[ase-users] Jacapo/Dacapo not working on Ubuntu 11.04

[Alex Eftimiades]

I am trying to run the unit cell optimization provided here: http://gilgamesh.cheme.cmu.edu/jacapo/jacapo/2-bulk/2.2-unitcell-optimization/2.2.0-unit-cell-optimization.html

I get:
 >>> print bulk.get_stresses()
None

That happens for all the examples on the page. Much worse errors  
occure if I try bulk.get_forces()
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/ase/atoms.py", line 571, in  
get_forces
	forces = self._calc.get_forces(self)
File  "/usr/lib/python2.7/dist-packages/ase/calculators/jacapo/ 
jacapo.py", line 2309, in get_forces
	forces = nc.variables['DynamicAtomForces'][-1]
KeyError: 'DynamicAtomForces'

I should note I manually transcribed that error output (as well as the  
ones described later in this message.) from another computer screen,  
so please try to look over any typos.

Now, I installed everything except decapo from apt-get repositories  
(including ase and gpaw.) Decapo did not install willingly. Here is  
the sequence of commands I used:
cd /opt
DIR=~/Downloads
svn checkout https://svn.fysik.dtu.dk/projects/dacapo/trunk dacapo
cd dacapo
mv psp psp2
mkdir psp
for m in `find ./psp2 -name '*.pseudo'`;do mv $m ./psp;done
rm -rf psp2
cd src
export NETCDF="/usr/lib"
export DACAPOPATH="/opt/dacapo/psp"
export BLASLAPACK="-L/usr/lib -lnetcdff -lnetcdf -L/usr/lib -lblas - 
llapack -L/usr/lib -lblas -llapack -lgfortran"
export FFTW="/usr/lib"
export MPIDIR="/usr/lib/openmpi"
export MPI_LIBDIR="$MPIDIR/lib"
export MPI_INCLUDEDIR="$MPIDIR/include"
export MPI_BINDIR="/usr/bin"
patch Makefile < $DIR/dacapo_patch_for_ubuntu.patch.patch	#This is a  
simple patch I made that seems to allow the program to compile with  
gfortran
make gfortran_fnosecond_underscore MP=mpi
echo "
export PATH=\$PATH:/opt/dacapo/src/gfortran_fnosecond_underscore_mpi
" >> ~/.bashrc
. ~/.bashrc

You can download the patch, dacapo_patch_for_ubuntu.patch.patch, from: http://sourceforge.net/projects/aeftimiamisc/files/installstuff/dacapo_patch_for_ubuntu.patch.patch/download
It deletes the compiler option -f90=$ 
(GFORTRAN_FNOSECOND_UNDERSCORE_FC90)' MPI_LIBDIR=$ 
{GFORTRAN_FNOSECOND_UNDERSCORE_MPIDIR}
which the mpi compiler does not recognize. I will try again with the  
serial version tomorrow. In the mean time has anyone gotten this  
successfully working on Ubuntu (recently.) I have looked through the  
listserves and followed everything they suggested.

I really just need something that can optimize the geometry and the  
unit cell. If anyone knows of any other (free) software that can do  
that, please let me know!


Thanks,
Alex


warning: extra tokens at end of #endif directive
and
Warning: Deleted feaure: End of expression in DO loop at (1) must be  
integer
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20110810/ccaf5e09/attachment.html>