Hi to all,
Does someone has already written an Ifeffit script calculating a contour
plot?
In 2003 Norbert opened this thread on "Scanning of Potential Surfaces in
EXAFS":
http://cars9.uchicago.edu/pipermail/ifeffit/2003-July/000398.html
Do you have any "wild code" to send me? :)
Thanks,
Mauro
--
Mauro Rovezzi
On Wednesday 29 March 2006 10:22, Mauro Rovezzi wrote:
Does someone has already written an Ifeffit script calculating a contour plot?
In 2003 Norbert opened this thread on "Scanning of Potential Surfaces in EXAFS":
http://cars9.uchicago.edu/pipermail/ifeffit/2003-July/000398.html
Do you have any "wild code" to send me? :)
That could certainly be done in pure Ifeffit, however I think that computing a contour would be better done using one of the scripting interfaces to Ifeffit. Ifeffit doesn't have any flow control. To compute a contour you would want to loop over values of at least two parameters. You can certainly just type out (or cut and paste and edit) Ifeffit commands to do something at each point in the contour, but that would be tedious and error prone to use once. And it would be horridly tedious and error prone to modify. So my advice would be to look at the Ifeffit buffer of Athena or Artemis to get an idea for what you want to do. Use that as the basis of the script, then use python or perl or some other high level language to do the looping and to gather up the results. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hello again, The reason I was looking through the Lytle database was that I was looking for a standard I could use for an iron boron compound (more iron than boron). The database has one as "raw" data, but I don't recognize the format. The headers look like: CUEDGE START STOP BEG FSCTS: 168620. 230500. 174080. 272000. 30. DELTA: 2000. 15. 90. 150. 210. DELEND: 217740. 214450. 200860. 187700. 174080. SEC: 1. 1. 1. 1. 1. Does anyone recognize this? Alternatively, does anyone have a standard for an iron boron compound? --Scott Calvin Sarah Lawrence College
On Wednesday 29 March 2006 13:13, Scott Calvin wrote:
Hello again,
The reason I was looking through the Lytle database was that I was looking for a standard I could use for an iron boron compound (more iron than boron). The database has one as "raw" data, but I don't recognize the format. The headers look like:
CUEDGE START STOP BEG FSCTS: 168620. 230500. 174080. 272000. 30. DELTA: 2000. 15. 90. 150. 210. DELEND: 217740. 214450. 200860. 187700. 174080. SEC: 1. 1. 1. 1. 1.
Does anyone recognize this?
Scott, The first column of the data is almost certainly encoder reading. Assume that the data were measured with a Si crystal and one of the common faces. If you assume that the CUEDGE is the encoder reading of 8979 eV and that 7112 eV must lie between 230500 and 174080, you should be able to figure out (using Bragg's law) what the number of steps per degree is and what the zero offset is. From there, it's just a few lines of Ifeffit to convert the data file into something Athena can grok. B P.S. I would *love* to know the beer back story also. Why don't I ever get research projects that involve beer? -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hi Scott, If I understand correctly, you want to transform the motor steps into energy values, am I right? Try with dspace= 1.92017 and stepdeg= 8000 You should get that a CUEDGE of 168620 gives 8977.32 eV Hope this info help you Best, Marco on 29/03/2006 15:13 Scott Calvin wrote:
Hello again,
The reason I was looking through the Lytle database was that I was looking for a standard I could use for an iron boron compound (more iron than boron). The database has one as "raw" data, but I don't recognize the format. The headers look like:
CUEDGE START STOP BEG FSCTS: 168620. 230500. 174080. 272000. 30. DELTA: 2000. 15. 90. 150. 210. DELEND: 217740. 214450. 200860. 187700. 174080. SEC: 1. 1. 1. 1. 1.
Does anyone recognize this?
Alternatively, does anyone have a standard for an iron boron compound?
--Scott Calvin Sarah Lawrence College
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Marco A. Alsina Estudiante de Magíster Ingeniería Hidráulica y Ambiental UC Vicuña Mackenna 4860, Macul Chile tel: (56 2) 354 4873
Hi Scott, If I understand correctly, you want to transform the motor steps into energy values, am I right? Try with dspace= 1.92017 and stepdeg= 8000 You should get that a CUEDGE of 168620 gives 8977.32 eV Hope this info help you Best, Marco on 29/03/2006 15:13 Scott Calvin wrote:
Hello again,
The reason I was looking through the Lytle database was that I was looking for a standard I could use for an iron boron compound (more iron than boron). The database has one as "raw" data, but I don't recognize the format. The headers look like:
CUEDGE START STOP BEG FSCTS: 168620. 230500. 174080. 272000. 30. DELTA: 2000. 15. 90. 150. 210. DELEND: 217740. 214450. 200860. 187700. 174080. SEC: 1. 1. 1. 1. 1.
Does anyone recognize this?
Alternatively, does anyone have a standard for an iron boron compound?
--Scott Calvin Sarah Lawrence College
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Marco A. Alsina División de Evaluación y Seguimiento Ambiental Comisión Nacional del Medio Ambiente Teatinos 254 Santiago, Chile tel: (56 2) 240 57 33 fax: (56 2) 240 57 82 Marco A. Alsina Estudiante de Magíster Ingeniería Hidráulica y Ambiental UC Vicuña Mackenna 4860, Macul tel: (56 2) 354 4873
I believe Marco's right, and that you want a script like this: macro read_lytle file group 8000 read_data ($1, group=$2, narrays=2) set (dspace = 1.92017, stpdeg = $3) set (r2d = 57.29577951, hc = 12398.61) set $2.energy = hc / (2 * dspace) / sin($2.1 / (r2d * stpdeg)) set $2.xmu = $2.2 end macro read_lytle beerbottle.dat Sorry the FAQ is so far out of date and the Wiki doesn't have such info. Perhaps someone else would be willing to write a How to Use the Lytle Database on the Wiki or (even better) convert all the data available to a more useful format. --Matt
Not so long ago I also did data mining at the Farrel Lytle database, and here is what I found based on typical values for common faces of Si crystal and step per degree values; CUEDGE dspace stpdeg energy 42147 1.92017 2000 8978.950759 84294 1.92017 4000 8978.950759 50880 3.13562 4000 8979.010145 168620 1.92017 8000 8977.324319 183931 0.96008 4000 8978.996359 337234 1.92017 16000 8977.476771 This should help when someone encounter data files where the dspace or stpdeg entries are missing, and of course fot the macro you will also need to set dspace as a variable; Too bad that macros doesnt support "if then" conditionals statemens macro read_lytle file group 1.92017 8000 read_data ($1, group=$2, narrays=2) set (dspace = $3, stpdeg = $4) set (r2d = 57.29577951, hc = 12398.61) set $2.energy = hc / (2 * dspace) / sin($2.1 / (r2d * stpdeg)) set $2.xmu = $2.2 end macro on 29/03/2006 17:23 Matt Newville wrote:
I believe Marco's right, and that you want a script like this: macro read_lytle file group 8000 read_data ($1, group=$2, narrays=2) set (dspace = 1.92017, stpdeg = $3) set (r2d = 57.29577951, hc = 12398.61) set $2.energy = hc / (2 * dspace) / sin($2.1 / (r2d * stpdeg)) set $2.xmu = $2.2 end macro
read_lytle beerbottle.dat
Sorry the FAQ is so far out of date and the Wiki doesn't have such info. Perhaps someone else would be willing to write a How to Use the Lytle Database on the Wiki or (even better) convert all the data available to a more useful format.
--Matt
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From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of Scott Calvin Sent: Wed 3/29/2006 1:58 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] F.W. Lytle spectrum... Hi all, I was just browsing the F. W. Lytle database, and came across this entry: febot.034.Z ftp://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/Fe/febot.034.Z FE IN BROWN BEER BOTTLE 7 8 3-19-82 There's got to be a good story behind that one... :) --Scott Calvin Sarah Lawrence College ... which, in turn, should be eligible for an IXS award to be established just for such stories. Anatoly
participants (7)
-
Bruce Ravel -
Frenkel, Anatoly -
Marco A. Alsina -
Marco A. Alsina -
Matt Newville -
Mauro Rovezzi -
Scott Calvin