21 September 2012

244. Molden on debian testing

Update: avogadro can write gamess input files, but seems to offer little in the way of showing detailed output from gamess output files. Also, some of the input files contain keywords which don't exist.

Original post:
Nothing beats a good GUI, so after butting heads with gabedit again (and losing - again. Although in this case I think I tried to make it do something it wasn't designed to) I've decided to try Molden.

To download, go here, make sure to be a good citizen and register yourself as a user (will help motivate funding for development) then download: http://www.cmbi.ru.nl/molden/howtoget.html

cd ~/tmp
wget ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.0.tar.gz
tar xvf molden5.0.tar.gz
cd molden5.0/

Edit makefile and remove -lXmu from line 20:

16 CC = cc
17 FC = gfortran
18 LIBS =  -lX11 -lm
19 LDR = ${FC} 
20 LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lX11 -lm

cd surf/

edit Makefile and change it from

 46 depend: $(DEPEND)
 47     @ echo making dependencies...
 48     @ echo ' ' > makedep
 49     @ makedepend $(INCLUDE) -f makedep $(DEPEND)


 46 depend: $(DEPEND)
 47     @ echo making dependencies...
 48     @ echo ' ' > makedep
 49     @ $(CC) $(INCLUDE) -M $(DEPEND) > makedep

Save and go back up one level, and run make:
 cd ../

You're pretty much done.

I like putting things in /opt, so
sudo mkdir /opt/molden
sudo chown $USER /opt/molden
cp ~/tmp/molden5.0/* -R /opt/molden

export PATH=$PATH:/opt/molden
in your ~/.bashrc

to run

Molden can read output files from gamess -- still exploring the exact capabilities, but e.g the convergence information can be accessed:

and you can get nifty contour plots of the electron density of orbitals etc.


If you don't edit the surf/Makefile as shown above you'll get

make[1]: Leaving directory `/home/me/tmp/molden5.0/ambfor'
make -C surf depend
make[1]: Entering directory `/home/me/tmp/molden5.0/surf'
making dependencies...
make[1]: makedepend: Command not found
make[1]: *** [depend] Error 127
make[1]: Leaving directory `/home/me/tmp/molden5.0/surf'


  1. Hi, My name is Ana and I'm working with Fedora 17, I have edit the surf/Make as you have show, but I'm getting the same problem:

    make[1]: leaving directory `/home/anaid/Molden/molden5.0/surf'
    making dependencies...
    /bin/sh: makedepend: command not found
    make[1]: *** [depend] Error 127
    make[1]: leaving directory `/home/anaid/Molden/molden5.0/surf'
    make: *** [surf/surf] Error 2

    Do you know what is happening?

    1. I think this is the key: "/bin/sh: makedepend: command not found"

      I don't have access to fedora 17 and so I can't test a solution for you. Doing a quick online search it seems that there's a makedepend package, so try

      sudo yum install makedepend

      Then try to compile again and report back.

    2. I spoke (wrote) too soon -- the package seems to be called imake

      sudo yum install imake