[ase-users] Appending Ulm-file does not work

[Simon Lamowski]

Dear Jens Jørgen,

thanks a lot! I change my example to reflect your answer and it worked.

I think, the documentation could be amended to make thinks more clear,
what is possible with the ulm-files.
Here is a suggestion for an addition to the Documentation
(https://wiki.fysik.dtu.dk/ase/ase/io/ulm.html):

An advanced example

The following script creates a ulm-file, containing two small lists,
closes the file and appends it later with an array.

>>> import numpy as np
>>> import ase.io.ulm as ulm
>>>
>>>
>>> ##write lists
... w = ulm.open('test.ulm', 'w')
>>> w.write(smalllist = [1, 1])
>>> w.write(list2 = [0, 2])
>>> w.close()
>>>
>>> ##append file with an array
... bigarray = np.arange(12,dtype=float).reshape((4, 3))
>>> print('bigarray\n', bigarray)
bigarray
 [[  0.   1.   2.]
 [  3.   4.   5.]
 [  6.   7.   8.]
 [  9.  10.  11.]]
>>> w2 = ulm.Writer('test.ulm', 'a')
>>> w2.add_array('bigarray', bigarray.shape, bigarray.dtype)
>>> for i in range(bigarray.shape[0]):
...     w2.fill(bigarray[i])
...
>>> w2.close()
>>>

The reader opens the file again and prints the data, which was written
first:

>>> ## open file again: this gives only the data from the
...
>>> R = ulm.Reader('test.ulm')
>>> d = R.asdict()
>>> print(d.keys() )
dict_keys(['list2', 'smalllist'])

To get all the data, it is possible to iterate over the items in the file.

>>> ## print all data in the file
... for r in ulm.Reader('test.ulm'):
...     dct = r.asdict()
...     for k in dct.keys():
...         print(k)
...         print(dct[k])
...
...
list2
[0 2]
smalllist
[1 1]
bigarray
[[  0.   1.   2.]
 [  3.   4.   5.]
 [  6.   7.   8.]
 [  9.  10.  11.]]
>>>

The different parts (items) of the file are numbered by the index
argument. Or in the usual way to get items:

>>> r[0].asdict().keys()
dict_keys(['list2', 'smalllist'])
>>> r.close()

The last command closes the file.
---
Thanks again.

Best regards,
Simon


On 01-03-2018 09:01, Jens Jørgen Mortensen wrote:
> On 02/28/2018 04:48 PM, Simon Lamowski via ase-users wrote:
>> Hello all!
>>
>> I was testing to append an ulm-file and found that it did not work.
>> Hence I attached a minimal example.
>>
>> Since I do not understand why it is not working, I hope that someone,
>> who is more familiar with the code can fix it.
>>
>> By the way, the add_array and fill is working, if the file is not closed
>> and reopened.
>>
>> Here are the versions, I use:
>> numpy: 1.14.0
>> scipy: 1.0.0
>> ase: 3.15.0
>> python: 3.4.6
>>
>> It fails as well for versions:
>> scipy: 0.19.1
>> ase: 3.13.0-python34
>> numpy: 1.13.2
>>
>> If you now a workaround, please answer.
> 
> When you first write to an ulm file, you write to the block with
> index=0.  When you open it in append mode and write some more things,
> that will go to the next block with index=1.
> 
> You can look inside an ulm file with:
> 
> [jensj at jordan ~]$ ase ulm test.ulm
> test.ulm  (tag: "", 2 items)
> item #0:
> {
>     smalllist: [1 1]}
> item #1:
> {
>     bigarray: <ndarray shape=(4, 3) dtype=float64>}
> 
> If you change your example to "reader = ulm.Reader('test.ulm', index=1)"
> and comment out the "print(dct['smalllist'])" line, then it should work.
> 
> Jens Jørgen
> 
>>
>>
>> Best regards
>>
>> Simon Lamowski
>>
>>
>>
>> _______________________________________________
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>> ase-users at listserv.fysik.dtu.dk
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> 

-- 
Simon Lamowski
PhD student
AG Pauly

visitor address:
University of Konstanz
Department of Physics
Universitätsstraße 10
Room Z1018
D-78464 Konstanz
Germany

postal address:
Simon Lamowski
University of Konstanz
Department of Physics
P.O. Box 699
D-78457 Konstanz
Germany

Phone:  +49 (0) 7531 88 3827
email: simon.lamowski at uni-konstanz.de

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