[ase-users] jacapo error

[John Kitchin]

I suppose your error means that dacapo.run is not on your path, ,
or the executables are not found.

you should be able to type: dacapo.run at the command line and get something
like:
10:27:42 1001> dacapo.run
 abort_calc: Syntax error: number_of_args < 1;
usage:/opt/dacapo-j/src-v2-3-5/dacapo-j/gfortran_fnosecond_underscore_serial/dacapo_gfortran_fnosecond_underscore_serial.run
netCDF_input_file [netCDF_output_file] [-innc netCDF_input_file] [-outnc
netCDF_out_file] [-out ASCII_output] [-scratch scratch_dir ] [-stop
stop_file_name]
 Not a netCDF
id
 clexit: exiting the program
"/opt/dacapo-j/src-v2-3-5/dacapo-j/gfortran_fnosecond_underscore_serial/dacapo_gfortran_fnosecond_underscore_serial.run
" failed

you may see different details, but overall it should resemble this.

you may also have to define these variables:
setenv DACAPOEXE_SERIAL $HOME/bin/dacapo_intellinux_serial.run
setenv DACAPOEXE_PARALLEL $HOME/bin/dacapo_intellinux_mpi.run

to point to the fortran executables.

j

>
> ------------------------------
>
> Message: 2
> Date: Tue, 08 Feb 2011 12:45:57 -0800
> From: Sharon H Chou <cnorahs at stanford.edu>
> Subject: [ase-users] [ase-user] jacapo error
> To: ase-users at listserv.fysik.dtu.dk
> Message-ID: <1297197957.1919.13.camel at mystic-architect-desktop>
> Content-Type: text/plain; charset="UTF-8"
>
> Thanks for debugging -
>
> I ran the bash command
> export DACAPOPATH=$HOME/ase/ase/calculators/jacapo/tools
> and copied the *.pseudo files into the directory above,
>
>
> When I ran the script below from
>
> http://gilgamesh.cheme.cmu.edu/doc/software/jacapo/3-surfaces/3.2-surface-relaxation/3.2.0-surface-relaxation.html
>
> #!/usr/bin/env python
> from ase.lattice.surface import *
> from ase.calculators.jacapo import *
>
> slab = fcc111('Al', size=(2,2,3), vacuum=10.0)
> slab.center()
>
> calc = Jacapo('3.2.1-Al-norelax.nc',
>              pw=300,
>              kpts=(2,2,1),
>              atoms=slab)
>
> print slab.get_potential_energy()
> print slab.get_forces()
>
>
> I got the error below,
>
> Traceback (most recent call last):
>  File "Al_3layers.py", line 13, in <module>
>    print slab.get_potential_energy()
>  File "/usr/lib/python2.6/dist-packages/ase/atoms.py", line 494, in
> get_potential_energy
>    return self.calc.get_potential_energy(self)
>  File
> "/usr/lib/python2.6/dist-packages/ase/calculators/jacapo/jacapo.py",
> line 2180, in get_potential_energy
>    self.calculate()
>  File
> "/usr/lib/python2.6/dist-packages/ase/calculators/jacapo/jacapo.py",
> line 2661, in calculate
>    f = open(txt, 'r')
> IOError: [Errno 2] No such file or directory: '3.2.1-Al-norelax.txt'
>
> Seems like it's looking for a text file that never got created, what
> lines should I add in the original script?
>
>
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