[Ifeffit] Larch-0.9.24 with Python2
Matt Newville
newville at cars.uchicago.edu
Wed Nov 5 10:28:42 CST 2014
Hi Matthias,
Yes, that looks correct. I also fixed the code so that it can work
with scipy 0.11 and later. I will work on changing the installation
to check for minimal version numbers.
On Wed, Nov 5, 2014 at 10:03 AM, Matthias Filez <Matthias.Filez at ugent.be> wrote:
> Dear Matt,
>
> We have upgraded to scipy 0.14.0 and this is what I get now when I run the script:
>
> Read ASCII File: <Group ascii_file examples/xafsdata/cu_rt01.xmu>
> ['array_labels', 'attrs', 'column_labels', 'data', 'energy', 'filename', 'header', 'i0', 'mu']
> After pre-edge:
> ['array_labels', 'attrs', 'column_labels', 'data', 'dmude', 'e0', 'edge_step', 'energy', 'filename', 'flat', 'header', 'i0', 'mu', 'nnorm', 'norm', 'norm1', 'norm2', 'norm_c0', 'norm_c1', 'norm_c2', 'norm_c3', 'nvict', 'post_edge', 'pre1', 'pre2', 'pre_edge', 'pre_offset', 'pre_slope']
> After autobk:
> ['array_labels', 'attrs', 'autobk_details', 'bkg', 'chi', 'chie', 'column_labels', 'data', 'dmude', 'e0', 'edge_step', 'energy', 'filename', 'flat', 'header', 'i0', 'k', 'mu', 'nnorm', 'norm', 'norm1', 'norm2', 'norm_c0', 'norm_c1', 'norm_c2', 'norm_c3', 'nvict', 'post_edge', 'pre1', 'pre2', 'pre_edge', 'pre_offset', 'pre_slope']
> [ 5.22014125e-01 4.68863165e-01 4.23387732e-01 3.84601353e-01
> 3.51517555e-01 3.23149862e-01 2.98511802e-01 2.76616899e-01
> 2.56478680e-01 2.37110672e-01 2.17526399e-01 1.96774248e-01
> 1.74202338e-01 1.49312809e-01 1.21645288e-01 9.07843838e-02
> 5.63993015e-02 1.85571728e-02 -2.03243717e-02 -5.75444687e-02
> -9.14850299e-02 -1.18154030e-01 -1.36108084e-01 -1.45468821e-01
> -1.47073697e-01 -1.50934997e-01 -1.54219769e-01 -1.56582731e-01
> -1.55007074e-01 -1.50082523e-01 -1.35737843e-01 -1.13771275e-01
> -8.25087559e-02 -4.62194044e-02 9.36626084e-04 4.42260206e-02
> 8.89877045e-02 1.27496716e-01 1.50717679e-01 1.52846156e-01
> 1.34118361e-01 1.02181582e-01 6.49568133e-02 3.22399885e-02
> 6.46113335e-03 -6.98123272e-03 -4.09343210e-03 1.83744265e-02
> 5.17624756e-02 8.65303295e-02 9.62396887e-02 7.69122752e-02
> 4.26727610e-02 7.49257701e-03 -1.81363351e-02 -3.96258643e-02
> -6.15635768e-02 -7.97519898e-02 -8.77310666e-02 -8.66687826e-02
> -8.15835644e-02 -7.32081259e-02 -6.02706951e-02 -4.24399368e-02
> -2.10497270e-02 5.08304985e-04 2.06241750e-02 3.91292189e-02
> 5.77145097e-02 7.15135419e-02 7.45516578e-02 6.38238728e-02
> 4.35580179e-02 2.02712305e-02 -4.46692821e-03 -2.41242981e-02
> -3.66799760e-02 -4.33587597e-02 -4.46705006e-02 -4.05827015e-02
> -3.30819589e-02 -2.70683602e-02 -2.59245042e-02 -2.90609922e-02
> -2.95609304e-02 -2.38858773e-02 -1.50880484e-02 -9.19969595e-03
> -8.33417313e-03 -7.93651142e-03 -3.05461694e-03 7.13301998e-03
> 1.82026094e-02 2.66824286e-02 3.30622138e-02 4.00340894e-02
> 4.90608443e-02 6.02648286e-02 7.00942393e-02 7.31115967e-02
> 6.75011510e-02 5.35389324e-02 3.48700770e-02 1.69745209e-02
> 1.72454146e-03 -1.20611024e-02 -2.27968218e-02 -2.76882865e-02
> -3.34147477e-02 -4.57197498e-02 -6.05078349e-02 -7.24893051e-02
> -7.70420692e-02 -7.26272010e-02 -6.11005811e-02 -4.55265529e-02
> -3.00707518e-02 -1.68398434e-02 -7.56863503e-03 -3.68954861e-03
> -3.43061853e-03 -3.06004774e-03 2.55862832e-03 1.71655046e-02
> 4.20159830e-02 6.75693679e-02 8.23617564e-02 8.56835153e-02
> 8.13427954e-02 7.37373718e-02 6.28271473e-02 4.67098172e-02
> 2.60081154e-02 2.82900268e-03 -2.26376028e-02 -4.78755329e-02
> -6.99617777e-02 -8.35343661e-02 -8.44844001e-02 -7.18198681e-02
> -5.08207746e-02 -2.73111366e-02 -8.63745041e-03 2.79708853e-03
> 8.16043004e-03 7.92863690e-03 5.11229300e-03 3.49449875e-03
> 3.87115590e-03 2.85022886e-03 -1.51356430e-04 -2.71617609e-03
> 7.99093220e-04 1.28770189e-02 2.97511624e-02 4.23481503e-02
> 4.61655216e-02 4.49878002e-02 4.16959342e-02 3.51358326e-02
> 2.30338982e-02 7.71870254e-03 -6.49914172e-03 -1.95979278e-02
> -2.91442689e-02 -3.34105565e-02 -3.22190201e-02 -2.83765449e-02
> -2.52463396e-02 -2.32145504e-02 -2.10720714e-02 -1.84390441e-02
> -1.47681365e-02 -1.01599056e-02 -4.95494275e-03 -3.16814647e-04
> 4.11336090e-03 7.87342088e-03 1.02960668e-02 1.29127543e-02
> 1.55124154e-02 1.78762099e-02 1.96778316e-02 2.12245457e-02
> 1.92318426e-02 1.52708347e-02 1.00532965e-02 3.93556366e-03
> -2.00861226e-04 -3.92225374e-03 -5.30239979e-03 -4.82306995e-03
> -4.47717083e-03 -6.19650760e-03 -1.00134814e-02 -1.42494639e-02
> -1.54978616e-02 -1.35397676e-02 -1.13623819e-02 -9.41262041e-03
> -7.58206760e-03 -5.06296458e-03 -2.48585060e-03 -4.00416183e-04
> 1.87050218e-03 3.62541073e-03 6.07766518e-03 7.21786016e-03
> 8.77502787e-03 9.95603332e-03 1.03558434e-02 9.73912155e-03
> 7.63280475e-03 5.35276100e-03 2.20653640e-03 -9.84994816e-05
> -1.37884146e-03 -1.12248811e-03 -8.47538380e-04 -6.26076861e-04
> -5.87386385e-04 -8.97700051e-04 -2.24337187e-03 -3.92268068e-03
> -4.69266928e-03 -4.80954070e-03 -4.76843389e-03 -5.05903965e-03
> -4.98518712e-03 -4.01197097e-03 -3.00891314e-03 -1.46903844e-03
> 3.53683094e-05 1.59446778e-03 3.12390382e-03 4.76890345e-03
> 5.59846498e-03 5.63295324e-03 5.09371953e-03 3.49773838e-03
> 1.79393075e-03 4.66522098e-04 -1.52569918e-04 -7.15600312e-04
> -9.34996770e-04 -1.13022725e-03 -8.06959189e-04 -8.41610248e-04
> -1.14800547e-03 -1.28965094e-03 -1.24884820e-03 -1.44400047e-03
> -2.04579669e-03 -2.17836113e-03 -2.08363191e-03 -1.81376431e-03
> -1.41088949e-03 -8.75421280e-04 -4.54586404e-04 8.29150513e-05
> 6.78654789e-04 1.04647304e-03 1.59651631e-03 1.75850262e-03
> 1.71743579e-03 1.72121567e-03 1.67674127e-03 1.26223831e-03
> 1.09938217e-03 6.79160864e-04 2.74810773e-04 2.51510300e-04
> -1.81502999e-05 -2.49024384e-04 -6.74164538e-04 -7.71579948e-04
> -8.51008782e-04 -7.46019036e-04 -7.91883682e-04 -1.02615516e-03
> -1.27411149e-03 -1.14412599e-03 -1.10888173e-03 -1.24436555e-03
> -5.70511174e-04 -2.67727213e-04 -5.10544602e-05 -7.44585105e-05
> 3.32434599e-04 6.16025534e-04 4.60911522e-04 4.52806510e-04
> 5.17149268e-04 8.86203824e-04 8.06249536e-04 7.62364216e-04
> 6.89168671e-04 6.48290053e-04 5.50507466e-04 5.00420100e-04
> 4.91031520e-04 1.90660816e-04 1.42033309e-04 7.11215401e-05
> -4.54097265e-05 -3.46351385e-05 -3.10631849e-05 -9.24403309e-05
> -1.47993095e-04 -2.10994331e-04 -2.82751339e-04 -2.75720314e-04
> -2.00919076e-04 -1.47717375e-04 -6.51029766e-05 -3.22735306e-05
> -1.15212367e-04 -1.80394605e-04 -1.91644236e-04 -2.09229079e-04
> -2.87571537e-04 -2.91770309e-04 -3.03029185e-04 -3.65472126e-04
> -2.40079196e-04 -2.57480565e-04 -2.13293922e-04 -2.23895882e-04
> -2.05898811e-04 -2.51361361e-04 -2.15835935e-04 -3.26122661e-04
> -3.60578368e-04 -3.48674339e-04 -2.51265522e-04 -9.42783246e-05
> 1.05407722e-05 1.35324496e-04 1.32768084e-04 2.38054795e-04
> 2.37051097e-04 2.60387811e-04 3.17263146e-04 4.05326800e-04
> 5.37145496e-04 6.98105861e-04 8.02577998e-04 8.44690107e-04
> 8.42747086e-04 9.18552333e-04]
>
> It seems to work! For certainty, is this consistent with what you obtain?
>
> Many thanks for your help,
> Matthias
>
> ________________________________________
> Van: ifeffit-bounces at millenia.cars.aps.anl.gov [ifeffit-bounces at millenia.cars.aps.anl.gov] namens Matt Newville [newville at cars.uchicago.edu]
> Verzonden: woensdag 5 november 2014 14:23
> Aan: XAFS Analysis using Ifeffit
> Onderwerp: Re: [Ifeffit] Larch-0.9.24 with Python2
>
> Hi Matthias,
>
> OK, having scipy 0.9.0 is almost certainly the problem. I'm not
> entirely sure how far back in scipy versions would be supported, but I
> believe that version 0.12 will work, and am certain that 0.13 will
> work. In fact, I'm pretty sure that version 0.13 is made several
> changes to the minimization package. I believe I may be relying on
> some of those changes for being able to use minimization method other
> than the default Levenberg-Marquardt least-squares algorithm (not
> that this is recommended for autobk() or feffit(), but it can
> sometimes be useful in other fitting problems).
>
> The version of numpy you have should be not be a problem.
>
> I'll set the required versions of scipy to 0.13 and numpy to 1.5.
>
>
> On Wed, Nov 5, 2014 at 1:39 AM, Matthias Filez <Matthias.Filez at ugent.be> wrote:
>> Dear Matt, Bruce,
>>
>> I verified the scipy version: 0.9.0.
>> The installed numpy version is 1.6.1.
>>
>> What versions are required?
>>
>> Thanks a lot!
>>
>> Matthias
>> ________________________________________
>> Van: ifeffit-bounces at millenia.cars.aps.anl.gov [ifeffit-bounces at millenia.cars.aps.anl.gov] namens Matt Newville [newville at cars.uchicago.edu]
>> Verzonden: dinsdag 4 november 2014 18:59
>> Aan: XAFS Analysis using Ifeffit
>> Onderwerp: Re: [Ifeffit] Larch-0.9.24 with Python2
>>
>> Hi Matthias,
>>
>> Hmm, looking at this more closely, my guess is that you're using an
>> older version scipy than I am. Can you verify what scipy version you
>> have?
>>
>> That is, I do see that the return value for this call did change
>> sometime in the past 2 years, though I'm not sure exactly which
>> version. I'll try to commit a patch to allow this older version to
>> github today. But, I suspect that older scipy versions might cause
>> other problems.
>>
>> I should probably put in a more exact check for required scipy version.
>>
>> --Matt
>> _______________________________________________
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>
>
> --Matt
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--Matt
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