September 2022 - Ifeffit - millenia.cars.aps.anl.gov

Parameters for parent function in wavelet transform analysis
by Scott Calvin 09 Feb '23

09 Feb '23

Hi all, I’ve never actually tried wavelet transform analysis before, so I’m trying to understand it better, but there’s one aspect that’s puzzling me: The Morlet wavelet has two parameters, eta and sigma. Eta controls how fast it wiggles, and sigma how quickly the function dies out. (Essentially, it’s like the basis function for a Fourier transform multiplied by a Gaussian envelope.) In wavelet analysis we pick a parent function, which is often a Morlet wavelet with particular values of eta and sigma that we have chosen. We then create a set of child functions from the parent function by shifting and dilating the function in k-space. Each child function is then used as a basis function for a transform of chi(k) calculated by integrating over a range of k-values, much like what is done to calculate a Fourier transform. Since the Morlet wavelet is localized in k-space, and the child functions are shifted to focus on different regions of k-space, our wavelet transform produces plots which are a function of k. But since dilating the parent function by different amounts yields child functions with different frequencies, the plots are also a function of R. Therefore the result is a two-dimensional (k and R) contour plot. So far, so good. But what I’m wondering about is the effect of the initial choice of eta and sigma for the parent function. The dimensionless product of eta and sigma has a clear effect. If (eta)(sigma) is small, the parent function will not have very many oscillations of significant size; it it’s large, it will have a lot of oscillations. So if we want good resolution in R (and thus relatively poor resolution in k), we want a big value of (eta)(sigma). In the limit as (eta)(sigma) becomes arbitrarily large, we recover the Fourier transform. If we want good resolution in k, we use a small value for (eta)(sigma). In the limit as (eta)(sigma) becomes arbitrarily small we recover chi(k). That still makes sense to me! But what difference do sigma and eta make individually? In other words, how is sigma = 0.5 and eta = 10.0 different from sigma = 1.0 and eta = 5.0? Since we end up creating child functions that dilate the parent function anyway, I can’t see that it should have any effect at all. And if those two parameters don’t make an independent effect, why do we pretend there are two independent-looking parameters? I’ve seen at least one early paper that suggests choosing eta so that it’s close to the path length you’re most interested in probing, but I can’t see how that actually makes any difference, given the dilation. I expect there’s a good chance I’m missing something obvious, or have a fundamental misunderstanding of part of the process, and look forward to learning more! Best, Scott Calvin Lehman College of the City University of New York

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Co2P spectrum
by Christian Wittee Lopes 21 Sep '22

21 Sep '22

Dear XAFS community, Does anyone have a spectrum of Co2P sample or standard? Thank you in advance. Best, Christian Wittee Lopes -- Christian Wittee Lopes Visiting Researcher - ANP/FINEP - PRH 50.1 Institute of Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS) chriswittee(a)gmail.com LinkedIn <https://www.linkedin.com/in/christian-wittee-lopes-561855219/> | ORCID <https://orcid.org/my-orcid?orcid=0000-0001-8420-1958> | Lattes <http://lattes.cnpq.br/4953371870936050>

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Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 12
by Dien.Li＠srnl.doe.gov 15 Sep '22

15 Sep '22

HI, Matt Attached please find the raw data in Athena, could you please also look at this as well as the Artemis file. Due to limited by L1,2 edge, the EXAFS data may just go up to K 9. Anyhow, thank you so much for your any directions. Dien Li -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, September 15, 2022 2:09 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 12 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11 (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Sep 2022 18:04:42 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11 Message-ID: <DM8PR09MB6232238674FEDB80096B6498C4499(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Please see this attachment. Thank you so much. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, September 15, 2022 1:42 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Sep 2022 17:41:19 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Message-ID: <DM8PR09MB6232C4DEDD6CCE2CF3984655C4499(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, Matt and EXAFS experts Thank you so much. Our sample is porous silica + PO4 ligand on surface/pore, then react with LaNO3 in solution. The model is that La is bonding with PO4 through both mono- (corner-sharing) and di-dentate (edge sharing) modes. Please see the attachment. The first three fits in history are fits with increasing paths, with fixed CN for the La-P11 and La-P14 path, the ss parameters are reasonable, but to fix CN at 3 for La-P14 is unreasonable, which requires La to bind with three different PO4 groups. The last three fits are fits with increasing paths, in which CN was fitted, the fitted parameters are reasonable, EXCEPT for the negative ss parameters for the path La-P11 (edge sharing) and La-P14 (corner sharing). By the way, the length for La-P14 is +0.3 A, it is large, but not completely unreasonable, because the bond distances of La-O polyhedron may change from 2.4 to 3.1 A. Is it possible to constrain ss parameter? If so, how to set up this constrain? Thank you so much for your further instruction. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, September 14, 2022 4:03 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch: Fitting error of the objective/model function (Matt Newville) 2. Re: Help for EXAFS fitting (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Sep 2022 13:28:38 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch: Fitting error of the objective/model function Message-ID: <CA+7ESbodGVSNHuzTHZoeb3iL-jUsWFpeYM7TqLQPkkSyMyE2DA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Fan, Sorry for the trouble. That seems like a strange error to me - I don't see why changing those expressions for E0s (even if they are "slightly complicated"!) should generate NaNs or Infinities. I don't think I've seen that happen with "feffit" fittings. Can you send me a Larch Session File with this fit in it? One suggestion is to place bounds (say +/- 20 eV) on those Parameters, say pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr', min=-20, max=20) But I'm not certain whether that would solve this problem. On Wed, Sep 14, 2022 at 7:53 AM <dxfan(a)post.kek.jp> wrote: > Dear All > > > > I am doing Temperature-dependent EXAFS experiment with a lot of data. > > > > Usually, we do these kinds of data fitting by several steps, like below: > > First, put every parameter free, and obtain the averaged value of amp. > > Second, set the amp to the averaged value, put other parameters free, and > then obtain the averaged value of del_e0. > > Third, set the amp and del_e0 to the averaged value, and fit again. > > > > In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). > > To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as > suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 > (1995): 151-153. > > The fitting parameters of Cubic model is this: > > setattr(pars, f'alpha', param(0, vary=True)) > > setattr(pars, f'amp', param(0, vary=True)) > > setattr(pars, f'del_e0_O', param(0, vary=True)) > > setattr(pars, f'del_e0_Sr', param(0, vary=True)) > > setattr(pars, f'del_e0_Ti', param(0, vary=True)) > > setattr(pars, f'sig2_O', param(.002, vary=True)) > > setattr(pars, f'sig2_Sr', param(.002, vary=True)) > > setattr(pars, f'sig2_Ti', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr1', param(.002, vary=True)) > > setattr(pars, f'sig2_p', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr2', param(.002, vary=True)) > > > > #del_e0 for each path > > pars.del_e0_1=param(expr='del_e0_O') > > pars.del_e0_2=param(expr='del_e0_O') > > pars.del_e0_3=param(expr='del_e0_Sr') > > pars.del_e0_4=param(expr='del_e0_Ti') > > pars.del_e0_5=param(expr='del_e0_O') > > pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') > > pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') > > > > In the first step, the fitting is fine, I obtained the averaged amp. > > However, in the second step, when I set amp to the averaged value, Error > happens for ?some? of the data. > > When I use different averaged amp value, the data that happens error is > different. > > The error is: > > Traceback (most recent call last): > > File "STO16_C_2.py", line 250, in <module> > > out = feffit(pars, dset) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line > 557, in feffit > > result = fit.leastsq() > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 1689, in leastsq > > lsout = scipy_leastsq(self.__residual, variables, **lskws) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", > line 423, in leastsq > > retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 601, in __residual > > return _nan_policy(np.asarray(out).ravel(), > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 2436, in _nan_policy > > raise ValueError(msg) > > ValueError: NaN values detected in your input data or the output of your > objective/model function - fitting algorithms cannot handle this! Please > read > https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-w… > for more information. > > > > I don?t know what happened, can somebody help me figure this out? > > > > PS: when I use only one del_e0 for every path, no such error happens. > > > > Best regards > > Fan > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11
by Dien.Li＠srnl.doe.gov 15 Sep '22

15 Sep '22

Please see this attachment. Thank you so much. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, September 15, 2022 1:42 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 11 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 15 Sep 2022 17:41:19 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Message-ID: <DM8PR09MB6232C4DEDD6CCE2CF3984655C4499(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, Matt and EXAFS experts Thank you so much. Our sample is porous silica + PO4 ligand on surface/pore, then react with LaNO3 in solution. The model is that La is bonding with PO4 through both mono- (corner-sharing) and di-dentate (edge sharing) modes. Please see the attachment. The first three fits in history are fits with increasing paths, with fixed CN for the La-P11 and La-P14 path, the ss parameters are reasonable, but to fix CN at 3 for La-P14 is unreasonable, which requires La to bind with three different PO4 groups. The last three fits are fits with increasing paths, in which CN was fitted, the fitted parameters are reasonable, EXCEPT for the negative ss parameters for the path La-P11 (edge sharing) and La-P14 (corner sharing). By the way, the length for La-P14 is +0.3 A, it is large, but not completely unreasonable, because the bond distances of La-O polyhedron may change from 2.4 to 3.1 A. Is it possible to constrain ss parameter? If so, how to set up this constrain? Thank you so much for your further instruction. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, September 14, 2022 4:03 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch: Fitting error of the objective/model function (Matt Newville) 2. Re: Help for EXAFS fitting (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Sep 2022 13:28:38 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch: Fitting error of the objective/model function Message-ID: <CA+7ESbodGVSNHuzTHZoeb3iL-jUsWFpeYM7TqLQPkkSyMyE2DA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Fan, Sorry for the trouble. That seems like a strange error to me - I don't see why changing those expressions for E0s (even if they are "slightly complicated"!) should generate NaNs or Infinities. I don't think I've seen that happen with "feffit" fittings. Can you send me a Larch Session File with this fit in it? One suggestion is to place bounds (say +/- 20 eV) on those Parameters, say pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr', min=-20, max=20) But I'm not certain whether that would solve this problem. On Wed, Sep 14, 2022 at 7:53 AM <dxfan(a)post.kek.jp> wrote: > Dear All > > > > I am doing Temperature-dependent EXAFS experiment with a lot of data. > > > > Usually, we do these kinds of data fitting by several steps, like below: > > First, put every parameter free, and obtain the averaged value of amp. > > Second, set the amp to the averaged value, put other parameters free, and > then obtain the averaged value of del_e0. > > Third, set the amp and del_e0 to the averaged value, and fit again. > > > > In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). > > To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as > suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 > (1995): 151-153. > > The fitting parameters of Cubic model is this: > > setattr(pars, f'alpha', param(0, vary=True)) > > setattr(pars, f'amp', param(0, vary=True)) > > setattr(pars, f'del_e0_O', param(0, vary=True)) > > setattr(pars, f'del_e0_Sr', param(0, vary=True)) > > setattr(pars, f'del_e0_Ti', param(0, vary=True)) > > setattr(pars, f'sig2_O', param(.002, vary=True)) > > setattr(pars, f'sig2_Sr', param(.002, vary=True)) > > setattr(pars, f'sig2_Ti', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr1', param(.002, vary=True)) > > setattr(pars, f'sig2_p', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr2', param(.002, vary=True)) > > > > #del_e0 for each path > > pars.del_e0_1=param(expr='del_e0_O') > > pars.del_e0_2=param(expr='del_e0_O') > > pars.del_e0_3=param(expr='del_e0_Sr') > > pars.del_e0_4=param(expr='del_e0_Ti') > > pars.del_e0_5=param(expr='del_e0_O') > > pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') > > pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') > > > > In the first step, the fitting is fine, I obtained the averaged amp. > > However, in the second step, when I set amp to the averaged value, Error > happens for ?some? of the data. > > When I use different averaged amp value, the data that happens error is > different. > > The error is: > > Traceback (most recent call last): > > File "STO16_C_2.py", line 250, in <module> > > out = feffit(pars, dset) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line > 557, in feffit > > result = fit.leastsq() > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 1689, in leastsq > > lsout = scipy_leastsq(self.__residual, variables, **lskws) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", > line 423, in leastsq > > retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 601, in __residual > > return _nan_policy(np.asarray(out).ravel(), > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 2436, in _nan_policy > > raise ValueError(msg) > > ValueError: NaN values detected in your input data or the output of your > objective/model function - fitting algorithms cannot handle this! Please > read > https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-w… > for more information. > > > > I don?t know what happened, can somebody help me figure this out? > > > > PS: when I use only one del_e0 for every path, no such error happens. > > > > Best regards > > Fan > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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Re: [Ifeffit] [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10
by Dien.Li＠srnl.doe.gov 15 Sep '22

15 Sep '22

Hi, Matt and EXAFS experts Thank you so much. Our sample is porous silica + PO4 ligand on surface/pore, then react with LaNO3 in solution. The model is that La is bonding with PO4 through both mono- (corner-sharing) and di-dentate (edge sharing) modes. Please see the attachment. The first three fits in history are fits with increasing paths, with fixed CN for the La-P11 and La-P14 path, the ss parameters are reasonable, but to fix CN at 3 for La-P14 is unreasonable, which requires La to bind with three different PO4 groups. The last three fits are fits with increasing paths, in which CN was fitted, the fitted parameters are reasonable, EXCEPT for the negative ss parameters for the path La-P11 (edge sharing) and La-P14 (corner sharing). By the way, the length for La-P14 is +0.3 A, it is large, but not completely unreasonable, because the bond distances of La-O polyhedron may change from 2.4 to 3.1 A. Is it possible to constrain ss parameter? If so, how to set up this constrain? Thank you so much for your further instruction. Dien -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, September 14, 2022 4:03 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 10 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch: Fitting error of the objective/model function (Matt Newville) 2. Re: Help for EXAFS fitting (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Sep 2022 13:28:38 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch: Fitting error of the objective/model function Message-ID: <CA+7ESbodGVSNHuzTHZoeb3iL-jUsWFpeYM7TqLQPkkSyMyE2DA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Fan, Sorry for the trouble. That seems like a strange error to me - I don't see why changing those expressions for E0s (even if they are "slightly complicated"!) should generate NaNs or Infinities. I don't think I've seen that happen with "feffit" fittings. Can you send me a Larch Session File with this fit in it? One suggestion is to place bounds (say +/- 20 eV) on those Parameters, say pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr', min=-20, max=20) But I'm not certain whether that would solve this problem. On Wed, Sep 14, 2022 at 7:53 AM <dxfan(a)post.kek.jp> wrote: > Dear All > > > > I am doing Temperature-dependent EXAFS experiment with a lot of data. > > > > Usually, we do these kinds of data fitting by several steps, like below: > > First, put every parameter free, and obtain the averaged value of amp. > > Second, set the amp to the averaged value, put other parameters free, and > then obtain the averaged value of del_e0. > > Third, set the amp and del_e0 to the averaged value, and fit again. > > > > In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). > > To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as > suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 > (1995): 151-153. > > The fitting parameters of Cubic model is this: > > setattr(pars, f'alpha', param(0, vary=True)) > > setattr(pars, f'amp', param(0, vary=True)) > > setattr(pars, f'del_e0_O', param(0, vary=True)) > > setattr(pars, f'del_e0_Sr', param(0, vary=True)) > > setattr(pars, f'del_e0_Ti', param(0, vary=True)) > > setattr(pars, f'sig2_O', param(.002, vary=True)) > > setattr(pars, f'sig2_Sr', param(.002, vary=True)) > > setattr(pars, f'sig2_Ti', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr1', param(.002, vary=True)) > > setattr(pars, f'sig2_p', param(.002, vary=True)) > > setattr(pars, f'sig2_Tr2', param(.002, vary=True)) > > > > #del_e0 for each path > > pars.del_e0_1=param(expr='del_e0_O') > > pars.del_e0_2=param(expr='del_e0_O') > > pars.del_e0_3=param(expr='del_e0_Sr') > > pars.del_e0_4=param(expr='del_e0_Ti') > > pars.del_e0_5=param(expr='del_e0_O') > > pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') > > pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') > > pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') > > > > In the first step, the fitting is fine, I obtained the averaged amp. > > However, in the second step, when I set amp to the averaged value, Error > happens for ?some? of the data. > > When I use different averaged amp value, the data that happens error is > different. > > The error is: > > Traceback (most recent call last): > > File "STO16_C_2.py", line 250, in <module> > > out = feffit(pars, dset) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line > 557, in feffit > > result = fit.leastsq() > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 1689, in leastsq > > lsout = scipy_leastsq(self.__residual, variables, **lskws) > > File > "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", > line 423, in leastsq > > retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 601, in __residual > > return _nan_policy(np.asarray(out).ravel(), > > File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", > line 2436, in _nan_policy > > raise ValueError(msg) > > ValueError: NaN values detected in your input data or the output of your > objective/model function - fitting algorithms cannot handle this! Please > read > https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-w… > for more information. > > > > I don?t know what happened, can somebody help me figure this out? > > > > PS: when I use only one del_e0 for every path, no such error happens. > > > > Best regards > > Fan > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

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Help for EXAFS fitting
by Dien.Li＠srnl.doe.gov 14 Sep '22

14 Sep '22

Hi, Matt and Carlo and other EXAFS experts Attached please find a fpj data file. The basic system is silica + PO4 ligand on surfaces, which was used for adsorption of La. We collected La L3-edge EAXFS data and did this fitting. I used two models of La binding as monodentate and bidentate. I saw the negative ss parameter. I saw this in some of my other EXAFS data fitting samples as well. I have two questions for help: 1. What might cause the negative ss parameters and how I may improve this, is this caused by incorrect structure models 2. If we can do some "stress" test to make sure the fitting is valid and meaningful. Please you can help look at and play this data set and direct me on how to do this correctly, thank you so much. Dien Li Savannah River National Laboratory

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Larch: Fitting error of the objective/model function
by dxfan＠post.kek.jp 14 Sep '22

14 Sep '22

Dear All I am doing Temperature-dependent EXAFS experiment with a lot of data. Usually, we do these kinds of data fitting by several steps, like below: First, put every parameter free, and obtain the averaged value of amp. Second, set the amp to the averaged value, put other parameters free, and then obtain the averaged value of del_e0. Third, set the amp and del_e0 to the averaged value, and fit again. In my case, my sample is perovskite structure (Ti K-edge of SrTiO3). To increase the fitting accuracy, I use three del_e0 for O, Ti, Sr as suggested in paper: Haskel, D., et al. Physica B: Condensed Matter 208 (1995): 151-153. The fitting parameters of Cubic model is this: setattr(pars, f'alpha', param(0, vary=True)) setattr(pars, f'amp', param(0, vary=True)) setattr(pars, f'del_e0_O', param(0, vary=True)) setattr(pars, f'del_e0_Sr', param(0, vary=True)) setattr(pars, f'del_e0_Ti', param(0, vary=True)) setattr(pars, f'sig2_O', param(.002, vary=True)) setattr(pars, f'sig2_Sr', param(.002, vary=True)) setattr(pars, f'sig2_Ti', param(.002, vary=True)) setattr(pars, f'sig2_Tr1', param(.002, vary=True)) setattr(pars, f'sig2_p', param(.002, vary=True)) setattr(pars, f'sig2_Tr2', param(.002, vary=True)) #del_e0 for each path pars.del_e0_1=param(expr='del_e0_O') pars.del_e0_2=param(expr='del_e0_O') pars.del_e0_3=param(expr='del_e0_Sr') pars.del_e0_4=param(expr='del_e0_Ti') pars.del_e0_5=param(expr='del_e0_O') pars.del_e0_6=param(expr='0.5*del_e0_O+0.5*del_e0_Ti') pars.del_e0_7=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_8=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_9=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_10=param(expr='(2*del_e0_O+del_e0_Ti)/3') pars.del_e0_11=param(expr='0.5*del_e0_O+0.5*del_e0_Sr') In the first step, the fitting is fine, I obtained the averaged amp. However, in the second step, when I set amp to the averaged value, Error happens for "some" of the data. When I use different averaged amp value, the data that happens error is different. The error is: Traceback (most recent call last): File "STO16_C_2.py", line 250, in <module> out = feffit(pars, dset) File "D:\anaconda3\envs\xraylarch\lib\site-packages\larch\xafs\feffit.py", line 557, in feffit result = fit.leastsq() File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 1689, in leastsq lsout = scipy_leastsq(self.__residual, variables, **lskws) File "D:\anaconda3\envs\xraylarch\lib\site-packages\scipy\optimize\minpack.py", line 423, in leastsq retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol, File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 601, in __residual return _nan_policy(np.asarray(out).ravel(), File "D:\anaconda3\envs\xraylarch\lib\site-packages\lmfit\minimizer.py", line 2436, in _nan_policy raise ValueError(msg) ValueError: NaN values detected in your input data or the output of your objective/model function - fitting algorithms cannot handle this! Please read https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-wh at-can-i-do for more information. I don't know what happened, can somebody help me figure this out? PS: when I use only one del_e0 for every path, no such error happens. Best regards Fan

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FW: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 3
by Dien.Li＠srnl.doe.gov 13 Sep '22

13 Sep '22

Hi Matt and all I sent this and an attachment before. I hope you can help figure out why I often get negative ss parameter from fitting? For this specific example, if I fit the CN, it yields CN of ~1, the monodendate structure is reasonable, but I got negative ss. However, if I fixed CN at 3, the ss is reasonable, but it needs to bind with three different PO4 on the surfaces, this is interesting but I am uncertain. Thank you so much for your any advice. Dien Li Savannah River National Laboratory -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Friday, September 9, 2022 12:32 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [EXTERNAL] Ifeffit Digest, Vol 235, Issue 3 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Help for EXAFS fitting (Dien.Li(a)srnl.doe.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 9 Sep 2022 16:31:38 +0000 From: "Dien.Li(a)srnl.doe.gov" <Dien.Li(a)srnl.doe.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help for EXAFS fitting Message-ID: <DM8PR09MB62323624C91F0A43DC7CB6D1C4439(a)DM8PR09MB6232.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, Matt and Carlo and other EXAFS experts Attached please find a fpj data file. The basic system is silica + PO4 ligand on surfaces, which was used for adsorption of La. We collected La L3-edge EAXFS data and did this fitting. I used two models of La binding as monodentate and bidentate. I saw the negative ss parameter. I saw this in some of my other EXAFS data fitting samples as well. I have two questions for help: 1. What might cause the negative ss parameters and how I may improve this, is this caused by incorrect structure models 2. If we can do some "stress" test to make sure the fitting is valid and meaningful. Please you can help look at and play this data set and direct me on how to do this correctly, thank you so much. Dien Li Savannah River National Laboratory

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Fitting multiple spectra simultaneously with Larch
by Van Stappen, Casey M 12 Sep '22

12 Sep '22

Dear Ifeffit team, I’d like to fit multiple EXAFS spectra simultaneously in Larch using several common parameters/relative restraints, but have not found a way to do so (yet). I’ve gone through Dr. Matt Newville’s youtube tutorials (generally very helpful), but this topic doesn’t seem to have been covered. Any suggestions? Thanks! Best, Casey Van Stappen ------------------------------------------------------------------------ Dr. Casey Van Stappen University of Texas at Austin Robert A. Welch Hall, 4.318 2350 Speedway Austin, TX 78705 USA Phone: +1 (512) 775-2658 E-mail: casey.vanstappen(a)austin.utexas.edu

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Icon Resolution issue in 14 inch
by Mohamad Numan 12 Sep '22

12 Sep '22

Dear Developers, I am using the Demeter package on my windows 11 laptop. I am facing some resolution issues in the icons of Athena and Artemis. The icons look pretty dull and very distressing to the eyes. Attaching a screenshot for your reference. I will be happy to hear an update from you. Thanks & Regards Mohamad Numan Ph.D. Student, IACS

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