Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp

2015-07-06 Thread Matt Newville
Ganesh -- gnuplot.exe is not being found in your PATH.Can you find it?
Any ideas why it might be missing?

--Matt

On Mon, Jul 6, 2015 at 6:58 PM, Ganesh Subramanian 
wrote:

> Sorry for not noticing. The log files are attached now. It is pretty much
> the same for all three cases of Athena, Artemis and Hephaestus.
>
> Ganesh
>
>
>
>
>>
>> Message: 2
>> Date: Mon, 06 Jul 2015 08:18:08 -0400
>> From: Bruce Ravel 
>> To: XAFS Analysis using Ifeffit 
>> Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
>> Message-ID: <559a7200.9050...@bnl.gov>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>> On 07/04/2015 06:10 PM, Ganesh Subramanian wrote:
>> > Hi.
>> >
>> > This is Ganesh and I am a first time user of the Demeter accessories.
>> >
>> > I downloaded and installed the files from the github site using the
>> > 0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7
>> > on my Macbook Pro (2012). It seemed to have installed fine, but the
>> > moment I click on the icons to open any of Athena, Artemis or
>> > Hephaestus, all of them show a command window, thats empty, and in a few
>> > seconds crash and close. No error windows or command line error prompts.
>> >
>> > Any idea on what might be wrong ?
>>
>>
>> It is basically impossible to answer a question like this without a look
>> at the log file, as explained here:
>>
>> http://bruceravel.github.io/demeter/pods/bugs.pod.html
>>
>> B
>>
>> --
>>   Bruce Ravel   bra...@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/
>>
>>
>>
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Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp

2015-07-06 Thread Ganesh Subramanian
Sorry for not noticing. The log files are attached now. It is pretty much
the same for all three cases of Athena, Artemis and Hephaestus.

Ganesh




>
> Message: 2
> Date: Mon, 06 Jul 2015 08:18:08 -0400
> From: Bruce Ravel 
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
> Message-ID: <559a7200.9050...@bnl.gov>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> On 07/04/2015 06:10 PM, Ganesh Subramanian wrote:
> > Hi.
> >
> > This is Ganesh and I am a first time user of the Demeter accessories.
> >
> > I downloaded and installed the files from the github site using the
> > 0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7
> > on my Macbook Pro (2012). It seemed to have installed fine, but the
> > moment I click on the icons to open any of Athena, Artemis or
> > Hephaestus, all of them show a command window, thats empty, and in a few
> > seconds crash and close. No error windows or command line error prompts.
> >
> > Any idea on what might be wrong ?
>
>
> It is basically impossible to answer a question like this without a look
> at the log file, as explained here:
>
> http://bruceravel.github.io/demeter/pods/bugs.pod.html
>
> B
>
> --
>   Bruce Ravel   bra...@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/
>
>
>


dartemis.log
Description: Binary data


dathena.log
Description: Binary data


dhephaestus.log
Description: Binary data
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Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Maxim Boyanov
Here's our room-temperature Fe-edge spectrum of scorodite. We measured it
mostly because we could, not because we really needed it--at the time we
were interested in the As edge data as a possible end phase in a geochemical
reactor. The sample and the Fe edge measurements aren't great and the
reference channel disappears once absorption in the sample becomes
significant (the energy axis was aligned as 7112 eV at the inflection point
of an Fe foil). We also took 2D powder diffraction in transmission on the
same tape-mounted sample, so if interested in verifying the purity of the
mineral I am attaching the integrated pattern. We did not prepare the
standard or follow up on these measurements, so use at your own risk :-).

Best,
Max.

Assoc. Prof. Maxim Boyanov
Bulgarian Academy of Sciences
Institute of Chemical Engineering
Sofia 1113, Bulgaria
tel: +359(88)821-9637



> -Original Message-
> From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-
> boun...@millenia.cars.aps.anl.gov] On Behalf Of Matthew Marcus
> Sent: Monday, July 6, 2015 11:51 AM
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] Fe K edge spectrum of scorodite
> 
> Do you by any chance has a room-temp spectrum?  Most of our data is taken
at
> RT or not much below, and so the LN2 spectrum won't be a perfect match.
>   mam
> 
> On 7/6/2015 9:12 AM, Case Van Genuchten wrote:
> > Dear Matthew,
> >
> > Sure, the raw data and/or spectrum can be added to the database.  For
this
> sample, the 1st derivative of the Fe foil was 7.112 keV.  I can also
provide
> individual scans for the database, if needed.  Is there any interest in
the As K-
> edge of this sample, too?  I have that one as well.
> > Case
> >
> > On Mon, Jul 6, 2015 at 5:48 PM, Matthew Marcus  > wrote:
> >
> > Thanks!  May I add it to the ALS 10.3.2 reference collection?
> >
> > What is the standard of energy calibration?  Is the Fe metal edge at
> 7110.75eV, 7112eV or what?
> >  mam
> >
> > On 7/6/2015 7:11 AM, Case Van Genuchten wrote:
> >
> > Dear Shaofeng,
> >
> > I am attaching the averaged, raw data and Fe K-edge EXAFS
spectrum
> (extracted using SixPack) of scorodite.  The mineral was prepared
following the
> procedure outlined in Paktunc et al. (2008).  The data were collected at
the
> Stanford Synchrotron Radiation Lightsource in transmission mode with the
> sample housed in a liquid nitrogen cryostat.  You can find additional
details on
> the preparation of the sample and data collection from the publication
where
> the spectrum is reported and modeled (van Genuchten et al. 2014,
Geochimica
> et Cosmochimica Acta).
> >
> > Please let me know if you have any other questions about data
> collection.
> >
> > Best,
> >
> > Case M. van Genuchten
> > Environmental Geochemistry Laboratory
> > Institute of Earth Surface Dynamics
> > University of Lausanne, Lausanne, CH
> >
> >
> >
> > On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang
> mailto:wangshaof...@iae.ac.cn>
> >> wrote:
> >
> >  Dear all,
> >  Can anyone have Fe K edge exafs spectrum of scorodite share
a copy?
> >  Thanks in advance.
> >  Shaofeng
> >  --
> >  Shaofeng Wang, Ph.D of Geochemistry
> >  Environmental Molecular Science Group
> >  Institute of Applied Ecology, Chinese Academy of Sciences
> >  Shenyang, 110016, China
> > wangshaof...@iae.ac.cn 
> >
> > www.iae.cas.cn  
> >
> >
> >
> >  ___
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> >
> >
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Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Matthew Marcus

Do you by any chance has a room-temp spectrum?  Most of our data is taken at RT 
or not much below, and so the LN2 spectrum won't be a perfect match.
mam

On 7/6/2015 9:12 AM, Case Van Genuchten wrote:

Dear Matthew,

Sure, the raw data and/or spectrum can be added to the database.  For this 
sample, the 1st derivative of the Fe foil was 7.112 keV.  I can also provide 
individual scans for the database, if needed.  Is there any interest in the As 
K-edge of this sample, too?  I have that one as well.
Case

On Mon, Jul 6, 2015 at 5:48 PM, Matthew Marcus mailto:mamar...@lbl.gov>> wrote:

Thanks!  May I add it to the ALS 10.3.2 reference collection?

What is the standard of energy calibration?  Is the Fe metal edge at 
7110.75eV, 7112eV or what?
 mam

On 7/6/2015 7:11 AM, Case Van Genuchten wrote:

Dear Shaofeng,

I am attaching the averaged, raw data and Fe K-edge EXAFS spectrum 
(extracted using SixPack) of scorodite.  The mineral was prepared following the 
procedure outlined in Paktunc et al. (2008).  The data were collected at the 
Stanford Synchrotron Radiation Lightsource in transmission mode with the sample 
housed in a liquid nitrogen cryostat.  You can find additional details on the 
preparation of the sample and data collection from the publication where the 
spectrum is reported and modeled (van Genuchten et al. 2014, Geochimica et 
Cosmochimica Acta).

Please let me know if you have any other questions about data 
collection.

Best,

Case M. van Genuchten
Environmental Geochemistry Laboratory
Institute of Earth Surface Dynamics
University of Lausanne, Lausanne, CH



On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang mailto:wangshaof...@iae.ac.cn> >> wrote:

 Dear all,
 Can anyone have Fe K edge exafs spectrum of scorodite share a copy?
 Thanks in advance.
 Shaofeng
 --
 Shaofeng Wang, Ph.D of Geochemistry
 Environmental Molecular Science Group
 Institute of Applied Ecology, Chinese Academy of Sciences
 Shenyang, 110016, China
wangshaof...@iae.ac.cn  
>
www.iae.cas.cn  



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Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Matthew Marcus

Here are my versions of processed files, made from what you sent.  The .e is 
the pre-edge removed, post-edge normalized, shifted so that the Fe K-edge is at 
7110.75eV.
The .b is k^3*chi(k), with E0 set so that it comes halfway up the edge jump.  
The .chi is the chi(k), with the abscissa interpolated to a regular grid, the 
way Artemis likes it.
mam

On 7/6/2015 9:12 AM, Case Van Genuchten wrote:

Dear Matthew,

Sure, the raw data and/or spectrum can be added to the database.  For this 
sample, the 1st derivative of the Fe foil was 7.112 keV.  I can also provide 
individual scans for the database, if needed.  Is there any interest in the As 
K-edge of this sample, too?  I have that one as well.
Case

On Mon, Jul 6, 2015 at 5:48 PM, Matthew Marcus mailto:mamar...@lbl.gov>> wrote:

Thanks!  May I add it to the ALS 10.3.2 reference collection?

What is the standard of energy calibration?  Is the Fe metal edge at 
7110.75eV, 7112eV or what?
 mam

On 7/6/2015 7:11 AM, Case Van Genuchten wrote:

Dear Shaofeng,

I am attaching the averaged, raw data and Fe K-edge EXAFS spectrum 
(extracted using SixPack) of scorodite.  The mineral was prepared following the 
procedure outlined in Paktunc et al. (2008).  The data were collected at the 
Stanford Synchrotron Radiation Lightsource in transmission mode with the sample 
housed in a liquid nitrogen cryostat.  You can find additional details on the 
preparation of the sample and data collection from the publication where the 
spectrum is reported and modeled (van Genuchten et al. 2014, Geochimica et 
Cosmochimica Acta).

Please let me know if you have any other questions about data 
collection.

Best,

Case M. van Genuchten
Environmental Geochemistry Laboratory
Institute of Earth Surface Dynamics
University of Lausanne, Lausanne, CH



On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang mailto:wangshaof...@iae.ac.cn> >> wrote:

 Dear all,
 Can anyone have Fe K edge exafs spectrum of scorodite share a copy?
 Thanks in advance.
 Shaofeng
 --
 Shaofeng Wang, Ph.D of Geochemistry
 Environmental Molecular Science Group
 Institute of Applied Ecology, Chinese Academy of Sciences
 Shenyang, 110016, China
wangshaof...@iae.ac.cn  
>
www.iae.cas.cn  



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6.8807500E+3 -5.6686879E-4
6.8907510E+3 4.0188098E-4
6.9007500E+3 1.9576439E-4
6.9107500E+3 6.6377126E-4
6.9207510E+3 7.3053432E-4
6.9307520E+3 4.2579199E-4
6.9407500E+3 5.1885990E-4
6.9507480E+3 8.5548572E-4
6.9607510E+3 1.1406525E-3
6.9707500E+3 1.1071908E-3
6.9807480E+3 9.7453779E-4
6.9907510E+3 9.5817003E-4
7.0007490E+3 9.1372709E-4
7.0107520E+3 1.3349763E-3
7.0207490E+3 1.0275797E-3
7.0307490E+3 1.3605076E-3
7.0407490E+3 1.6912761E-3
7.0507480E+3 1.6655628E-3
7.0607500E+3 2.3310543E-3
7.0707500E+3 3.0608769E-3
7.0807490E+3 3.4280701E-3
7.0907510E+3 4.6546218E-3
7.0911001E+3 5.1562926E-3
7.0914482E+3 5.1379598E-3
7.0918018E+3 5.1800186E-3
7.0921509E+3 5.1840505E-3
7.0924990E+3 4.9898361E-3
7.0928481E+3 5.0541580E-3
7.0932021E+3 5.1741299E-3
7.0935508E+3 5.1947828E-3
7.0938999E+3 5.5255872E-3
7.0942490E+3 5.5841443E-3
7.0945981E+3 5.4232348E-3
7.0949521E+3 5.7453403E-3
7.0953008E+3 5.6040450E-3
7.0956499E+3 5.8876155E-3
7.0959990E+3 5.8254543E-3
7.0963481E+3 6.0572238E-3
7.0966982E+3 6.2847678E-3
7.0970518E+3 6.5249893E-3
7.0974009E+3 6.7258098E-3
7.0977500E+3 6.5698550E-3
7.0981001E+3 6.4360630E-3
7.0984492E+3 6.5597185E-3
7.0987988E+3 6.7354134E-3
7.0991479E+3 6.7586658E-3
7.0994980E+3 7.1900967E-3
7.0998521E+3 7.3942537E-3
7.1002021E+3 7.2445427E-3
7.1005518E+3 7.2462349E-3
7.1009009E+3 7.3070318E-3
7.1012510E+3 8.0021702E-3
7.101

Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Matthew Marcus

Thanks.  I have an As-edge spectrum for scorodite.
mam

On 7/6/2015 9:12 AM, Case Van Genuchten wrote:

Dear Matthew,

Sure, the raw data and/or spectrum can be added to the database.  For this 
sample, the 1st derivative of the Fe foil was 7.112 keV.  I can also provide 
individual scans for the database, if needed.  Is there any interest in the As 
K-edge of this sample, too?  I have that one as well.
Case

On Mon, Jul 6, 2015 at 5:48 PM, Matthew Marcus mailto:mamar...@lbl.gov>> wrote:

Thanks!  May I add it to the ALS 10.3.2 reference collection?

What is the standard of energy calibration?  Is the Fe metal edge at 
7110.75eV, 7112eV or what?
 mam

On 7/6/2015 7:11 AM, Case Van Genuchten wrote:

Dear Shaofeng,

I am attaching the averaged, raw data and Fe K-edge EXAFS spectrum 
(extracted using SixPack) of scorodite.  The mineral was prepared following the 
procedure outlined in Paktunc et al. (2008).  The data were collected at the 
Stanford Synchrotron Radiation Lightsource in transmission mode with the sample 
housed in a liquid nitrogen cryostat.  You can find additional details on the 
preparation of the sample and data collection from the publication where the 
spectrum is reported and modeled (van Genuchten et al. 2014, Geochimica et 
Cosmochimica Acta).

Please let me know if you have any other questions about data 
collection.

Best,

Case M. van Genuchten
Environmental Geochemistry Laboratory
Institute of Earth Surface Dynamics
University of Lausanne, Lausanne, CH



On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang mailto:wangshaof...@iae.ac.cn> >> wrote:

 Dear all,
 Can anyone have Fe K edge exafs spectrum of scorodite share a copy?
 Thanks in advance.
 Shaofeng
 --
 Shaofeng Wang, Ph.D of Geochemistry
 Environmental Molecular Science Group
 Institute of Applied Ecology, Chinese Academy of Sciences
 Shenyang, 110016, China
wangshaof...@iae.ac.cn  
>
www.iae.cas.cn  



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Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Case Van Genuchten
Dear Matthew,

Sure, the raw data and/or spectrum can be added to the database.  For this
sample, the 1st derivative of the Fe foil was 7.112 keV.  I can also
provide individual scans for the database, if needed.  Is there any
interest in the As K-edge of this sample, too?  I have that one as well.
Case

On Mon, Jul 6, 2015 at 5:48 PM, Matthew Marcus  wrote:

> Thanks!  May I add it to the ALS 10.3.2 reference collection?
>
> What is the standard of energy calibration?  Is the Fe metal edge at
> 7110.75eV, 7112eV or what?
> mam
>
> On 7/6/2015 7:11 AM, Case Van Genuchten wrote:
>
>> Dear Shaofeng,
>>
>> I am attaching the averaged, raw data and Fe K-edge EXAFS spectrum
>> (extracted using SixPack) of scorodite.  The mineral was prepared following
>> the procedure outlined in Paktunc et al. (2008).  The data were collected
>> at the Stanford Synchrotron Radiation Lightsource in transmission mode with
>> the sample housed in a liquid nitrogen cryostat.  You can find additional
>> details on the preparation of the sample and data collection from the
>> publication where the spectrum is reported and modeled (van Genuchten et
>> al. 2014, Geochimica et Cosmochimica Acta).
>>
>> Please let me know if you have any other questions about data collection.
>>
>> Best,
>>
>> Case M. van Genuchten
>> Environmental Geochemistry Laboratory
>> Institute of Earth Surface Dynamics
>> University of Lausanne, Lausanne, CH
>>
>>
>>
>> On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang > > wrote:
>>
>> Dear all,
>> Can anyone have Fe K edge exafs spectrum of scorodite share a copy?
>> Thanks in advance.
>> Shaofeng
>> --
>> Shaofeng Wang, Ph.D of Geochemistry
>> Environmental Molecular Science Group
>> Institute of Applied Ecology, Chinese Academy of Sciences
>> Shenyang, 110016, China
>> wangshaof...@iae.ac.cn 
>> www.iae.cas.cn 
>>
>>
>>
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Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Matthew Marcus

Thanks!  May I add it to the ALS 10.3.2 reference collection?

What is the standard of energy calibration?  Is the Fe metal edge at 7110.75eV, 
7112eV or what?
mam

On 7/6/2015 7:11 AM, Case Van Genuchten wrote:

Dear Shaofeng,

I am attaching the averaged, raw data and Fe K-edge EXAFS spectrum (extracted 
using SixPack) of scorodite.  The mineral was prepared following the procedure 
outlined in Paktunc et al. (2008).  The data were collected at the Stanford 
Synchrotron Radiation Lightsource in transmission mode with the sample housed 
in a liquid nitrogen cryostat.  You can find additional details on the 
preparation of the sample and data collection from the publication where the 
spectrum is reported and modeled (van Genuchten et al. 2014, Geochimica et 
Cosmochimica Acta).

Please let me know if you have any other questions about data collection.

Best,

Case M. van Genuchten
Environmental Geochemistry Laboratory
Institute of Earth Surface Dynamics
University of Lausanne, Lausanne, CH



On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang mailto:wangshaof...@iae.ac.cn>> wrote:

Dear all,
Can anyone have Fe K edge exafs spectrum of scorodite share a copy?
Thanks in advance.
Shaofeng
--
Shaofeng Wang, Ph.D of Geochemistry
Environmental Molecular Science Group
Institute of Applied Ecology, Chinese Academy of Sciences
Shenyang, 110016, China
wangshaof...@iae.ac.cn 
www.iae.cas.cn 



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Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Case Van Genuchten
Dear Shaofeng,

I am attaching the averaged, raw data and Fe K-edge EXAFS spectrum
(extracted using SixPack) of scorodite.  The mineral was prepared following
the procedure outlined in Paktunc et al. (2008).  The data were collected
at the Stanford Synchrotron Radiation Lightsource in transmission mode with
the sample housed in a liquid nitrogen cryostat.  You can find additional
details on the preparation of the sample and data collection from the
publication where the spectrum is reported and modeled (van Genuchten et
al. 2014, Geochimica et Cosmochimica Acta).

Please let me know if you have any other questions about data collection.

Best,

Case M. van Genuchten
Environmental Geochemistry Laboratory
Institute of Earth Surface Dynamics
University of Lausanne, Lausanne, CH



On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang 
wrote:

>   Dear all,
>
> Can anyone have Fe K edge exafs spectrum of scorodite share a copy?
>
> Thanks in advance.
>
> Shaofeng
>
> --
> Shaofeng Wang, Ph.D of Geochemistry
> Environmental Molecular Science Group
> Institute of Applied Ecology, Chinese Academy of Sciences
> Shenyang, 110016, China
> wangshaof...@iae.ac.cn
> www.iae.cas.cn
>
>
>
>
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Scorodite_Fe_K_edge_EXAFS.chi
Description: Binary data


Scorodite_Fe_K_edge_Raw
Description: Binary data
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Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp

2015-07-06 Thread Bruce Ravel

On 07/04/2015 06:10 PM, Ganesh Subramanian wrote:

Hi.

This is Ganesh and I am a first time user of the Demeter accessories.

I downloaded and installed the files from the github site using the
0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7
on my Macbook Pro (2012). It seemed to have installed fine, but the
moment I click on the icons to open any of Athena, Artemis or
Hephaestus, all of them show a command window, thats empty, and in a few
seconds crash and close. No error windows or command line error prompts.

Any idea on what might be wrong ?



It is basically impossible to answer a question like this without a look 
at the log file, as explained here:


   http://bruceravel.github.io/demeter/pods/bugs.pod.html

B

--
 Bruce Ravel   bra...@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/
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