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

[Jens Jørgen Mortensen]

On 03/01/2018 02:55 PM, Simon Lamowski wrote:
> 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):

Thanks!  I'll add that to the docs.

Jens Jørgen

>
> 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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