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

[Sungsik Kim]

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<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__'
>>
>
>
> --
> *************************************
>  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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