Error using python script : neb_combine.py

Hi,

I am new to using python and not able to find solution for my problem. I want to use one of lammps post-processing python scripts “neb_combine.py”. But this is the error I run into

[[email protected]…4594… TEST]$ ./neb_combine.py -o output -r dump.neb.*
Traceback (most recent call last):
File “./neb_combine.py”, line 13, in ?
path = os.environ[“LAMMPS_PYTHON_TOOLS”]
File “/usr/lib64/python2.4/UserDict.py”, line 17, in getitem
def getitem(self, key): return self.data[key]
KeyError: ‘LAMMPS_PYTHON_TOOLS’

Possibly it is about setting the right path in the python script to access files in /lammps/tools/python/pizza.

  1. if I set it to

Path = os.environ["/home/agoyal/MD/LAMMPS/lammps-16Aug13/tools/python/pizza"] which is the right path for /pizza on my machine. I still get the error.

  1. Or, even if I copy files from /pizza to present working directory. It doesn’t work.

  2. If I set LAMMPS_PYTHON_TOOLS=/home/agoyal/MD/LAMMPS/lammps-16Aug13/tools/python
    In my ./bashrc and then run “neb_combine.py” it gives

ImportError: No module named dump

So do I need to install install.py or install some modules to use python Or may be I am doing something fundamentally wrong.

Please advise.

Thanks in Advance,

Anuj

Hi,

I am new to using python and not able to find solution for my problem. I
want to use one of lammps post-processing python scripts "neb_combine.py".
But this is the error I run into

[[email protected] TEST]$ ./neb_combine.py -o output -r dump.neb.*
Traceback (most recent call last):
  File "./neb_combine.py", line 13, in ?
   path = os.environ["LAMMPS_PYTHON_TOOLS"]
  File "/usr/lib64/python2.4/UserDict.py", line 17, in __getitem__
  def __getitem__(self, key): return self.data[key]
KeyError: 'LAMMPS_PYTHON_TOOLS'

Possibly it is about setting the right path in the python script to access
files in /lammps/tools/python/pizza.

1. if I set it to

Path =
os.environ["/home/agoyal/MD/LAMMPS/lammps-16Aug13/tools/python/pizza"] which
is the right path for /pizza on my machine. I still get the error.

this is complete nonsense. this part of the code is to query an
environment variable not the path directly.

2. Or, even if I copy files from /pizza to present working directory. It
doesn't work.

3. If I set
LAMMPS_PYTHON_TOOLS=/home/agoyal/MD/LAMMPS/lammps-16Aug13/tools/python
In my ./bashrc and then run "neb_combine.py" it gives

ImportError: No module named dump

of course you get this error message, because this is not correct.

So do I need to install install.py or install some modules to use python Or
may be I am doing something fundamentally wrong.

all you need to do is read the README file (there is a reason it has
this name) in the tools/python directory. it explains how you should
use the scripts and provide access to the python support modules.
plain and simple.

axel.

Sorry, but I did go through README.

It works now. As I downloaded pizza toolkit from LAMMPS site and setenv in
my bash file as

Export
LAMMPS_PYTHON_TOOLS=/home/agoyal/MD/LAMMPS/lammps-16Aug13/pizza-11Sep13/src

Thanks,
Anuj

Sorry, but I did go through README.

but you didn't pay attention

It works now. As I downloaded pizza toolkit from LAMMPS site and setenv in

this is not necessary. the distribution of files shipped with LAMMPS
is sufficient, but you *HAVE* to use the correct path, and you
obviously didn't.

axel.