Gaussian '16 is now available on Odyssey. To use it, add the following lines to /.bashrc: source new-modules.sh. /n/sw/g16nehalem/setup.bash Two builds of. Recently I was working on an issue where an application was not retaining the umask setting set in the root users profile or /etc/profile. After looking into the issue a bit it seemed that the application in question only applied the umask setting that was set in /etc/bashrc and would not even accept the values being the applications own start scripts.
This question already has an answer here:.3 answersI've been trying to install Android developer tools on Eclipse, and I followed the information in.Like the video said, I added the following two lines of code to the.bashrc file: export PATH=$(PATH):-/android-sdk/tools/export PATH=$(PATH):-/android-sdk/platform-tools/It seems, however, that this did not help me to install the Android files on Eclipse, as I am still having problems with that. What's more, it seems that I can't make any command in the terminal without getting a major error now! Every time I try to make a command in the terminal I get the following message:The command could not be located because '/usr/bin' is not included inthe PATH environment variable.Is there away to restore.bashrc to its default? Idea: There exist backup copies of.bashrc,.profile etc. In /etc/skel/. So one could replace a corrupt.bashrc simply by overwitting from there.Caution: if you replace the.bashrc file with a fresh one, it will remove any other modification(s) you have made to it. For example, one could add aliases, custom function or PATH in.bashrc.
When you replace the file, all those modifications will be lost. Better you can keep a copy of your modified.bashrc before replacing it. Later, you can carefully extract the required part from it. To keep a backup copy of your modified.bashrc in your home directory with name mybashrc use the following in a terminal, /bin/cp /.bashrc /mybashrcWhy /bin/cp: In case if you have messed with your $PATH variable when changed /.bashrc all the executable will be unavailable from your terminal and cp will not work anymore. So it is recommended to call cp with its full path as /bin/cp while you are trying to copy something with corrupt /.bashrc.Finally, use the following command in your terminal to replace the /.bashrc with a fresh copy, /bin/cp /etc/skel/.bashrc /It will replace your corrupt /.bashrc with a fresh one. After that, you need to source the /.bashrc so that the change takes place immediately, write in the terminal,. /.bashrcor, source /.bashrcor, if that does not work you can close the terminal and open it again.
If you can't get a working shell Via the file browser. Open the file browser, go to the home directory, press Ctrl H so that hidden files are shown. Edit.bashrc as needed. Open the file browser, go to /etc/skel, press Ctrl H so that hidden files are shown. Copy.bashrc to your home folder to restore it to the default.Via the run menu. Press Alt F2, type gedit.bashrc, press Enter.
Edit as needed. Press Alt F2, use the command /bin/cp /etc/skel/.bashrc / as given in to restore it to the default.Via the terminal.Open the terminal, and ignore that you don't have a shell.
Go to Edit → Preferences → Profiles:.Either create a new profile, or edit the current profile, to change the command:Use either /bin/bash -norc or /bin/bash -rcfile=/etc/skel/.bashrc. Start a new tab (with the custom profile, if you created one). Use the working shell as needed. Delete the custom profile, or uncheck the custom command option if you edited the default profile, once you're done.If you have SSHRun SSH with a custom command, which should help you bypass the.bashrc: ssh -t dashThe dash shell (aka /bin/sh) is minimal, but sufficient for restoring the.bashrc. If you can't get a GUI and don't have SSHBoot into recovery mode , which will get you a root shell.
Look in /home for your user's home directory. Via the TTYYou can enter the TTY by pressing ctrl+ alt+ f1 where you have to login with your user-name and your password. Ctrl+ alt+ f7 will bring you back to your GUI later.Now copy the existing raw.bashrc from /etc/skel to your home directory by cp /etc/skel/.bashrc /Maybe even bring the rest over if you're not sure if your.profile was changed too. Cp /etc/skel/.profile /Now to get the.bashrc to have immediate effect you might want to source it with: source /.bashrcIf you did replace your.profile as well you need to reboot to make it take effect.
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 ingenerating the internal coordinates for the TS during QST2 andQST3 optimizations.d. The maximum number of steps allowed ever in an optimization (i.e.,include later restarts) can be reduced. This is sometimes usefulfor very large systems in order to reduce memory and disk usage.e. The program now checks if the standard orientation of a moleculehas flipped by 180 degrees during an optimization and avoids theflip.
This avoids jumps when animating optimizations, IRCs, etc.in GaussView and improves SCF convergence.f. The memory allocation for generation of internal coordinates isnow proportional to the amount of memory provided by%mem. Thisallows jobs with very large numbers of atoms or internalcoordinates which previously failed to run if enough memory isprovided.g. By default, internal coordinates for potential hydrogen bonds arenot generated automatically.
Bond coordinates are still added toconnect otherwise disjoint fragments, so coordinates for hydrogenbonds which connect fragments will still be included.2. Single-point BD calculations now default to frozen-core, with thecore orbitals uncorrelated but updated using the BD Fock matrix.The previous default was to leave the core orbitals unchanged fromthe HF values, or from the orbitals read in with BD=Read. The newdefault produces energies which are independent of the choice ofstarting orbitals. Gradients with BD still require and defaults tofull rather than frozen-core. The OldFCBD keyword requests theold-style frozen-core.3 The memory required by very large ONIOM(MO:MM) and pure MM frequencycalculations has been reduced.4. On some machines fully direct integral transformation and fully directMP2 are chosen if there is a large amount of memory, but the semidirectalgorithms are faster. Tran=SemiDirect in the Default.Route file nowforces the SemiDirect algorithm for MP2 as well as the transformationin higher level post-SCF calculations.
(All method keywords such asMP2 are ignored in the Default.Route file, because otherwise theywould force that model in all calculations.)5. Output=Wfn and Output=WfX with post-SCF methods now defaults toDensity=Current and Pop=NOAB, both of which are necessary forthe post-SCF density to be stored in the.wfn/.wfx file. Problemswith the orientation of the forces in these files and in generatingthem with ROHF wavefunctions and/or linearly dependent basis setshave also been fixed. Core densities are stored in the wfx filefor calculations which use ECPs, so that AIM and other analysis canbe done correctly for these cases.6. Several customers have used the file generated for COSMORS as inputto their local simulation programs, so this capability has been putback into G09.7. Polar=Gamma has been added as more descriptive option for requestingsecond hyperpolarizabilities.
It is synonym for Polar=(DCSHG,Cubic).8. The definition of improper torsions in the Amber force field is dependenton the ordering of atoms in the molecule. Calculations in the Amberprogram on typical proteins are consistent because of the standardordering of atoms withing residues and residues within a PDB file, butfor general molecules produced with GaussView the results depend onthe order of atoms in an arbitrary way. G09 has been changed to averageover the 6 possible orders of atoms in an Amber improper torsion, makingthe results slightly different than the standard Amber force field, butmaking 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 requeststhe previous default.11.
Printing during Pop=MK with IOp33 increased has been restored to includethe data required for RESP charge fitting. However, G09 can now generatethe data file for AnteChamber directly, by setting IOp(6/50=1) in thePop=MK job, and this is the recommended method for generating input forRESP.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 compoundjob; 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 ofusing SCVS.16.
TB and TW can now be used to specify memory and disk allocations inunits of terabytes and terawords, respectively.17. Pop=SaveBio in Stable=Opt jobs caused the stability calculation tobe wrong or fail.
This now works properly, saving the biorthogonalorbitals 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 withmore than 999 atoms.21. A bug in DFTB using interpolated (not analytic) parameters withd functions was fixed.22.
A rare problem with uncompleted write statements on slow filesystems was fixed.23. Problems with some combinations of charge and multiplicity infragments 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 largeunit cells were fixed.26. Inconsistencies in how the geometry was modified in some cases bySymm=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 finishare now restartable.30. A bug in reading ECPs with ONIOM when the same ECP was placed onmultiple centers was fixed.31. The combination of IRC and Freq, which did the frequency calculationat the last point of the IRC rather than the TS, is now rejected.32. Several unsupported combinations of Douglas-Kroll-Hess with propertiesnow generate an error message rather than incorrect answers.33.
A bug in generating the default (Harris) initial guess when using ECPson charged species was fixed. The quality of the initial guess whenusing ECPs has also been improved.34. Several defaults for whether to use FMM and other integral optionshave been updated for better performance on current models of CPU.35.
FormChk now writes -1 rather than. to the formatted checkpointfile if the value exceeds 10^13-1. This allows unfchk and otherutilities to process the resulting fchk file.36. A bug affecting geom=check after numerical frequencies when usingONIOM was fixed.37. The Direct option is available for SAC-CI.
This requests anintegral-direct algorithm suitable for larger molecules.38. A%oldchk link0 command has been added. The contents of thecheckpoint file specified by%oldchk are copied to the checkpointfile of the current job step at the start of the job step.This allows data to be picked up from a previous calculationwithout destroying anything on the chk file from it.39.
The combination of BD or W1BD with SCRF, which does not workcorrectly, 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 onthe route line to turn off use of the ATLAS matrix multiplicationroutines.41.
A problem in reported transition moments between excited statescomputed in SAC-CI jobs was fixed.42. Empirical dispersion with DFT and ghost atoms now runs. Empiricaldispersion and PBC now produces an error message, since it is notimplemented.43. 'Opt Freq' with ROHF/RODFT now works correctly, doing Freq=Numerwith the restricted open-shell wavefunction in the second job step.44. Franck-Condon calculations now function correctly for forbiddentransitions.45.
The route generator rejects the combination of TD and double-hybridDFT methods, which never worked (previously, TD was done based ononly the SCF part of the double-hybrid).46. IRC=(RCFC,GradientOnly) calculations now correctly use the Hessianfrom the chk file.47. Diffuse (aug-) functions were added for cc-pVDZ for the firsttransition row.48. A memory allocation bug for very large systems which could causea 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 thecurrent (Power7) processors. To compile a version for thePower5 or Power6 machines, instead of just 'bldg09' you mustgive 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 atg09testscomtest726.gjf for an example of using it.3. A problem with the G09W front-end writing out multi-stepjobs when the -Link1- lines were truncated was fixed.Corrections to deprecated features:1. Problems with setting non-integer nuclear charges in Massage input havebeen corrected. There is now a ZNuc function in Massage input whichchanges 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 includesa new integral-direct algorithm - SACCI=(Direct.) - which ismuch faster for large systems.3. The ExtraOverlay route keyword did not function in A.02; this hasbeen 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 textfiles or an input and a checkpoint file can be merged. See thewebsite for examples.7. Problems with the dummy basis set used with molecular mechanicswhen the system was highly charged or very high spin were fixed.8. Polar=(Cubic,DCSHG) can now be used to numerically differentiatefrequency-dependent hyperpolarizabilities (betas) to produce secondhyperpolarizabilities (gammas). These polarizabilities are nowprinted in the standard coordinate systems (i.e., with componentsof beta along and perpendicular to the dipole moment).9.
WfnX files, used by the newer versions of AIMPAC, can now be writtenvia Output=WfnX.10. Performance for very large MM systems (20K atoms) has been improved,especially when range limits are applied to the Coulomb andVan der Waals terms. There is a new route option, Geom=Huge, whichturns off various actions, useful in QM calculations butunnecessary 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 makedata from newer DFTB parameter files acceptable. These files stillrequire some modification to be used with G09; refer to the web sitefor 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 theatomic densities required for the model for the first 18 elements.An alternative version, Pop=HLYGAt, uses the HLY fitting scheme butwith Gaussian's standard atomic densities, which are available forthe 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 tomake the virial condition satisfied exactly, has been added.16. The use of IOp's to specify user-selected ranges for integrals hasbeen updated in order to make it more general.17. The default algorithm for optimizations when minimizing in a regionof 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 secondarystructure is now done (by default for systems with.