Hi All,
Sorry for the trouble, but I don't see how to create a new bug report
on gna.org. I followed the link from the nmr-relax.com website, but
all I see is how to browse already reported bugs/items.
Thanks,
Doug
On Aug 29, 2007, at 11:55 AM, Edward d'Auvergne wrote:
> Hi,
>
> This is definitely a bug and will occur whenever there is a spin
> system loaded into the system but which has not been used in the
> analysis (because of deselection or missing relaxation data). The
> problem is that self.relax.data.res[run][i].model does not exist for
> all spin systems in your system. Would you be able to create a bug
> report for this issue? Thanks. There are three places in the
> 'convergence()' function in which this failure will occur, but I'll
> fix all of these once the bug report is complete so I can point to the
> bug report in the SVN commit messages.
>
> Cheers,
>
> Edward
>
>
> On 8/29/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> Hi Edward,
>>
>> I am just picking back up on my relaxation analysis, and noticed that
>> the CONV_LOOP = 1 function is full_analysis.py does not seem to work
>> properly. I get the following error:
>>
>> """
>> #####################
>> # Convergence tests #
>> #####################
>>
>>
>> Chi-squared test:
>> chi2 (k-1): 164.3021658998544
>> chi2 (k): 168.91097779838205
>> The chi-squared value has not converged.
>>
>> Identical model-free models test:
>> Traceback (most recent call last):
>> File "/opt/relax/1.2/relax", line 454, in ?
>> Relax()
>> File "/opt/relax/1.2/relax", line 166, in __init__
>> self.interpreter.run()
>> File "/opt/relax/1.2/prompt/interpreter.py", line 213, in run
>> run_script(intro=self.relax.intro_string, local=self.local,
>> script_file=self.relax.script_file, quit=1)
>> File "/opt/relax/1.2/prompt/interpreter.py", line 388, in
>> run_script
>> console.interact(intro, local, script_file, quit)
>> File "/opt/relax/1.2/prompt/interpreter.py", line 340, in
>> interact_script
>> execfile(script_file, local)
>> File "full_analysis.py", line 574, in ?
>> Main(self.relax)
>> File "full_analysis.py", line 247, in __init__
>> converged = self.convergence(run=name)
>> File "full_analysis.py", line 368, in convergence
>> curr_models = curr_models + self.relax.data.res[run][i].model
>> AttributeError: Element instance has no attribute 'model'
>> """
>>
>> Thanks,
>> Doug
>>
>> On Jun 27, 2007, at 11:22 AM, Edward d'Auvergne wrote:
>>
>>> Hi,
>>>
>>> To commit changes to the repository, you need to become a relax
>>> developer. There is detailed information in the relax manual about
>>> this long process. Alternatively if you run the command svn diff to
>>> create a patch file, I can then apply the patch and make the commit
>>> for you. In this case however I am making the changes to the 1.3
>>> repository line and then back porting to the 1.2 line (this is the
>>> origin of the relax_data_store error you saw before). Therefore if
>>> you post what the changes are, I will manually apply them to 1.3 and
>>> then back port to 1.2.
>>>
>>> Cheers,
>>>
>>> Edward
>>>
>>>
>>> P.S. The change to line 290 was unnecessary as far as I can see (I
>>> could be wrong though). And I also replaced the looping over
>>> LOCAL_TM_MODELS and MF_MODELS with a single test within the model-
>>> free
>>> model loop which already exists - just to simplify the code. The
>>> changes have been committed to the repository.
>>>
>>>
>>>
>>>
>>> On 6/27/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>>>> Another update. I had to change a few more lines, but the script
>>>> seems to work properly now.
>>>>
>>>> % diff OLD.py NEW.py
>>>> 229a230,231
>>>>> if name in self.relax.data.run_names:
>>>>> run.delete(name)
>>>> 290a293,294
>>>>> if 'final' in self.relax.data.run_names:
>>>>> run.delete('final')
>>>> 524a529,531
>>>>> for name_to_remove in LOCAL_TM_MODELS:
>>>>> if name_to_remove in self.relax.data.run_names:
>>>>> run.delete(name_to_remove)
>>>> 526a534,536
>>>>> for name_to_remove in MF_MODELS:
>>>>> if name_to_remove in self.relax.data.run_names:
>>>>> run.delete(name_to_remove)
>>>>
>>>>
>>>> If you would like me to commit these changes, just let me know
>>>> where
>>>> I can find instructions on how to do so.
>>>>
>>>> Thanks,
>>>>
>>>> Doug
>>>>
>>>>
>>>>
>>>> On Jun 26, 2007, at 3:58 AM, Edward d'Auvergne wrote:
>>>>
>>>>> Whoops, that should have been 'self.relax.data.run_names'! It's
>>>> all
>>>>> fixed in the repository.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Edward
>>>>>
>>>>>
>>>>> On 6/25/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>>>>>> Hi Edward,
>>>>>>
>>>>>> A new error, that appears before the first round of iteration
>>>> starts
>>>>>> after executing the script:
>>>>>>
>>>>>>
>>>> -------------------------------------------------------------------
>>>> --
>>>>>> ---
>>>>>> ----------------------------
>>>>>> Traceback (most recent call last):
>>>>>> File "/home/dkojetin/bin/relax", line 454, in ?
>>>>>> Relax()
>>>>>> File "/home/dkojetin/bin/relax", line 166, in __init__
>>>>>> self.interpreter.run()
>>>>>> File "/opt/relax/1.2/prompt/interpreter.py", line 213, in run
>>>>>> run_script(intro=self.relax.intro_string, local=self.local,
>>>>>> script_file=self.relax.script_file, quit=1)
>>>>>> File "/opt/relax/1.2/prompt/interpreter.py", line 388, in
>>>>>> run_script
>>>>>> console.interact(intro, local, script_file, quit)
>>>>>> File "/opt/relax/1.2/prompt/interpreter.py", line 340, in
>>>>>> interact_script
>>>>>> execfile(script_file, local)
>>>>>> File "n3.py", line 578, in ?
>>>>>> Main(self.relax)
>>>>>> File "n3.py", line 230, in __init__
>>>>>> self.load_tensor()
>>>>>> File "n3.py", line 499, in load_tensor
>>>>>> if 'previous' in self.relax.data.runs:
>>>>>> AttributeError: Data instance has no attribute 'runs'
>>>>>>
>>>>>>
>>>>>> Doug
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jun 25, 2007, at 8:54 AM, Edward d'Auvergne wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Sorry, that relax_data_store was 1.3 line specific and I
>>>> forgot to
>>>>>>> change that for the 1.2 line. The repository code should now
>>>> have
>>>>>>> that fixed.
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Edward
>>>>>>>
>>>>>>>
>>>>>>> On 6/25/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> Here is the error reported by the modified full_analysis.py
>>>> script
>>>>>>>> (named n.py in the below Traceback):
>>>>>>>>
>>>>>>>> #--start
>>>>>>>>
>>>>>>
>>>> -------------------------------------------------------------------
>>>> --
>>>>>>>> ---
>>>>>>>> ----------------------------
>>>>>>>> Traceback (most recent call last):
>>>>>>>> File "/home/dkojetin/bin/relax", line 454, in ?
>>>>>>>> Relax()
>>>>>>>> File "/home/dkojetin/bin/relax", line 166, in __init__
>>>>>>>> self.interpreter.run()
>>>>>>>> File "/opt/relax/1.2/prompt/interpreter.py", line 213, in
>>>> run
>>>>>>>> run_script(intro=self.relax.intro_string,
>>>> local=self.local,
>>>>>>>> script_file=self.relax.script_file, quit=1)
>>>>>>>> File "/opt/relax/1.2/prompt/interpreter.py", line 388, in
>>>>>>>> run_script
>>>>>>>> console.interact(intro, local, script_file, quit)
>>>>>>>> File "/opt/relax/1.2/prompt/interpreter.py", line 340, in
>>>>>>>> interact_script
>>>>>>>> execfile(script_file, local)
>>>>>>>> File "n.py", line 577, in ?
>>>>>>>> Main(self.relax)
>>>>>>>> File "n.py", line 229, in __init__
>>>>>>>> self.load_tensor()
>>>>>>>> File "n.py", line 498, in load_tensor
>>>>>>>> if relax_data_store.has_key('previous'):
>>>>>>>> NameError: global name 'relax_data_store' is not defined
>>>>>>>>
>>>>>>>> #--end
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Doug
>>>>>>>>
>>>>>>>>
>>>>>>>> On Jun 25, 2007, at 4:42 AM, Edward d'Auvergne wrote:
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I've just made modifications to the 1.2 and 1.3 repository
>>>>>> lines to
>>>>>>>>> hopefully fix this problem. Could you try again to see if
>>>> the
>>>>>>>> script
>>>>>>>>> works this time?
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>>
>>>>>>>>> Edward
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 6/25/07, Douglas Kojetin <[EMAIL PROTECTED]>
>>>> wrote:
>>>>>>>>>> Hi Edward,
>>>>>>>>>>
>>>>>>>>>> I gave the new script a try, setting CONV_LOOP = 1, but it
>>>>>>>> reported
>>>>>>>>>> an error after optimizing the first round:
>>>>>>>>>>
>>>>>>>>>> """
>>>>>>>>>> Convergence:
>>>>>>>>>> [ No ]
>>>>>>>>>>
>>>>>>>>>> relax> run.create(run='previous', run_type='mf')
>>>>>>>>>> RelaxError: The run 'previous' already exists.
>>>>>>>>>> """
>>>>>>>>>>
>>>>>>>>>> If you have any suggestions for changes to the script, send
>>>>>>>> them my
>>>>>>>>>> way and I'll give it a try.
>>>>>>>>>>
>>>>>>>>>> Doug
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Jun 24, 2007, at 11:47 AM, Edward d'Auvergne wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> The simplest way to do this would be to use a while loop
>>>>>> using a
>>>>>>>>>>> modified version of the convergence() function which
>>>> returns
>>>>>>>> 1 or 0
>>>>>>>>>>> depending on whether the results have converged
>>>> (exactly like
>>>>>>>> your
>>>>>>>>>>> suggestion). I have added this looping ability to the
>>>>>>>>>>> full_analysis.py script in the relax repository (to both
>>>>>> the 1.2
>>>>>>>>>> and
>>>>>>>>>>> 1.3 lines). This is not activated by default though
>>>> and the
>>>>>>>>>> scripts
>>>>>>>>>>> in the repository are significantly different from that in
>>>>>> the
>>>>>>>>>> relax
>>>>>>>>>>> 1.2.10 version (all the variables which should be
>>>> modified by
>>>>>>>>>> the user
>>>>>>>>>>> have been shifted to the top of the script). Would you be
>>>>>>>> able to
>>>>>>>>>>> test if this automatic looping over all rounds of
>>>>>> optimisation
>>>>>>>>>> until
>>>>>>>>>>> convergence actually works? There could possibly be bugs
>>>>>>>> lurking
>>>>>>>>>>> there. Thanks.
>>>>>>>>>>>
>>>>>>>>>>> The problem that you encountered with the calling of the
>>>>>>>> __init__()
>>>>>>>>>>> function is because this function should not be called.
>>>>>>>> Using that
>>>>>>>>>>> type of approach, the looping should have been outside
>>>> of the
>>>>>>>> Main
>>>>>>>>>>> class to work.
>>>>>>>>>>>
>>>>>>>>>>> Cheers,
>>>>>>>>>>>
>>>>>>>>>>> Edward
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 6/16/07, Douglas Kojetin <[EMAIL PROTECTED]>
>>>>>> wrote:
>>>>>>>>>>>> Hi All,
>>>>>>>>>>>>
>>>>>>>>>>>> Is it possible to edit full_analysis.py so the
>>>>>> optimization of
>>>>>>>>>> MII to
>>>>>>>>>>>> MV (self.round > 0) is done automatically by looping
>>>> until
>>>>>>>>>>>> convergence?
>>>>>>>>>>>
>>>>>>>>>>> Do you mean that the script will automatically
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> I tried to do this by modifying the following in
>>>>>>>>>>>> convergence() [near the end]:
>>>>>>>>>>>>
>>>>>>>>>>>> """
>>>>>>>>>>>> # Final print out.
>>>>>>>>>>>> ##################
>>>>>>>>>>>>
>>>>>>>>>>>> print "\nConvergence:"
>>>>>>>>>>>> if chi2_converged and models_converged and
>>>>>>>>>> params_converged:
>>>>>>>>>>>> print " [ Yes ]"
>>>>>>>>>>>> return 1
>>>>>>>>>>>> else:
>>>>>>>>>>>> print " [ No ]"
>>>>>>>>>>>> return 0
>>>>>>>>>>>> """
>>>>>>>>>>>>
>>>>>>>>>>>> then modifying __init__(), at the end of the "elif
>>>>>>>> DIFF_MODEL ==
>>>>>>>>>>>> 'sphere' or DIFF_MODEL == 'prolate' or DIFF_MODEL ==
>>>>>>>> 'oblate' or
>>>>>>>>>>>> DIFF_MODEL == 'ellipsoid':" statement:
>>>>>>>>>>>>
>>>>>>>>>>>> """
>>>>>>>>>>>> # Test for convergence.
>>>>>>>>>>>> test=self.convergence(run=name)
>>>>>>>>>>>>
>>>>>>>>>>>> if test == 0:
>>>>>>>>>>>> __init__(self.relax)
>>>>>>>>>>>> #Main(self.relax)
>>>>>>>>>>>> """
>>>>>>>>>>>>
>>>>>>>>>>>> but it did not work properly. I think the problem has
>>>>>>>>>> something to
>>>>>>>>>>>> do with the call to __init__() or Main(). I'll see if
>>>> I can
>>>>>>>>>> dig up
>>>>>>>>>>>> the error reported by relax.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Doug
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> relax (http://nmr-relax.com)
>>>>>>>>>>>>
>>>>>>>>>>>> This is the relax-users mailing list
>>>>>>>>>>>> [email protected]
>>>>>>>>>>>>
>>>>>>>>>>>> To unsubscribe from this list, get a password
>>>>>>>>>>>> reminder, or change your subscription options,
>>>>>>>>>>>> visit the list information page at
>>>>>>>>>>>> https://mail.gna.org/listinfo/relax-users
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>
>>
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