Hi,
If you can see the list of bugs, then you are at the main bug tracker
page. There should be a menu at the top which says 'Bugs'. Click on
this link and then select 'Submit'. You should be then able to submit
a report as described in the relax manual. If you have a Gna! account
already then don't forget to log in prior to submitting the report.
If you don't have a Gna! account, then don't bother setting one up.
This is not important at all!
Cheers,
Edward
On 8/29/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
> 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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