Error in Running XANES on FEFF8.4 for Cobalt based cluster
Dear all, I was trying to simulate XANES using FEFF8.4 at Cobalt K edge. This is for a cluster and not a crystal. I encountered two problems. 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') 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') Sorry for the long email, and thank you for any suggestions. Ganesh
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/
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/
participants (2)
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Bruce Ravel -
Ganesh Subramanian