View source for Mod:Hunt Research Group/mac setup

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==== For NEW computers: make a group ====
::if you are a new user on an existing computer, the groups will already be set up!
::open accounts in system prefs
::click on the + button
::choose groups on pulldown menu
::type in a name and add those users you want to belong to the group
::in this case call the group "gaussian"
::exit

==== set-up the terminal ====
::you will find the terminal app in the <b>Utilities folder</b> in your <b>Applications</b> directory
::drag this app onto your <b>Dock</b>, you will be using it a lot!
::open a terminal
::check you are in your home directory type "ls" to list the files/folders

==== set-up your .bashrc_profile ====
::create the file ".bash_profile" 
::copy and paste the following into it
<pre>
#echo "bash_profile"
. ~/.bashrc
</pre>

==== set-up your .bashrc ====
::create the file ".bashrc"
::copy and paste the following into it
<pre>
# .bashrc
# WARNING: had to make .bash_profile and added  execute to this file
#
#  important stuff
#
# tells the computer where to look for personal scripts
   export PATH=$PATH:/Users/$USER/bin:/usr/local/bin
#
# change the prompt
   export PS1="[\$USER@\h]\$PWD \$ "
#
# control-R lets you search backward through history
   HISTSIZE=100
   HISTCONTROL=erasedups
   HISTIGNORE="cd:exit"
   EDITOR=vi
   export EDITOR
#
#  gaussian
#
# where to fine the executable
   export g16root="/Applications"
# set the default memory
   export GAUSS_MEMDEF="500MB"
# where to put the LARGE temporary files when running gaussian
   export GAUSS_SCRDIR="/Users/$USER/Work/Jobs/tmp"
# script which sets many variables for gaussian
   source $g16root/g16/bsd/g16.profile
#
#   gaussview
#
# where to find gaussview
   export GV_DIR="/Applications/gv"
# libraries 
   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${GV_DIR}/lib
# allow start from the comand line in mac terminal
   alias gv="open $GV_DIR/gview.app"
#  
#  alias definitions            
#
   alias home="cd"
   alias force="grep -i 'Maximum Force'"
   alias dist="grep -i 'Maximum Disp'"
#
</pre>

::<b>edit key lines</b> for the version of gaussian and gaussview that you have
::make sure you have a <b>~/Work/Jobs/tmp" directory</b>
::type "source ~/.bashrc" into your terminal to active all the alias commands. 
::if you are using visualisation tools you may want to add some of the following into your .bashrc
<pre>
#
#  image magic
#
   export PATH="$PATH:/Applications/ImageMagick-7.0.3/bin"
   export MAGICK_HOME="/Applications/ImageMagick-7.0.3"
#   export DYLD_LIBRARY_PATH="$MAGICK_HOME/lib/"
#
#  multiwfn
#
   export KMP_STACKSIZE=64000000
   export Multiwfnpath="/Applications/Multiwfn_3.4_bin_Mac"
   export DYLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/Applications/Multiwfn 
#
#  nciplot
#
   export NCIPLOT_HOME=/Applications/nciplot-3.0/src/nciplot
   export OMP_NUM_THREADS=2
   alias nciplot="/Applications/nciplot-3.0/src/nciplot"
#
#  vmd
#
   alias vmd="open /Applications/VMD_1.9.3.app"
#
</pre>
::again <b>edit key lines</b> for the version of gaussian and gaussview that you have

==== set-up your .login ====
::create the file ".login" 
::this is needed because gaussview looks for csh stuff
::copy and paste the following into it
<pre>
setenv g16root /Applications
source $g16root/g16/bsd/g16.login
setenv GAUSS_SCRDIR /Users/$USER/Work/Jobs/tmp
setenv GV_DIR /Applications/gv
setenv GAUSS_EXEDIR /Applications/g16
</pre>
::of course you may need to change <b>version specific information</b> (or directory structure)
::the directory tmp should exist before you run any jobs.

==== set-up working directories ====
::make a directory called "work", keep ALL your files here
::inside work make a directory called "jobs", keep all your gaussian jobs here
::inside work make a directory called "testing" ie full path is /Users/name/work/jobs/testing 
::inside work make a directory called tmp (this is where you should direct gaussview to put temporary files)

==== run a test job ====
::cd into your testing directory
::vi a file "test.com" and copy and paste the following into it
::ps don't forget the last line must be blank
<pre>
%chk=test.chk
%mem=500MB
%nproc=1
# hf/3-21g geom=connectivity

Title Card Required

0 1
 C
 H                  1              B1
 H                  1              B2    2              A1
 H                  1              B3    3              A2    2              D1
 H                  1              B4    3              A3    2              D2

   B1             1.07000000
   B2             1.07000000
   B3             1.07000000
   B4             1.07000000
   A1           109.47120255
   A2           109.47125080
   A3           109.47121829
   D1          -119.99998525
   D2           120.00000060

 1 2 1.0 3 1.0 4 1.0 5 1.0
 2
 3
 4
 5

</pre>

==== For NEW computers: install gaussian ====
::if you are a new user on an existing computer, the groups will already be set up!
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Work/Gaussian_Images/G16_A03_mac
</pre>
::read the "readme" file
::change to the cshell
<pre>
csh
</pre>
::tell the script where gaussian (G16) is to be installed
<pre>
    setenv g16root "/Applications"
</pre>
::now goto the g16root directory
<pre>
    cd $g16root
</pre>
::read and extract the files
<pre>
bzip2 -d -c /Users/tricia/Work/Gaussian_Images/G16_A03_mac/tar/*.tbz | tar xvf -
</pre>
::this will unpack and copy the contents of the tar file you should see a stream of file names, when this stops and the prompt returns
::ensure that the group permissions are set
<pre>
chgrp -R gaussian g16 
</pre>
::check this has worked, type "ls -al"
::you should see a list with something like the following
<pre>
drwxr-x---  195 tricia  gaussian   6630 30 Dec  2016 g16
</pre>
::goto the gaussian directory and run the install script
<pre>
cd g16
./bsd/install
</pre>
::you are not quite ready to run as the variables g16root, GAUSS_SCRDIR and the g16.login script need to be set in your .bashrc file ... this was done in the terminal instructions above
:: you may also want to get rid of the pesky error "-bash: ulimit: open files: cannot modify limit: Invalid argument" which shows up because you have asked "source $g16root/g16/bsd/g16.profile" in your .bashrc
:::goto the direcotry g16/bsd
:::edit the file g16.profile, goto the end and hash out the following command
<pre>
#turned off by tricia to stop error message
#ulimit -n hard
</pre>
::now you are ready to run a test job
:::nohup means don't stop if you logout
:::the trailing & means run in the background
<pre>
cd work/jobs/testing
nohup g09 test & 
</pre>
::ls to see that the job is running and that test.chk and test.log files are being generated.
::check that the job finishes ok

====For NEW computers: install gaussview ====
::assuming you are still in shell and that g16root is set
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Mount/GV5_09_mac
cd cd /Users/tricia/Mount/GV6_17_mac
</pre>
::if you look inside these directories you will see the compressed gv files, they are compressed in different ways
::read the "readme" file for each version of gv
::then go back to the g16root directory, this is normally /Applications
::from there unpack the files
<pre>
tar -xvf tar -xvf /Users/tricia/Mount/GV5_09_mac/tar/*.tgz
</pre>
::move the gv directory to gv5
<pre>
bzip2 -d -c /Users/tricia/Mount/GV6_17_mac/*.tbz | tar xvf -
</pre>
::move the gv directory to gv5
::now change the group premisions to the same as those for g09/g16
<pre>
chgrp -R gaussian gv5 
chgrp -R gaussian gv6 
</pre>

::gaussview uses csh, so you need to have a .login if you want to run from the launcher
::check that you have the following in your .login
::you will need to manually change between gv5 and gv6!
::if you do change your .login you will need to re-execute the .login within csh
<pre>
csh
source .login
</pre>
<pre>
setenv g16root /Applications
source $g16root/g16/bsd/g16.login
setenv GAUSS_SCRDIR /Users/$USER/Work/tmp
setenv GV_DIR /Applications/gv6
#setenv GV_DIR /Applications/gv5
setenv GAUSS_EXEDIR /Applications/g16
#setenv GAUSS_EXEDIR /Applications/g09
</pre>

====For NEW computers: install GMMX ====
::assuming you are still in c-shell and that g16root is set
::goto the directory where the file is stored
<pre>
cd /Users/tricia/Mount/GMMX_MacOSX
</pre>
::double click on the file gmmx-m64.tbz
::this will be expanded into your downloads directory
::drag the gmmx file into the gv folder
::change the group to "gaussian" group (via appleI or via chmod)

====For OLD computers: setup for gaussian and gaussview====
::you will need to be added to the gaussian group on your computer before you have access to gaussview and gaussian
::goto <b>System Preferences</b>
::click on <b>Users and Groups</b>
::<b>unlock</b> this pane by entering an administrators name and password, if you are not an administrator come and see me
::click on <b>Groups</b> (appears after all the users)
::click on the group  <b>gaussian</b> and then tick the box next to your name on the right hand panel
::<b>lock</b> and leave this panel
::<b>reboot</b> your computer (this step is required!)
::check to see that you have access to the gaussian and gaussview directories

=====set-up quick starting of gaussview=====
::goto the Applications folder and click on the gv folder
::drag the gaussview icon into the launcher
::double click to start gaussview
::if you get an error saying that it cannot find gaussian directories then
:::cd to the gv directory
:::cd into the data directory
:::edit the gpath.txt file (and give the correct path to the gaussian application)
<pre>
/Applications/g09
</pre>
:::quit gaussview and then restart it, your problem should be fixed

=====set-up preferences=====
::now we need to set some directories in the preferences of gaussview
::click on preferences
::choose the "File?Directory" option
::under the starting directory, choose Specify, click on the "..." button and pick your work/jobs directory
::under the scratch directory, choose "Use GAUSS_SCRDIR"
=====test run a job=====
::start a terminal
::type "gv" in the window (and press return)
::or start gaussview view by clicking on the icon in the Dock
::choose "open" and goto your /work/jobs/testing directory, open your test.com file
::submit it to run (save as test_1.com) so that you don't overwrite the other test job
::check that it finishes OK
::open your test molecule's com file