Unusual amout of time to generate NBOs

Unusual amout of time to generate NBOs

Postby HenriqueJunior » Mon Jun 27, 2016 1:22 am

Dear NBO forum,
I'm using ORCA 3.0.3 with the latest NBO6 update.
Working with coordination complexes I have to deal with unpaired electrons, in this case, Cu, Fe, Co mostly. The problem is that when I try to use NBO, even the more simple structures are taking an absurd amount of time (6 hours for a structure with 1 metallic center and 2 ligands with less than 15 atoms each). The calculation seems to be stuck for hours and then I give up.
My main structure is relatively big, ~150 atoms with 6 metallic centers. After running for 15 hours the last update in my files as stuck for more than 13 hours. For all this time ORCA keeps using 100% CPU in 8 threads and NBO 1 more thread with 100% too, it is too much CPU and too much time. My .47 file is big: 283M.
Here is what I have in my .nboout file that is bein generated by ORCA (yes, 13+ hours without a single update to the file):
Code: Select all
                                 Natural Population
 ---------------------------------------------------------
   Core                     149.99811 ( 99.9987% of  150)
   Valence                  298.82645 ( 99.6088% of  300)
   Natural Minimal Basis    448.82456 ( 99.7388% of  450)
   Natural Rydberg Basis      1.17544 (  0.2612% of  450)
 ---------------------------------------------------------

    Atom No         Natural Electron Configuration
 ----------------------------------------------------------------------------
     Cu  1      [core]4s( 0.18)3d( 4.96)4p( 0.01)4d( 0.01)
     Cu  2      [core]4s( 0.16)3d( 4.96)4p( 0.01)4d( 0.01)
     Cu  3      [core]4s( 0.17)3d( 4.96)4p( 0.01)4d( 0.01)
      O  4      [core]2s( 0.84)2p( 2.55)
      O  5      [core]2s( 0.84)2p( 2.54)
      O  6      [core]2s( 0.88)2p( 2.69)
      O  7      [core]2s( 0.84)2p( 2.55)
      O  8      [core]2s( 0.87)2p( 2.69)
      O  9      [core]2s( 0.80)2p( 2.42)
      O 10      [core]2s( 0.84)2p( 2.54)
      O 11      [core]2s( 0.79)2p( 2.43)
      O 12      [core]2s( 0.84)2p( 2.54)
      O 13      [core]2s( 0.79)2p( 2.43)
      O 14      [core]2s( 0.84)2p( 2.55)
      O 15      [core]2s( 0.88)2p( 2.70)
      C 16      [core]2s( 0.42)2p( 1.44)3p( 0.01)
      C 17      [core]2s( 0.46)2p( 1.73)3p( 0.01)
      H 18            1s( 0.40)
      C 19      [core]2s( 0.40)2p( 1.37)3p( 0.01)
      C 20      [core]2s( 0.41)2p( 1.39)3p( 0.01)
      C 21      [core]2s( 0.46)2p( 1.63)3p( 0.01)
      H 22            1s( 0.40)
      C 23      [core]2s( 0.46)2p( 1.73)3p( 0.01)
      H 24            1s( 0.40)
      C 25      [core]2s( 0.42)2p( 1.45)3p( 0.01)
      C 26      [core]2s( 0.46)2p( 1.63)3p( 0.01)
      H 27            1s( 0.40)
      C 28      [core]2s( 0.41)2p( 1.37)3p( 0.01)
      C 29      [core]2s( 0.42)2p( 1.45)3p( 0.01)
      C 30      [core]2s( 0.40)2p( 1.36)3p( 0.01)
      C 31      [core]2s( 0.41)2p( 1.38)3p( 0.01)
      C 32      [core]2s( 0.46)2p( 1.65)
      H 33            1s( 0.41)
      C 34      [core]2s( 0.40)2p( 1.35)3p( 0.01)
      C 35      [core]2s( 0.46)2p( 1.62)3p( 0.01)
      H 36            1s( 0.41)
      C 37      [core]2s( 0.44)2p( 1.44)3p( 0.01)
      H 38            1s( 0.43)
      C 39      [core]2s( 0.49)2p( 1.54)
      H 40            1s( 0.43)
      H 41            1s( 0.43)
      H 42            1s( 0.42)
      C 43      [core]2s( 0.49)2p( 1.55)
      H 44            1s( 0.43)
      H 45            1s( 0.43)
      H 46            1s( 0.42)
      C 47      [core]2s( 0.41)2p( 1.02)3p( 0.02)3d( 0.01)
      C 48      [core]2s( 0.46)2p( 1.73)3p( 0.01)
      H 49            1s( 0.40)
      C 50      [core]2s( 0.49)2p( 1.55)
      H 51            1s( 0.43)
      H 52            1s( 0.44)
      H 53            1s( 0.43)
      C 54      [core]2s( 0.44)2p( 1.44)3p( 0.01)
      H 55            1s( 0.43)
      C 56      [core]2s( 0.46)2p( 1.66)
      H 57            1s( 0.41)
      C 58      [core]2s( 0.47)2p( 1.65)
      H 59            1s( 0.41)
      C 60      [core]2s( 0.44)2p( 1.44)3p( 0.01)
      H 61            1s( 0.43)
      C 62      [core]2s( 0.41)2p( 1.02)3p( 0.02)3d( 0.01)
      C 63      [core]2s( 0.40)2p( 1.02)3p( 0.02)3d( 0.01)
     Cu 64      [core]4s( 0.18)3d( 4.96)4p( 0.01)4d( 0.01)
     Cu 65      [core]4s( 0.16)3d( 4.96)4p( 0.01)4d( 0.01)
     Cu 66      [core]4s( 0.17)3d( 4.96)4p( 0.01)4d( 0.01)
      O 67      [core]2s( 0.84)2p( 2.55)
      O 68      [core]2s( 0.84)2p( 2.54)
      O 69      [core]2s( 0.88)2p( 2.69)
      O 70      [core]2s( 0.84)2p( 2.55)
      O 71      [core]2s( 0.87)2p( 2.69)
      O 72      [core]2s( 0.80)2p( 2.42)
      O 73      [core]2s( 0.84)2p( 2.54)
      O 74      [core]2s( 0.79)2p( 2.43)
      O 75      [core]2s( 0.84)2p( 2.54)
      O 76      [core]2s( 0.79)2p( 2.43)
      O 77      [core]2s( 0.84)2p( 2.55)
      O 78      [core]2s( 0.88)2p( 2.70)
      C 79      [core]2s( 0.42)2p( 1.44)3p( 0.01)
      C 80      [core]2s( 0.46)2p( 1.73)3p( 0.01)
      H 81            1s( 0.40)
      C 82      [core]2s( 0.40)2p( 1.37)3p( 0.01)
      C 83      [core]2s( 0.41)2p( 1.39)3p( 0.01)
      C 84      [core]2s( 0.46)2p( 1.63)3p( 0.01)
      H 85            1s( 0.40)
      C 86      [core]2s( 0.46)2p( 1.73)3p( 0.01)
      H 87            1s( 0.40)
      C 88      [core]2s( 0.42)2p( 1.45)3p( 0.01)
      C 89      [core]2s( 0.46)2p( 1.63)3p( 0.01)
      H 90            1s( 0.40)
      C 91      [core]2s( 0.41)2p( 1.37)3p( 0.01)
      C 92      [core]2s( 0.42)2p( 1.45)3p( 0.01)
      C 93      [core]2s( 0.40)2p( 1.36)3p( 0.01)
      C 94      [core]2s( 0.41)2p( 1.38)3p( 0.01)
      C 95      [core]2s( 0.46)2p( 1.65)
      H 96            1s( 0.41)
      C 97      [core]2s( 0.40)2p( 1.35)3p( 0.01)
      C 98      [core]2s( 0.46)2p( 1.62)3p( 0.01)
      H 99            1s( 0.41)
      C100      [core]2s( 0.44)2p( 1.44)3p( 0.01)
      H101            1s( 0.43)
      C102      [core]2s( 0.49)2p( 1.54)
      H103            1s( 0.43)
      H104            1s( 0.43)
      H105            1s( 0.42)
      C106      [core]2s( 0.49)2p( 1.55)
      H107            1s( 0.43)
      H108            1s( 0.43)
      H109            1s( 0.42)
      C110      [core]2s( 0.41)2p( 1.02)3p( 0.02)3d( 0.01)
      C111      [core]2s( 0.46)2p( 1.73)3p( 0.01)
      H112            1s( 0.40)
      C113      [core]2s( 0.49)2p( 1.55)
      H114            1s( 0.43)
      H115            1s( 0.44)
      H116            1s( 0.43)
      C117      [core]2s( 0.44)2p( 1.44)3p( 0.01)
      H118            1s( 0.43)
      C119      [core]2s( 0.46)2p( 1.66)
      H120            1s( 0.41)
      C121      [core]2s( 0.47)2p( 1.65)
      H122            1s( 0.41)
      C123      [core]2s( 0.44)2p( 1.44)3p( 0.01)
      H124            1s( 0.43)
      C125      [core]2s( 0.41)2p( 1.02)3p( 0.02)3d( 0.01)
      C126      [core]2s( 0.40)2p( 1.02)3p( 0.02)3d( 0.01)
      F127      [core]2s( 0.93)2p( 2.76)
      F128      [core]2s( 0.93)2p( 2.75)
      F129      [core]2s( 0.93)2p( 2.75)
      F130      [core]2s( 0.93)2p( 2.76)
      F131      [core]2s( 0.93)2p( 2.75)
      F132      [core]2s( 0.93)2p( 2.75)
      F133      [core]2s( 0.93)2p( 2.76)
      F134      [core]2s( 0.93)2p( 2.75)
      F135      [core]2s( 0.93)2p( 2.75)
      F136      [core]2s( 0.93)2p( 2.76)
      F137      [core]2s( 0.93)2p( 2.75)
      F138      [core]2s( 0.93)2p( 2.75)
      F139      [core]2s( 0.93)2p( 2.76)
      F140      [core]2s( 0.93)2p( 2.75)
      F141      [core]2s( 0.93)2p( 2.75)
      F142      [core]2s( 0.93)2p( 2.76)
      F143      [core]2s( 0.93)2p( 2.75)
      F144      [core]2s( 0.93)2p( 2.75)


 NATURAL BOND ORBITAL ANALYSIS, alpha spin orbitals:

                            Occupancies       Lewis Structure    Low   High
         Max    Occ     -------------------  -----------------   occ   occ
  Cycle  Ctr   Thresh    Lewis   non-Lewis     CR  BD  nC  LP    (L)   (NL)
 ============================================================================
    1     2     0.95   437.22987  12.77013    150 162   0 138    24     30
    2     2     0.94   437.22154  12.77846    150 154   0 146    22     30
    3     2     0.93   437.24049  12.75951    150 150   0 150    18     30
    4     2     0.91   438.55005  11.44995    150 154   0 146    14     30
    5     2     0.90   439.17303  10.82697    150 156   0 144    12     30

Any ideas?
HenriqueJunior
 
Posts: 3
Joined: Wed Feb 03, 2016 5:02 am

Re: Unusual amout of time to generate NBOs

Postby ericg » Tue Jun 28, 2016 1:29 am

Thank you for reporting this issue. Several others have brought it to my attention also.

I recognize what the problem is (the search hasn't failed, rather it's exploring an excessive number of bonding arrangements) and I am considering how to fix it. I should have a solution by next week and will post updated distributions of the source and binaries at that time.

Eric
ericg
 
Posts: 270
Joined: Sat Dec 29, 2012 9:31 am

Re: Unusual amout of time to generate NBOs

Postby negoty » Tue Jun 28, 2016 10:58 pm

Allow me to chip in. I encountered te same problems but on windows (I'm using NBOPro6). For a test calculation I tried a Cr hexacarbonyl complex but after more than a day nothing has happened and the .nbo file has not been updated for 24 hours.
My main compound is a 100 atom Mo complex which showed the same behaviour and I aborted the calculation after running it for a whole week.

Will the fix you mentioned include the windows versions as well?
negoty
 
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Re: Unusual amout of time to generate NBOs

Postby ericg » Thu Jun 30, 2016 6:40 am

All distributions of NBO6, including the windows distribution, should be fixed when posted next week.

Eric
ericg
 
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Re: Unusual amout of time to generate NBOs

Postby ericg » Sun Jul 10, 2016 7:05 pm

The NBO6 distributions that are posted on July 11, 2016 fix the issue with excessively long NBO searches. All binary and source distributions have been updated, with the exception of the Windows distribution, which should be updated in the next day or so.

Eric
ericg
 
Posts: 270
Joined: Sat Dec 29, 2012 9:31 am

Re: Unusual amout of time to generate NBOs

Postby negoty » Mon Jul 11, 2016 9:44 am

Thanks for the quick reply Eric!

However I have to report that the updated version does not seem to change anything for me. I'm currently trying to do an NBO analysis on Cr(CO)6 and so far NBO has produced this output (left out everything up to that point):

Code: Select all
 NATURAL BOND ORBITAL ANALYSIS:

                            Occupancies       Lewis Structure    Low   High
         Max    Occ     -------------------  -----------------   occ   occ
  Cycle  Ctr   Thresh    Lewis   non-Lewis     CR  BD  nC  LP    (L)   (NL)
 ============================================================================
    1     2     1.90   104.74674   3.25326     21  21   0  12     6     15


The .nbo file has not been updated for 7 hours. Am I right in the assumption that such a molecule shouldn't take that long to analyze or am I being impatient?

Regards, Benedikt
negoty
 
Posts: 7
Joined: Tue Jun 28, 2016 10:48 pm

Re: Unusual amout of time to generate NBOs

Postby ericg » Mon Jul 11, 2016 9:25 pm

The calculation certainly shouldn't take so long. The B3LYP/sdd testcase that I use for Cr(C6H6)2 only takes a minute or so.

Check to ensure that you have the most recent version of NBO. Use the VERSION keyword:

$nbo version $end

The current version should be reported as NBO 6.0.13 (11-Jul-2016).

Eric
ericg
 
Posts: 270
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Re: Unusual amout of time to generate NBOs

Postby negoty » Wed Jul 13, 2016 3:14 am

Greetings,
You're right Eric, my version is still the older one from May (6.0.12). Sorry, it seems I overread that the windows version was to be updated later. Has this happened already? The download page states that the downloaded item is the July version, that's why I thought it should be working but apparently it doesn't.

Regards, Benedikt
negoty
 
Posts: 7
Joined: Tue Jun 28, 2016 10:48 pm

Re: Unusual amout of time to generate NBOs

Postby ericg » Mon Jul 18, 2016 3:05 pm

The Windows binary distribution of NBO 6.0.13 has been uploaded and should be available for download tomorrow morning (after 2:00am CDT July 19).

Eric
ericg
 
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Re: Unusual amout of time to generate NBOs

Postby negoty » Thu Jul 21, 2016 5:14 am

Works very well so far. Thanks a lot, Eric!
negoty
 
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