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#1 2018-04-18 16:01:47

mig_riv
Member
Registered: 2017-11-30
Posts: 3

[SOLVED] EMBQ does not print out charges

Dear Molcas users,

I have been attempting to use the embq module described here:
http://www.molcas.org/documentation/manual/node78.html
To generate point charges. I am encountering a couple of problems.

1. When I follow the example at the bottom of the page, the calculation produces a [prefix].Embq_cell.xyz but not the other outputs such as EMBQ_ncQ.dat
I see no error in the log file, everything looks as though it has run as intended. Where are the other output files?

2. I then modify the example to change it to another, larger unit cell and quantum cluster (and the appropriate numbers of atoms). The quantum cluster is recognized but encounters the error below:

------------------------------------------
Generate Electrostatic Embedding Potential
------------------------------------------

Error: cannot read EmbQ_CQM

Found errors while reading EmbQ input
The program is terminated

---------------------------------------------------------------------------------------------
  Nr.    Label          Type            Offset          Length     Atime          Address
---------------------------------------------------------------------------------------------
  1     CARQM           REAL    17515354640190      21600000           5        [0x7f70e480f010]
  2     CARNCQ          REAL    17515351939902      21600000           6        [0x7f70e3375010]
  3     CHGNCQ          REAL    17515351039806       7200000           7        [0x7f70e2c97010]
---------------------------------------------------------------------------------------------
Maximal available memory for Molcas = 7289632000
--- Stop Module:  embq at Wed Apr 18 15:52:00 2018 /rc=0 ---

     Happy landing!

--- Stop Module:  auto at Wed Apr 18 15:52:00 2018 /rc=0 ---

Any clue where I could look to get more information on this error? I do not know what EmbQ_CQM is or any of the other keywords.

Any suggestions would be very welcome!

My Molcas version is v8.0.15-06-18

Kind regards,

Miguel

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#2 2018-04-19 08:24:11

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 558

Re: [SOLVED] EMBQ does not print out charges

I have a suspicion... Try modifying the data/embq.prgm file and remove or replace the "+" signs from the filenames.

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#3 2018-04-19 09:55:31

mig_riv
Member
Registered: 2017-11-30
Posts: 3

Re: [SOLVED] EMBQ does not print out charges

That worked for the first problem! Thank you. The '+' character is definitely allowed in filenames on my system so I am not sure where it went wrong.

The problem didn't get resolved though. The run still gets stuck on the error I mentioned.

The input file I am using for it is:

&EMBQ &END
Elmoment
3
Teterahedra
1 1 1 1 0 0 0 0
Shift
0.5
Print
3
30.0
Calculate
2
UCvectors
12.1199998856         0.0000000000         0.0000000000
 0.0000000000        10.2849998474         0.0000000000
-5.4720203118         0.0000000000        11.2441994632
UCatoms
148
  4.031579   3.221460   4.582038  0.5880
  5.284447   3.803897   4.831403 -0.3862
  2.951172   3.424654   5.492674 -0.3877
  3.874181   2.467695   3.476297 -0.6398
  5.477075   4.600411   5.950437 -0.0275
  6.092446   3.596827   4.129731  0.2014
  3.188198   4.247078   6.614505 -0.0892
  1.659384   2.761890   5.224879  0.7085
  2.882818   2.137047   3.557238  0.4550
  4.423934   4.831952   6.845565 -0.2294
  6.454712   5.046370   6.140204  0.1303
  2.387788   4.444135   7.325895  0.1391
  0.539315   2.935918   6.111159 -0.4559
  1.561928   2.021928   4.178832 -0.5735
  4.572755   5.469828   7.716325  0.1435
 -0.643562   2.269033   5.923049 -0.0966
  0.645311   3.623277   6.948004  0.1823
 -1.844261   2.395459   6.688277  0.1753
 -0.686432   1.574010   5.077487  0.1507
 -2.018255   3.330438   7.738915 -0.1858
 -2.962707   1.591188   6.362206 -0.1858
 -3.210466   3.453319   8.414458 -0.2877
 -1.193757   3.983766   8.027028  0.1538
  7.957207   1.691009   7.031828 -0.2877
  9.254672   0.873675   5.546171  0.1538
  7.791581   2.628411   8.088444  0.2376
 -3.286154   4.190674   9.209383  0.1668
  7.129033   1.054068   6.731268  0.1668
  6.617686   2.732802   8.762922 -0.0140
  6.472355   3.714830   9.826108 -0.2665
  5.504099   1.848374   8.449214 -0.2665
  6.664975   4.732556   9.452737  0.1044
  5.452685   3.674679  10.220088  0.1044
 -4.948064   3.513581  10.650958  0.1044
  5.804852   0.793396   8.537853  0.1044
  4.686213   2.039521   9.150740  0.1044
  5.136179   2.017037   7.425323  0.1044
  1.295569   4.967964  10.204138  0.5880
  2.548437   4.385527  10.453502 -0.3862
  0.215162   4.764770  11.114774 -0.3877
  1.138170   5.721729   9.098396 -0.6398
  8.213086   3.589013   0.328337 -0.0275
  3.356437   4.592596   9.751830  0.2014
  5.924208   3.942346   0.992405 -0.0892
 -1.076626   5.427534  10.846978  0.7085
  0.146809   6.052377   9.179337  0.4550
  7.159944   3.357472   1.223465 -0.2294
  9.190722   3.143054   0.518105  0.1303
  5.123798   3.745288   1.703795  0.1391
  3.275325   5.253506   0.489059 -0.4559
 -1.174082   6.167496   9.800931 -0.5735
  7.308766   2.719596   2.094226  0.1435
  2.092448   5.920390   0.300949 -0.0966
  3.381321   4.566147   1.325904  0.1823
  0.891749   5.793964   1.066177  0.1753
 -3.422442   6.615414  10.699586  0.1507
  0.717755   4.858986   2.116815 -0.1858
 -0.226697   6.598236   0.740106 -0.1858
 -0.474456   4.736105   2.792358 -0.2877
  1.542253   4.205658   2.404928  0.1538
 10.693218   6.498415   1.409728 -0.2877
  6.518661   7.315749  11.168270  0.1538
 10.527591   5.561013   2.466345  0.2376
 -0.550144   3.998749   3.587284  0.1668
  9.865044   7.135355   1.109168  0.1668
  9.353696   5.456622   3.140823 -0.0140
  9.208366   4.474594   4.204008 -0.2665
  8.240109   6.341050   2.827114 -0.2665
  9.400986   3.456868   3.830638  0.1044
  8.188695   4.514745   4.597989  0.1044
 -2.212053   4.675842   5.028858  0.1044
  8.540862   7.396027   2.915754  0.1044
  7.422223   6.149903   3.528640  0.1044
  7.872189   6.172387   1.803223  0.1044
  4.494706   8.363961   7.970863  0.5880
  3.241839   8.946397   7.721498 -0.3862
  5.575113   8.567154   7.060227 -0.3877
  4.652105   7.610195   9.076604 -0.6398
  3.049210   9.742911   6.602464 -0.0275
  2.433839   8.739327   8.423170  0.2014
  5.338087   9.389578   5.938397 -0.0892
  6.866902   7.904390   7.328023  0.7085
  5.643467   7.279547   8.995663  0.4550
  4.102351   9.974452   5.707336 -0.2294
  2.071573  10.188870   6.412697  0.1303
  6.138497   9.586635   5.227007  0.1391
  7.986970   8.078418   6.441742 -0.4559
  6.964357   7.164428   8.374069 -0.5735
  3.953530   0.327328   4.836576  0.1435
 -2.950153   7.411533   6.629853 -0.0966
  7.880974   8.765777   5.604897  0.1823
 -1.749453   7.537959   5.864624  0.1753
 -2.907283   6.716510   7.475414  0.1507
 -1.575459   8.472938   4.813987 -0.1858
 -0.631008   6.733688   6.190695 -0.1858
 -0.383248   8.595819   4.138443 -0.2877
  9.720042   9.126266   4.525873  0.1538
  0.569078   6.833509   5.521073 -0.2877
 -0.728386   6.016175   7.006731  0.1538
  0.734705   7.770911   4.464457  0.2376
 -0.307560   9.333174   3.343518  0.1668
  1.397252   6.196569   5.821633  0.1668
  1.908600   7.875302   3.789979 -0.0140
  2.053930   8.857329   2.726793 -0.2665
  3.022186   6.990874   4.103687 -0.2665
  1.861310   9.875056   3.100163  0.1044
  3.073601   8.817179   2.332813  0.1044
  1.354349   8.656081   1.901943  0.1044
  2.721434   5.935897   4.015048  0.1044
  3.840072   7.182021   3.402162  0.1044
  3.390107   7.159538   5.127578  0.1044
  7.230716  10.110463   2.348763  0.5880
  5.977849   9.528027   2.099398 -0.3862
  8.311124   9.907270   1.438127 -0.3877
  7.388115   0.579229   3.454504 -0.6398
  8.379478   0.909877   3.373564 -0.0275
  5.785220   8.731513   0.980364  0.2014
  5.169849   9.735096   2.801071 -0.0892
  8.074098   9.084846   0.316297  0.7085
  9.602912   0.285034   1.705923  0.4550
  9.700367   1.024996   2.751969 -0.2294
  6.838362   8.499972   0.085237  0.1303
  4.807583   8.285554   0.790597  0.1391
  3.402487   8.887788  10.849106 -0.4559
 10.722980   0.111006   0.819643 -0.5735
  1.217520   7.862096  10.458675  0.1435
 -0.214143   0.777891   1.007753 -0.0966
  5.144964   9.708647  11.226997  0.1823
  0.986557   0.651465   0.242525  0.1753
 -0.171272   1.472914   1.853314  0.1507
 -4.311469  10.001486  10.436086 -0.1858
  2.105003   1.455736   0.568595 -0.1858
 -3.119258   9.878605   9.760542 -0.2877
  6.984032   9.348158  10.147973  0.1538
 -2.166932   1.355915  11.143173 -0.2877
  2.007624   2.173249   1.384631  0.1538
 -2.001305   0.418513  10.086556  0.2376
 -3.043570   9.141250   8.965617  0.1668
  4.133262   1.992856   0.199534  0.1668
 -0.827410   0.314122   9.412078 -0.0140
 -0.682079   9.617095   8.348892 -0.2665
  0.286177   1.198550   9.725787 -0.2665
 -0.874699   8.599368   8.722263  0.1044
  0.337590   9.657245   7.954913  0.1044
 -1.381660   9.818342   7.524042  0.1044
 -0.014576   2.253528   9.637147  0.1044
  1.104062   1.007403   9.024261  0.1044
  0.654097   1.029886  10.749678  0.1044
QMatoms
37
     C  -4.889284  -0.174537   2.348763
     C  -6.142151  -0.756973   2.099398
     C  -3.808876  -0.377730   1.438127
     O  -4.731885   0.579229   3.454504
     H  -3.740522   0.909877   3.373564
     C  -6.334780  -1.553487   0.980364
     H  -6.950151  -0.549904   2.801071
     C  -4.045902  -1.200154   0.316297
     C  -2.517088   0.285034   1.705923
     O  -2.419633   1.024996   2.751969
     C  -5.281638  -1.785028   0.085237
     H  -7.312417  -1.999446   0.790597
     H  -3.245493  -1.397212  -0.395093
     C  -1.397020   0.111006   0.819643
     H  -5.430460  -2.422904  -0.785524
     C  -0.214143   0.777891   1.007753
     H  -1.503016  -0.576353  -0.017202
     C   0.986557   0.651465   0.242525
     H  -0.171272   1.472914   1.853314
     C   1.160551  -0.283514  -0.808113
     C   2.105003   1.455736   0.568595
     C   2.352762  -0.406395  -1.483657
     H   0.336052  -0.936842  -1.096226
     C   3.305088   1.355915  -0.101026
     H   2.007624   2.173249   1.384631
     C   3.470715   0.418513  -1.157643
     H   2.428450  -1.143750  -2.278582
     H   4.133262   1.992856   0.199534
     N   4.644610   0.314122  -1.832121
     C   4.789941  -0.667905  -2.895307
     C   5.758197   1.198550  -1.518412
     H   4.597321  -1.685632  -2.521936
     H   5.809610  -0.627755  -3.289286
     H   4.090360  -0.466658  -3.720157
     H   5.457444   2.253528  -1.607052
     H   6.576082   1.007403  -2.219938
     H   6.126117   1.029886  -0.494521
End of Input

I tried to keep it as close as possible to the example which worked. Maybe I am understanding some parameters incorrectly?

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#4 2018-04-19 15:27:36

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 558

Re: [SOLVED] EMBQ does not print out charges

mig_riv wrote:

That worked for the first problem! Thank you. The '+' character is definitely allowed in filenames on my system so I am not sure where it went wrong.

It is a limitation in the way Molcas handles filenames. I believe with OpenMolcas you don't have this limitation, but then you don't have EMBQ either.

The problem didn't get resolved though. The run still gets stuck on the error I mentioned.

I guess that's because QMatoms should contain only the coordinates, not the atomic symbols/labels (and teterahedra should be tetrahedra, or at least tetr-whatever).

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#5 2018-04-19 15:34:11

mig_riv
Member
Registered: 2017-11-30
Posts: 3

Re: [SOLVED] EMBQ does not print out charges

Ah, good catch! Rookie mistakes smile

There are some other errors with the construction of the quantum cluster with respect to the unit cell that I provided but I think I can solve those. Thanks for all the help.

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