Abhijeet Gaur | 3 Aug 13:49 2015
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Re: Ifeffit Digest, Vol 150, Issue 2

Hi Scott,

              Thanks for your quick reply. So, I have to add more paths to the fitting and then try to determine the size of the particle.

             Also, I want to add some analysis details to confirm that I am on the right path.

             The value of amp is obtained from fitting of metal foil, i.e., 0.84 (0.03) and is kept fixed during the fitting of the sample.

              S02 is defined by the formula  S02 = amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))).

With thanks

Abhijeet


            


Message: 2
Date: Mon, 3 Aug 2015 07:11:53 -0400
From: Scott Calvin <scalvin-LBZPvM76S0LYFPJBu9q2oodd74u8MsAO@public.gmane.org>
To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Subject: Re: [Ifeffit] Measuring particle size by coordination number
Message-ID: <C61F6046-713C-4EC2-8F7A-536ECC43DEA5-WZtszHR+tOk@public.gmane.org>
Content-Type: text/plain; charset="utf-8"

Hi Abhijeet,

The formula looks poorly when it is only applied with one path.

The strength of this approach, and of Anatoly Frenkel?s alternative strategy for finding particle sizes, is that it compares coordination numbers for different shells, helping to break the correlations between N, S02, and sigma2.

Even then, it tends to report sizes that are small compared to those provided by other techniques, but compares sizes between different samples quite well.

?Scott Calvin
Sarah Lawrence College





--
Dr. Abhijeet Gaur
Post doctoral fellow in the  Institute for Chemical Technology and Polymer Chemistry 
Karlsruher Institut für Technologie (KIT), Karlsruhe Germany.
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Abhijeet Gaur | 3 Aug 10:41 2015
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Measuring particle size by coordination number

Hi all,

             Sorry, I may be asking a question already asked in the mailing list, but I am unable to get it from the earlier discussions. 

                I am reading one of the research article ´´ Determination of crystallite size in a magnetic nanocomposite  using extended x-ray absorption fine structure´´ .J. Appl. Phys,. vol 94, page 778, 2003

               In this paper there is a formula N_nano = [1-3/4(r/R)+1/16(r/R)^3]N_bulk, which you said can be used in the Artemis for extracting the  particle size.

               I am trying to use this formula for determination of size of Ni particles in an Ni / Al2O3 catalyst. From TEM the size determined is around 4 nm. 

               So, I am trying to fit the theoretical model of Ni metal to the sample data in the Artemis

               I defined a guessed parameter R and then put the whole formula for S02 = amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))).

               The value of R I am getting is 0.81 (0.05) which is quite small. 

               Is there something I am missing in the formula or I have to define the N seprately for sample cooridnation number. 

              Currently, I am using only the first path in the fitting.  

          

With thanks 


Abhijeet Gaur


--
Dr. Abhijeet Gaur
Post doctoral fellow in the  Institute for Chemical Technology and Polymer Chemistry 
Karlsruher Institut für Technologie (KIT), Karlsruhe Germany.
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Adora Graham | 31 Jul 01:38 2015
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Vanadium-Chromium Prussian Blue Analog XANES fitting

Hello, 

First of all, I am still very new to XAS analysis, so please excuse any misunderstandings I may have. 

I have a series of compounds nominally consisting of KxVx[Cr(CN)6] Prussian blue analogs (where x is ~1) with Cr(III) and presumably V(II) present in the system. From other evidence, the V(II) may be oxidizing to V(III). I have XAS data collected at the V and Cr K-edges from APS and have been struggling through trying to analyze my data using Athena. 

I am trying to get two things out of this data:

First, I would like to get the oxidation state of the Vanadium sites. If they are not V(II), to get the ratio of V(II) to V(III) present, if possible. I have been trying to follow a similar analysis to Wong (Phys. Rev. B, 1984, 30, 10, 5596-5610). However, I seem to be running into the issue of finding standards with a similar ligand set to my sample. I have XAS data for the following standards: VO, V2O3, V2O4, V2O5, V(acac)3, VO(acac), VOSO4, and VSO4. I start with VSO4 as my initial vanadium source, so that could be useful for a comparison. Our initial idea was to use the vanadium oxides to give a standard curve to then extrapolate the oxidation state of my compound, but using this gives me an oxidation state of ~4.2 which seems unreasonable for my system. I am kind of lost otherwise as to what else I could do with this. 

Second, I would like to get the ratio of V to Cr. I was told I could compare the un-normalized K-edge heights of the vanadium to that of the chromium to get this ratio. This doesn't seem right, as I would think that there should be some relative intensity factor involved. Also, this gives me a fairly unreasonable value of 4:1, since XPS measurements give me values of around 1:1. 

Can you point me in the right direction for these issues? 

I've also attached the project files for one of my samples. 

Thanks, 
Adora
Attachment (AGB02-083-Cr merged.prj): application/octet-stream, 24 KiB
Attachment (AGB02-083-V merged.prj): application/octet-stream, 11 KiB
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Fowler, Joseph W. | 30 Jul 17:58 2015

Re: HELP: failed to install gcc49 on mac (v10.6.8)

Dear Ie-Rang,

I’m the demeter maintainer on MacPorts, but I admit I am anything but a MacPorts guru.

I notice that the error you showed is a failure to install gcc49. I don’t know if that new GCC is compatible with your old version of OS X, but that’s an issue that’s beyond my expertise. You might edit your variants file (it’s /opt/local/etc/macports/variants.conf on my installation) to insist on an earlier version by adding a line containing, e.g., “+gcc47” or whatever is your installed and preferred version of GCC.

In fact, the port demeter does not depend (directly) on gcc, which you can see by issuing the command

> port echo depof:demeter
> port echo depof:demeter-devel

So it looks to me like you have several steps to get ready for installing demeter.

I admit that I recently discovered—but have not fixed—a flaw in the demeter port description file. The code depends on ports p5.16-file-which and p5.16-math-round, but these are not made explicit. I need to figure out how to add these to the explicit dependency list. I’m just back from vacation and a conference, so I have no excuses now. If you get far enough that you can install *but not run* demeter’s executables, then a workaround for this is

> sudo port install p5.16-file-which p5.16-math-round

And for MacPorts users in general: I understand that the project as a whole is in the process of trying to move to Perl 5.22 instead of 5.16. I’ll be updating the port file to reflect that change, too.

Joe Fowler
NIST Boulder Laboratories



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Today's Topics:

  1. HELP: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon)
  2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel)
  3. Error in Running XANES on FEFF8.4 for Cobalt based cluster
     (Ganesh Subramanian)

From: Ie-Rang Jeon <jeon <at> northwestern.edu>
Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)
Date: July 29, 2015 at 1:11:08 PM MDT
To: "ifeffit-yJARRRr6MatGzrOJDQI3KQ@public.gmane.org.aps.anl.gov" <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Reply-To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>


Hello,

I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got.
Could you please help me to figure out what the problem is?

Thank you.
Ie-Rang


-----------------------------------

--->  Building gcc49
Error: org.macports.build for port gcc49 returned: command execution failed
Error: Failed to install gcc49
Please see the log file for port gcc49 for details:
   /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log
Error: The following dependencies were not installed:
.
.
.
Error: Processing of port demeter-devel failed






From: Bruce Ravel <bravel <at> bnl.gov>
Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)
Date: July 29, 2015 at 1:21:06 PM MDT
To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Reply-To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>


On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote:
Hello,

I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got.
Could you please help me to figure out what the problem is?

Thank you.
Ie-Rang

Perhaps there's anything useful in that log file?
B




-----------------------------------

--->  Building gcc49
Error: org.macports.build for port gcc49 returned: command execution failed
Error: Failed to install gcc49
Please see the log file for port gcc49 for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log
Error: The following dependencies were not installed:
.
.
.
Error: Processing of port demeter-devel failed


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--
Bruce Ravel  ------------------------------------ bravel-IGkKxAqZmp0@public.gmane.org

National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973

Homepage:    http://bruceravel.github.io/home/
Software:    https://github.com/bruceravel
Demeter:     http://bruceravel.github.io/demeter/



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Ganesh Subramanian | 30 Jul 00:01 2015
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Error in Running XANES on FEFF8.4 for Cobalt based cluster

Dear all,

I was trying to simulate XANES using FEFF8.4 at Cobalt K edge. This is for a cluster and not a crystal. I encountered two problems.

1. Using the FOLP card: The actual cluster size is about 180 atoms extending upto 18 A in radial distance from the central cobalt atom. But there are quite a few instances of Hydrogen atoms that are too close. I tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to get a syntax type error, that i cant figure out. I checked the crystal structure and the smallest hydrogen bond distance is 0.89 A. (I have attached the corresponding input and log file with suffix 'full cluster')

2. SCF for small cluster: Since the problem with the hydrogen distances persisted, I decided to run the calculation for a smaller cluster (about 50 atoms). I used the conditions as prescribed for small clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were too close (within this smaller cluster, there were about 3 of them, and none in the first or second shell of co-ordination) were removed manually. Now, I did not have the error on distances, did not require the FOLP card to be manually altered, but the log1 file seems to suggest that the SCF is not calculated. I cant figure why that is the case. (I have attached the corresponding input and log file with suffix 'small cluster')

Sorry for the long email, and thank you for any suggestions. 

Ganesh



 * This feff8 input file was generated by TkAtoms 3.0beta7
 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001

 TITLE MeCbl-Groundstate-Kedge

 *  Co K edge energy = 7712.0 eV
 EDGE      K
 S02       1.0

 *         pot    xsph  fms   paths genfmt ff2chi
 CONTROL   0      1     1     1     1      1
 PRINT     1      0     0     0     0      0

                          *** ixc=0 means to use Hedin-Lundqvist
 *         ixc  [ Vr  Vi ]
 EXCHANGE  0 0 0.5

                          *** Radius of small cluster for
                          *** self-consistency calculation
                          *** A sphere including 2 shells is
                          *** a good choice
                          *** l_scf = 0 for a solid, 1 for a molecule
 *         r_scf  [ l_scf   n_scf   ca ]
 SCF       7.0

                          *** Upper limit of XANES calculation.
                          *** This *must* be uncommented to
                          *** make Feff calculate full multiple
                          *** scattering rather than a path expansion
 

 *         kmax   [ delta_k  delta_e ]
 XANES     7.0 0.05 0.05

                          *** Radius of cluster for Full Multiple
                          *** Scattering calculation
                          *** l_fms = 0 for a solid, 1 for a molecule
 *         r_fms     l_fms
 FMS        8  0

                          *** Energy grid over which to calculate
                          *** DOS functions
 *         emin  emax   eimag
 LDOS      -30   20     0.1

                          *** for EXAFS:  RMAX  10.0 and uncomment
                          *** the EXAFS card
 RPATH     0.1
 *EXAFS     20

 POTENTIALS
 *    ipot   Z  element            l_scmt  l_fms   stoichiometry
        0   27   Cu                 3       2       1
        1    1    H                 3       2       76
        2    6    C                 3       3       63
        3    7    N                 3       2       13
	4    8    O		    3       2       14
	5   15    P		    3	    2       1

	
FOLP 1 0.8	
	

 ATOMS                          * this list contains 178 atoms
 *   x          y          z      ipot  tag           distance
0	0	0	0	Co	0.000	0
-0.73	1.487	0.476	3	N	1.724	1
1.314	0.811	-0.784	3	N	1.732	2
0.708	-1.561	-0.381	3	N	1.756	3
-1.175	-0.832	1.088	3	N	1.805	4
-1.293	0.017	-1.587	2	C	2.047	5
-1.628	1.352	1.298	2	C	2.483	6
-1.646	0.059	2.026	2	C	2.611	7
1.44	2.014	-0.847	2	C	2.617	8
1.674	-1.773	-1.033	2	C	2.648	9
0.065	-2.651	-0.292	2	C	2.668	10
-0.361	2.622	0.395	2	C	2.676	11
2.151	0.331	-1.562	2	C	2.679	12
-1.518	-1.905	1.163	2	C	2.699	13
0.567	2.92	-0.473	2	C	3.012	14
0.08	0.589	2.961	1	H2	3.020	15
2.423	-0.876	-1.633	2	C	3.050	16
-1.094	-2.832	0.333	2	C	3.054	17
-0.8	0.26	3.233	2	C	3.341	18
3.026	0.892	1.392	1	H5	3.448	19
2.801	-1.786	1.549	1	H4	3.665	20
-0.699	-0.591	3.706	1	H2	3.817	21
-2.038	2.748	1.975	2	C	3.950	22
3.001	1.502	2.085	3	N	3.951	23
2.924	-1.048	-2.449	1	H	3.955	24
-2.994	-0.645	2.527	2	C	3.971	25
0.795	-3.712	-1.166	2	C	3.971	26
2.129	-3.213	-1.116	2	C	4.013	27
-2.497	-2.107	2.332	2	C	4.014	28
2.966	1.351	-2.354	2	C	4.020	29
-1.385	3.613	1.102	2	C	4.023	30
2.808	2.449	-1.53	2	C	4.028	31
-3.946	-0.621	0.726	1	H2	4.060	32
-1.22	0.906	3.817	1	H2	4.108	33
3.601	-1.355	1.522	3	N	4.138	34
0.4	-2.921	-3.025	1	H3	4.224	35
2.795	1.217	2.932	1	H5	4.230	36
3.712	-0.574	1.974	1	H4	4.243	37
2.702	-3.406	0.874	1	H4	4.435	38
4.152	1.702	-0.187	1	H4	4.491	39
1.539	1.977	-3.728	1	H4	4.492	40
-2.692	3.586	-0.467	1	H5	4.508	41
-4.202	-0.405	1.635	2	C	4.527	42
0.992	4.397	-0.487	2	C	4.534	43
-1.711	-4.229	0.511	2	C	4.591	44
0.324	-3.792	-2.611	2	C	4.615	45
2.573	-3.326	-1.961	1	H	4.640	46
-3.249	-2.646	2.035	1	H	4.658	47
0.848	3.782	2.591	1	H5	4.662	48
2.648	3.255	-2.035	1	H	4.663	49
-4.396	0.54	1.668	1	H2	4.733	50
2.434	1.58	-3.774	2	C	4.761	51
3.07	-3.715	0.032	2	C	4.819	52
4.035	2.577	-0.579	2	C	4.823	53
-2.343	4.256	0.132	2	C	4.860	54
0.942	4.76	0.419	1	H5	4.870	55
-2.008	-3.447	-2.876	4	O	4.918	56
2.387	0.722	-4.248	1	H4	4.926	57
1.913	4.468	-0.817	1	H5	4.928	58
3.571	2.835	1.893	2	C	4.937	59
-1.272	-3.474	3.311	1	H3	4.965	60
-2.371	-4.204	1.233	1	H3	4.982	61
4.608	0.219	-1.892	1	H4	4.986	62
2.954	4.008	0.364	1	H4	4.992	63
-2.15	-4.501	-0.323	1	H3	4.999	64
-2.008	-2.903	3.566	2	C	5.018	65
-1.016	-4.862	0.731	1	H3	5.021	66
0.402	4.897	-1.066	1	H5	5.028	67
4.663	-1.852	0.661	2	C	5.061	68
-1.698	-2.269	4.238	1	H3	5.098	69
4.416	0.956	-2.49	2	C	5.159	70
-1.11	-4.263	-2.692	2	C	5.163	71
3.778	3.538	0.562	2	C	5.206	72
-2.527	-0.411	4.554	1	H2	5.224	73
-3.349	-0.384	4.007	2	C	5.236	74
-0.805	4.863	1.856	2	C	5.267	75
0.695	-5.198	-0.718	2	C	5.293	76
-1.873	4.943	-0.384	1	H5	5.300	77
-3.606	3.081	2.397	2	C	5.314	78
0.233	4.451	2.953	2	C	5.347	79
-3.997	2.297	2.804	1	H6	5.396	80
-0.231	-5.406	-0.483	1	H3	5.432	81
0.884	-4.417	-3.085	1	H3	5.460	82
1.27	-5.344	0.058	1	H3	5.493	83
-4.12	3.289	1.597	1	H6	5.508	84
4.504	-3.18	-0.063	2	C	5.514	85
-0.239	4.077	3.714	1	H5	5.520	86
-0.344	5.427	1.215	1	H5	5.572	87
-3.767	0.496	4.091	1	H2	5.583	88
3.081	-4.692	0.037	1	H4	5.613	89
-3.079	4.665	0.624	1	H5	5.624	90
3.353	3.63	2.752	4	O	5.656	91
3.034	2.184	-4.253	1	H4	5.662	92
4.852	2.817	-1.061	1	H4	5.710	93
4.982	1.715	-2.261	1	H4	5.734	94
4.753	-3.085	-0.99	1	H4	5.752	95
4.594	0.684	-3.408	1	H4	5.761	96
5.741	-1.287	0.682	4	O	5.923	97
-5.504	-1.166	1.925	2	C	5.946	98
-3.965	-1.064	4.316	1	H2	5.957	99
-1.532	5.363	2.25	1	H5	6.014	100
0.986	-5.782	-1.456	1	H3	6.043	101
4.504	4.191	0.625	1	H4	6.184	102
5.093	-3.823	0.371	1	H4	6.379	103
-3.137	-3.745	4.192	2	C	6.437	104
-1.354	-5.657	-2.958	3	N	6.526	105
-6.51	-0.299	0.368	1	H2	6.527	106
-3.728	4.254	3.361	2	C	6.580	107
-3.357	-4.455	3.581	1	H3	6.629	108
-5.673	-1.993	2.814	4	O	6.639	109
-3.922	-3.183	4.359	1	H3	6.672	110
1.04	5.696	3.398	2	C	6.714	111
-6.604	-0.9	1.038	3	N	6.745	112
-0.67	-6.255	-2.898	1	H4	6.926	113
-3.184	4.243	4.455	4	O	6.927	114
-2.205	-5.954	-3.062	1	H4	7.049	115
-2.008	-2.626	6.339	1	H3	7.149	116
2.05	4.854	4.989	1	H	7.256	117
1.146	6.695	2.696	4	O	7.308	118
-2.661	-4.358	5.503	2	C	7.507	119
1.88	5.649	4.578	3	N	7.510	120
-7.399	-1.324	1.159	1	H2	7.605	121
-2.08	-3.52	6.488	3	N	7.669	122
-5.054	5.341	2.22	1	H6	7.681	123
-4.624	5.338	3.025	3	N	7.683	124
-1.79	-3.874	7.269	1	H3	8.429	125
-2.707	-5.556	5.796	4	O	8.473	126
-4.723	6.046	3.601	1	H6	8.475	127
3.657	6.544	4.239	1	H1	8.612	128
2.832	6.767	4.691	2	C	8.707	129
2.453	7.572	4.317	1	H1	9.055	130
2.371	6.047	7.196	4	O	9.694	131
3.109	6.938	6.24	2	C	9.836	132
4.243	4.4	7.706	4	O	9.836	133
2.05	4.336	8.879	4	O	10.092	134
2.487	7.667	6.344	1	H	10.257	135
3.134	5.213	8.292	5	P	10.284	136
5.001	7.829	5.91	1	H3	11.011	137
4.405	7.736	6.675	2	C	11.127	138
4.862	7.25	7.385	1	H3	11.434	139
4.151	8.613	6.996	1	H3	11.847	140
3.704	6.108	9.46	4	O	11.854	141
1.918	6.772	9.906	1	H	12.152	142
2.77	6.616	10.359	2	C	12.600	143
1.926	5.091	11.435	1	H	12.664	144
2.576	5.791	11.594	2	C	13.213	145
3.243	8.973	9.298	1	H5	13.322	146
3.747	5.16	11.995	4	O	13.585	147
4.45	5.645	11.736	1	Ho	13.762	148
3.257	7.86	11.008	2	C	13.913	149
3.026	9.122	10.227	2	C	14.034	150
2.093	9.407	10.314	1	H5	14.116	151
4.226	7.792	11.079	1	H	14.189	152
1.139	6.856	12.625	1	H	14.412	153
0.369	4.49	13.692	1	H	14.414	154
2.102	6.749	12.652	2	C	14.493	155
-0.411	1.976	14.446	1	Hm	14.586	156
2.678	7.948	12.285	4	O	14.875	157
0.876	4.432	14.508	2	C	15.195	158
3.873	10.094	10.746	4	O	15.244	159
-0.602	2.494	15.243	2	C	15.457	160
-1.431	2.98	15.122	1	Hm	15.479	161
2.535	6.358	13.975	3	N	15.561	162
1.962	5.3	14.722	2	C	15.769	163
0.525	3.474	15.488	2	C	15.882	164
3.697	10.21	11.612	1	Ho	15.898	165
-0.685	1.893	16.011	1	Hm	16.137	166
3.591	6.904	14.652	2	C	16.590	167
4.144	7.623	14.332	1	H	16.754	168
2.748	5.246	15.931	2	C	16.996	169
1.317	3.409	16.675	2	C	17.071	170
3.751	6.267	15.816	3	N	17.421	171
2.4	4.291	16.901	2	C	17.602	172
1.334	1.524	17.528	1	Hm	17.645	173
0.955	2.397	17.753	2	C	17.940	174
-0.016	2.324	17.812	1	Hm	17.963	175
2.917	4.228	17.732	1	H	18.461	176
1.301	2.698	18.608	1	Hm	18.848	177    
 END

 Feff 8.40
  XANES:
 FOLP:
 Expert option, please read documentation carefully and check your results.
 MeCbl-Groundstate-Kedge
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       20      24
   20  3.02600E+00  8.92000E-01  1.39200E+00
   24  3.00100E+00  1.50200E+00  2.08500E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       21      35
   21  2.80100E+00 -1.78600E+00  1.54900E+00
   35  3.60100E+00 -1.35500E+00  1.52200E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       24      37
   24  3.00100E+00  1.50200E+00  2.08500E+00
   37  2.79500E+00  1.21700E+00  2.93200E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       35      38
   35  3.60100E+00 -1.35500E+00  1.52200E+00
   38  3.71200E+00 -5.74000E-01  1.97400E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      106     114
  106 -1.35400E+00 -5.65700E+00 -2.95800E+00
  114 -6.70000E-01 -6.25500E+00 -2.89800E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      106     116
  106 -1.35400E+00 -5.65700E+00 -2.95800E+00
  116 -2.20500E+00 -5.95400E+00 -3.06200E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      107     113
  107 -6.51000E+00 -2.99000E-01  3.68000E-01
  113 -6.60400E+00 -9.00000E-01  1.03800E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      113     122
  113 -6.60400E+00 -9.00000E-01  1.03800E+00
  122 -7.39900E+00 -1.32400E+00  1.15900E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      117     123
  117 -2.00800E+00 -2.62600E+00  6.33900E+00
  123 -2.08000E+00 -3.52000E+00  6.48800E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      118     121
  118  2.05000E+00  4.85400E+00  4.98900E+00
  121  1.88000E+00  5.64900E+00  4.57800E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      123     126
  123 -2.08000E+00 -3.52000E+00  6.48800E+00
  126 -1.79000E+00 -3.87400E+00  7.26900E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      124     125
  124 -5.05400E+00  5.34100E+00  2.22000E+00
  125 -4.62400E+00  5.33800E+00  3.02500E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      125     128
  125 -4.62400E+00  5.33800E+00  3.02500E+00
  128 -4.72300E+00  6.04600E+00  3.60100E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      148     149
  148  3.74700E+00  5.16000E+00  1.19950E+01
  149  4.45000E+00  5.64500E+00  1.17360E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      160     166
  160  3.87300E+00  1.00940E+01  1.07460E+01
  166  3.69700E+00  1.02100E+01  1.16120E+01
 Run continues in case you really meant it.

 * This feff8 input file was generated by TkAtoms 3.0beta7
 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001

 TITLE MeCbl-Groundstate-Kedge

 *  Co K edge energy = 7712.0 eV
  EDGE      K
 * S02       1.0

 *         pot    xsph  fms   paths genfmt ff2chi
 CONTROL   1      1     1     1     1      1
 PRINT     1      0     0     0     0      0

                          *** ixc=0 means to use Hedin-Lundqvist
 *         ixc  [ Vr  Vi ]
 EXCHANGE  0 0 0.5

                          *** Radius of small cluster for
                          *** self-consistency calculation
                          *** A sphere including 2 shells is
                          *** a good choice
                          *** l_scf = 0 for a solid, 1 for a molecule
 *         r_scf  [ l_scf   n_scf   ca ]
 SCF       5 1 

                          *** Upper limit of XANES calculation.
                          *** This *must* be uncommented to
                          *** make Feff calculate full multiple
                          *** scattering rather than a path expansion
 

 *         kmax   [ delta_k  delta_e ]
 XANES     4.5 

                          *** Radius of cluster for Full Multiple
                          *** Scattering calculation
                          *** l_fms = 0 for a solid, 1 for a molecule
 *         r_fms     l_fms
 FMS        5  1

                          *** Energy grid over which to calculate
                          *** DOS functions
 *         emin  emax   eimag
 LDOS      -30   20     0.1

                          *** for EXAFS:  RMAX  10.0 and uncomment
                          *** the EXAFS card
 RPATH     -1
 EXAFS     20

 POTENTIALS
 *    ipot   Z  element            l_scmt  l_fms   stoichiometry
        0   27   Cu                 3       2       1
        1    1    H                 3       2       14
        2    6    C                 3       3       25
        3    7    N                 3       2       6
 *	4    8    O		    3       2       14
 *	5   15    P		    3	    2       1

 * FOLP 1 0.8	

 ATOMS                          * this list contains 178 atoms
 *   x          y          z      ipot  tag           distance
0	0	0	0	Co	0.000	0
-0.73	1.487	0.476	3	N	1.724	1
1.314	0.811	-0.784	3	N	1.732	2
0.708	-1.561	-0.381	3	N	1.756	3
-1.175	-0.832	1.088	3	N	1.805	4
-1.293	0.017	-1.587	2	C	2.047	5
-1.628	1.352	1.298	2	C	2.483	6
-1.646	0.059	2.026	2	C	2.611	7
1.44	2.014	-0.847	2	C	2.617	8
1.674	-1.773	-1.033	2	C	2.648	9
0.065	-2.651	-0.292	2	C	2.668	10
-0.361	2.622	0.395	2	C	2.676	11
2.151	0.331	-1.562	2	C	2.679	12
-1.518	-1.905	1.163	2	C	2.699	13
0.567	2.92	-0.473	2	C	3.012	14
0.08	0.589	2.961	1	H2	3.020	15
2.423	-0.876	-1.633	2	C	3.050	16
-1.094	-2.832	0.333	2	C	3.054	17
-0.8	0.26	3.233	2	C	3.341	18
-0.699	-0.591	3.706	1	H2	3.817	21
-2.038	2.748	1.975	2	C	3.950	22
3.001	1.502	2.085	3	N	3.951	23
2.924	-1.048	-2.449	1	H	3.955	24
-2.994	-0.645	2.527	2	C	3.971	25
0.795	-3.712	-1.166	2	C	3.971	26
2.129	-3.213	-1.116	2	C	4.013	27
-2.497	-2.107	2.332	2	C	4.014	28
2.966	1.351	-2.354	2	C	4.020	29
-1.385	3.613	1.102	2	C	4.023	30
2.808	2.449	-1.53	2	C	4.028	31
-3.946	-0.621	0.726	1	H2	4.060	32
-1.22	0.906	3.817	1	H2	4.108	33
3.601	-1.355	1.522	3	N	4.138	34
0.4	-2.921	-3.025	1	H3	4.224	35
2.702	-3.406	0.874	1	H4	4.435	38
4.152	1.702	-0.187	1	H4	4.491	39
1.539	1.977	-3.728	1	H4	4.492	40
-2.692	3.586	-0.467	1	H5	4.508	41
-4.202	-0.405	1.635	2	C	4.527	42
0.992	4.397	-0.487	2	C	4.534	43
-1.711	-4.229	0.511	2	C	4.591	44
0.324	-3.792	-2.611	2	C	4.615	45
2.573	-3.326	-1.961	1	H	4.640	46
-3.249	-2.646	2.035	1	H	4.658	47
0.848	3.782	2.591	1	H5	4.662	48
2.648	3.255	-2.035	1	H	4.663	49
-4.396	0.54	1.668	1	H2	4.733	50
END

 Calculating potentials ...
    free atom potential and density for atom type    0
    free atom potential and density for atom type    1
    free atom potential and density for atom type    2
    free atom potential and density for atom type    3
    initial state energy
    overlapped potential and density for unique potential    0
    overlapped potential and density for unique potential    1
    overlapped potential and density for unique potential    2
    overlapped potential and density for unique potential    3
    muffin tin radii and interstitial parameters
 iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph)
    0  1.24151E+00  1.13966E+00  1.15000E+00
    1  9.41337E-01  6.67025E-01  1.15000E+00
    2  1.43160E+00  1.26080E+00  1.15000E+00
    3  9.18708E-01  5.74238E-01  1.15000E+00
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Ie-Rang Jeon | 29 Jul 21:11 2015

HELP: failed to install gcc49 on mac (v10.6.8)

Hello,

I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages
that I got.
Could you please help me to figure out what the problem is?

Thank you.
Ie-Rang

-----------------------------------

--->  Building gcc49
Error: org.macports.build for port gcc49 returned: command execution failed
Error: Failed to install gcc49
Please see the log file for port gcc49 for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log
Error: The following dependencies were not installed: 
.
.
.
Error: Processing of port demeter-devel failed
Kenneth Latham | 28 Jul 06:59 2015
Picon

Setting ranges in peak fitting

Hi Bruce, 

To clarify this further, I am peak fitting a number of peaks under the carbon edge. For example, I know from
the literature that the 1s-p transition for the C=C should be located between 284.5 to 285.5 eV, so I would
fit a peak at about 285 eV to start with. I would then move on to fitting additional peaks based on their
literature values with what I know about the material/where obvious peaks are in the NEXAFS.

The problem now comes when I tell Athena to fit, it will start to move the peaks all over the place to obtain the
best fit, typically placing them in locations where functionalities don't appear under the NEXAFS. In
other words, it would move peaks away from where I would expect them to be based on the literature. This can
be partially stopped by fixing all but one peak, fitting it and then and applying this procedure to every
peak multiple times.

What I was wondering is if Athena has the ability to set a range that each peak is allowed to move, i.e., the C=C
center would be restricted to values between 284.5-285.5 eV. Hence I could set up the ranges and fit
quickly based on those.

Cheers, 
Ken Latham

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Subject: Ifeffit Digest, Vol 149, Issue 23

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Today's Topics:

   1. Setting ranges in peak fitting Athena (Kenneth Latham)
   2. Re: Setting ranges in peak fitting Athena (Ravel, Bruce)
   3. Re: Setting ranges in peak fitting Athena (Matt Newville)

----------------------------------------------------------------------

Message: 1
Date: Fri, 24 Jul 2015 00:14:18 +0000
From: Kenneth Latham <Kenneth.Latham@...>
To: "ifeffit@..."
        <ifeffit@...>
Subject: [Ifeffit] Setting ranges in peak fitting Athena
Message-ID:
        <CY1PR02MB1416E3DBC230406B078F9A07AA810@...>

Content-Type: text/plain; charset="iso-8859-1"

Hi Bruce,

Is it possible to set a range of values that the the center (or any other values) can be between for line shapes
when peak fitting in Athena? Similar to what you can do in CasaXPS.

If not, do you know of a program that can handle NEXAFS  peak fitting and has that feature?

Cheers,
Ken

------------------------------

Message: 2
Date: Fri, 24 Jul 2015 13:14:03 +0000
From: "Ravel, Bruce" <bravel@...>
To: XAFS Analysis using Ifeffit <ifeffit@...>
Subject: Re: [Ifeffit] Setting ranges in peak fitting Athena
Message-ID: <xp7hq5h11j0ygmcc2btiht0f.1437743641853@...>
Content-Type: text/plain; charset="us-ascii"

Hi Ken,

I'm sorry, but I don't quite understand your question.  And I have no idea what casaXPS is, so that reference
doesn't help me.

Are you asking whether you can put gaps in the fit range?

B

On July 23, 2015, at 8:16 PM, Kenneth Latham
<Kenneth.Latham@...> wrote:

Hi Bruce,

Is it possible to set a range of values that the the center (or any other values) can be between for line shapes
when peak fitting in Athena? Similar to what you can do in CasaXPS.

If not, do you know of a program that can handle NEXAFS  peak fitting and has that feature?

Cheers,
Ken

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Message: 3
Date: Fri, 24 Jul 2015 11:05:45 -0500
From: Matt Newville <newville@...>
To: XAFS Analysis using Ifeffit <ifeffit@...>
Subject: Re: [Ifeffit] Setting ranges in peak fitting Athena
Message-ID:
        <CA+7ESbo5Z27OdFi3a5D0S9rDX8v3x=8E1WtEvEhuthtUHB1ARQ@...>
Content-Type: text/plain; charset="utf-8"

I thought maybe Ken was asking about having box constraints or min/max
constraints on parameter values.   But that is kind of a guess.

Hi Ken,

I'm sorry, but I don't quite understand your question.  And I have no idea
what casaXPS is, so that reference doesn't help me.

Are you asking whether you can put gaps in the fit range?

B

On July 23, 2015, at 8:16 PM, Kenneth Latham <Kenneth.Latham@...>
wrote:

 Hi Bruce,

Is it possible to set a range of values that the the center (or any other
values) can be between for line shapes when peak fitting in Athena? Similar
to what you can do in CasaXPS.

If not, do you know of a program that can handle NEXAFS  peak fitting and
has that feature?

Cheers,
Ken

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End of Ifeffit Digest, Vol 149, Issue 23
****************************************
Anatoly I Frenkel | 28 Jul 05:02 2015

Two postdoctoral positions

Dear subscribers,

Please pass along this information to anyone who may be interested in this opportunities.

Physics Department of Yeshiva University in New York City has two openings for postdoctoral research associate positions, beginning in September 2015. The first position is for the project: "Collaborative research: Toolkit to characterize and design bi-functional nanoparticle catalysts." The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II and other synchrotrons for X-ray absorption spectroscopy measurements. Required qualifications: Ph.D. in physics, chemistry or materials science, expert knowledge of XAS methods, including analysis and modeling of nanoparticles, and experience with in situ characterization methods by XAS and other techniques.

The second position is for the project "Multidisciplinary research for the advancement of filtration materials: Uptake, decomposition, and catalysis for Agent-POM/MOF Chemistry". The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II and other synchrotrons for high energy XRD-PDF characterization of novel POM/MOF materials in reaction conditions. Required qualifications: Ph.D. in chemistry, chemical engineering or materials science, expert knowledge of XRD-PDF technique and data analysis, experience with analysis of MOFs, experience with in situ and/or operando methods of synchrotron characterization.
 
The research will be performed under the direction of Prof. Anatoly Frenkel. Applicants should forward cover letter with contact information of three references and CV to anatoly.frenkel-BsWGWzZNy/s@public.gmane.org Yeshiva University is an Equal Opportunity Employer.

Anatoly Frenkel, Ph.D., Professor and Chair,
Department of Physics, Yeshiva University
245 Lexington Avenue, New York, NY 10016
http://www.yu.edu/faculty/afrenkel
Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc
Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel-OKzqDoqOkpk@public.gmane.org
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Kenneth Latham | 24 Jul 02:14 2015
Picon

Setting ranges in peak fitting Athena

Hi Bruce, 

Is it possible to set a range of values that the the center (or any other values) can be between for line shapes
when peak fitting in Athena? Similar to what you can do in CasaXPS.

If not, do you know of a program that can handle NEXAFS  peak fitting and has that feature?

Cheers, 
Ken
Ellen Daugherty | 21 Jul 01:48 2015

Plotting chi(k) linear combination fit in energy

Hello,

I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: "chi data cannot be plotted in energy." Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue.

Thank you!

Ellen

--
Ph.D. Candidate
Research Assistant, Borch Lab
Department of Chemistry
Colorado State University
Attachment (Sample.nor): application/octet-stream, 62 KiB
Attachment (Standard 1.nor): application/octet-stream, 67 KiB
Attachment (Standard 2.nor): application/octet-stream, 67 KiB
Attachment (Standard 3.nor): application/octet-stream, 67 KiB
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alexander.thoma | 20 Jul 16:52 2015
Picon

Artemis Crashing on Opening Project Files (Windows 7)

Hi all,

 

I couldn’t seem to find anything like this on the mailing list, I’m having issues reopening saved Artemis (0.9.21) projects on Windows 7, the program opens and runs through the ‘importing’ text in the bottom left of the control window before shutting down immediately with no error message or warning before any other windows appear. The problem seems to occur sporadically with projects with fits from crystal structures and all the time with those done with quick first shell fits, and doesn’t occur with project files where no fits have been made. Attached is the log file for one of the non-opening projects, any suggestions?

 

Many thanks,

Alex

 

 

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Attachment (dartemis.log): application/octet-stream, 2460 bytes
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