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 <douglas.kojetin@xxxxxxxxx> 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 <douglas.kojetin@xxxxxxxxx> 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 <douglas.kojetin@xxxxxxxxx> 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 <douglas.kojetin@xxxxxxxxx>
>> 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
>> >> >> >> relax-users@xxxxxxx
>> >> >> >>
>> >> >> >> 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
>> >> >> >>
>> >> >>
>> >> >>
>> >>
>> >>
>>
>>
Re: looping the optimization in full_analysis.py