Only PCM CH2CL2 fails

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abbott_cn
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Only PCM CH2CL2 fails

Post by abbott_cn » 13 Jun 2018, 06:48

Dear all,
When I included PCM in my calculation,
at the moment, only solvent CH2CL2 report error.
And all other solvents run well.



I got the following error message:
@ Reason: TOO MANY VERTICES IN TESSERA: BYE BYE...

I have modified pcmdef.h file as suggested by http://wiki.ctcc.no/doku.php?id=public:howto:dalton_pcm.

[root@node1 include]# diff pcmdef.h pcmdef.h.old
4,5c4,5
< PARAMETER (MXSP = 2000, MXTS = 25*MXSP, MXTSPT = 2*MXTS)
< PARAMETER (MXVER = 35000)
---
> PARAMETER (MXSP = 200, MXTS = 25*MXSP, MXTSPT = 2*MXTS)
> PARAMETER (MXVER = 25000)

by increasing MXSP to 2000, MXVER to 35000. Re-compile, but the same error message.

I have tested that if I replace the solvent name CH2CL2 with any one of these solvents C2H4CL2, CH3OH, THF, DMSO, CH3CN,
the calculation runs without any warning or error message.

I have attached the .dal, .mol, and .log files, though .dal and .mol are inlcuded in the .log file.
Attachments
Os-gr-opt-g16-small-BS.mol
(1.96 KiB) Downloaded 28 times
dalton.dal
(252 Bytes) Downloaded 38 times
dalton.out
(33.84 KiB) Downloaded 38 times

abbott_cn
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Re: Only PCM CH2CL2 fails

Post by abbott_cn » 14 Jun 2018, 13:16

Update,
the same .dal file, but another .mol file, yes another molecule,
there's no error.

xiongyan21
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Re: Only PCM CH2CL2 fails

Post by xiongyan21 » 23 Jun 2018, 10:37

Your input gave the following error

PEDRA ERROR: Too many PCM spheres, MXSP must be at least 313
PEDRA ERROR: in .../DALTON/include/pcmdef.h

--- SEVERE ERROR, PROGRAM WILL BE ABORTED ---
Date and time (Darwin) : Sat Jun 23 17:07:24 2018
Host name :

@ MPI MASTER, node no.: 0
@ Reason: PEDRA: TOO MANY SPHERES, -MXSP- MUST BE LARGER.

Total CPU time used in DALTON: 4.52 seconds
Total wall time used in DALTON: 4.58 seconds


QTRACE dump of internal trace stack

========================
level module
========================
5 PEDRA
4 HERCTL
3 HERMIT
2 DALTON
1 DALTON main
========================

Although modifying the input perhaps could make the calculation finish, which I have tried, but it might not meet your requirements.
...
** WARNING ** A VERY POOR TESSELATION HAS BEEN CHOSEN
IT IS VALUABLE ALMOST ONLY FOR TESTING
...
@ *** DIIS converged in 17 iterations !
...

...
**************************************************************************************
*** @ Excit. operator sym 1 & ref. state sym 1 => excited state symmetry 1 ( A ) ***
**************************************************************************************



@ Excited state no: 1 in symmetry 1 ( A )
----------------------------------------------

@ Excitation energy : ...
@ ... eV; ... cm-1; ... kJ / mol

@ Total energy : ... au

@ Operator type: X1SPNORB
@ Spin-orbit coupling constant (X1SPNORB) : ... cm-1
... au

...


The dominant contributions:

I A K_IA K_AI <|I|*|A|> <I^2*A^2> Weight Contrib
...
Time used in polarization propagator calculation is 2067.65 CPU seconds for symmetry 1

Total CPU time used in RESPONSE: 34 minutes 28 seconds
Total wall time used in RESPONSE: 34 minutes 34 seconds


.-------------------------------------------.
| End of Dynamic Property Section (RESPONS) |
`-------------------------------------------'

Total CPU time used in DALTON: 1 hour 17 minutes 42 seconds
Total wall time used in DALTON: 1 hour 17 minutes 54 seconds


Date and time (Darwin) : Sat Jun 23 18:47:10 2018
Host name :
You can try it by youself, because I have discarded the log file.

abbott_cn
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Re: Only PCM CH2CL2 fails

Post by abbott_cn » 10 Aug 2018, 14:47

Still no luck.

I switched to ADF, which is more user-friendly for fresh users.

tlovell
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Too Many Vertices Error

Post by tlovell » 20 Nov 2018, 18:44

I’m trying to calculate the two photon cross section in THF for the molecules that I make. I’ve spent a lot of time on the forum trying to trouble shoot my problems, but I’ve hit a wall. I initially got an error that said “TOO MANY SPHERES”. I did as the forum suggested and increased the MXSP and recompiled Dalton. However now I’m getting the error “TOO MANY VERTICES IN TESSERA: BYE BYE…”. I looked at both threads regarding this and the manual, but I can’t figure it out. Any help as to how to fix this would be greatly appreciated.

Ps. I’m a new Dalton user and not a computational guru, which maybe why I can’t figure this out

kennethruud
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Re: Only PCM CH2CL2 fails

Post by kennethruud » 20 Nov 2018, 22:46

Dear Terri,

I note you use a sphere on each individual atom. This is in general not recommended and may lead to the errors you observe for larger molecules. I would recommend only using a sphere on the heavy (that is, carbon) atoms, using a radius of 2.28 Å (in order to get this, you should also set .ALPHA to 1.0 in the *PCMCAV section). See the manual for more details.


Best regards,

Kenneth

tlovell
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Re: Only PCM CH2CL2 fails

Post by tlovell » 21 Nov 2018, 00:46

Kenneth,
Thanks for your quick response! I did as you suggested and I'm no longer getting the "too many vertices" error. However, my job seem to just stop. It doesn't give a direct error message as it did in the past so I'm not really sure how to proceed to troubleshoot. Do you know how to proceed?

Thank you!
Terri
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exH228_8mCPP.out
(18.01 KiB) Downloaded 8 times

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magnus
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Re: Only PCM CH2CL2 fails

Post by magnus » 21 Nov 2018, 14:33

This is because you have to add the same number of alphas as NESFP, so in your case you have to add 48 lines with 1.0 under .ALPHA

tlovell
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Re: Only PCM CH2CL2 fails

Post by tlovell » 21 Nov 2018, 18:08

Thank you! Unfortunately when I correct the .ALPHA mistake I'm back to the "Too many vertices" error. Is it possible that the molecule is too big? I'm hoping the answer to that is no and that there is a way to make it work.
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exH228_3_8mCPP.out
(51.54 KiB) Downloaded 9 times

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magnus
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Re: Only PCM CH2CL2 fails

Post by magnus » 21 Nov 2018, 22:24

Unfortunately, I'm not very familiar with the PCM part of Dalton. You may want to consider using LSDalton instead depending on which properties you are interested in.

tlovell
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Re: Only PCM CH2CL2 fails

Post by tlovell » 22 Nov 2018, 01:30

I'm interested in the two-photon absorption cross sections, which aren't mentioned in the LSDalton manual...

Also, I used the same input file, but applied it to two other molecules (Cy3 and JCM874) and those jobs appear to be working (they've been running for 7 hours). If anyone knows how to modify the exH228_3_8mcpp file above to make it work, or if you know I can't get it to work, please let me know!

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magnus
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Re: Only PCM CH2CL2 fails

Post by magnus » 22 Nov 2018, 11:08

The problem is that the PCM implementation in Dalton hasn't been maintained for a long time.

There is TPA in LSDalton (described in section 4.8.13) and since the release on Monday (2018.0) also including PCM via the PCMSolver library (described in section 4.13). To use it, LSDalton has to be setup and built including -DENABLE_PCMSOLVER=ON.

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