Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster

30 Aug 2015


      Hi Ganesh,
It is common to see the
WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
warning from feff when you have H atoms since the bonds tend to be very
short. However, these are not the ones that are causing the problem. These
warning can be ignored if the structure is reasonable. If the structure at
the bottom of this email is the input structure that you used, then there
is indeed an oxygen atom that is less than 0.1 angstrom from a carbon atom,
which is of course unphysical. That is probably what is causing the
problem, however, there are some other things that could be causing
problems as well. In particular, there are what I like to call "floating
atoms" in your file, i.e., single atoms or several atoms that are
disconnected from the rest of the cluster. I am sending a new input file
below that has fixed this problem. I  deleted the O atom that was too close
to the C atom, and deleted all of the structure that wasn't connected to
the central atom by a string of bonds. You might worry about weather the C
or O atom is the one that should have been deleted in the structure, but
you can always test using both possibilities. I doubt that it will make
much difference since C and O look pretty similar, and the O atom is pretty
far from the Co. Also, the H atoms look a bit messed up, but I don't think
that will make much of a difference either. You can check by taking the H
atoms out and running and see if the results change much.
Cheers,
Josh Kas

*  Al K edge energy = 1559.0 eV
EDGE      K
S02       1.0

*         pot    xsph  fms   paths genfmt ff2chi
CONTROL   1      1     1     1     1      1
PRINT     1      0     0     0     0      0

*                         *** ixc=0 means to use Hedin-Lundqvist
*         ixc  [ Vr  Vi ]
EXCHANGE  0    0       0
CORRECTIONS    0       1

*                         *** Radius of small cluster for
*                         *** self-consistency calculation
*                         *** A sphere including 2 shells is
*                         *** a good choice
*                         *** l_scf = 0 for a solid, 1 for a molecule
*         r_scf  [ l_scf   n_scf   ca ]
SCF       5         0

*                         *** scattering rather than a path expansion
*         kmax   [ delta_k  delta_e ]
XANES     8.0

*                         *** Radius of cluster for Full Multiple
*                         *** Scattering calculation
*                         *** l_fms = 0 for a solid, 1 for a molecule
*         r_fms     l_fms
FMS     6       0
*                         *** Energy grid over which to calculate
*                         *** DOS functions
*         emin  emax   eimag
*LDOS      -30   20     0.1

FOLP 3 0.8

POTENTIALS
  0     27      Co      -1      -1
  1     6       C       -1      -1
  2     15      P       -1      -1
  3     1       H       -1      -1
  4     7       N       -1      -1
  5     8       O       -1      -1

ATOMS
	0.000000        0.000000        0.000000        0       Co
 0.000000        1
	-0.877000       -1.130000       1.209000        4       N
1.872888        2
	0.706000        0.763000        1.563000        4       N
1.877119        3
	-0.886000       -0.853000       -1.472000       4       N
1.918173        4
	1.117000        1.157000        -1.052000       4       N
1.921729        5
	1.456000        -1.334000       -0.126000       1       C
1.978729        6
	-1.601000       1.453000        -0.068000       4       N
2.163107        7
	1.122000        -2.209000       0.163000        3       H
2.482969        8
	1.765000        -1.394000       -1.054000       3       H
2.483823        9
	2.201000        -1.061000       0.448000        3       H
2.484115        10
	-0.328000       -1.105000       2.581000        1       C
2.826689        11
	1.045000        1.233000        -2.389000       1       C
2.884378        12
	0.051000        0.367000        2.864000        1       C
2.887869        13
	1.756000        1.481000        1.751000        1       C
2.888408        14
	-0.659000       -0.537000       -2.771000       1       C
2.898464        15
	-1.715000       -2.120000       1.053000        1       C
2.923086        16
	-1.810000       -1.877000       -1.395000       1       C
2.957238        17
	2.263000        1.829000        -0.603000       1       C
2.971535        18
	-2.864000       1.125000        -0.216000       1       C
3.084603        19
	0.509000        -1.655000       2.598000        3       H
3.122132        20
	-3.165000       0.225000        -0.264000       3       H
3.183951        21
	-1.881000       -2.521000       -0.717000       3       H
3.226095        22
	0.212000        0.468000        -3.185000       1       C
3.226173        23
	0.260000        -3.225000       -0.293000       3       H
3.248703        24
	-1.605000       2.854000        0.000000        1       C
3.274346        25
	-1.931000       0.869000        2.513000        3       H
3.286197        26
	2.614000        1.957000        0.706000        1       C
3.340850        27
	-2.232000       -2.499000       -0.241000       1       C
3.359301        28
	-2.287000       -2.542000       0.830000        3       H
3.518669        29
	-1.207000       1.214000        3.075000        1       C
3.519413        30
	-1.019000       2.145000        2.831000        3       H
3.695125        31
	0.186000        -3.470000       1.287000        3       H
3.705653        32
	-2.458000       -2.943000       -0.050000       1       C
3.834777        33
	0.288000        -3.903000       0.413000        1       C
3.935343        34
	-1.387000       -1.820000       3.396000        1       C
4.094995        35
	2.553000        -0.694000       3.132000        3       H
4.099862        36
	1.198000        0.646000        3.906000        1       C
4.136346        37
	0.236000        0.648000        -4.119000       3       H
4.176333        38
	1.974000        1.827000        3.218000        1       C
4.194059        39
	1.979000        2.281000        -2.920000       1       C
4.200691        40
	-1.954000       -2.872000       2.399000        1       C
4.221576        41
	-1.356000       -1.474000       -3.722000       1       C
4.226665        42
	3.077000        2.276000        -1.823000       1       C
4.239273        43
	-2.379000       -2.161000       -2.783000       1       C
4.251429        44
	-3.699000       2.187000        -0.292000       4       N
4.307068        45
	-2.114000       -1.164000       3.595000        3       H
4.329886        46
	4.151130        0.213470        -1.476130       3       H
4.410942        47
	-3.398000       -2.805000       -0.293000       3       H
4.415912        48
	-2.914000       3.318000        -0.141000       1       C
4.418190        49
	-1.477000       1.171000        4.015000        3       H
4.435425        50
	0.084000        -2.932000       -3.384000       3       H
4.478296        51
	-0.139000       -3.903000       2.219000        3       H
4.491847        52
	1.145000        -4.375000       0.380000        3       H
4.538287        53
	2.138000        -0.543000       4.017000        1       C
4.582814        54
	1.599000        -1.345000       4.232000        3       H
4.719709        56
	4.110000        1.128000        -2.086000       1       C
4.745090        57
	2.947000        1.705000        3.417000        3       H
4.823663        58
	-3.841000       -0.653000       -2.863000       3       H
4.834921        59
	3.949000        2.548000        1.146000        1       C
4.837377        60
	-3.203000       -3.637000       -0.340000       1       C
4.858248        61
	-0.314000       -2.507000       -4.171000       1       C
4.876565        62
	2.363000        1.996000        -3.799000       3       H
4.898998        63
	-1.074000       -4.151000       2.377000        1       C
4.902490        64
       -2.168000       -4.410000       0.005000        1       C
4.914097        65
	-2.368000       -3.147000       -2.947000       3       H
4.918927        66
	1.290000        3.658000        -3.054000       1       C
4.936799        67
	-0.837000       -4.889000       0.206000        1       C
4.964406        68
	0.666000        3.369000        3.643000        3       H
5.006512        69
	1.635000        3.289000        3.463000        1       C
5.048080        70
	-3.849000       -1.643000       -2.849000       1       C
5.062712        71
	-4.475000       -1.815000       1.737000        3       H
5.131961        72
	0.388000        -2.058000       -4.689000       3       H
5.135429        73
	-4.326000       -1.930000       -2.031000       3       H
5.154041        74
	-1.382000       -4.745000       1.662000        3       H
5.214134        75
	-4.736000       1.135000        1.925000        5       O
5.236750        76
	-2.871000       -4.398000       0.183000        3       H
5.255334        77
	-3.300000       -3.904000       -1.277000       3       H
5.268961        78
	-4.074000       -3.355000       0.011000        3       H
5.277653        79
	-1.914000       -0.761000       -4.955000       1       C
5.366055        80
	0.046000        3.646000        -3.941000       1       C
5.369070        81
	-1.698000       -3.672000       -3.533000       3       H
5.371115        82
	-2.633000       -0.152000       -4.682000       3       H
5.373725        83
	-0.880000       -2.379000       4.741000        1       C
5.376906        84
	-3.372000       -3.278000       2.760000        1       C
5.452822        85
	0.671000        1.054000        5.308000        1       C
5.453074        86
	-0.293000       -1.712000       5.177000        3       H
5.460597        87
	-4.181000       -1.407000       3.261000        3       H
5.485848        88
	-1.200000       -0.248000       -5.388000       3       H
5.525581        89
	3.795000        3.637000        -1.723000       1       C
5.531593        90
	0.151000        1.882000        5.232000        3       H
5.562243        91
	-5.154000       2.141000        -0.214000       1       C
5.585105        92
	-0.348000       -3.198000       4.579000        3       H
5.596030        93
	-4.430000       -2.157000       2.662000        1       C
5.600339        94
	0.099000        0.341000        5.663000        3       H
5.674121        95
	-0.746000       -3.186000       -4.728000       3       H
5.749878        96
       -1.148000       -4.612000       3.238000        3       H
5.750921        97
	-5.597000       1.049000        -0.967000       5       O
5.775976        98
	-4.998000       1.024000        2.714000        3       H
5.778787        99
	-1.369000       -4.479000       -3.414000       4       N
5.795774        100
	-3.647000       -4.018000       2.164000        3       H
5.841903        101
	4.578000        3.552000        -1.141000       3       H
5.905647        102
	-1.672000       -4.987000       -2.760000       3       H
5.939979        103
	3.263000        -0.429000       5.058000        1       C
6.034449        104
	-5.655000       1.939000        1.236000        1       C
6.104625        105
	5.047000        1.380000        -3.248000       1       C
6.158418        106
	-6.144000       -0.550000       0.157000        3       H
6.170566        107
	-3.372000       -3.628000       3.685000        3       H
6.173491        108
	1.428000        1.198000        5.912000        3       H
6.198882        109
	-3.234000       -5.327000       -0.151000       1       C
6.233658        110
	-0.566000       -6.250000       0.206000        1       C
6.278956        111
	-5.537000       2.986000        -0.588000       3       H
6.318252        112
	-0.435000       -4.923000       -4.197000       1       C
6.483823        113
	-4.129000       -5.031000       -0.254000       3       H
6.513380        114
	4.649000        1.240000        -4.419000       5       O
6.532868        115
	-4.629000       -2.157000       -4.093000       1       C
6.544688        116
	-6.579000       0.277000        -0.201000       1       C
6.587896        117
	3.946000        0.575000        5.254000        5       O
6.595912        118
	-2.062000       -2.707000       5.670000        1       C
6.612760        119
	-0.029000       -4.281000       -5.051000       5       O
6.621209        120
	-2.897000       -4.497000       3.921000        5       O
6.632485        121
	-5.819000       2.808000        1.704000        3       H
6.682009        122
	-4.241000       -1.749000       -4.909000       3       H
6.718881        123
	2.890000        -2.118000       5.767000        3       H
6.789427        124
	-2.956000       -1.850000       5.836000        5       O
6.798480        125
	3.365000        -1.387000       5.883000        4       N
6.917852        126
	-5.795000       -2.719000       3.077000        1       C
7.102318        127
	6.519000        1.843000        -2.135000       3       H
7.102974        128
       -6.958000       1.182000        0.953000        1       C
7.121734        129
	-5.572000       -1.864000       -4.025000       3       H
7.121959        130
	6.265000        1.753000        -2.972000       4       N
7.152344        131
	-4.584000       -3.642000       -4.220000       1       C
7.217037        132
	-6.768000       -0.507000       -2.663000       3       H
7.290709        133
	-4.900000       -4.410000       -3.269000       5       O
7.358292        134
	-6.097000       -1.290000       4.274000        3       H
7.556758        135
	-2.049000       -3.867000       6.278000        4       N
7.652802        136
	-7.386000       0.433000        2.084000        5       O
7.686582        137
	-1.394000       -4.435000       6.126000        3       H
7.690275        138
	-7.333000       -0.912000       -2.191000       5       O
7.707471        139
	-6.196000       -3.784000       2.591000        5       O
7.708590        140
	3.913000        -1.320000       6.566000        3       H
7.756695        141
	-7.697000       -0.106000       -1.106000       1       C
7.776778        142
	-6.460000       -2.026000       3.953000        4       N
7.839801        143
	-7.673000       1.820000        0.672000        3       H
7.914475        144
	6.835000        1.912000        -3.624000       3       H
7.969087        145
	-4.202000       -4.117000       -5.391000       4       N
7.979309        146
	-3.986000       -3.564000       -6.042000       3       H
8.068213        147
	-8.116000       0.720000        -1.452000       3       H
8.276241        148
	-6.953000       -4.513000       1.270000        5       O
8.385957        149
	-2.691000       -4.077000       6.838000        3       H
8.403669        150
	-8.380000       -0.585000       -0.571000       3       H
8.419778        151
	-4.162000       -4.987000       -5.524000       3       H
8.526839        152
	-8.821000       0.724000        2.726000        2       P
9.260955        153
	-7.794000       -2.418000       4.430000        1       C
9.285368        154
	-8.760000       -1.946000       2.636000        3       H
9.352701        155
	-7.884000       -3.402000       4.375000        3       H
9.636996        156
	-8.812000       -0.362000       3.897000        5       O
9.642043        157
	-8.891000       -1.772000       3.614000        1       C
9.759655        158
	-7.894000       -2.154000       5.378000        3       H
9.791723        159
	-8.993000       2.042000        3.320000        5       O
9.801337        160
       -9.840000       0.431000        1.688000        5       O
9.993033        161
	-10.251000      -2.267000       4.070000        1       C
11.259982       162
	-10.331000      -3.225000       3.886000        3       H
11.499182       163
	-10.955000      -1.781000       3.591000        3       H
11.665302       164
	-10.348000      -2.113000       5.035000        3       H
11.700303       165
END

On Fri, Aug 28, 2015 at 2:03 PM, 
wrote:
...
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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. Re: Error in Running XANES on FEFF8.4 for Cobalt based
      cluster (Ganesh Subramanian)
----------------------------------------------------------------------
Message: 1
Date: Fri, 28 Aug 2015 14:03:16 -0700
From: Ganesh Subramanian 
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt
        based   cluster
Message-ID:
        
Content-Type: text/plain; charset="utf-8"
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:
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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" <
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
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--
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/

Joshua Kas

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