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

Re: [Ifeffit] Deglitching
by Matt Newville 04 Sep '15

04 Sep '15

Hi Martina, On Sep 3, 2015 12:58 PM, "Martina Ralle" <rallem(a)ohsu.edu> wrote: > Hi Matt, > > > > I have a quick question. When I try to deglitch in Athena it won't let me > pick a point for deglitching. No matter where I double click it always > chooses 8990. > > > > Have others encountered this error? I am running athena on a Windows 7 64 > bit machine. The latest (not beta) version. > > > Sorry for the trouble. I haven't seen (or heard of) that myself, but I'll ask the ifeffit mailing list where maybe someone has a better idea what the trouble could be. > -martina > > > > Martina Ralle, Ph.D. > > Assistant Professor > > Department of Molecular and Medical Genetics > > Mail Code L103 > > OHSU > > 3181 SW Sam Jackson Pk Rd > > Portland, OR 97239 > > Phone 503 494-3225(o) 503 888-6128(m) > > >

2 1

Spline range and FT range
by 이국승(에너지환경소재연구팀) 02 Sep '15

02 Sep '15

Hi everyone, While I was processing my data, I found that the FT features are changing as I change the spline range. I think the change is severe as my data contain a lot of noises at high-k regions (above 12k). The change is remarkable even when FT range is fixed and even when the spline range is far from the low and high limits of FT range. When data are imported into athena, the defalut values for spline ranges from 0 to the end of measured data and the high limit of FT range is set to a value of the high limit of spline range minus 2. There must be a relationship. Could anyone explain these things and general rules for setting the spline range? Thank you in advance. Best wishes, Kug-Seung Lee ________________________________ Kug-Seung Lee, Ph. D. Staff Scientist 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011 ________________________________

3 3

Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster (Joshua Kas)
by Ganesh Subramanian 01 Sep '15

01 Sep '15

Dear Josh, Thanks for the altered input. It seems fine now as you mention. I ran the XANES calculations and compared with the existing literature of experimental XANES and it looks good. Thanks again, Ganesh On Sun, Aug 30, 2015 at 1:19 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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: Error in Running XANES on FEFF8.4 for Cobalt based > cluster (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 30 Aug 2015 13:18:51 -0700 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: > < > CAHuhYRnxrcfiveDOkS7T2Lx5C3bEZg4LeNffOJeq0dZLYJpRcg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Ganesh, > It is common to see the > WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. > warning from feff when you have H atoms since the bonds tend to be very > short. However, these are not the ones that are causing the problem. These > warning can be ignored if the structure is reasonable. If the structure at > the bottom of this email is the input structure that you used, then there > is indeed an oxygen atom that is less than 0.1 angstrom from a carbon atom, > which is of course unphysical. That is probably what is causing the > problem, however, there are some other things that could be causing > problems as well. In particular, there are what I like to call "floating > atoms" in your file, i.e., single atoms or several atoms that are > disconnected from the rest of the cluster. I am sending a new input file > below that has fixed this problem. I deleted the O atom that was too close > to the C atom, and deleted all of the structure that wasn't connected to > the central atom by a string of bonds. You might worry about weather the C > or O atom is the one that should have been deleted in the structure, but > you can always test using both possibilities. I doubt that it will make > much difference since C and O look pretty similar, and the O atom is pretty > far from the Co. Also, the H atoms look a bit messed up, but I don't think > that will make much of a difference either. You can check by taking the H > atoms out and running and see if the results change much. > Cheers, > Josh Kas > > * Al K edge energy = 1559.0 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 > CORRECTIONS 0 1 > > * *** 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 0 > > * *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 8.0 > > * *** Radius of cluster for Full Multiple > * *** Scattering calculation > * *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 6 0 > * *** Energy grid over which to calculate > * *** DOS functions > * emin emax eimag > *LDOS -30 20 0.1 > > FOLP 3 0.8 > > POTENTIALS > 0 27 Co -1 -1 > 1 6 C -1 -1 > 2 15 P -1 -1 > 3 1 H -1 -1 > 4 7 N -1 -1 > 5 8 O -1 -1 > > ATOMS > 0.000000 0.000000 0.000000 0 Co > 0.000000 1 > -0.877000 -1.130000 1.209000 4 N > 1.872888 2 > 0.706000 0.763000 1.563000 4 N > 1.877119 3 > -0.886000 -0.853000 -1.472000 4 N > 1.918173 4 > 1.117000 1.157000 -1.052000 4 N > 1.921729 5 > 1.456000 -1.334000 -0.126000 1 C > 1.978729 6 > -1.601000 1.453000 -0.068000 4 N > 2.163107 7 > 1.122000 -2.209000 0.163000 3 H > 2.482969 8 > 1.765000 -1.394000 -1.054000 3 H > 2.483823 9 > 2.201000 -1.061000 0.448000 3 H > 2.484115 10 > -0.328000 -1.105000 2.581000 1 C > 2.826689 11 > 1.045000 1.233000 -2.389000 1 C > 2.884378 12 > 0.051000 0.367000 2.864000 1 C > 2.887869 13 > 1.756000 1.481000 1.751000 1 C > 2.888408 14 > -0.659000 -0.537000 -2.771000 1 C > 2.898464 15 > -1.715000 -2.120000 1.053000 1 C > 2.923086 16 > -1.810000 -1.877000 -1.395000 1 C > 2.957238 17 > 2.263000 1.829000 -0.603000 1 C > 2.971535 18 > -2.864000 1.125000 -0.216000 1 C > 3.084603 19 > 0.509000 -1.655000 2.598000 3 H > 3.122132 20 > -3.165000 0.225000 -0.264000 3 H > 3.183951 21 > -1.881000 -2.521000 -0.717000 3 H > 3.226095 22 > 0.212000 0.468000 -3.185000 1 C > 3.226173 23 > 0.260000 -3.225000 -0.293000 3 H > 3.248703 24 > -1.605000 2.854000 0.000000 1 C > 3.274346 25 > -1.931000 0.869000 2.513000 3 H > 3.286197 26 > 2.614000 1.957000 0.706000 1 C > 3.340850 27 > -2.232000 -2.499000 -0.241000 1 C > 3.359301 28 > -2.287000 -2.542000 0.830000 3 H > 3.518669 29 > -1.207000 1.214000 3.075000 1 C > 3.519413 30 > -1.019000 2.145000 2.831000 3 H > 3.695125 31 > 0.186000 -3.470000 1.287000 3 H > 3.705653 32 > -2.458000 -2.943000 -0.050000 1 C > 3.834777 33 > 0.288000 -3.903000 0.413000 1 C > 3.935343 34 > -1.387000 -1.820000 3.396000 1 C > 4.094995 35 > 2.553000 -0.694000 3.132000 3 H > 4.099862 36 > 1.198000 0.646000 3.906000 1 C > 4.136346 37 > 0.236000 0.648000 -4.119000 3 H > 4.176333 38 > 1.974000 1.827000 3.218000 1 C > 4.194059 39 > 1.979000 2.281000 -2.920000 1 C > 4.200691 40 > -1.954000 -2.872000 2.399000 1 C > 4.221576 41 > -1.356000 -1.474000 -3.722000 1 C > 4.226665 42 > 3.077000 2.276000 -1.823000 1 C > 4.239273 43 > -2.379000 -2.161000 -2.783000 1 C > 4.251429 44 > -3.699000 2.187000 -0.292000 4 N > 4.307068 45 > -2.114000 -1.164000 3.595000 3 H > 4.329886 46 > 4.151130 0.213470 -1.476130 3 H > 4.410942 47 > -3.398000 -2.805000 -0.293000 3 H > 4.415912 48 > -2.914000 3.318000 -0.141000 1 C > 4.418190 49 > -1.477000 1.171000 4.015000 3 H > 4.435425 50 > 0.084000 -2.932000 -3.384000 3 H > 4.478296 51 > -0.139000 -3.903000 2.219000 3 H > 4.491847 52 > 1.145000 -4.375000 0.380000 3 H > 4.538287 53 > 2.138000 -0.543000 4.017000 1 C > 4.582814 54 > 1.599000 -1.345000 4.232000 3 H > 4.719709 56 > 4.110000 1.128000 -2.086000 1 C > 4.745090 57 > 2.947000 1.705000 3.417000 3 H > 4.823663 58 > -3.841000 -0.653000 -2.863000 3 H > 4.834921 59 > 3.949000 2.548000 1.146000 1 C > 4.837377 60 > -3.203000 -3.637000 -0.340000 1 C > 4.858248 61 > -0.314000 -2.507000 -4.171000 1 C > 4.876565 62 > 2.363000 1.996000 -3.799000 3 H > 4.898998 63 > -1.074000 -4.151000 2.377000 1 C > 4.902490 64 > -2.168000 -4.410000 0.005000 1 C > 4.914097 65 > -2.368000 -3.147000 -2.947000 3 H > 4.918927 66 > 1.290000 3.658000 -3.054000 1 C > 4.936799 67 > -0.837000 -4.889000 0.206000 1 C > 4.964406 68 > 0.666000 3.369000 3.643000 3 H > 5.006512 69 > 1.635000 3.289000 3.463000 1 C > 5.048080 70 > -3.849000 -1.643000 -2.849000 1 C > 5.062712 71 > -4.475000 -1.815000 1.737000 3 H > 5.131961 72 > 0.388000 -2.058000 -4.689000 3 H > 5.135429 73 > -4.326000 -1.930000 -2.031000 3 H > 5.154041 74 > -1.382000 -4.745000 1.662000 3 H > 5.214134 75 > -4.736000 1.135000 1.925000 5 O > 5.236750 76 > -2.871000 -4.398000 0.183000 3 H > 5.255334 77 > -3.300000 -3.904000 -1.277000 3 H > 5.268961 78 > -4.074000 -3.355000 0.011000 3 H > 5.277653 79 > -1.914000 -0.761000 -4.955000 1 C > 5.366055 80 > 0.046000 3.646000 -3.941000 1 C > 5.369070 81 > -1.698000 -3.672000 -3.533000 3 H > 5.371115 82 > -2.633000 -0.152000 -4.682000 3 H > 5.373725 83 > -0.880000 -2.379000 4.741000 1 C > 5.376906 84 > -3.372000 -3.278000 2.760000 1 C > 5.452822 85 > 0.671000 1.054000 5.308000 1 C > 5.453074 86 > -0.293000 -1.712000 5.177000 3 H > 5.460597 87 > -4.181000 -1.407000 3.261000 3 H > 5.485848 88 > -1.200000 -0.248000 -5.388000 3 H > 5.525581 89 > 3.795000 3.637000 -1.723000 1 C > 5.531593 90 > 0.151000 1.882000 5.232000 3 H > 5.562243 91 > -5.154000 2.141000 -0.214000 1 C > 5.585105 92 > -0.348000 -3.198000 4.579000 3 H > 5.596030 93 > -4.430000 -2.157000 2.662000 1 C > 5.600339 94 > 0.099000 0.341000 5.663000 3 H > 5.674121 95 > -0.746000 -3.186000 -4.728000 3 H > 5.749878 96 > -1.148000 -4.612000 3.238000 3 H > 5.750921 97 > -5.597000 1.049000 -0.967000 5 O > 5.775976 98 > -4.998000 1.024000 2.714000 3 H > 5.778787 99 > -1.369000 -4.479000 -3.414000 4 N > 5.795774 100 > -3.647000 -4.018000 2.164000 3 H > 5.841903 101 > 4.578000 3.552000 -1.141000 3 H > 5.905647 102 > -1.672000 -4.987000 -2.760000 3 H > 5.939979 103 > 3.263000 -0.429000 5.058000 1 C > 6.034449 104 > -5.655000 1.939000 1.236000 1 C > 6.104625 105 > 5.047000 1.380000 -3.248000 1 C > 6.158418 106 > -6.144000 -0.550000 0.157000 3 H > 6.170566 107 > -3.372000 -3.628000 3.685000 3 H > 6.173491 108 > 1.428000 1.198000 5.912000 3 H > 6.198882 109 > -3.234000 -5.327000 -0.151000 1 C > 6.233658 110 > -0.566000 -6.250000 0.206000 1 C > 6.278956 111 > -5.537000 2.986000 -0.588000 3 H > 6.318252 112 > -0.435000 -4.923000 -4.197000 1 C > 6.483823 113 > -4.129000 -5.031000 -0.254000 3 H > 6.513380 114 > 4.649000 1.240000 -4.419000 5 O > 6.532868 115 > -4.629000 -2.157000 -4.093000 1 C > 6.544688 116 > -6.579000 0.277000 -0.201000 1 C > 6.587896 117 > 3.946000 0.575000 5.254000 5 O > 6.595912 118 > -2.062000 -2.707000 5.670000 1 C > 6.612760 119 > -0.029000 -4.281000 -5.051000 5 O > 6.621209 120 > -2.897000 -4.497000 3.921000 5 O > 6.632485 121 > -5.819000 2.808000 1.704000 3 H > 6.682009 122 > -4.241000 -1.749000 -4.909000 3 H > 6.718881 123 > 2.890000 -2.118000 5.767000 3 H > 6.789427 124 > -2.956000 -1.850000 5.836000 5 O > 6.798480 125 > 3.365000 -1.387000 5.883000 4 N > 6.917852 126 > -5.795000 -2.719000 3.077000 1 C > 7.102318 127 > 6.519000 1.843000 -2.135000 3 H > 7.102974 128 > -6.958000 1.182000 0.953000 1 C > 7.121734 129 > -5.572000 -1.864000 -4.025000 3 H > 7.121959 130 > 6.265000 1.753000 -2.972000 4 N > 7.152344 131 > -4.584000 -3.642000 -4.220000 1 C > 7.217037 132 > -6.768000 -0.507000 -2.663000 3 H > 7.290709 133 > -4.900000 -4.410000 -3.269000 5 O > 7.358292 134 > -6.097000 -1.290000 4.274000 3 H > 7.556758 135 > -2.049000 -3.867000 6.278000 4 N > 7.652802 136 > -7.386000 0.433000 2.084000 5 O > 7.686582 137 > -1.394000 -4.435000 6.126000 3 H > 7.690275 138 > -7.333000 -0.912000 -2.191000 5 O > 7.707471 139 > -6.196000 -3.784000 2.591000 5 O > 7.708590 140 > 3.913000 -1.320000 6.566000 3 H > 7.756695 141 > -7.697000 -0.106000 -1.106000 1 C > 7.776778 142 > -6.460000 -2.026000 3.953000 4 N > 7.839801 143 > -7.673000 1.820000 0.672000 3 H > 7.914475 144 > 6.835000 1.912000 -3.624000 3 H > 7.969087 145 > -4.202000 -4.117000 -5.391000 4 N > 7.979309 146 > -3.986000 -3.564000 -6.042000 3 H > 8.068213 147 > -8.116000 0.720000 -1.452000 3 H > 8.276241 148 > -6.953000 -4.513000 1.270000 5 O > 8.385957 149 > -2.691000 -4.077000 6.838000 3 H > 8.403669 150 > -8.380000 -0.585000 -0.571000 3 H > 8.419778 151 > -4.162000 -4.987000 -5.524000 3 H > 8.526839 152 > -8.821000 0.724000 2.726000 2 P > 9.260955 153 > -7.794000 -2.418000 4.430000 1 C > 9.285368 154 > -8.760000 -1.946000 2.636000 3 H > 9.352701 155 > -7.884000 -3.402000 4.375000 3 H > 9.636996 156 > -8.812000 -0.362000 3.897000 5 O > 9.642043 157 > -8.891000 -1.772000 3.614000 1 C > 9.759655 158 > -7.894000 -2.154000 5.378000 3 H > 9.791723 159 > -8.993000 2.042000 3.320000 5 O > 9.801337 160 > -9.840000 0.431000 1.688000 5 O > 9.993033 161 > -10.251000 -2.267000 4.070000 1 C > 11.259982 162 > -10.331000 -3.225000 3.886000 3 H > 11.499182 163 > -10.955000 -1.781000 3.591000 3 H > 11.665302 164 > -10.348000 -2.113000 5.035000 3 H > 11.700303 165 > END > > On Fri, Aug 28, 2015 at 2:03 PM, < > ifeffit-request(a)millenia.cars.aps.anl.gov> > wrote: > > > 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: Error in Running XANES on FEFF8.4 for Cobalt based > > cluster (Ganesh Subramanian) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 28 Aug 2015 14:03:16 -0700 > > From: Ganesh Subramanian <gunkanna(a)gmail.com> > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > based cluster > > Message-ID: > > <CAAb9e-c_jTi=+KbQi6gPzYVNnSoikXAF= > > eYHtKkfSHWE+_y-kw(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Bruce, > > > > Thanks for the response and sorry for the delay in getting back to you. > > > > I retried the FEFF simulation using structural information from another > > article (Randaccio, Lucio, et al. *Inorganic chemistry* 39.15 (2000): > > 3403-3413). The structural data from this article seems to be widely used > > by many others in simulating for optical absorption. But here with FEFF, > I > > still run into the same issue of "ATOMS VERY CLOSE TOGETHER" and a couple > > of other issues. With two different articles suggesting smaller bond > > distances for a few of their atoms, it seems like the distances are what > > they are. > > > > I have attached the log files and input file for this trial run. > > > > Is there any way to circumvent this error without altering the structure > ? > > > > Thanks, > > > > Ganesh > > > > > > > From: Bruce Ravel <bravel(a)bnl.gov> > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > > based cluster > > > Message-ID: <55BA3978.4080801(a)bnl.gov> > > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > > > On 07/29/2015 06:01 PM, Ganesh Subramanian wrote: > > > > 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') > > > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > > when you have atoms that are separated by 1.75 Angstroms or less. That > > > message has nothing to do with the FOLP setting. > > > > > > > 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') > > > > > > When I ran feff 8.40, I got same the contents of the log1.dat file, but > > > with these additional lines: > > > > > > Core-valence separation > > > WARNING: fatal error in subroutine corval. Try > > > to reduce ca1 in SCF card. If does not help, > > > SEND bug report to AUTHORS > > > CORVAL-1 > > > > > > I don't quite know what that means, but it gives some hints. The > source > > > code corval.f tells us that is "Finds the core-valence separation for > > > the cluster of atoms." I simply am not knowledgeable enough about the > > > details of Feff to know why your cluster triggered this warning. > > > > > > B > > > > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > 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/ > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Thu, 30 Jul 2015 10:51:30 -0400 > > > From: Bruce Ravel <bravel(a)bnl.gov> > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > > based cluster > > > Message-ID: <55BA39F2.4090609(a)bnl.gov> > > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > > > On 07/30/2015 10:49 AM, Bruce Ravel wrote: > > > >> 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') > > > > > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at > you > > > > when you have atoms that are separated by 1.75 Angstroms or less. > That > > > > message has nothing to do with the FOLP setting. > > > > > > Oops! That message is triggered for atoms separated by 1.75 bohr, > which > > > is about 0.92 Angstrom. > > > > > > B > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > 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/ > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Thu, 30 Jul 2015 15:58:12 +0000 > > > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > > > To: "ifeffit(a)millenia.cars.aps.anl.gov" > > > <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > > Message-ID: <D1759C33-50D0-46D4-84D0-4D649CA779A8(a)nist.gov> > > > Content-Type: text/plain; charset="windows-1252" > > > > > > 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 > > > > > > > > > On Jul 29, 2015, at 4:01 PM, ifeffit-request(a)millenia.cars.aps.anl.gov > > > <mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: > > > > > > Send Ifeffit mailing list submissions to > > > ifeffit(a)millenia.cars.aps.anl.gov<mailto: > > 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: 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(a)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(a)millenia.cars.aps.anl.gov" < > > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > Reply-To: XAFS Analysis using Ifeffit < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > > > > > 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(a)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(a)millenia.cars.aps.anl.gov> > > > Reply-To: XAFS Analysis using Ifeffit < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > > > > > 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 > > > > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > 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/ > > > > > > > > > > > >

1 0

Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster
by Joshua Kas 30 Aug '15

30 Aug '15

Hi Ganesh, It is common to see the WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. warning from feff when you have H atoms since the bonds tend to be very short. However, these are not the ones that are causing the problem. These warning can be ignored if the structure is reasonable. If the structure at the bottom of this email is the input structure that you used, then there is indeed an oxygen atom that is less than 0.1 angstrom from a carbon atom, which is of course unphysical. That is probably what is causing the problem, however, there are some other things that could be causing problems as well. In particular, there are what I like to call "floating atoms" in your file, i.e., single atoms or several atoms that are disconnected from the rest of the cluster. I am sending a new input file below that has fixed this problem. I deleted the O atom that was too close to the C atom, and deleted all of the structure that wasn't connected to the central atom by a string of bonds. You might worry about weather the C or O atom is the one that should have been deleted in the structure, but you can always test using both possibilities. I doubt that it will make much difference since C and O look pretty similar, and the O atom is pretty far from the Co. Also, the H atoms look a bit messed up, but I don't think that will make much of a difference either. You can check by taking the H atoms out and running and see if the results change much. Cheers, Josh Kas * Al K edge energy = 1559.0 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 CORRECTIONS 0 1 * *** 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 0 * *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 8.0 * *** Radius of cluster for Full Multiple * *** Scattering calculation * *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6 0 * *** Energy grid over which to calculate * *** DOS functions * emin emax eimag *LDOS -30 20 0.1 FOLP 3 0.8 POTENTIALS 0 27 Co -1 -1 1 6 C -1 -1 2 15 P -1 -1 3 1 H -1 -1 4 7 N -1 -1 5 8 O -1 -1 ATOMS 0.000000 0.000000 0.000000 0 Co 0.000000 1 -0.877000 -1.130000 1.209000 4 N 1.872888 2 0.706000 0.763000 1.563000 4 N 1.877119 3 -0.886000 -0.853000 -1.472000 4 N 1.918173 4 1.117000 1.157000 -1.052000 4 N 1.921729 5 1.456000 -1.334000 -0.126000 1 C 1.978729 6 -1.601000 1.453000 -0.068000 4 N 2.163107 7 1.122000 -2.209000 0.163000 3 H 2.482969 8 1.765000 -1.394000 -1.054000 3 H 2.483823 9 2.201000 -1.061000 0.448000 3 H 2.484115 10 -0.328000 -1.105000 2.581000 1 C 2.826689 11 1.045000 1.233000 -2.389000 1 C 2.884378 12 0.051000 0.367000 2.864000 1 C 2.887869 13 1.756000 1.481000 1.751000 1 C 2.888408 14 -0.659000 -0.537000 -2.771000 1 C 2.898464 15 -1.715000 -2.120000 1.053000 1 C 2.923086 16 -1.810000 -1.877000 -1.395000 1 C 2.957238 17 2.263000 1.829000 -0.603000 1 C 2.971535 18 -2.864000 1.125000 -0.216000 1 C 3.084603 19 0.509000 -1.655000 2.598000 3 H 3.122132 20 -3.165000 0.225000 -0.264000 3 H 3.183951 21 -1.881000 -2.521000 -0.717000 3 H 3.226095 22 0.212000 0.468000 -3.185000 1 C 3.226173 23 0.260000 -3.225000 -0.293000 3 H 3.248703 24 -1.605000 2.854000 0.000000 1 C 3.274346 25 -1.931000 0.869000 2.513000 3 H 3.286197 26 2.614000 1.957000 0.706000 1 C 3.340850 27 -2.232000 -2.499000 -0.241000 1 C 3.359301 28 -2.287000 -2.542000 0.830000 3 H 3.518669 29 -1.207000 1.214000 3.075000 1 C 3.519413 30 -1.019000 2.145000 2.831000 3 H 3.695125 31 0.186000 -3.470000 1.287000 3 H 3.705653 32 -2.458000 -2.943000 -0.050000 1 C 3.834777 33 0.288000 -3.903000 0.413000 1 C 3.935343 34 -1.387000 -1.820000 3.396000 1 C 4.094995 35 2.553000 -0.694000 3.132000 3 H 4.099862 36 1.198000 0.646000 3.906000 1 C 4.136346 37 0.236000 0.648000 -4.119000 3 H 4.176333 38 1.974000 1.827000 3.218000 1 C 4.194059 39 1.979000 2.281000 -2.920000 1 C 4.200691 40 -1.954000 -2.872000 2.399000 1 C 4.221576 41 -1.356000 -1.474000 -3.722000 1 C 4.226665 42 3.077000 2.276000 -1.823000 1 C 4.239273 43 -2.379000 -2.161000 -2.783000 1 C 4.251429 44 -3.699000 2.187000 -0.292000 4 N 4.307068 45 -2.114000 -1.164000 3.595000 3 H 4.329886 46 4.151130 0.213470 -1.476130 3 H 4.410942 47 -3.398000 -2.805000 -0.293000 3 H 4.415912 48 -2.914000 3.318000 -0.141000 1 C 4.418190 49 -1.477000 1.171000 4.015000 3 H 4.435425 50 0.084000 -2.932000 -3.384000 3 H 4.478296 51 -0.139000 -3.903000 2.219000 3 H 4.491847 52 1.145000 -4.375000 0.380000 3 H 4.538287 53 2.138000 -0.543000 4.017000 1 C 4.582814 54 1.599000 -1.345000 4.232000 3 H 4.719709 56 4.110000 1.128000 -2.086000 1 C 4.745090 57 2.947000 1.705000 3.417000 3 H 4.823663 58 -3.841000 -0.653000 -2.863000 3 H 4.834921 59 3.949000 2.548000 1.146000 1 C 4.837377 60 -3.203000 -3.637000 -0.340000 1 C 4.858248 61 -0.314000 -2.507000 -4.171000 1 C 4.876565 62 2.363000 1.996000 -3.799000 3 H 4.898998 63 -1.074000 -4.151000 2.377000 1 C 4.902490 64 -2.168000 -4.410000 0.005000 1 C 4.914097 65 -2.368000 -3.147000 -2.947000 3 H 4.918927 66 1.290000 3.658000 -3.054000 1 C 4.936799 67 -0.837000 -4.889000 0.206000 1 C 4.964406 68 0.666000 3.369000 3.643000 3 H 5.006512 69 1.635000 3.289000 3.463000 1 C 5.048080 70 -3.849000 -1.643000 -2.849000 1 C 5.062712 71 -4.475000 -1.815000 1.737000 3 H 5.131961 72 0.388000 -2.058000 -4.689000 3 H 5.135429 73 -4.326000 -1.930000 -2.031000 3 H 5.154041 74 -1.382000 -4.745000 1.662000 3 H 5.214134 75 -4.736000 1.135000 1.925000 5 O 5.236750 76 -2.871000 -4.398000 0.183000 3 H 5.255334 77 -3.300000 -3.904000 -1.277000 3 H 5.268961 78 -4.074000 -3.355000 0.011000 3 H 5.277653 79 -1.914000 -0.761000 -4.955000 1 C 5.366055 80 0.046000 3.646000 -3.941000 1 C 5.369070 81 -1.698000 -3.672000 -3.533000 3 H 5.371115 82 -2.633000 -0.152000 -4.682000 3 H 5.373725 83 -0.880000 -2.379000 4.741000 1 C 5.376906 84 -3.372000 -3.278000 2.760000 1 C 5.452822 85 0.671000 1.054000 5.308000 1 C 5.453074 86 -0.293000 -1.712000 5.177000 3 H 5.460597 87 -4.181000 -1.407000 3.261000 3 H 5.485848 88 -1.200000 -0.248000 -5.388000 3 H 5.525581 89 3.795000 3.637000 -1.723000 1 C 5.531593 90 0.151000 1.882000 5.232000 3 H 5.562243 91 -5.154000 2.141000 -0.214000 1 C 5.585105 92 -0.348000 -3.198000 4.579000 3 H 5.596030 93 -4.430000 -2.157000 2.662000 1 C 5.600339 94 0.099000 0.341000 5.663000 3 H 5.674121 95 -0.746000 -3.186000 -4.728000 3 H 5.749878 96 -1.148000 -4.612000 3.238000 3 H 5.750921 97 -5.597000 1.049000 -0.967000 5 O 5.775976 98 -4.998000 1.024000 2.714000 3 H 5.778787 99 -1.369000 -4.479000 -3.414000 4 N 5.795774 100 -3.647000 -4.018000 2.164000 3 H 5.841903 101 4.578000 3.552000 -1.141000 3 H 5.905647 102 -1.672000 -4.987000 -2.760000 3 H 5.939979 103 3.263000 -0.429000 5.058000 1 C 6.034449 104 -5.655000 1.939000 1.236000 1 C 6.104625 105 5.047000 1.380000 -3.248000 1 C 6.158418 106 -6.144000 -0.550000 0.157000 3 H 6.170566 107 -3.372000 -3.628000 3.685000 3 H 6.173491 108 1.428000 1.198000 5.912000 3 H 6.198882 109 -3.234000 -5.327000 -0.151000 1 C 6.233658 110 -0.566000 -6.250000 0.206000 1 C 6.278956 111 -5.537000 2.986000 -0.588000 3 H 6.318252 112 -0.435000 -4.923000 -4.197000 1 C 6.483823 113 -4.129000 -5.031000 -0.254000 3 H 6.513380 114 4.649000 1.240000 -4.419000 5 O 6.532868 115 -4.629000 -2.157000 -4.093000 1 C 6.544688 116 -6.579000 0.277000 -0.201000 1 C 6.587896 117 3.946000 0.575000 5.254000 5 O 6.595912 118 -2.062000 -2.707000 5.670000 1 C 6.612760 119 -0.029000 -4.281000 -5.051000 5 O 6.621209 120 -2.897000 -4.497000 3.921000 5 O 6.632485 121 -5.819000 2.808000 1.704000 3 H 6.682009 122 -4.241000 -1.749000 -4.909000 3 H 6.718881 123 2.890000 -2.118000 5.767000 3 H 6.789427 124 -2.956000 -1.850000 5.836000 5 O 6.798480 125 3.365000 -1.387000 5.883000 4 N 6.917852 126 -5.795000 -2.719000 3.077000 1 C 7.102318 127 6.519000 1.843000 -2.135000 3 H 7.102974 128 -6.958000 1.182000 0.953000 1 C 7.121734 129 -5.572000 -1.864000 -4.025000 3 H 7.121959 130 6.265000 1.753000 -2.972000 4 N 7.152344 131 -4.584000 -3.642000 -4.220000 1 C 7.217037 132 -6.768000 -0.507000 -2.663000 3 H 7.290709 133 -4.900000 -4.410000 -3.269000 5 O 7.358292 134 -6.097000 -1.290000 4.274000 3 H 7.556758 135 -2.049000 -3.867000 6.278000 4 N 7.652802 136 -7.386000 0.433000 2.084000 5 O 7.686582 137 -1.394000 -4.435000 6.126000 3 H 7.690275 138 -7.333000 -0.912000 -2.191000 5 O 7.707471 139 -6.196000 -3.784000 2.591000 5 O 7.708590 140 3.913000 -1.320000 6.566000 3 H 7.756695 141 -7.697000 -0.106000 -1.106000 1 C 7.776778 142 -6.460000 -2.026000 3.953000 4 N 7.839801 143 -7.673000 1.820000 0.672000 3 H 7.914475 144 6.835000 1.912000 -3.624000 3 H 7.969087 145 -4.202000 -4.117000 -5.391000 4 N 7.979309 146 -3.986000 -3.564000 -6.042000 3 H 8.068213 147 -8.116000 0.720000 -1.452000 3 H 8.276241 148 -6.953000 -4.513000 1.270000 5 O 8.385957 149 -2.691000 -4.077000 6.838000 3 H 8.403669 150 -8.380000 -0.585000 -0.571000 3 H 8.419778 151 -4.162000 -4.987000 -5.524000 3 H 8.526839 152 -8.821000 0.724000 2.726000 2 P 9.260955 153 -7.794000 -2.418000 4.430000 1 C 9.285368 154 -8.760000 -1.946000 2.636000 3 H 9.352701 155 -7.884000 -3.402000 4.375000 3 H 9.636996 156 -8.812000 -0.362000 3.897000 5 O 9.642043 157 -8.891000 -1.772000 3.614000 1 C 9.759655 158 -7.894000 -2.154000 5.378000 3 H 9.791723 159 -8.993000 2.042000 3.320000 5 O 9.801337 160 -9.840000 0.431000 1.688000 5 O 9.993033 161 -10.251000 -2.267000 4.070000 1 C 11.259982 162 -10.331000 -3.225000 3.886000 3 H 11.499182 163 -10.955000 -1.781000 3.591000 3 H 11.665302 164 -10.348000 -2.113000 5.035000 3 H 11.700303 165 END On Fri, Aug 28, 2015 at 2:03 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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: Error in Running XANES on FEFF8.4 for Cobalt based > cluster (Ganesh Subramanian) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 28 Aug 2015 14:03:16 -0700 > From: Ganesh Subramanian <gunkanna(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: > <CAAb9e-c_jTi=+KbQi6gPzYVNnSoikXAF= > eYHtKkfSHWE+_y-kw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Bruce, > > Thanks for the response and sorry for the delay in getting back to you. > > I retried the FEFF simulation using structural information from another > article (Randaccio, Lucio, et al. *Inorganic chemistry* 39.15 (2000): > 3403-3413). The structural data from this article seems to be widely used > by many others in simulating for optical absorption. But here with FEFF, I > still run into the same issue of "ATOMS VERY CLOSE TOGETHER" and a couple > of other issues. With two different articles suggesting smaller bond > distances for a few of their atoms, it seems like the distances are what > they are. > > I have attached the log files and input file for this trial run. > > Is there any way to circumvent this error without altering the structure ? > > Thanks, > > Ganesh > > > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > based cluster > > Message-ID: <55BA3978.4080801(a)bnl.gov> > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 07/29/2015 06:01 PM, Ganesh Subramanian wrote: > > > 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') > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > when you have atoms that are separated by 1.75 Angstroms or less. That > > message has nothing to do with the FOLP setting. > > > > > 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') > > > > When I ran feff 8.40, I got same the contents of the log1.dat file, but > > with these additional lines: > > > > Core-valence separation > > WARNING: fatal error in subroutine corval. Try > > to reduce ca1 in SCF card. If does not help, > > SEND bug report to AUTHORS > > CORVAL-1 > > > > I don't quite know what that means, but it gives some hints. The source > > code corval.f tells us that is "Finds the core-valence separation for > > the cluster of atoms." I simply am not knowledgeable enough about the > > details of Feff to know why your cluster triggered this warning. > > > > B > > > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > 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/ > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 30 Jul 2015 10:51:30 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > based cluster > > Message-ID: <55BA39F2.4090609(a)bnl.gov> > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 07/30/2015 10:49 AM, Bruce Ravel wrote: > > >> 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') > > > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > > when you have atoms that are separated by 1.75 Angstroms or less. That > > > message has nothing to do with the FOLP setting. > > > > Oops! That message is triggered for atoms separated by 1.75 bohr, which > > is about 0.92 Angstrom. > > > > B > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > 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/ > > > > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 30 Jul 2015 15:58:12 +0000 > > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > > To: "ifeffit(a)millenia.cars.aps.anl.gov" > > <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > Message-ID: <D1759C33-50D0-46D4-84D0-4D649CA779A8(a)nist.gov> > > Content-Type: text/plain; charset="windows-1252" > > > > 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 > > > > > > On Jul 29, 2015, at 4:01 PM, ifeffit-request(a)millenia.cars.aps.anl.gov > > <mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: > > > > Send Ifeffit mailing list submissions to > > ifeffit(a)millenia.cars.aps.anl.gov<mailto: > 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: 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(a)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(a)millenia.cars.aps.anl.gov" < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > 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(a)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(a)millenia.cars.aps.anl.gov> > > Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > 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 > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > 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/ > > > > > > > >

1 0

Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster
by Ganesh Subramanian 28 Aug '15

28 Aug '15

Dear Bruce, Thanks for the response and sorry for the delay in getting back to you. I retried the FEFF simulation using structural information from another article (Randaccio, Lucio, et al. *Inorganic chemistry* 39.15 (2000): 3403-3413). The structural data from this article seems to be widely used by many others in simulating for optical absorption. But here with FEFF, I still run into the same issue of "ATOMS VERY CLOSE TOGETHER" and a couple of other issues. With two different articles suggesting smaller bond distances for a few of their atoms, it seems like the distances are what they are. I have attached the log files and input file for this trial run. Is there any way to circumvent this error without altering the structure ? Thanks, Ganesh > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: <55BA3978.4080801(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 07/29/2015 06:01 PM, Ganesh Subramanian wrote: > > 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') > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > when you have atoms that are separated by 1.75 Angstroms or less. That > message has nothing to do with the FOLP setting. > > > 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') > > When I ran feff 8.40, I got same the contents of the log1.dat file, but > with these additional lines: > > Core-valence separation > WARNING: fatal error in subroutine corval. Try > to reduce ca1 in SCF card. If does not help, > SEND bug report to AUTHORS > CORVAL-1 > > I don't quite know what that means, but it gives some hints. The source > code corval.f tells us that is "Finds the core-valence separation for > the cluster of atoms." I simply am not knowledgeable enough about the > details of Feff to know why your cluster triggered this warning. > > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > 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/ > > > ------------------------------ > > Message: 3 > Date: Thu, 30 Jul 2015 10:51:30 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: <55BA39F2.4090609(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 07/30/2015 10:49 AM, Bruce Ravel wrote: > >> 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') > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > when you have atoms that are separated by 1.75 Angstroms or less. That > > message has nothing to do with the FOLP setting. > > Oops! That message is triggered for atoms separated by 1.75 bohr, which > is about 0.92 Angstrom. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > 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/ > > > ------------------------------ > > Message: 4 > Date: Thu, 30 Jul 2015 15:58:12 +0000 > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > Message-ID: <D1759C33-50D0-46D4-84D0-4D649CA779A8(a)nist.gov> > Content-Type: text/plain; charset="windows-1252" > > 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 > > > On Jul 29, 2015, at 4:01 PM, ifeffit-request(a)millenia.cars.aps.anl.gov > <mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@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: 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(a)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(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov > > > Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > 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(a)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(a)millenia.cars.aps.anl.gov> > Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > 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 > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > 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/ > > > >

1 0

Academic Career Opportunity in X-ray Spectroscopy at the University of Leeds
by Sven L. M. Schroeder 23 Aug '15

23 Aug '15

Dear colleagues I would like to advertise an exciting career opportunity for an X-ray spectroscopist at the University of Leeds. Leeds is one of the top 10 research-intensive Universities in the UK. Through our international academic recruitment programme ( http://250greatminds.leeds.ac.uk ) we wish to consolidate our strategic relationship with Diamond Light Source by appointing a University Academic Fellow in Structure-Function Determination in Complex Soft Matter Systems Chemical product and process engineering can now take advantage of structure analysis with a broad range of X-ray techniques that have become available at the UKs synchrotron radiation source, DIAMOND. The focus of the research is to determine structure information across length scales, ideally in situ under process conditions, and from molecular to macroscopic dimensions, and to combine such information with multi-scale models to generate a seamless understanding of the relationships between microstructure, processing conditions and product performance. The Fellowship is an exciting opportunity for an engineer or physical scientist with an interest in determining structural/performance relationships in complex products, particularly soft matter systems, with synchrotron radiation techniques. Salary: £38,511 to £45,954 Closing Date: Wednesday 30 September 2015 Reference: ENGPE1026 Career Pathway: Successful completion of a 5 year probationary period leading to appointment to Grade 9, Associate Professor. More particulars are available at: https://jobs.leeds.ac.uk/Upload/vacancies/files/2719/ENGPE1026 - UAF in Structure-Function Determination in Complex Soft Matter1.pdf <https://jobs.leeds.ac.uk/Upload/vacancies/files/2719/ENGPE1026%20-%20UAF%20 in%20Structure-Function%20Determination%20in%20Complex%20Soft%20Matter1.pdf> For informal enquiries about the role please feel free to contact me as per details below. -- Sven L. M. Schroeder Royal Academy of Engineering Bragg Centenary Chair School of Chemical and Process Engineering | Institute for Particle Science and Engineering (IPSE) | University of Leeds | Leeds LS2 9JT | UK Room 2.22 | Engineering Building T +44 (0)113 343 2401 | PA/secretary (Kirn Jutlla) +44 (0)113 343 2404 | F +44 (0)113 343 2384 E <mailto:s.l.m.schroeder@leeds.ac.uk> s.l.m.schroeder(a)leeds.ac.uk | W <https://www.engineering.leeds.ac.uk/people/staff/s.l.m.schroeder> https://www.engineering.leeds.ac.uk/people/staff/s.l.m.schroeder

1 0

Re: [Ifeffit] XANES simulation K-edges
by Joshua Kas 19 Aug '15

19 Aug '15

Hi Debora, The edge energies are very difficult to calculate, and FEFF only calculates them to roughly 5% accuracy. In this case the accuracy is actually much better. However, relative edge energies between different systems may be more reliable. Most comparisons between theoretical and experimental XANES allow for a shift of the edge to align the spectra. If the comparison is of several systems, a single shift should be used for all of them. Cheers, Josh Kas On Wed, Aug 19, 2015 at 10:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > 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. XANES simulation K-edges (Debora Meira) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Aug 2015 08:50:47 +0000 > From: Debora Meira <debsmeira(a)hotmail.com> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XANES simulation K-edges > Message-ID: <BLU181-W70FD27721CD14A2C97998CAD670(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > I'd like to know which kind of concern I should have for feff to simulate > the XANES for K-edges. I'm asking because I'm trying to simulate Sn K-edge > and I have around 30 eV energy shift for the edge position. Can it be > related with a wrong parameter for one of the cards? > Thank you, Debora Meira >

1 0

XANES simulation K-edges
by Debora Meira 19 Aug '15

19 Aug '15

Dear all, I'd like to know which kind of concern I should have for feff to simulate the XANES for K-edges. I'm asking because I'm trying to simulate Sn K-edge and I have around 30 eV energy shift for the edge position. Can it be related with a wrong parameter for one of the cards? Thank you, Debora Meira

1 0

MacPorts now contains Demeter 0.9.22 (and requires Perl 5.22)
by Fowler, Joseph W. 14 Aug '15

14 Aug '15

Dear Bruce: Wait a minute! In fact, I updated the Mac Ports package demeter within the last two weeks to use Demeter version 0.9.22. Mac users might want to use the latest version and should consider doing a "port self update && port upgrade demeter". Users who installed the development version port called demeter-devel will also land on 0.9.22 if they upgrade to the latest. Note that the latest Mac Ports version is known as 0.9.22_1, where the revision number _1 corresponds to the upgrade from Perl 5.16 to 5.22 (which the MacPorts team is pushing on). For many users, there will be numerous dependency upgrades when you upgrade to 0.9.22_1, but I found they took only a few minutes in my particular case. This change in Perl versions could conceivably cause problems, but I haven't heard of any. Best wishes, Joe Fowler (MacPorts maintainer for demeter) ________________________________ From: Bruce Ravel <bravel(a)bnl.gov> Sent: Tuesday, August 11, 2015 6:55 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Energy shift after deglitch I don't see the behavior you describe when I follow your recipe. Perhaps it got fixed when I fixed this fellow's issue...? http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-May/012496.html Of course, the Mac package is a fair bit behind at this point. B On 08/06/2015 06:10 PM, George Sterbinsky wrote: > Hello, > > I am writing to report a bug in Athena running on OSX 10.10.4. Here are > the steps to reproduce the problem. I'm not sure that all steps are > necessary. > > 1. Open Athena and import the attached project, which contains two > groups that are both marked. > 2. Change plot range to plot from -30 to 30 eV. > 3. Select the "deglitch and truncate" window. > 4. Select group "Ref data.merge". > 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to > -20. > 6. Click replot margins. > 7. Click remove points. > 8. Click return to main window. > 9. Click the derivative check box to plot marked groups as normalized > derivative. > 10. Click mu(E) button to plot marked groups as derivative of mu(E). > > When the last step is done the groups appear to shift with respect to > each other. One can switch between Normalized and mu(E) and see the > shift come and go. > > Thank you, > George > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov 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/

2 3

La2Zr2O7 EXAFS fitting
by herve muguerra 14 Aug '15

14 Aug '15

Dear All, First of all, I am still very new in EXAFS analysis, so please excuse me for any misunderstandings. My sample is a crystalized La2Zr2O7 thin layer (thickness = 100 nm) on a NiW substrate and we have realized EXAFS measurements by grazing angle under primary vacuum at Lathanum L3 edge (ESRF, Grenoble, France). My objectives are to establish the local distortions due to the different constraints in the oxide thin layer. The La2zr2O7 crystalized in a pyrochlore structure (SG = Fd-3m ; a = 10.78A). First scattering path La-O2.1 2.3352A La-O1.1 2.6453A But I have a problem: I observe the first peaks at 1.28A and 1.80A on the EXAFS spectra as a function of R. How do you explain this feature? Can you point me in the right direction for these issues? I attached the project file La_80_LZO_1000.prj of my sample: LAHM045 to LAHM50 = 6 different scans La_80_LZO_1000 = Data merge Thanks Best regards Hervé Muguerra

2 1