[ase-users] Lammps Reader

[Ask Hjorth Larsen]

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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ase-users mailing list
>>> ase-users at listserv.fysik.dtu.dk
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>
>