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Gaussian 16 Tips

Portal job status

If a portal job is paused (comment = job held, too many failed attempts to run) try

qstat –f jobid

Gaussian error messages

https://www.ace-net.ca/wiki/Gaussian_Error_Messages

Installation

For OS X Lion (10.7), at the Disk level, make sure you have set the invisible system files to visible using eg 

sudo defaults write com.apple.finder AppleShowAllFiles YES

and go to /etc to find file called bashrc. To the bottom of this file, add the lines 

export g16root=/Applications
. $g16root/g16/bsd/g16.profile
export GAUSS_EXEDIR=/Applications/gaussian16/g16

Test this has taken by opening the terminal, and typing g16 This should produce the response Entering Gaussian System, Link 0=g16.

In /Applications/g16/bsd edit the file g16.profile such that 

#ulimit -n hard

to suppress an error message, and you might also add 

export GAUSS_SCRDIR="$gr/g09/scratch"

where a directory scratch has been created (in the g09 folder in this instance) and given write privs.


This one also worked

export g16root=/Applications

. $g16root/g16/bsd/g16.profile

export GAUSS_SCRDIR=/Applications/g16/bsd/scratch

export GV_DIR /Applications/gv


in the $HOME level .profile file --Rzepa 11:08, 10 October 2012 (BST)

This is a C-shell method

Edit /etc/cshrc to include 

if ( ! $?DISPLAY ) then
setenv DISPLAY localhost:0.0
endif

setenv g16root /Applications/g16
setenv GAUSS_SCRDIR $HOME/work
source $g16root/g16/bsd/g16.login

limit stacksize unlimited
set path = ($path $HOME/bin)

setenv GV_DIR /Applications/gv
alias gv $GV_DIR/gview.app/Contents/MacOS/gview

Setting Execute permissions on Gaussian files in MacOS Big Sur

xattr -dr com.apple.quarantine /applications/g16

Recommended method 

bash Shell
$ cd
$ touch .bash_profile
$ ln -s .bash_profile my_profile

export g16root=/Applications
. $g16root/g16/bsd/g16.profile


Defaults

http://www.gaussian.com/g_tech/g_ur/m_defroute.htm

Solvation Energies

The CPM-type solvation fields now use a smoothed out cavity which ensures that energy derivatives are reliable, and resulting in far faster geometry and Hessian calculation. The final energy reported with such a field using eg the scrf(cpcm,solvent=name) keyword now includes by default the various solvation and free energy of cavitation terms. This is a difference from G03, which itemized these.

For systems where entropy differences may be significant, the following protocol is considered the currently best practice.

  1. Optimise fully at the gas phase to get a total gas phase energy.
  2. Repeat with solvation using a PCM model to get an optimized solvation geometry
  3. Using the PCM geometry, calculate the frequencies to get the thermal corrections.
  4. Do a single point calculation at the SMD level using the optimized PCM geometry to get a total solvation energy
  5. Subtract the SMD and gas phase energies to get a solvation energy

Symm=cs

To maintain eg cs symmetry.

.fchk Errors

Number of basis functions                  I              277
Number of independent functions            I              274

where the two numerical values differ. Change the spelling of independent to independant. Then open this .fchk file. Problem fixed with G09 B.01.

IOP(3/32=2)

Program does not check the eigenvalues of the overlap matrix looking for linear dependencies via small eigenvalues. Means that the mismatch in the above cannot occur.

IOp(1/20=1)

Flags that the input cartesian coordinates are in units of Bohr rather than Angstrom. Used when other programs write out such coordinates.

Detailed install instructions

I am assuming that the setup you sent me here corresponds with the lines in your ".cshrc" or ".tcshrc" files and not the ".login" file. When launching GV for Mac OS X by clicking on its icon the program looks for the Gaussian setup in the ".login" file (regardless of which shell is in use). So, you would need to have a ".login" file in the home directory with the following lines:

setenv g09root /gaussian09 setenv GAUSS_SCRDIR $HOME/work source $g09root/g09/bsd/g09.login setenv GV_DIR /Gv-5.09/gv


Assuming the "g09" directory is in "/gaussian09" (in you other message you mentioned that "g09" is in "/Applications", if so, change the first line accordingly). This will provide the G09 setup when GV is launched by clicking on its icon.

For the command line execution, if you use "bash" then there would be no issues by adding the corresponding setup in the ".profile" or ".bash_profile" or ".bashrc" files, so GV can be started from the command line.

If you use "csh" or "tcsh", unfortunately there is a conflict that has not been resolved yet. As mentioned above, when launching GV by clicking on its icon, the program looks at the ".login" file. When running from the command line with "csh" or "tcsh" shell, GV will crash if the ".login" file exists. We will fix this issue but, in the meantime, I would suggest a modification of your "gv" alias to add to the ".cshrc" or ".tcshrc":

setenv g09root /gaussian09 setenv GAUSS_SCRDIR $HOME/work source $g09root/g09/bsd/g09.login

limit stacksize unlimited set path = ($path $HOME/bin)

setenv GV_DIR /Gv-5.09/gv alias gv "mv ~/.login ~/.login.shadow ; $GV_DIR/gview.app/Contents/MacOS/gview & ; sleep 2 ; mv ~/.login.shadow ~/.login"


Note that this is just the way you had it already but the "gv" alias now hides the ".login" file (if it exists), launches GV, and restores the ".login" file once GV has started running (just added a two second wait before restoring the file back).

Regarding doing a system-wide setup, you may add the following lines to the "/etc/csh.cshrc":

setenv g09root /gaussian09 setenv GAUSS_SCRDIR $HOME/work source $g09root/g09/bsd/g09.login

limit stacksize unlimited set path = ($path $HOME/bin)

setenv GV_DIR /Gv-5.09/gv alias gv "mv ~/.login ~/.login.shadow ; $GV_DIR/gview.app/Contents/MacOS/gview & ; sleep 2 ; mv ~/.login.shadow ~/.login"


So, all users that use "csh" or "tcsh" shells would not need to add anything in their own files, the "/etc/csh.cshrc" file is always sourced first when starting a "csh" or "tcsh" shell. This way all the users would have command line access to G09 and GV.

For access by clicking on GV icon, all the need do is to add the following line to their ".login" files:

source /etc/csh.login

And you would have added the following lines to the "/etc/csh.login" file:

setenv g09root /gaussian09 setenv GAUSS_SCRDIR $HOME/work source $g09root/g09/bsd/g09.login setenv GV_DIR /Gv-5.09/gv


By editing these "/etc/csh.login" and "/etc/csh.cshrc" file, if you make changes to the location of G09 or GV, or if you install a newer version later, those changes would be transparent to the users.

Combining two calculations from the .fchk files

GaussView can combine the data from two checkpoint files (or two formatted checkpoint files) in this case. If you go to "File" -> "Open", in the "Open Files" dialog that will appear:

  1. in the "File name:" box type the names of the two checkpoint files, the one in the reverse direction first, and the one in the forward direction second. Enclose each name in quotes and have a space between the two names, for example:
    "irc-reverse.chk" "irc-forward.chk"
  2. in the "Target:" menu (two lines below), select "Single new molecule group for all files", which means that it will open the first file (irc-reverse.chk) and import the IRC points from that job, followed by opening the second file (irc-forward.chk) and importing the IRC points from that job on the same molecule group window.
  3. You should have now all the structures there and if you go to "Results" -> "IRC/Path", you will see the same expected information that you have when you run an IRC job that computes points in both directions.
  4. One thing you may notice though is that the TS geometry (zero reaction coordinate) appears twice and that is because that point was present in the checkpoint files of both reverse and forward IRCs. If you want to create a movie, for example, you would probably want to have only one TS geometry so it doesn't look like the movie has a delay at the TS because there are twice frames for that structure than for the rest of the IRC points. You can delete one of the two structures by going through the structures in GaussView and when you get to one of the two TS structures do "Edit" -> "Delete".
  5. A Python program File:Irc merge.tar.gz that can combine the IRC data from two formatted checkpoint files reads two formatted checkpoint file (fchk) from two different IRC jobs (in principle, one in the forward and one in the reverse directions), it combines the IRC data from these two files and writes a new Gaussian formatted checkpoint file with the combined data.
  6. you'll need to extract it (e.g. "tar xvfz irc_merge.tar.gz") first and possibly make it executable ("chmod +x irc_merge.py"). After this, you may run this programs in the following example:
  7. irc_merge.py IRC-example1.fchk IRC-example2.fchk IRC-combined.fchk

The resulting formatted checkpoint file “IRC-combined.fchk" can be visualized in GaussView and it will contain the combined IRC data from the other two files. Please, note that “irc_merge.py" is a relatively simple program that makes use of some modules in the "readfchk.py" file, a file that is also included in the attachment. You will need to keep both files on the same directory or to keep the "readfchk.py" file in a directory in your PYTHONPATH.

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