitions. 45. The route generator rejects the combination of TD and double-hybrid DFT methods, which never worked (previously, TD was done based on only the SCF part of the double-hybrid). 46. IRC=(RCFC,GradientOnly) calculations now correctly use the Hessian from the chk file. 47. Diffuse (aug-) functions were added for cc-pVDZ for the first transition row. 48. A memory allocation bug for very large systems which could cause a failure with the message "NIJ > Max2 in MMCore" was fixed. Changes specific to IBM AIX/Power machines: 1. When building from source, the default is to build for the current (Power7) processors. To compile a version for the Power5 or Power6 machines, instead of just "bldg09" you must give the command "bldg09 all ibmp5". Changes specific to the Windows versions: 1. A Windows64 version is now available. 2. The external keyword functions correctly. Look at g09\tests\com\test726.gjf for an example of using it. 3. A problem with the G09W front-end writing out multi-step jobs when the --Link1-- lines were truncated was fixed. Corrections to deprecated features: 1. Problems with setting non-integer nuclear charges in Massage input have been corrected. There is now a ZNuc function in Massage input which changes the nuclear charge but not the atomic number. 2. A problem with AIM analysis on Windows only was fixed. Changes between Gaussian 09 Revisions A.02 and B.01: 1. A bug in MP2 frequencies with PCM was fixed. 2. An updated version of the SAC-CI code is included. This includes a new integral-direct algorithm -- SACCI=(Direct,...) -- which is much faster for large systems. 3. The ExtraOverlay route keyword did not function in A.02; this has been corrected. 4. "Opt Freq" with TD now runs both job steps properly. 5. NewZMat now writes out secondary structure information, if present, with -opdb. 6. NewZMat can now merge data from two input files. Either two text files or an input and a checkpoint file can be merged. See the website for examples. 7. Problems with the dummy basis set used with molecular mechanics when the system was highly charged or very high spin were fixed. 8. Polar=(Cubic,DCSHG) can now be used to numerically differentiate frequency-dependent hyperpolarizabilities (betas) to produce second hyperpolarizabilities (gammas). These polarizabilities are now printed in the standard coordinate systems (i.e., with components of beta along and perpendicular to the dipole moment). 9. WfnX files, used by the newer versions of AIMPAC, can now be written via Output=WfnX. 10. Performance for very large MM systems (>20K atoms) has been improved, especially when range limits are applied to the Coulomb and Van der Waals terms. There is a new route option, Geom=Huge, which turns off various actions, useful in QM calculations but unnecessary and expensive with enormous MM runs. 11. MaxDisk can now be specified in the Default.Route file. 12. The free-format input routines have been generalized in order to make data from newer DFTB parameter files acceptable. These files still require some modification to be used with G09; refer to the web site for details. 13. The full tensors for ECD using TDDFT (including the quadrupole component) are now printed. 14. The Hu, Lu, and Wang charge fitting model (JCTC 3, 1004-1013, 2007) is now available via Pop=HLY. The authors only parametrized the atomic densities required for the model for the first 18 elements. An alternative version, Pop=HLYGAt, uses the HLY fitting scheme but with Gaussian's standard atomic densities, which are available for the entire periodic table. For systems which can be done either way, the difference in atomic charges is usually between 1% and 5%. 15. The SCVS method of Todd Keith, which scales the molecule in order to make the virial condition satisfied exactly, has been added. 16. The use of IOp's to specify user-selected ranges for integrals has been updated in order to make it more general. 17. The default algorithm for optimizations when minimizing in a region of incorrect curvature has been improved. 18. The initial guess for AM1 and PM6 has been improved. 19. More analysis of input ONIOM and MM parameters with respect to secondary structure is now done (by default for systems with <10,000 atoms when secondary structure information is available). The net MM charges on residues and average distances between residues are reported. 20. Various performance improvements, including ones for larger numbers of SMP processors and for SCF frequency calculations. Usage Notes: 1. If CIS frequencies are to be used with the Herzberg-Teller or Franck-Condon-Herzberg-Teller analysis, the CIS frequencies must be done numerically (Freq=Numer rather than Freq). This is because the transition dipole derivatives are not computed during the analytic force constant evaluation. The corresponding HF frequency calculation on the ground state, which is also required, can be done analytically as usual. 2. CIS and CASSCF frequencies with PCM solvation must also be done numerically using Freq=Numer. 3. The linear scaling (FMM-based) algorithms are now Linda-parallel, so Linda parallel jobs on large molecules do not need to specify NoFMM, and will run faster with the default algorithms chosen by the program. 4. Opt=GDIIS is still present but deprecated; the new default optimization algorithm (Opt=GEDIIS) is better than GDIIS for the few cases where GDIIS was better than the G03 default (Opt=RFO). 5. Optimizations of large molecules which have many very low frequency vibrational modes with DFT will often proceed more reliably when a larger DFT integration grid is requested (Int=UltraFine). 6. Density fitting can be made the default for jobs using pure DFT functionals by adding the DenFit keyword to the route (-#-) line in the Default.Route file. Fitting is faster than doing the Coulomb term exactly for systems up to several hundred atoms (depending on basis set), but is slower than exact Coulomb using linear scaling techniques (which are turned on automatically with exact Coulomb) for very large systems. 7. The default IRC algorithm has changed; refer to the User's Guide for details. The default is to report only the energies and reaction coordinate at each point on the path; if geometrical parameters along the path are desired, these should be defined as redundant internal coordinates via Geom=ModRedundant or as input to the IRC code via IRC=Report=Read. Changes in Usage and Defaults between Gaussian 03 and Gaussian 09: 1. There are many changes in the PCM algorithms: a. The default surface integration is new and gives continuous potential energy surfaces. It is strongly recommended for all new studies. The route option SCRF=G03Defaults restores most of the defaults to those in G03, but should be used only for comparison with previous calculations done using G03. b. When using the default IEFPCM solvation method or SCRF=CPCM, Gaussian 03 computed and reported non-electrostatic contributions to the solvation energy but did not include these in the energies and they were not included in the energies used for geometry optimizations, frequencies, etc. By default Gaussian 09 does not compute these values at all. c. The new SMD solvation model is recommended for absolute solvation energies and other properties for which the non-electrostatic solvation terms are significant. When SCRF=SMD is specified, the SMD non-electrostatic terms are included in the basic energies (the SCF energy reported in the "SCF Done" line, correlated energies, etc.) and are included in the geometry optimization and frequency calculations. The non-electrostatic energy is also reported separately. Absolute solvation energies should be computed by doing a gas-phase optimization and frequency calculation on the system, followed by the same calculations with SCRF=SMD or SCRF=(SMD,Solvent=...). d. The SCFVac PCM input option has been removed. If a preliminary gas-phase energy is desired, do this in a separate job step before the solvated calculation. e. If the quality of the PCM integration grid is to be changed, the keyword PTSDens should be used in the PCM input section. This specifies the density of integration points in points per Angstrom^2. The old keyword TSAre specifies the area per tessera and hence implies use of the old integration scheme involving tesserae, which is inferior. The default is approximately 5 points per A^2, so PTSDens=10.0 will cause about twice as many points to be used compared to the default. 2. MP and CC calculations now default to a partial transformation (Tran=IABC). This is faster on most systems, especially when several processors are used. A full transformation can be requested using Tran=Full. 3. The default SCF convergence is 10^-8 on the density for all calculations, including single points. 4. The physical constants used by default are those from the 2006 CODATA tables; those used in Gaussian 03 can be requested via Constants=1998. 5. AM1, PM3, and PM3MM by default use the new semi-empirical code, which has proper analytic first and second derivatives but which gives slightly different total energies because it computes the overlap integrals via 6-Gaussian expansions rather than over Slater functions. AM1=Old and Use=L402 both request use of the old (MOPAC 6) code, through the regular links or through link 402, respectively. The new code is strongly recommended except when comparison with results from Gaussian 03 is required. 6. Stable=Opt defaults to the usual (L502) SCF procedure for the initial SCF but then uses SCF=QC for additional SCF calculations, if they are required. Changes between Gaussian 09 Revision A.01 and A.02: 1. The logic for handling extra negative eigenvalues of the Hessian during minimizations has been improved. 2. The combination of DFT and General SCF, automatically turned on if DFT is requested along with Int=DKHSO, does not work and is now rejected by the route generator. 3. ONIOM input is now checked for divalent link atoms. The position of these atoms is ill-defined unless the distance scale factors are set to 1, and the model is usually poor if the scale factor is forced to be 1. Since this input is normally an error, it is now rejected by link 101. IOp 132 can be used to force acceptance of this input, but this is strongly discouraged. 4. Semidirect integral transformation is the the default. This code parallelizes better than the fully direct or in-core algorithms and is similar in speed on a single processor. 5. A bug which caused ONIOM=InputFiles to fail when PDB secondary structure information was included in the input has been fixed. Building from source code: 1. Building Gaussian 09 with Linda requires Linda version 8.2; the executables will not build with previous version of Linda. 2. Building on Intel Macs requires a case-sensitive file system. In order to build the ia32 version you must specify: bsd/bldg09 all mac32 as there is no way for the build script to determine that it is running on a x86 rather than x86-64 machine and the default is to build for x86-64. 3. When building from source on IBM Power systems, the default is to build for the current (Power7) processors. To compile a version for the Power5 or Power6 machines, instead of just "bldg09" you must give the command "bldg09 all ibmp5". Missing Reference: The G09 User's Guide omitted the paper Clemente08 from the bibliography. It is: F. Clemente, T. Vreven, and M. J. Frisch, in Quantum Biochemistry, Ed. C. Matta (Wiley VCH, 2008).