August 2017 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 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. Re: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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XAFS short course in BNL: Nov 1-3, 2017
by Anatoly Frenkel 08 Feb '18

08 Feb '18

Dear subscribers: Please share with your group members or others, who may be interested, the following information about the short course on XAFS spectroscopy: Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to Nanomaterials* Dates: *November 1-3, 2017* Location: *Brookhaven National Laboratory* The course is open for applications at this web site: https://www.bnl.gov/exafs2017/ <https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5Kclqc…> The course will be useful for those scientists who are familiar with the foundations of XAFS experiment, theory and data analysis, and seek training in advanced methods. The course will include lectures, software demonstrations, and data analysis sessions. The emphasis will be on applications of XAFS to nanomaterials but we will welcome all participants who are interested in modern analysis methods. The course instructors will use examples from their research during presentations. The topics covered will include: -Theory of XANES, -XANES data analysis, -Structural refinement using XANES, with emphasis on the following methods: -Molecular dynamics, -Reverse Monte Carlo. -Machine Learning methods During the data analysis practicum on November 3, participants will get an opportunity to work with research projects with the help of the course instructors. The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC). Best regards, Anatoly ------------------------------------------------------------------- Anatoly I. Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Peak locations for Phosphorus in Carbon K-edge
by Kenneth Latham 27 Aug '17

27 Aug '17

Dear All, I have analysed some phosphoric acid activated carbons via NEXAFS and was wondering if anyone had come across any references or knew where the transition/peak for the C-O-P or C-P-O bonding arrangement occurs in the carbon K-edge region. The samples I am examining are a series at different heat treatment steps and lose a lot of oxygen functionality, so finding where C-O-P or C-P-O transitions occur would be very useful in understanding the chemical transitions that are occurring. Regards, Ken

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Re: [Ifeffit] Ifeffit Digest, Vol 174, Issue 8
by Carmelo Prestipino 18 Aug '17

18 Aug '17

Hi Hiroyuki, I done a small interface to Larch to work with a lot of files http://soonready.github.io/PrestoPronto/ It is not nice as Athena and it has not all its possibility but if you are used to Athena you should not get lost (the name of parameter is the same ). It is not fast how it should be but give a try, maybe could be useful Carmelo On Thu, Aug 17, 2017 at 7:00 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: How to use Larch as backend for Athena and Artemis on > Windows (Bruce Ravel) > 2. Re: How to use Larch as backend for Athena and Artemis on > Windows (ASAKURA, Hiroyuki) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Aug 2017 13:17:13 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] How to use Larch as backend for Athena and > Artemis on Windows > Message-ID: <1956f39f-85f4-7a92-a989-24a5436df426(a)bnl.gov> > Content-Type: text/plain; charset=utf-8; format=flowed > > > Hi Hiroyuki, > > Sorry I didn't respond yesterday. Yesterday was a bit of crazy day... > > I suppose that this is still a work in progress. I believe that Demeter > works with Larch on Windows, but it is certainly not as easy or > convenient yet as it should be. > > In the place where Demeter got installed on your computer, there is a > folder called \perl\site\bin -- you can look at the properties of the > Athena desktop icon to see where that is. In that folder is the > "dathena.bat" file which the Athena desktop icon points at. > > You should also find a file called "lathena.bat". Try running that or > pointing your desktop icon at it instead. > > The difference between "lathena.bat" and "dathena.bat" is line 25 that > sets an environment variable that Demeter uses to decide which of > ifeffit or larch to use. > > Obviously, there are number of other ways to get this environment > variable set. The bottom line is, yes, there is a switch. The switch > is the DEMETER_BACKEND environment variable. > > Unfortunately, that switch cannot be in the configuration files, > although what you tired in item 2 of your email was a sensible guess. > It turns out that the choice of larch/ifeffit has to made long before > the configuration files are read. > > Do let me know how you get on. While Demeter + larch should work, there > are still almost certainly problems. I need to get a new version of the > Demeter installer out soon, so it would be nice to get some feedback in > this area. > > As for using Demeter + larch + 100s of file -- it should work after a > fashion. But I worry that Athena's performance might not be what you > are hoping for. Athena does a lot of things that are more user-friendly > than performance-friendly.... > > > Cheers, > B > > > On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote: > > Dear all, > > > > I would like to use the latest Larch as backend for Athena and Artemis > > on Windows to handle hundreds of XAS data (, hopefully). > > But, I'm stuck. I would appreciate any comments and suggestions. > > > > Matt announced it is now possible on this list, but I still cannot do it > > on Windows. > > > > [Ifeffit] Larch 0.9.33 > > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017- > April/009091.html > > > >> The "server mode" for Athena and Artemis now works on all platforms and > I > >> strongly encourage everyone to use this over the ifeffit back end. > > > > Here is what I did. > > > > Environment: > > Windows 10 Pro (Japanese) > > Demeter 0.9.25 (via official website) > > Python 3.6 (official distribution) > > > > 1. Installation of the latest Larch > > > >> git clone https://github.com/xraypy/xraylarch.git (sha1: > >> 5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d) > >> cd xraylarch > >> python setup.py install > > # Some dependency related to XRD is not fulfilled. > > > > 2. Start Larch server > > > >> cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts > >> python larch_server start > > larch_server port=4966: started > > > > I found a parameter of peakfit backend in demeter.ini and changed to > > larch, but did not work (as expected). > > > > In the dathena.log, Athena still uses ifeffit as backend. > > > >> perl version: v5.18.2 > >> backend: ifeffit > > > > Should I compile Demeter package by myself to use the Larch backend? > > Or, is there any "switch" to use Larch? > > > > Thanks in advance, > > > > ASAKURA, Hiroyuki > > > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Aug 2017 18:21:51 +0900 > From: "ASAKURA, Hiroyuki" <asakura(a)moleng.kyoto-u.ac.jp> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] How to use Larch as backend for Athena and > Artemis on Windows > Message-ID: > <2d60a548-06bf-5cdf-02f7-154ab039924a(a)moleng.kyoto-u.ac.jp> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear Bruce, > > I do appreciate your prompt response! > > Now, I managed to run Athena with Larch backend on Windows 10 and handle > about 100 XAS data at once. > Athena with Ifeffit backend stalls when handling about 40 XAS spectra at > least in my case. > Unfortunately, there seems to be a bit severe performance issue with a > large number of spectra, as noted. > > Here is what I did. > > 0. Install an official Git package > 1-1. Download "64-bit Git for Windows Setup" via > https://git-scm.com/download/win > 1-2. Install Git with default options except for "Use Git from the > Windows Command Prompt" and "Use Windows' default console window" > Note: You can use any options you want. > > 1. Install an official Demeter package > 1-1. Download "Demeter 0.9.25 (32 bit)" via https://bruceravel.github.io/ > demeter/ > 1-2. Install Demeter with default options > Note: I cannot run 64 bit version with Larch. > > 2. Install an official Python package > 2-1. Download "Windows x86-64 web-based installer" via > https://www.python.org/downloads/release/python-362/ > 2-2. Custom Install Python with default options except for "Add Python > 3.6 to PATH" (checked) > > 3. Install unofficial Numpy and Scipy, Python libraries > 3-1. Download numpy?1.13.1+mkl?cp36?cp36m?win_amd64.whl and > scipy?0.19.1?cp36?cp36m?win_amd64.whl via http://www.lfd.uci.edu/~ > gohlke/pythonlibs/ > 3-2. pip install numpy-1.13.1+mkl-cp36-cp36m-win_amd64.whl > 3-3. pip install scipy?0.19.1?cp36?cp36m?win_amd64.whl > > 4. Install Larch and its dependencies > 4-1. Start a command prompt > 4-2. git clone https://github.com/xraypy/xraylarch.git > 4-3. cd xraylarch > 4-4. pip install lmfit > 4-5. pip install h5py > 4-6. pip install pillow > 4-7. pip install requests > 4-8. pip install sqlalchemy > 4-9. pip install matplotlib > 4-10. pip install pypiwin32 > 4-11. pip install wxpython > 4-12. pip install wxmplot > 4-13. pip install wxutils > 4-14. python setup.py install > 4-15. larch --version > 4-16. You will see "larch command-line version 0.2". > Note: I installed Larch dependencies except for pyFAI, CifFile, fabio, > tomopy, scikit-image. > > 5. Run Larch and Athena with Larch > 5-1. Start a new command prompt > 5-2. larch -rc > 5-3. Start another new command prompt > 5-4.cd %APPDATA%\DemeterPerl\perl\site\bin > 5-5. lathena.bat > > It works. > Athena is the most user-friendly XAS processing tool I have used. > > Thanks so much! > > Best regards, > > ASAKURA, Hiroyuki > > > On 2017/08/17 2:17, Bruce Ravel wrote: > > > > Hi Hiroyuki, > > > > Sorry I didn't respond yesterday. Yesterday was a bit of crazy day... > > > > I suppose that this is still a work in progress. I believe that Demeter > works with Larch on Windows, but it is certainly not as easy or convenient > yet as it should be. > > > > In the place where Demeter got installed on your computer, there is a > folder called \perl\site\bin -- you can look at the properties of the > Athena desktop icon to see where that is. In that folder is the > "dathena.bat" file which the Athena desktop icon points at. > > > > You should also find a file called "lathena.bat". Try running that or > pointing your desktop icon at it instead. > > > > The difference between "lathena.bat" and "dathena.bat" is line 25 that > sets an environment variable that Demeter uses to decide which of ifeffit > or larch to use. > > > > Obviously, there are number of other ways to get this environment > variable set. The bottom line is, yes, there is a switch. The switch is > the DEMETER_BACKEND environment variable. > > > > Unfortunately, that switch cannot be in the configuration files, > although what you tired in item 2 of your email was a sensible guess. It > turns out that the choice of larch/ifeffit has to made long before the > configuration files are read. > > > > Do let me know how you get on. While Demeter + larch should work, there > are still almost certainly problems. I need to get a new version of the > Demeter installer out soon, so it would be nice to get some feedback in > this area. > > > > As for using Demeter + larch + 100s of file -- it should work after a > fashion. But I worry that Athena's performance might not be what you are > hoping for. Athena does a lot of things that are more user-friendly than > performance-friendly.... > > > > > > Cheers, > > B > > > > > > On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote: > >> Dear all, > >> > >> I would like to use the latest Larch as backend for Athena and Artemis > on Windows to handle hundreds of XAS data (, hopefully). > >> But, I'm stuck. I would appreciate any comments and suggestions. > >> > >> Matt announced it is now possible on this list, but I still cannot do > it on Windows. > >> > >> [Ifeffit] Larch 0.9.33 > >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017- > April/009091.html > >> > >>> The "server mode" for Athena and Artemis now works on all platforms > and I > >>> strongly encourage everyone to use this over the ifeffit back end. > >> > >> Here is what I did. > >> > >> Environment: > >> Windows 10 Pro (Japanese) > >> Demeter 0.9.25 (via official website) > >> Python 3.6 (official distribution) > >> > >> 1. Installation of the latest Larch > >> > >>> git clone https://github.com/xraypy/xraylarch.git (sha1: > 5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d) > >>> cd xraylarch > >>> python setup.py install > >> # Some dependency related to XRD is not fulfilled. > >> > >> 2. Start Larch server > >> > >>> cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts > >>> python larch_server start > >> larch_server port=4966: started > >> > >> I found a parameter of peakfit backend in demeter.ini and changed to > larch, but did not work (as expected). > >> > >> In the dathena.log, Athena still uses ifeffit as backend. > >> > >>> perl version: v5.18.2 > >>> backend: ifeffit > >> > >> Should I compile Demeter package by myself to use the Larch backend? > >> Or, is there any "switch" to use Larch? > >> > >> Thanks in advance, > >> > >> ASAKURA, Hiroyuki > >> > >> > > > > > > -- > ASAKURA, Hiroyuki (Ph.D) > Program-Specific Assistant Professor (ESICB) > T. Tanaka Lab., ESICB, Kyoto University, Japan > asakura(a)moleng.kyoto-u.ac.jp > http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/ > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 174, Issue 8 > *************************************** > -- Carmelo Prestipino Sciences Chimiques de Rennes, UMR 6226 Solid State and Materials Chemistry group (CSM) Campus de Beaulieu, Bât 10B, bureau 123 263 avenue du Général Leclerc F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959

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How to use Larch as backend for Athena and Artemis on Windows
by ASAKURA, Hiroyuki 17 Aug '17

17 Aug '17

Dear all, I would like to use the latest Larch as backend for Athena and Artemis on Windows to handle hundreds of XAS data (, hopefully). But, I'm stuck. I would appreciate any comments and suggestions. Matt announced it is now possible on this list, but I still cannot do it on Windows. [Ifeffit] Larch 0.9.33 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html > The "server mode" for Athena and Artemis now works on all platforms and I > strongly encourage everyone to use this over the ifeffit back end. Here is what I did. Environment: Windows 10 Pro (Japanese) Demeter 0.9.25 (via official website) Python 3.6 (official distribution) 1. Installation of the latest Larch > git clone https://github.com/xraypy/xraylarch.git (sha1: 5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d) > cd xraylarch > python setup.py install # Some dependency related to XRD is not fulfilled. 2. Start Larch server > cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts > python larch_server start larch_server port=4966: started I found a parameter of peakfit backend in demeter.ini and changed to larch, but did not work (as expected). In the dathena.log, Athena still uses ifeffit as backend. > perl version: v5.18.2 > backend: ifeffit Should I compile Demeter package by myself to use the Larch backend? Or, is there any "switch" to use Larch? Thanks in advance, ASAKURA, Hiroyuki -- ASAKURA, Hiroyuki (Ph.D) T. Tanaka Lab., ESICB, Kyoto University, Japan asakura(a)moleng.kyoto-u.ac.jp http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/

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How to use Larch as backend for Athena and Artemis on Mac (Re: Ifeffit Digest, Vol 174, Issue 8)
by Luke Higgins 17 Aug '17

17 Aug '17

Dear All, Following the excellent guide that Hiroyuki & Bruce gave for running larch on Demeter on Windows (Ifeffit Digest, Vol 174, Issue 8). The following steps worked for me to run larch/Demeter on MacOS (Sierra 10.12.6). 1) Install Demeter using the advice from: https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h… 2) Installed Anaconda and larch using the following guide: http://cars.uchicago.edu/xraylarch/installation/index.html (Python & larch from source is fine: but then use Hiroyuki’s step 3&4 advice [attached below]) 3) In a new terminal window check larch by: larch --version You should see "larch command-line version 0.2". 4) Running larch and Demeter, run in a new terminal window: larch --port=4966 –rc 5) Open Demeter.pm in a text editor (which for me was buried in: /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter.pm) and change line 44 to: $ENV{DEMETER_BACKEND} ||= 'larch'; 6) This has changed both Athena and Artemis to using larch – haven’t fully tested yet, but looks good. Best Wishes, Luke (from Hhiroyuki, installing python and larch from source files:) 3. Install unofficial Numpy and Scipy, Python libraries 3-1. Download numpy‑1.13.1+mkl‑cp36‑cp36m‑win_amd64.whl and scipy‑0.19.1‑cp36‑cp36m‑win_amd64.whl via http://www.lfd.uci.edu/~gohlke/pythonlibs/ 3-2. pip install numpy-1.13.1+mkl-cp36-cp36m-win_amd64.whl 3-3. pip install scipy‑0.19.1‑cp36‑cp36m‑win_amd64.whl 4. Install Larch and its dependencies 4-1. Start a command prompt 4-2. git clone https://github.com/xraypy/xraylarch.git 4-3. cd xraylarch 4-4. pip install lmfit 4-5. pip install h5py 4-6. pip install pillow 4-7. pip install requests 4-8. pip install sqlalchemy 4-9. pip install matplotlib 4-10. pip install pypiwin32 4-11. pip install wxpython 4-12. pip install wxmplot 4-13. pip install wxutils 4-14. python setup.py install 4-15. larch --version 4-16. You will see "larch command-line version 0.2". Note: I installed Larch dependencies except for pyFAI, CifFile, fabio, tomopy, scikit-image.

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Artemis can't open project file and crashes
by Michelle Hammerton 11 Aug '17

11 Aug '17

Hello, I wonder if anyone can help me. Artemis (version 0.9.25) is unable to open the most recent project files that I have created and just crashes. These files also can't be opened on a different computer. I get the following message in the dartemis log file: You must define a method name at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\vendor\lib\Class\MOP\Mixin\HasMethods.pm line 96 Class::MOP::Mixin::HasMethods::has_method('Class::MOP::Class::Immutable::Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0xb49ab58)', '') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 424 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x10140bd0)', ' :') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 447 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x10140bd0)', 'space = I 41/a m d :2') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 382 Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x10140bd0)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 198 Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x10140bd0)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\racrw\atoms.inp') called at accessor Demeter::Atoms::file (defined at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 202) line 10 Demeter::Atoms::file('Demeter::Atoms=HASH(0x10140bd0)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Atoms\Xtal.pm line 667 Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x1afa1b38)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 1388 Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x1522a180)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp', 'CuCr2O4_I41-amd2_2006190') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis\Project.pm line 351 Demeter::UI::Artemis::Project::read_project('HASH(0xf7cdf60)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 996 Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x1522a180)', 'Wx::CommandEvent=SCALAR(0x15dc4558)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 440 Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x1522a180)', 'Wx::CommandEvent=SCALAR(0x15dc4558)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 50 eval {...} at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 50 So I guess I need to define a method name? What could it be and how do I define it? Thank you for your help (in advance!) Best wishes, Michelle *Michelle Hammerton Msc.* University of Amsterdam <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Demeter on Windows with Inkscape (and possibly other programs)
by Bruce Ravel 10 Aug '17

10 Aug '17

Windows users: I got an interesting bug report today from a fellow who develops a popular open source program for vector graphics editing (Inkscape). Apparently, there is a problem in Demeter's installer that has an impact on the ability of that program (and possibly others) in accessing system font files. The issue with Inkscape is described here: https://github.com/bruceravel/demeter/issues/51 I mention this here on the mailing list in an effort to help the folks who maintain Inkscape. If you use Demeter and Inkscape on your Windows machine, there is a problem and it is my fault :( The simplest solution is to uninstall Demeter, then continue using Inkscape. If that's not true or if someone needs a better solution right now, post here and I will help you work out a solution. I think the real fix to the problem is simple and I will work on a new installer this month. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Athena Crashing on Mac
by Daniel Austin Sheffield Uni 04 Aug '17

04 Aug '17

Hi, I emailed relatively recently about Artemis crashing on my MacBook Pro. This is the email i sent: 'I was using Artemis on Mac and it crashed. Now when i try to reopen Artemis it attempts restore what i was doing from an autosave file but it becomes unresponsive and is just stuck on the screen posted below. Does anyone know how i can fix it? Do i have to uninstall and then reinstall the software? i have left it running for over an hour but it still hasn’t worked. Thanks for any help’ Now the exact same thing is occurring with Athena. One of the replies from the previous email instructed me to remove parts of the programme code. I did so an Artemis worked perfectly after, i just needed to save often. The full email that instructed me on this can be found below: Hi Daniel, I had a similar issue, but my solution hasn’t been put up yet on the list: With respect to the error that Katherine Davies reported (02/16/2016; RE: [Ifeffit] problem with Artemis crashing on mac), I came across the same problem when running Artemis on Mac. I believe this issue is caused by a piece of code found in “artemis.pm” (Demeter/UI/artemis.pm) line 512-521: 512 sub process_argv { 513 my ($app, @args) = @_; 514 if (Demeter->co->default("artemis", "autosave") and autosave_exists()) { 515 import_autosave(); 516 } elsif ($args[0]) { # and -e $args[0]) { 517 my $file = File::Spec->rel2abs( $args[0] ); 518 read_project(\%frames, $file) if Demeter->is_zipproj($file, 0, 'fpj'); 519 }; 520 }; I think the error is due to not shutting down the program correctly causing this code to fail. A fix is to comment out lines 514-516 & 519, save the file and reboot Artemis (to edit artemis.pm you will need to make the file writable)– thus getting you past startup and allowing you to turn off the autosave settings from within Artemis as suggested. Put the code back as it was after you have finished. Hope this helps. Best, Luke Higgins I tried searching for similar code in the Athena programme but couldn’t find it. Does anyone have a similar solution, or any solution, to this problem? Thank you so much

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Artemis Crashing
by Daniel Austin Sheffield Uni 02 Aug '17

02 Aug '17

Hi, I was using Artemis on Mac and it crashed. Now when i try to reopen Artemis it attempts restore what i was doing from an autosave file but it becomes unresponsive and is just stuck on the screen posted below. Does anyone know how i can fix it? Do i have to uninstall and then reinstall the software? i have left it running for over an hour but it still hasn’t worked. Thanks for any help, Daniel

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