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problem running with >3000 bqs (point charges)
From NWChem
Viewed 114 times, With a total of 8 Posts
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Clicked A Few Times
Threads 2
Posts 6
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| 10:05:54 AM PDT - Wed, May 2nd 2012 |
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Hello everyone,
I am trying to run a cluster calculation with a set of point charges (>10,000 PCs). I am specifying the PCs directly in the geometry section (input file will be pasted as a reply to the thread).
1. The first error I received complained I was using >3000 atoms, exceeding nw_max_atom. I proceeded to increase nw_max_atom in the src code to 11,000 and recompile
2. the next error I received, after increasing the limit, was that there were too many bonds found (8*nw_max_atom=88000) and the word "autoz" was printed
3. I added the lines to may input file: nocenter noautoz according to another thread that had been posted in this forum by someone with similar problems
The new error is now:
------------------------------------------------------------------------
rtdb_cput: abuf is too small, need=20495
geom_rtdb_store: write to rtdb failedgeometry -> geometry
geom_rtdb_store: open geometies: 1
1 geom_rtdb_store: "geometry" -> "geometry"
geom_rtdb_store: geometries in last accessed data base: 1
geometry
geom_input: geom_rtdb_store failed 0
------------------------------------------------------------------------
I know that in response to the other thread posted in this forum, niri suggested loading the bqs in a separate file. However, I haven't found further details on how this can be done.
Any help would be greatly appreciated!
Regards,
Dalal
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Clicked A Few Times
Threads 2
Posts 6
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| 10:08:45 AM PDT - Wed, May 2nd 2012 |
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input file
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title ...
basis
...
end
ecp
...
end
geometry units au noprint nocenter noautoz
symmetry c1
MN -0.01869177127493 0.05584790221506 0.01137447398337
MN 4.21053283168732 -4.17314571018542 0.01259498044196
ZN -0.09169633313320 -4.24242516527811 4.34406587841085
O 4.22509157777151 0.07377900945757 -0.00271240780482
O 4.20549799920798 -4.14166987295850 4.09323659827758
O 4.14758569437111 -4.14485678377820 -4.10730881872117
O 4.14609207242937 -8.35061709405547 -0.00476631375466
O 8.22429072544983 -4.15424255293304 -0.00231644199101
O 0.11594570794496 -4.03277212381728 -0.10750395197484
O 0.01354320809358 0.04793100913462 4.10336236287029
O 0.01107934092478 -0.00813494960166 -4.11659637484793
O -0.00016426395916 4.06516399059956 -0.00222626880216
O -4.19232034774105 -0.00791041235965 -0.00495728171523
O -4.11438964949746 -4.14775332336534 4.11744406510852
O 0.00683478930291 -8.26784355968200 4.11777137528741
O 0.01203425697808 -4.14404817012199 8.26884406802041
bqa 4.15537166111718 0.000000000000000 4.15537166111718 Charge 12.0
bqa 4.15537166111718 0.000000000000000 -4.15537166111718 Charge 12.0
---
bq1 0.0000 -4.1554 -8.3107 Charge -2.0
bq1 0.0000 -8.3107 -4.1554 Charge -2.0
bq1 -4.1554 -4.1554 -4.1554 Charge -2.0
---
bq2 0.0000 -12.4661 -4.1554 Charge 2.0
bq2 0.0000 -8.3107 -8.3107 Charge 2.0
bq2 0.0000 -4.1554 -12.4661 Charge 2.0
---
end
charge -1
scf
uhf
nopen 9
...
direct
maxiter 500
end
task scf
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Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Vet
Threads 3
Posts 309
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| 11:23:32 AM PDT - Thu, May 3rd 2012 |
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bq
#
# Format is charge, x, y, z
#
12.0 4.15537166111718 0.000000000000000 4.15537166111718
12.0 4.15537166111718 0.000000000000000 -4.15537166111718
---
-2.0 0.0000 -4.1554 -8.3107
-2.0 0.0000 -8.3107 -4.1554
-2.0 -4.1554 -4.1554 -4.1554
---
2.0 0.0000 -12.4661 -4.1554
2.0 0.0000 -8.3107 -8.3107
2.0 0.0000 -4.1554 -12.4661
---
end
Alternatively
bq
load mypointcharges
end
Where the file mypointcharges would contain the data in the format:
bq 4.15537166111718 0.000000000000000 4.15537166111718 12.0
bq 4.15537166111718 0.000000000000000 -4.15537166111718 12.0
---
bq 0.0000 -4.1554 -8.3107 -2.0
bq 0.0000 -8.3107 -4.1554 -2.0
bq -4.1554 -4.1554 -4.1554 -2.0
---
bq 0.0000 -12.4661 -4.1554 2.0
bq 0.0000 -8.3107 -8.3107 2.0
bq 0.0000 -4.1554 -12.4661 2.0
Bert
Quote:Dkanan May 2nd 5:08 pmtitle ...
basis
...
end
ecp
...
end
geometry units au noprint nocenter noautoz
symmetry c1
MN -0.01869177127493 0.05584790221506 0.01137447398337
MN 4.21053283168732 -4.17314571018542 0.01259498044196
ZN -0.09169633313320 -4.24242516527811 4.34406587841085
O 4.22509157777151 0.07377900945757 -0.00271240780482
O 4.20549799920798 -4.14166987295850 4.09323659827758
O 4.14758569437111 -4.14485678377820 -4.10730881872117
O 4.14609207242937 -8.35061709405547 -0.00476631375466
O 8.22429072544983 -4.15424255293304 -0.00231644199101
O 0.11594570794496 -4.03277212381728 -0.10750395197484
O 0.01354320809358 0.04793100913462 4.10336236287029
O 0.01107934092478 -0.00813494960166 -4.11659637484793
O -0.00016426395916 4.06516399059956 -0.00222626880216
O -4.19232034774105 -0.00791041235965 -0.00495728171523
O -4.11438964949746 -4.14775332336534 4.11744406510852
O 0.00683478930291 -8.26784355968200 4.11777137528741
O 0.01203425697808 -4.14404817012199 8.26884406802041
bqa 4.15537166111718 0.000000000000000 4.15537166111718 Charge 12.0
bqa 4.15537166111718 0.000000000000000 -4.15537166111718 Charge 12.0
---
bq1 0.0000 -4.1554 -8.3107 Charge -2.0
bq1 0.0000 -8.3107 -4.1554 Charge -2.0
bq1 -4.1554 -4.1554 -4.1554 Charge -2.0
---
bq2 0.0000 -12.4661 -4.1554 Charge 2.0
bq2 0.0000 -8.3107 -8.3107 Charge 2.0
bq2 0.0000 -4.1554 -12.4661 Charge 2.0
---
end
charge -1
scf
uhf
nopen 9
...
direct
maxiter 500
end
task scf |
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Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Gets Around
Threads 4
Posts 82
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| 11:47:12 AM PDT - Thu, May 3rd 2012 |
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Hi Dalal,
This can be done with the file option. We just noticed that we forgot to document this clearly.
I assume you are using the 6.0 or 6.1 version.
Specify your geometry in angstroms in the geometry block
geometry
...
end
For large numbers of bq charges, use the bq block in your input file.
bq
load bq_charges
end
where bq_charges is your bq charges file. The name of this file is fixed.
The format is
bq x y z charge
...
Make sure the bq charges are in the same units as your geometry. I typically specify them both in angstroms.
Let me know if there are issues.
Best regards,
-Niri
niri.govind@pnnl.gov
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Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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| 11:47:58 AM PDT - Thu, May 3rd 2012 |
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Hi Dalal,
Send me an email directly and I can send you a working example.
Best regards,
-Niri
niri.govind@pnnl.gov
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Posts 6
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| 4:01:52 AM PDT - Fri, May 4th 2012 |
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two more curiosities
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Dear Niri,
Thanks very much for the reply. It was very helpful and worked just fine. One question: it seems that the summed up charge of the PCs does not get added to the total charge of the system. Is that correct? i.e. my point charges add up to a total charge of -42, while my cluster has a charge of +42. Adding those together gives and overall neutral system. However, when the PCs are loaded in a separate file, the total electron count is incorrect if I set the "charge" tag to be 0 (charge of cluster + PCs). It is corrected when I set the charge tag to be +42 (the charge of just the cluster).
One more curiosity: is this in any way implemented in NWchem version 5.1 too?
Best regards,
Dalal
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Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Gets Around
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Posts 82
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| 6:46:33 AM PDT - Fri, May 4th 2012 |
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Dear Dalal,
That's correct. The charges on the subsystems are printed out separately. You should set the charge tag to +42 if your background PCs are -42 so that your total system is neutral. The charge tag is associated with the explicit QM part of your calculation. If you want to perform a charged calculation, for example, adding an electron. In this case you would just set the charge tag in the input to +41, so that your total system is -1 and similarly if you want to remove an electron.
We reworked this interface significantly in the 6.0 and 6.1 releases. Is there a specific reason you would like to use NWChem 5.1 ?
Best,
-Niri
niri.govind@pnnl.gov
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Clicked A Few Times
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Posts 6
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| 10:04:23 AM PDT - Sun, May 6th 2012 |
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Hello Niri,
I compiled NWChem versions 6.1 and 5.1 (6.1 with gfortran and 5.1 with the ifort compiler). However, I can only get version 5.1 to run past the SCF cycle set up. Version 5.1 runs fine, without errors, and converges the UHF wavefunction of my cluster. However, using the same input files, version 6.1 crashes at the start of the SCF module with the error:
Last System Error Message from Task 0:: Inappropriate ioctl for device
0:0:movecs_fragment: failed reading frag header:: 1
(rank:0 hostname:r1c2n8 pid:29850):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/armci.c:ARMCI_Error():208 cond:0
0: ARMCI aborting 1 (0x1).
0: ARMCI aborting 1 (0x1).
system error message: Invalid argument
These tests are all on clusters without any point charges present. When I do include point charges (as you prescribed, for version 6.1) the calculation crashes in the same place, but I can see in the beginning of the output file that the PCs where read in correctly.
I need assistance deciphering this error and/or using NWChem 5.1 in a way that can treat >3000 PCs.
I'd be happy to take this conversation over to email if you prefer (dkanan@princeton.edu).
Regards,
Dalal
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Niri Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Gets Around
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Posts 82
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| 5:04:04 PM PDT - Mon, May 7th 2012 |
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Dear Dalal,
Can you send me your input (*.nw) and bq charges file directly ?
Best regards,
-Niri
niri.govind@pnnl.gov
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