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 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster Message-ID: <55BA3978.4080801@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@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 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster Message-ID: <55BA39F2.4090609@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@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." To: "ifeffit@millenia.cars.aps.anl.gov" Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) Message-ID: 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@millenia.cars.aps.anl.gov mailto:ifeffit-request@millenia.cars.aps.anl.gov wrote:

Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov

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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 Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) Date: July 29, 2015 at 1:11:08 PM MDT To: "ifeffit@millenia.cars.aps.anl.gov"

...

Reply-To: XAFS Analysis using Ifeffit

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 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 Reply-To: XAFS Analysis using Ifeffit

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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ------------------------------------ bravel@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/