Error in running lammps using python file

LAMMPS LAMMPS Beginners
1

Hi,

I am trying to run lammps using python using the following script:

from lammps import lammps
lmp = lammps()
lmp.file("+input.cntMS")

But i get the following error:
Note: The lammps input file “input.cntMS” is in the same directory as the poython script “cnt.py”

 /bin/python3 /home/vinayak/Documents/vinayak-phd/codes_vinayak/lammps/cnt/MS/cnt.py
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
ERROR on proc 0: Cannot open input script input.cntMS: No such file or directory (src/input.cpp:334)
Last command: (unknown)
Traceback (most recent call last):
  File "/home/vinayak/Documents/vinayak-phd/codes_vinayak/lammps/cnt/MS/cnt.py", line 4, in <module>
    lmp.file("input.cntMS")
  File "/home/vinayak/.local/lib/python3.8/site-packages/lammps/core.py", line 564, in file
    self.lib.lammps_file(self.lmp, path)
  File "/home/vinayak/.local/lib/python3.8/site-packages/lammps/core.py", line 49, in __exit__
    raise self.lmp._lammps_exception
Exception: ERROR on proc 0: Cannot open input script input.cntMS: No such file or directory (src/input.cpp:334
Total wall time: 0:00:00

I don’t get this error if i specify the full path of the lammps input file in the python script as follows:

from lammps import lammps
lmp = lammps()
lmp.file("/home/vinayak/Documents/vinayak-phd/codes_vinayak/lammps/cnt/MS/input.cntMS")

What is the reason for this? How can i get away with specifying the complete path even when the files are in the same directory?

Thanks
Vinayak

2

The inputs you provide and the error messages are not consistent.
If you have a file “input.cntMS” in your current folder and execute lmp.file("+input.cntMS")
you should get an error, namely this (because the filename is misspelled):

[akohlmey@notamac test]$ ls
input.cntMS  log.lammps  test.py
[akohlmey@notamac test]$ rm log.lammps 
[akohlmey@notamac test]$ ls
input.cntMS  test.py
[akohlmey@notamac test]$ cat input.cntMS 
print "hello!"
[akohlmey@notamac test]$ cat test.py 
from lammps import lammps
lmp = lammps()
lmp.file("+input.cntMS")
[akohlmey@notamac test]$ python test.py
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
ERROR on proc 0: Cannot open input script +input.cntMS: No such file or directory (src/input.cpp:334)
Last command: (unknown)
Traceback (most recent call last):
  File "/home/akohlmey/compile/lammps/build-test/test/test.py", line 3, in <module>
    lmp.file("+input.cntMS")
  File "/home/akohlmey/.local/lib/python3.10/site-packages/lammps/core.py", line 563, in file
    with ExceptionCheck(self):
  File "/home/akohlmey/.local/lib/python3.10/site-packages/lammps/core.py", line 49, in __exit__
    raise self.lmp._lammps_exception
Exception: ERROR on proc 0: Cannot open input script +input.cntMS: No such file or directory (src/input.cpp:33
Total wall time: 0:00:00

However, if I change the python code to refer to the input file correctly, it does execute as expected:

[akohlmey@notamac test]$ cat test.py
from lammps import lammps
lmp = lammps()
lmp.file("input.cntMS")
[akohlmey@notamac test]$ python test.py
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
hello!
Total wall time: 0:00:00

So the reason why you don’t get the expected result is between your chair and your computer.

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