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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: 1,079
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 InputI 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: 1,079
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.
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 
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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