[ase-users] Installation of ASE-DACAPO On Ubuntu 12.10
Sungsik Kim
sungsik312 at gmail.com
Sun Feb 10 19:38:18 CET 2013
Hello,
Thank you so much.
now first example(CO) works well after I fixed DACAPOPATH to $HOME/psp.
I got -590.938274618 without any error.
About installation of DACAPO on Ubuntu 11.04
I used "sudo apt-get install dacapo", sudo apt-get install Dacapo" and
"sudo apt-get dacapo",
I got
##################################################################################
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package dacapo
##################################################################################
About asetest, I did it by different way.
cd ase
cd tools
python testase.py
I got an error in jacapo/jacapo.py (ScriptTestCase) ... Segmentation fault.
except it, everything is fine.
##################################################################################
python 2.7.1+ GCC 4.5.2 64bit ELF on Linux x86_64 Ubuntu 11.04 natty
Ag-Cu100.py (ScriptTestCase) ... ok
CO2_Au111.py (ScriptTestCase) ... ok
COCu111_2.py (ScriptTestCase) ... ok
ag.py (ScriptTestCase) ... ok
atom.py (ScriptTestCase) ... ok
bader.py (ScriptTestCase) ... ok
basin.py (ScriptTestCase) ... ok
build.py (ScriptTestCase) ... ok
center.py (ScriptTestCase) ... ok
com.py (ScriptTestCase) ... ok
constr_setpos.py (ScriptTestCase) ... ok
coverage.py (ScriptTestCase) ... ok
crystal.py (ScriptTestCase) ... ok
dependency_gtk.py (ScriptTestCase) ... ok
dependency_matplotlib.py (ScriptTestCase) ... ok
dihedralconstraint.py (ScriptTestCase) ... ok
dimer.py (ScriptTestCase) ... ok
dimer_method.py (ScriptTestCase) ... ok
distance.py (ScriptTestCase) ... ok
distmom.py (ScriptTestCase) ... ok
eam_test.py (ScriptTestCase) ... ok
emt.py (ScriptTestCase) ... ok
emt1.py (ScriptTestCase) ... ok
emt2.py (ScriptTestCase) ... ok
emt_h3o2m.py (ScriptTestCase) ... ok
eos.py (ScriptTestCase) ... ok
eoswoase.py (ScriptTestCase) ... ok
example.py (ScriptTestCase) ... ok
geometry.py (ScriptTestCase) ... ok
h2.py (ScriptTestCase) ... ok
hcp.py (ScriptTestCase) ... ok
maxwellboltzmann.py (ScriptTestCase) ... ok
md.py (ScriptTestCase) ... ok
n2.py (ScriptTestCase) ... ok
neb.py (ScriptTestCase) ... ok
neighbor.py (ScriptTestCase) ... ok
noncollinear.py (ScriptTestCase) ... ok
properties.py (ScriptTestCase) ... ok
pull.py (ScriptTestCase) ... ok
repeat_FixAtoms.py (ScriptTestCase) ... ok
replay.py (ScriptTestCase) ... ok
rotate.py (ScriptTestCase) ... ok
rotate_euler.py (ScriptTestCase) ... ok
scaled_positions.py (ScriptTestCase) ... ok
scientificpython_bug.py (ScriptTestCase) ... ok
set_get_angle.py (ScriptTestCase) ... ok
stm.py (ScriptTestCase) ... ok
strain.py (ScriptTestCase) ... ok
strain_emt.py (ScriptTestCase) ... ok
things.py (ScriptTestCase) ... ok
unitcellfilter.py (ScriptTestCase) ... ok
vacancy.py (ScriptTestCase) ... ok
verlet.py (ScriptTestCase) ... ok
vib.py (ScriptTestCase) ... ok
vtk_data.py (ScriptTestCase) ... ok
vtk_pipeline.py (ScriptTestCase) ... ok
abinit/abinit_cmdline.py (ScriptTestCase) ... ok
aims/aims_cmdline.py (ScriptTestCase) ... ok
castep/castep_interface.py (ScriptTestCase) ... ok
cmr/ase_rw.py (ScriptTestCase) ... ok
cmr/cmr_rw.py (ScriptTestCase) ... ok
cmr/reactions.py (ScriptTestCase) ... ok
cmr/reactions_run.py (ScriptTestCase) ... ok
cmr/reactions_test.py (ScriptTestCase) ... ok
cmr/reactions_xsimple.py (ScriptTestCase) ... ok
cmr/rw.py (ScriptTestCase) ... ok
elk/elk_cmdline.py (ScriptTestCase) ... ok
exciting/exciting.py (ScriptTestCase) ... ok
fio/abinit.py (ScriptTestCase) ... ok
fio/info.py (ScriptTestCase) ... ok
fio/magmom.py (ScriptTestCase) ... ok
fio/netcdf.py (ScriptTestCase) ... ok
fio/oi.py (ScriptTestCase) ... ok
fio/oldtraj.py (ScriptTestCase) ... ok
fio/trajectory.py (ScriptTestCase) ... ok
fio/v_sim.py (ScriptTestCase) ... ok
fleur/fleur_cmdline.py (ScriptTestCase) ... ok
gaussian/gaussian_cmdline.py (ScriptTestCase) ... ok
gaussian/water.py (ScriptTestCase) ... ok
gromacs/test_gromacs.py (ScriptTestCase) ... ok
jacapo/jacapo.py (ScriptTestCase) ... Segmentation fault
##################################################################################
Even though I fixed DACAPOPATH, I still got the same error in Molecular
Reaction Barrier(1.8).
It is because jacapo.py has segmentation fault?
why is jacapo.py's fault occurred?
Thank you for your help.
Sincerely
Sungsik
2013/2/10 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
> 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, '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>
>
>> 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__'
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20130210/3c009333/attachment.html>
More information about the ase-users
mailing list