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

Re: [Ifeffit] XANES temperature estimation (Robert Gordon)
by Gabriele Garofalo 21 Nov '22

21 Nov '22

Hi Gordon, I have just one spectrum per sample, all taken at different T (unknown, due to technical problems) and P (known). I'd like to find T and using an EoS is not a viable option. I was thinking that maybe, assuming that the Debye-Waller term is explained only by thermal disorder, the Debye temperature is P independent, and there are no structural or electronic transformations, I could retrieve T by fitting the Debye-Waller term and using the reference spectra. Is this possible? Best regards Gabriele > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 21 Nov 2022 16:16:50 +0100 > From: Gabriele GAROFALO <gabriele.garofalo(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] XANES temperature estimation > Message-ID: <0ce690cc-ca47-5507-76b3-848bba8d7db8(a)esrf.fr> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi everyone, > > I'd like to estimate the temperature of some samples from some XANES > spectra, is there a way to do that? I couldn't find an answer in the > mailing list archive. > > Thanks! > > > > ------------------------------ > > Message: 2 > Date: Mon, 21 Nov 2022 10:23:10 -0500 > From: Anatoly Frenkel <anatoly.frenkel(a)stonybrook.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XANES temperature estimation > Message-ID: <B288F5DB-33C3-4F6C-A4A3-D41D713157B1(a)stonybrook.edu> > Content-Type: text/plain; charset=utf-8 > > Only evaporation temperature, when XANES spectrum disappears?:) > > Anatoly > >> On Nov 21, 2022, at 10:20 AM, Gabriele GAROFALO >> <gabriele.garofalo(a)esrf.fr> wrote: >> >> ?Hi everyone, >> >> I'd like to estimate the temperature of some samples from some XANES >> spectra, is there a way to do that? I couldn't find an answer in the >> mailing list archive. >> >> Thanks! >> >> _______________________________________________ >> 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 > > > > ------------------------------ > > Message: 3 > Date: Mon, 21 Nov 2022 09:13:19 -0800 > From: Robert Gordon <ragordon(a)alumni.sfu.ca> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XANES temperature estimation > Message-ID: > <CA+FiM0EvUpbWH2=WzqjKTRMwZsw2w-DSgJ-2J9XgAVAScbiSTg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Gabriele, > > To qualify Anatoly's cheerful, pre-morning coffee response, if your > samples > are part of a sequence of measurements > of a material whose XANES has been measured at different temperatures, > and > said XANES does have some changes > owing to changes in physical or electronic behavior with temperature > (i.e. > a phase transition), then you could estimate > where your samples fit within that determined behavior. > > Are you familiar with how temperature dependence manifests in a typical > XAFS measurement? > ...through the Debye-Waller term..the effects of which become less > pronounced at lower k... > > Temperature is more typically a controlled parameter during > measurements. > > So no, not really...unless there is a known behavior for comparison. > > -R.

2 1

XANES temperature estimation
by Gabriele GAROFALO 21 Nov '22

21 Nov '22

Hi everyone, I'd like to estimate the temperature of some samples from some XANES spectra, is there a way to do that? I couldn't find an answer in the mailing list archive. Thanks!

3 2

How to normalize tens of thousands of XAS data?
by 张驰 15 Nov '22

15 Nov '22

How to normalize tens of thousands of XAS data? I measured a series of the spectra of sample over time by in situ XAS, the results contained tens of thousands of sets of XAS data, and it was impossible to normalize each set of data individually.I would like to ask where to find the normalized source code of Athena, I can modify the code so I can use my computer to achieve a large number of processing.Thanks!

2 1

found some issues found in larch (read-in issues)
by Mangold, Stefan (IPS) 26 Oct '22

26 Oct '22

Dear All, dear Matt, all tests were done on Macs (one M1 & one Intel) with the latest version your software & latest OS. 1. Read-In of spec files works, but only one file at once. Even if multiple files are selected 2. If one tries to load text-files it is possible to load data form multiple files as long as you don’t try to load also the reference spectra. If you load the reference also the read-in stopps at the transmission/fluorescence spectrum of the second file selected. 3. Trouble, that I sometimes can’t unmount network volumes after reading from them, larch saved on local discs. MacOS claims that python has files open; no other python program running 4. unable to save the data of one XAS-viewer while having two xas-viewer open. best regards Stefan Mangold

3 3

Xraylarch installation
by Dien.Li＠srnl.doe.gov 14 Oct '22

14 Oct '22

Dear Matt With help of our IT folk, we downloaded Larch for windows binary installer file and installed the xraylarch 9.65 on my computer, however, the LARCH subdirectory with the five application platforms (e.g., XAS viewer) were NOT generated automatically. We tried to uninstall and install three times, it is still the same, could you please suggest what we may do to correct this? Thank you so much. Dien Li Savannah River National Laboratory

1 0

[Larch] S02 value larger than 1
by dxfan＠post.kek.jp 04 Oct '22

04 Oct '22

Dear All, � I have a very common question, which is already asked many times: the S02 value is larger than 1. I measure the Sr K-edge EXAFS of SrTiO3 with temperature dependence. The S02 value is larger than 1. I check the book of “XAFS for everyone”, in which say maybe because of the distorted data or wrong structure model. I check the data measured by other beamline with the same sample, the S02 value still is larger than 1. I change the background reduction parameters, same result. I also modify the model, still same result. � I am very confused with these results. I attached the data, FEFF paths, and the fitting python Code the package. Can anyone help me check my fitting procedure. � Best regards, Fan

1 0

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>

3 3

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

1 0

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

1 0

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

1 0