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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 Utilities folder in your Applications directory
drag this app onto your Dock, 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
#echo "bash_profile"
. ~/.bashrc

set-up your .bashrc

create the file ".bashrc"
copy and paste the following into it
# .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 $GV_DIR/gview.app"
#  
#  alias definitions            
#
   alias home="cd"
   alias force="grep -i 'Maximum Force'"
   alias dist="grep -i 'Maximum Disp'"
#
edit key lines for the version of gaussian and gaussview that you have
make sure you have a ~/Work/Jobs/tmp" directory
type "source ~/.bashrc" into your terminal to active all the alias commands.
if you are using visualisation tools you may want to add some of the following into your .bashrc
#
#  image magic
#
   export PATH="$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"
#
again edit key lines 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
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
of course you may need to change version specific information (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
%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

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
cd /Users/tricia/Work/Gaussian_Images/G16_A03_mac
read the "readme" file
change to the cshell
csh
tell the script where gaussian (G16) is to be installed
    setenv g16root "/Applications"
now goto the g16root directory
    cd $g16root
read and extract the files
bzip2 -d -c /Users/tricia/Work/Gaussian_Images/G16_A03_mac/tar/*.tbz | tar xvf -
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
chgrp -R gaussian g16
check this has worked, type "ls -al"
you should see a list with something like the following
drwxr-x---  195 tricia  gaussian   6630 30 Dec  2016 g16
goto the gaussian directory and run the install script
cd g16
./bsd/install
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
#turned off by tricia to stop error message
#ulimit -n hard
now you are ready to run a test job
nohup means don't stop if you logout
the trailing & means run in the background
cd work/jobs/testing
nohup g09 test &
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
cd /Users/tricia/Mount/GV5_09_mac
cd cd /Users/tricia/Mount/GV6_17_mac
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
tar -xvf tar -xvf /Users/tricia/Mount/GV5_09_mac/tar/*.tgz
move the gv directory to gv5
bzip2 -d -c /Users/tricia/Mount/GV6_17_mac/*.tbz | tar xvf -
move the gv directory to gv5
now change the group premisions to the same as those for g09/g16
chgrp -R gaussian gv5 
chgrp -R gaussian gv6
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
csh
source .login

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

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
cd /Users/tricia/Mount/GMMX_MacOSX
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 System Preferences
click on Users and Groups
unlock this pane by entering an administrators name and password, if you are not an administrator come and see me
click on Groups (appears after all the users)
click on the group gaussian and then tick the box next to your name on the right hand panel
lock and leave this panel
reboot 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)
/Applications/g09
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
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