download error: "Unknown database type: xyz"

[eszter137]

Is it possible that the xyz type is not supported for downloading a database?

$ abcd download -q "E_MP2_3b>0.01" data_MP2_3b_gt_001eV.xyz
Traceback (most recent call last):
  File "/home/es732/miniconda3/bin/abcd", line 8, in <module>
    sys.exit(main())
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/parser.py", line 121, in main
    callback_func(**kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/decorators.py", line 15, in wrapper
    func(*args, config=config, **kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/decorators.py", line 48, in wrapper
    func(*args, db=db, query=query, **kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/commands.py", line 41, in download
    write(filename, list(db.get_atoms(query=query)), format=fileformat)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/io/formats.py", line 507, in write
    **kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/parallel.py", line 233, in new_func
    return func(*args, **kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/io/formats.py", line 528, in _write
    io.write(filename, images, append=append, **kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/io/db.py", line 32, in write_db
    con = ase.db.connect(filename, serial=True, append=append, **kwargs)
  File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/db/core.py", line 188, in connect
    raise ValueError('Unknown database type: ' + type)
ValueError: Unknown database type: xyz

When the query results in no structures, it creates an empty file:

$ abcd download -q "E_MP2_3b>0.5" data_MP2_3b_gt_05eV.xyz

$ ls -rtl 
# [...]
-rw-r--r--  1 es732 es732         0 Mar 16 09:56 data_MP2_3b_gt_05eV.xyz

[gabor1]

For the moment you need to specify "-f xyz" and then it works

-- Gábor

On 16 Mar 2020, at 09:58, eszter137 notifications@github.com wrote:

 Is it possible that the xyz type is not supported for downloading a database? Interestingly, the error is dependent on the query's parameter name. In the first case, there's an error; and in the second case, it seems to be running but creates only an empty file in the current working directory:

$ abcd download -q "E_MP2_TTM_3b>0.5" mww_MP2_TTM_3b_gt_05eV.xyz Traceback (most recent call last): File "/home/es732/miniconda3/bin/abcd", line 8, in sys.exit(main()) File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/parser.py", line 121, in main callback_func(kwargs) File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/decorators.py", line 15, in wrapper func(*args, config=config, *kwargs) File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/decorators.py", line 48, in wrapper func(args, db=db, query=query, kwargs) File "/home/es732/miniconda3/lib/python3.7/site-packages/abcd/frontends/commandline/commands.py", line 41, in download write(filename, list(db.get_atoms(query=query)), format=fileformat) File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/io/formats.py", line 507, in write *kwargs) File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/parallel.py", line 233, in new_func return func(args, kwargs) File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/io/formats.py", line 528, in _write io.write(filename, images, append=append, kwargs) File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/io/db.py", line 32, in write_db con = ase.db.connect(filename, serial=True, append=append, **kwargs) File "/home/es732/miniconda3/lib/python3.7/site-packages/ase/db/core.py", line 188, in connect raise ValueError('Unknown database type: ' + type) ValueError: Unknown database type: xyz $ abcd download -q "E_MP2_3b>0.5" data_MP2_3b_gt_05eV.xyz results in an empty file:

$ ls -rtl

[...]

-rw-r--r-- 1 es732 es732 0 Mar 16 09:56 data_MP2_3b_gt_05eV.xyz — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[eszter137]

Thank you; it worked. (Maybe it'd be good to add this to the examples.md that contained this line:

abcd download -q formula~W128 data.xyz

)