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

[Marcin Dulak]

Hi,

i think we need to split the problem into smaller ones:
1. please try to install the serial version of dacapo first.
You should not need any patches - maybe the right underscoring 
conventions for you system is gfortran_fsecond_underscore
and not gfortran_fnosecond_underscore. Please check you underscoring 
convention as described here 
https://listserv.fysik.dtu.dk/pipermail/ase-users/2009-September/000362.html
2. are you able to run the simple example CO from 
https://wiki.fysik.dtu.dk/ase/ase/calculators/jacapo.html?
To the problem of the optimizer I get in a separate post.

Best regards,

Marcin

Alex Eftimiades wrote:
> 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


-- 
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Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk

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