dump2pdb.py

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1

Dear LAMMPS Users

I am trying to convert LAMMPS dump file (which I created via the command
“dump id6 nonwater atom 10000 test.atom”) to pdb format.

And I have the following error:

% python dump2pdb.py test.atom 1 2 3 4 5 file1 file2
0
read 1 snapshots
1 snapshots selected out of 1
assigned columns: id type x y z
Unscaling dump …
Traceback (most recent call last):
File “dump2pdb.py”, line 34, in
d = dump(dumpfile)
File “/home/user/lammps-16Mar18/tools/python/dump.py”, line 233, in init
self.read_all()
File “/home/user/lammps-16Mar18/tools/python/dump.py”, line 286, in read_all
if self.scale_original == 1: self.unscale()
File “/home/user/lammps-16Mar18/tools/python/dump.py”, line 523, in unscale
for snap in self.snaps: self.unscale_one(snap,x,y,z)
File “/home/user/lammps-16Mar18/tools/python/dump.py”, line 539, in unscale_one
if atoms != None:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

I would be really grateful for any little help.

Best Wishes

Lunna

2

it seems like the python code expects behavior from older python
versions, that is not available with more recent python versions.

if you edit the dump.py file by replacing all lines that have:

      if atoms != None:

with:

      if type(atoms) != types.NoneType:

then it should work again.

axel.

3

Dear Axel

Thank you so much. It works now.

Best Wishes
Lunna