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

Strange problems with Artemis
by Jatinkumar Rana 27 Aug '10

27 Aug '10

Dear users, I am facing a strange problem with Artemis and i don't know how to get rid of it. I hope any expert in the mailing lists would help me solving this problem. I have EXAFS data on Fe and Mn K-edge for Arrojadite mineral. Since the crystal structure of this mineral is not known we did neutron diffraction to refine the structure. To support the neutron diffraction results, we planned to do EXAFS on this mineral (Fe and Mn k-edge). We have around 8 different atomic species (i.e. Na,K,Fe,Mn,Al,Cr,O,P) in the mineral and some of the sites are fractionally occupied. Since ATOMS can not handle more than 7 potentials and site occupancy other than unity i have made following changes : 1) replaced Cr with Al, mainly because Cr is present in a few ppm only (relative importance). 2) set all site occupancy to 1 Even after doing the above changes, i got following error message when i run FEFF ************** Feff 6L.02 WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 11 20 11 -3.01973 -0.20361 1.44233 20 -3.54653 -0.05083 0.83053 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 46 62 46 -0.40014 -0.20361 5.03633 62 0.12666 -0.05083 5.64813 Run continues... Sodium Potassium Aluminium Chromium Iron Manganese Phosphate Hydrate Al Cr Fe7.53 H2 K1.21 Mn6 Na3 O50 P12 Kallfa\&s, Christoph Crystal structure, chemical composition and thermal behaviour of arrojadite Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 free atom potential and density for atom type 4 free atom potential and density for atom type 5 free atom potential and density for atom type 6 free atom potential and density for atom type 7 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 overlapped potential and density for unique potential 4 overlapped potential and density for unique potential 5 overlapped potential and density for unique potential 6 overlapped potential and density for unique potential 7 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 3 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 4 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 5 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 6 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 7 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... Rmax 7.0000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table nfound nheap nheapx nsc r 1000 469 469 3 5.2890 2000 730 730 3 5.7147 3000 907 907 3 5.9455 4000 1040 1040 3 6.1157 5000 1177 1177 3 6.2616 6000 1319 1319 3 6.3835 7000 1412 1413 3 6.4825 8000 1443 1444 3 6.5749 9000 1469 1473 3 6.6585 10000 1432 1474 3 6.7377 11000 1367 1474 3 6.8062 12000 1202 1474 3 6.8680 13000 870 1474 3 6.9289 14000 251 1474 3 6.9856 . . . . . .. . This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). This may be due to the presence of hydrogen atoms in your feff.inp file, in which case this is an innocuous warning and may be ignored. However, this may indicate a problem constructing the Atoms list. The most common cause of this problem is a mistake in the crystallographic data used on the Atoms page. You may have incorrect values for lattice constants or angles or incorrect values for site coordinates. You may need a shift vector to move the lattice into its standard setting. Please be aware that Atoms works with 5 digits of precision. Thus, if you have a site with a coordinate of 1/3, you should use either "1/3" or "0.33333" on the Atoms page. Using insufficient precision, say "0.333" is a common cause of this error message. Artemis has continued on the possibility that the warning is caused by hydrogen atoms, but be warned that the feff.inp may require your attention. ************************************ I have attached both *original.cif file* (with all 8 atomic species and fractional occupancy) and *modified.cif file* (Cr replaced by Al and all site occupancy set to 1) with this mail for your perusal. I hope some experts in the mailing list would suggest me some solutions. Many more thanks in advance for your valuable time and suggestions.... Best regards, Rana

1 0

debye function
by Kleber Daum Machado 24 Aug '10

24 Aug '10

Hi, I'd like to know the explicit mathematical expressions that are represented by the functions debye(temp,thetad) and eins(temp,thetae). Are they given in some documentation file or article? Thank you very much Kleber

3 3

Re: [Ifeffit] updating ifeffit manually
by hemantha aranwela 19 Aug '10

19 Aug '10

Hi Matt, Thanks for the information. I could not get the runner.exe to work. So installed the updates directly as you suggested. It works perfectly. Aranwela These were the steps I have followed. Updating Ifeffit manually (if, somehow, it does not update automatically) 1. Check the latest update installed (typically in C:\Program Files\Ifeffit\config\iff_xxx). In my case it was iff_009.2. Then check the current available update level from the cars webpage: http://cars9.uchicago.edu/~ifeffit/updates/current.datAt present it is at 013. 3. Download the missing updates from http://cars9.uchicago.edu/~ifeffit/updates/iff_XXX.zip Remember you need to change XXX to the appropriate file # (to 010 for an example). ( I had to download iff_010, iff_011, iff_012 and iff_013 and saved them on to the desktop). 4. These are zipped files. Need to unzip those into the C:\Program Files\Ifeffit folder. But one has to do this in sequence (it is said). ( In my case I unzipped 010 first then 011, next 012 and 013 after that. Unzipping is easy in windows 7. Just right click on the zipped folder and select ‘extract all’ then browse to the Ifeffit folder (In my case C:\Program Files\Ifeffit). It will prompt you to choose between two or three options. (In all cases I chose ‘copy and replace’ or just ‘replace’. That’a all. Everything should work perfectly. Date: Mon, 16 Aug 2010 14:06:47 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 7 Message-ID: <AANLkTinvBiq0ES9TLN2Air38tWw4VgCroOSJbsCSNU7X(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Aranwela, Thanks for the report. I do think this is a permissions problem. That's not to say it's not a real problem, just that it should be solvable. I just tested this by resetting the "update level" in config/current.dat, and forcing the updater to run. It worked fine to download and install the update. That was on a Mac running Windows 7 (64 bit) as a virtual machine. The account I used does have full Administrator control. The process running the updater definitely needs to be be able to write to C:\Program Files\Ifeffit (or wherever you installed to). Would you be willing to try to download the update zip file (say, iff_013.zip) and unzip it into your installation directory, as described at http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater and let us know what does and doesn't work? I'm sure that others would find your report helpful. Cheers, --Matt

2 1

Updating Ifeffit manually
by hemantha aranwela 19 Aug '10

19 Aug '10

Hi Matt, Thanks for the information. I could not get the runner.exe to work. So installed the updates directly as you suggested. It works perfectly. Aranwela These were the steps I have followed. Updating Ifeffit manually (if, somehow, it does not update automatically) 1. Check the latest update installed (typically in C:\Program Files\Ifeffit\config\iff_xxx). In my case it was iff_009. 2. Then check the current available update level from the cars webpage: http://cars9.uchicago.edu/~ifeffit/updates/current.dat At present it is at 013. 3. Download the missing updates from http://cars9.uchicago.edu/~ifeffit/updates/iff_XXX.zip Remember you need to change XXX to the appropriate file # (to 010 for an example). ( I had to download iff_010, iff_011, iff_012 and iff_013 and saved them on to the desktop). 4. These are zipped files. Need to unzip those into the C:\Program Files\Ifeffit folder. But one has to do this in sequence (it is said). ( In my case I unzipped 010 first then 011, next 012 and 013 after that. Unzipping is easy in windows 7. Just right click on the zipped folder and select ‘extract all’ then browse to the Ifeffit folder (In my case C:\Program Files\Ifeffit). It will prompt you to choose between two or three options. (In all cases I chose ‘copy and replace’ or just ‘replace’. That’a all. Everything should work perfectly. Date: Mon, 16 Aug 2010 14:06:47 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 7 Message-ID: <AANLkTinvBiq0ES9TLN2Air38tWw4VgCroOSJbsCSNU7X(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Aranwela, Thanks for the report. I do think this is a permissions problem. That's not to say it's not a real problem, just that it should be solvable. I just tested this by resetting the "update level" in config/current.dat, and forcing the updater to run. It worked fine to download and install the update. That was on a Mac running Windows 7 (64 bit) as a virtual machine. The account I used does have full Administrator control. The process running the updater definitely needs to be be able to write to C:\Program Files\Ifeffit (or wherever you installed to). Would you be willing to try to download the update zip file (say, iff_013.zip) and unzip it into your installation directory, as described at http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater and let us know what does and doesn't work? I'm sure that others would find your report helpful. Cheers, --Matt

1 0

Re: [Ifeffit] IFEFFIT update (windows7)
by hemantha aranwela 19 Aug '10

19 Aug '10

Hi Todd, Thanks for the information. But I have already tried that. Doesn't work for me. But since it has worked for you I guess the problem is still in my computer. Unfortunately I do not know what it is. So, I am going to download and install updates directly as Matt has suggested. Thanks. Aranwela Date: Tue, 17 Aug 2010 08:52:28 -0600 From: "Monson, Todd" <tmonson(a)sandia.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] updating Athena in Win 7 Message-ID: <AC050BA7EAC9A34E9A05BC31C3AA2E8B186774E38A(a)ES02SNLNT.srn.sandia.gov> Content-Type: text/plain; charset="us-ascii" Aranwela, It sounds like you're having the same problem that I was having. You need to change the permissions in the Ifeffit folder under program files. There is a good discussion of this that worked for me under Vol. 90, Issue 5 of the Ifeffit digest. This is a copy of the portion of that conversion that you need: "Right click on the IFEFFIT folder in Program Files and select Properties. Select the Security tab and then click the Edit button. For all of the group or user names listed make sure Allow is marked for all permissions (Checking Full Control should select all of the permissions in the list below it). Hit the Apply button and then the OK button. Then try opening Athena again and see if it successfully runs through the update process. " Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

2 1

Help with cif file
by Kleper Rocha 18 Aug '10

18 Aug '10

3 2

updating Athena in Win 7
by Monson, Todd 17 Aug '10

17 Aug '10

Aranwela, It sounds like you're having the same problem that I was having. You need to change the permissions in the Ifeffit folder under program files. There is a good discussion of this that worked for me under Vol. 90, Issue 5 of the Ifeffit digest. This is a copy of the portion of that conversion that you need: "Right click on the IFEFFIT folder in Program Files and select Properties. Select the Security tab and then click the Edit button. For all of the group or user names listed make sure Allow is marked for all permissions (Checking Full Control should select all of the permissions in the list below it). Hit the Apply button and then the OK button. Then try opening Athena again and see if it successfully runs through the update process. " Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

1 0

Help with cif file
by Kleper Rocha 17 Aug '10

17 Aug '10

1 0

Re: [Ifeffit] PYTHON scripting on MacOS & XP (Joel Brugger)
by Brugger, Joel (SAM) 17 Aug '10

17 Aug '10

Hi Matt, Thanks for the update. We had trouble getting the XP version to work. We're running Win XP under parallels on the Mac. Ifeffit (1.2.11), python (2.5) and the wrapper installed successfully. The ifeffit.py shell (in the python/scripts directory) does not recognise any python commands. And opening python in the ifeffit directory - it does not recognise ifeffit in the "import ifeffit" command. What are we doing wrong? Thanks, Joel & Barbara

2 1

incorporating feff 8 into Artemis
by Jatinkumar Rana 17 Aug '10

17 Aug '10

Dear All, Recently, I have decided to upgrade to Feff8.20. We have got Feff820a.exe file. I would like to know if there is any specific procedure to replace older Feff6 with this Feff820a.exe in artemis ? Thank you very much in advance !!! Best regards, Rana

2 1