[ase-users] Installation of ASE-DACAPO On Ubuntu 12.10

[Marcin Dulak]

Hi,

the first problem you report (CO) points to setting DACAPOPATH.
I think it should be export DACAPOPATH="$HOME/psp".
Please also run ase tests:
https://wiki.fysik.dtu.dk/ase/download.html#run-the-tests
This performs some relevant netcdf tests.

On Ubuntu 11.04 you can install dacapo with:
sudo apt-get dacapo
This will install also the pseudopotentials under 
DACAPOPATH=/usr/share/dacapo-psp

Best regards,

Marcin

On 02/10/13 15:29, Sungsik Kim wrote:
> Hello,
>
> I did with newly installing ubuntu 12.10. I still got the same errors 
> - dacapo.run and serials
>
> Fortunately, I succeeded in compiling dacapo on Ubuntu 11.04. So I do 
> not need to install dacapo on ubuntu 12.10 anymore.
>
> Thank you for your help.
>
> Even though I compiled by using "make gfortran_fnosecond_undersocre" 
> on ubuntu 11.04,
>
> I got other errors when running some examples.
>
> First example, total energy of a CO molecule, 
> https://wiki.fysik.dtu.dk/ase/ase/calculators/jacapo.html
>
> I got error below
> #####################################################################
> Traceback (most recent call last):
>   File "/home/sungsik/skim/skim1.py", line 15, in <module>
>     print CO.get_potential_energy()
>   File "/home/sungsik/ase/ase/atoms.py", line 627, in get_potential_energy
>     return self._calc.get_potential_energy(self)
>   File "/home/sungsik/ase/ase/calculators/jacapo/jacapo.py", line 
> 2330, in get_potential_energy
>     self.calculate()
>   File "/home/sungsik/ase/ase/calculators/jacapo/jacapo.py", line 
> 2866, in calculate
>     raise DacapoAbnormalTermination(s % txt)
> DacapoAbnormalTermination: Dacapo output txtfile (CO.txt) did not end 
> normally.
>  setuop:
>
>  setuop: ----------------------------------------------------------------
>  setuop: species  chemical  friction  dynamic mass
>  setuop: number    symbol    [0..1]       [u]
>  setuop: ----------------------------------------------------------------
>  setuop:    1         C     0.500000    3.000000
>  setuop:    2         O     0.500000    3.000000
>  setuop: ----------------------------------------------------------------
>
> #####################################################################
>
> Second example is molecular reaction barriers(1.8), This is really 
> what I need to calculate.
> http://gilgamesh.cheme.cmu.edu/doc/software/jacapo/1-molecules/1.7-reaction-barriers/1.7.0-reaction-barriers.html
> First part, I got an error
> ######################################################################
> Traceback (most recent call last):
>   File "skim2.py", line 22, in <module>
>     qn.run(fmax=0.05)
>   File "/home/sungsik/ase/ase/optimize/optimize.py", line 114, in run
>     f = self.atoms.get_forces()
>   File "/home/sungsik/ase/ase/atoms.py", line 669, in get_forces
>     forces = self._calc.get_forces(self)
>   File "/home/sungsik/ase/ase/calculators/jacapo/jacapo.py", line 
> 2355, in get_forces
>     forces = nc.variables['DynamicAtomForces'][-1]
> KeyError: 'DynamicAtomForces'
> #######################################################################
>
> Second part for NEB calculation for the first part, I got error like below
> ########################################################################
> Traceback (most recent call last):
>   File "skim3.py", line 6, in <module>
>     initial = read('1.7.1-initial.traj')
>   File "/home/sungsik/ase/ase/calculators/jacapo/jacapo.py", line 81, 
> in read
>     calc = Jacapo(ncfile)
>   File "/home/sungsik/ase/ase/calculators/jacapo/jacapo.py", line 263, 
> in __init__
>     self.set_nc(nc)
>   File "/home/sungsik/ase/ase/calculators/jacapo/jacapo.py", line 
> 1237, in set_nc
>     self._set_frame_number()
>   File "/home/sungsik/ase/ase/calculators/jacapo/jacapo.py", line 692, 
> in _set_frame_number
>     nc = netCDF(self.nc <http://self.nc>, 'r')
>   File "/usr/lib/python2.7/dist-packages/Scientific/IO/NetCDF.py", 
> line 177, in NetCDFFile
>     return apply(_NetCDFFile, args)
> IOError: netcdf: No such file or directory
> ##########################################################################
>
> Can you tell me why I got errors like these? I think that I set 
> environmental variable correctly.
> I do not why I got these error,
>
> Just in case, here is my procedure to install dacapo on Ubuntu 11.04.
>
> sudo apt-get install liblapack-dev
> sudo apt-get install libnetcdf-dev
> sudo apt-get install netcdf-bin
> sudo apt-get install fftw-dev
> sudo apt-get install subversion
> sudo apt-get install gfortran
> sudo apt-get install python-scientific
> sudo apt-get install grace
> sudo apt-get install rasmol
> sudo apt-get install gnuplot
> sudo apt-get install python-pexpect
> sudo apt-get install python-vtk
> sudo apt-get install python-matplotlib
> sudo apt-get install python-gnuplot
> svn checkout https://svn.fysik.dtu.dk/projects/ase/trunk ase
> sudo apt-get install python-ase
> svn co https://svn.fysik.dtu.dk/projects/dacapo/trunk dacapo
> cd
> mkdir psp
> cp -pr dacapo/psp/*/*/*.pseudo psp
> export NETCDF="/usr/lib"
> export DACAPOPATH="/home/psp"
> export BLASLAPACK="-L/usr/lib -lnetcdff -lnetcdf -L/usr/lib -lblas 
> -llapack -L/usr/lib -lblas -llapack -lgfortran"
> export FFTW="/usr/lib"
> cd ~/dacapo/src
> make gfortran_fnosecond_underscore
> export VTK_TK_WIDGET_PATH=/usr/lib
> export PYTHONPATH=${HOME}/dacapo/
> Python:${HOME}/ase
> export 
> PATH=${HOME}/bin:${HOME}/ase/ase/tools:${HOME}/dacapo/Python/Dacapo/Tools:${PATH}
> export 
> DACAPOEXE_SERIAL=${HOME}/dacapo/src/gfortran_fnosecond_underscore_serial/dacapo.run
>
> Thanks, again.
>
> Sincerely
>
> Sungsik
>
>
> 2013/2/9 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk 
> <mailto:Marcin.Dulak at fysik.dtu.dk>>
>
>     Hi,
>
>     please verify that the required nf_* functions are there,
>     following
>     https://listserv.fysik.dtu.dk/pipermail/ase-users/2009-September/000362.html
>     You need to build in a fresh directory (dacapo Makefile does not
>     have "make clean" option).
>
>     Best regards,
>
>     Marcin
>
>     On 02/09/13 22:39, Sungsik Kim wrote:
>
>         undefined reference to `nf_open__'
>

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