[ase-users] Lammps Reader

[Jonathan]

It seems that it originates from the lammpsdata.py file not being able 
to parse it.

I think I have an older version of ASE than you as there was a change to 
this file in Nov, but the error seems to be in the same place.

Jon

On 19/12/2017 13:08, Ask Hjorth Larsen wrote:
> Hi Jonathan, (please reply to list)
>
> 2017-12-19 14:04 GMT+01:00 Jonathan <jonathan.bean at york.ac.uk>:
>> Hi Ask
>>
>> Below is the trace
>>
>> Traceback (most recent call last):
>>    File "greens_function_probe.py", line 80, in <module>
>>      a = read(str(abs(x1+3)) + str(abs(y1+3)) + str(abs(z1+3)) + "GFprobe" +
>> suffix)
>>    File "/home/jb2191/.local/lib/python2.7/site-packages/ase/io/formats.py",
>> line 428, in read
>>      parallel=parallel, **kwargs))
>>    File "/home/jb2191/.local/lib/python2.7/site-packages/ase/io/formats.py",
>> line 485, in _iread
>>      for dct in io.read(fd, *args, **kwargs):
>>    File "/home/jb2191/.local/lib/python2.7/site-packages/ase/io/formats.py",
>> line 313, in wrap_read_function
>>      yield read(filename, **kwargs)
>>    File
>> "/home/jb2191/.local/lib/python2.7/site-packages/ase/io/lammpsdata.py", line
>> 167, in read_lammps_data
>>      (style, len(fields)))
>> TypeError: %d format: a number is required, not str
>>
>>
>> The name of the file is not hard-coded but is called
>> "000GFprobe.lammps-data"
> I get this error instead:
>
> askhl at jormungandr:~$ ase -T gui 000GFprobe.lammps-data
> Traceback (most recent call last):
>    File "/home/askhl/src/ase/bin/ase", line 3, in <module>
>      main()
>    File "/home/askhl/src/ase/ase/cli/main.py", line 69, in main
>      f(args)
>    File "/home/askhl/src/ase/ase/gui/ag.py", line 67, in run
>      images.read(args.filenames, string2index(args.image_number))
>    File "/home/askhl/src/ase/ase/gui/images.py", line 145, in read
>      i = read(filename, index, filetype)
>    File "/home/askhl/src/ase/ase/io/formats.py", line 435, in read
>      **kwargs))
>    File "/home/askhl/src/ase/ase/io/formats.py", line 496, in _iread
>      for dct in io.read(fd, *args, **kwargs):
>    File "/home/askhl/src/ase/ase/io/formats.py", line 322, in wrap_read_function
>      yield read(filename, **kwargs)
>    File "/home/askhl/src/ase/ase/io/lammpsdata.py", line 167, in read_lammps_data
>      "".format(style, len(fields)))
> RuntimeError: Style 'full' not supported or invalid number of fields 5
>
>
> (I probably can't help much with lammps, but maybe someone else on the
> list can, if the full scripts/error messages are available)
>
> Best regards
> Ask
>
>> Jonathan
>>
>>
>> On 19/12/2017 13:00, Ask Hjorth Larsen wrote:
>>> Hi,
>>>
>>> 2017-12-18 20:11 GMT+01:00 Jonathan via ase-users
>>> <ase-users at listserv.fysik.dtu.dk>:
>>>> Hello All
>>>>
>>>> I've just been trying to read in a lammp-data type file into the ASE
>>>> reader
>>>> but I am getting the following error message
>>>>
>>>> "TypeError: %d format: a number is required, not str"
>>> Please provide the full stack trace and the exact command or script to
>>> reproduce it.
>>>
>>> Best regards
>>> Ask
>>>
>>>> But this file (see below) works fine with LAMMPS
>>>>
>>>> "LAMMPS Description
>>>>
>>>> 4 atoms
>>>> 1 atom types
>>>> -33.100000 33.100000 xlo xhi
>>>> -33.100000 33.100000 ylo yhi
>>>> -33.100000 33.100000 zlo zhi
>>>>
>>>> Atoms
>>>>
>>>> 1 1    -33.10000000   -33.10000000   -33.10000000
>>>> 2 1    -31.44500000   -31.44500000   -31.44500000
>>>> 3 1    -33.10000000   -33.10000000   -29.79000000
>>>> 4 1    -31.44500000   -31.44500000   -28.13500000"
>>>>
>>>> Not sure whether anyone has any insights into this.
>>>>
>>>> Jonathan
>>>>
>>>>
>>>>
>>>>
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>>