From owner-chemistry %-% at %-% ccl.net Mon Sep 11 10:57:01 2017 From: "Igors Mihailovs igorsm!=!cfi.lu.lv" To: CCL Subject: CCL:G: Gaussian SCRF error "No solvent atoms in DisRep" Message-Id: <-52996-170911063843-24756-j95lfIbFS+LJRzqeSP53bw^_^server.ccl.net> X-Original-From: Igors Mihailovs Content-Language: en-US Content-Type: multipart/alternative; boundary="------------2A3D99DFE872EA0B49E737C0" Date: Mon, 11 Sep 2017 13:41:02 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm#,#cfi.lu.lv] This is a multi-part message in MIME format. --------------2A3D99DFE872EA0B49E737C0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Dear Dr. Klamt, Actually, this was just /p/-nitroaniline (C6H6N2O2). But this was CPCM + SMD calculation. As Dr. Zou said, SMD is constructed over IEFPCM (if I use the right words), at least in /Gaussian/. I actually got to check it without SMD option (same molecule), and in this case 1) the "error on total polarization charges" is 0.00492 for CPCM and 0.00493 for IEFPCM, so, seems to me, it's all right with CPCM in /Gaussian/, for all that. I also checked some archived files, in which a molecule of 71 atom has this number -0.00015 for CPCM; another one is 88 atoms and the error value is 0.01296 (but here it was a 'generic' solvent; similar case has 0.01106 for 92 atoms); and I also found a rather big molecule with 258 atoms, for which CPCM "error on total polarization charges" is 0.01800 for one conformer and 0.02019 for another one. 2) yes, escaped charge is not reported now also for CPCM, so it is probably due to a threshold. So, in fact, Dr. Zou told all I needed at the moment. It's just that SMD is a model which was not build with CPCM. And CPCM alone is as good (from that "error" side) as IEFPCM. 3) there is an IOp option (3/70=20000) to "Do COSMO style CPCM: Klamt radii, iterative (implies g03defaults)", and it does not return any "error on total polarization charges" (maybe this is why You were confused by this message). The corresponding part of output is (same molecule/solvent): Gaussian default C-PCM: No special actions if energy rises. Inv3: Mode=1 IEnd= 6203532. Iteration 1 A*A^-1 deviation from unit magnitude is 3.55D-15 for 771. Iteration 1 A*A^-1 deviation from orthogonality is 2.58D-15 for 583 203. Iteration 1 A^-1*A deviation from unit magnitude is 3.55D-15 for 771. Iteration 1 A^-1*A deviation from orthogonality is 1.56D-15 for 1219 49. Error on total polarization charges = 0.00492 SCF Done: E(RB3LYP) = -492.131647316 A.U. after 13 cycles NFock= 13 Conv=0.26D-08 -V/T= 2.0086 Gaussian "COSMO-style C-PCM": No special actions if energy rises. Integral accuracy reduced to 1.0D-05 until final iterations. Initial convergence to 1.0D-05 achieved. Increase integral accuracy. SCF Done: E(RB3LYP) = -492.120662663 A.U. after 15 cycles NFock= 15 Conv=0.48D-08 -V/T= 2.0086 Seems to be two quite different algorithms – and thereactuallyare two different algorithms, as IOp(3/140) possible values suggest: Override PCM solution method. 0Leave unchanged. 1Force inversion. 2Force iterative. 3Force simultaneous in L502. (/Gaussian 09 IOp Reference/, 2nd ed., p. 72). Looks like that "error on total polarization charges" appears only for the inversion method of solving PCM (the first case, as I can guess). I am starting to feel uneasy if this discussion does not fall under 'reverse engineering' or something else which is not permitted under /Gaussian/ license... Yours sincerely, Igors Mihailovs ISSP UL On 10/09/17 14:25, Andreas Klamt klamt_-_cosmologic.de wrote: > Dear Igors, > > Can you tell me how big the molecule with escaped charge of 0.46 e is? > This either means, that too small radii have been used somewhere, or > that the molecule is very big, so that even with COSMO (C-PCM) the > error is that large. By the way, this error does not depend on epsilon. > > And what does the > "Error on total polarization charges = 0.30616 "mean? > It is claimed to be only 0.01 for IEFPCM. > > Andreas > > > Am 09.09.2017 um 21:24 schrieb Igors Mihailovs igorsm###cfi.lu.lv: >> Dear Dr. Zou, >> >> Thank You for the further clarification! >> >> One another thing I am a little curious about -- only in CPCM+SMD >> calculation the escaped charge is /reported/ (in my case, enormous >> 0.46984). Is that because of some threshold for things to appear in >> output, or due to a different algorithm in use (for IEFPCM, even with >> #P there is no sign of escaped charge)? >> >> Dear Dr. Klamt, >> >> That's why I was surprised by the results I had got, because I have >> read before, well, at least the abstract of the article You cited >> (due to the lack of access) /and/ Your article of 2011 (DOI: >> 10.1002/wcms.56 ) where You argued >> that, although it was proven that the best value of /x/ in the >> equation for COSMO is 0.5, "[u]nfortunately, several >> reimplementations of COSMO, including C-PCM, set the value of /x/ to >> zero either by default or fixed." Can this be the reason? Or is it >> simply because SMD model in Gaussian is optimized for IEFPCM, not >> CPCM?(Maybe Dr. Zou can comment on that.) >> You also mention that "in the literature the COSMO approximation is >> often claimed to be applicable only to polar solvents, it needs to be >> emphasized that for neutral compounds the COSMO approximation with x >> = 0.5 provides very accurate results down to ε = 2". Maybe this is >> why COSMO is not that popular? On the other hand, if, as Dr. Zou >> said, the differences in computational cost arise only in really >> large molecules, maybe software developers just feel it is not that >> urgent to implement COSMO if they already have another methods >> implemented… >> >> By "the equation" I mean the equation of COSMO scaling factor for >> unscreened charge density, >> >> /f/ (/ε/) = (/ε/ – 1) / (/ε/ + /x/) >> >> --------------------------------------------------------------------------- >> >> To mention some other details, the differing part in the output is >> the following: >> >> ***** CPCM_SMD.out >> No special actions if energy rises. >> Using charges instead of weights in PCMQM. >> Inv3: Mode=1 IEnd= 5838075. >> Iteration 1 A*A^-1 deviation from unit magnitude is 2.78D-15 >> for 865. >> Iteration 1 A*A^-1 deviation from orthogonality is 1.65D-15 >> for 711 187. >> Iteration 1 A^-1*A deviation from unit magnitude is 3.11D-15 >> for 813. >> Iteration 1 A^-1*A deviation from orthogonality is 1.65D-15 >> for 1142 64. >> Escaped charge = 0.46984 >> Error on total polarization charges = 0.30616 >> SCF Done: E(RB3LYP) = -492.141763479 A.U. after 13 cycles >> NFock= 13 Conv=0.34D-08 -V/T= 2.0086 >> SMD-CDS (non-electrostatic) energy (kcal/mol) = -1.55 >> >> ***** IEFPCM_SMD.OUT >> No special actions if energy rises. >> Inv3: Mode=1 IEnd= 5838075. >> Iteration 1 A*A^-1 deviation from unit magnitude is 3.55D-15 >> for 317. >> Iteration 1 A*A^-1 deviation from orthogonality is 2.67D-15 >> for 629 474. >> Iteration 1 A^-1*A deviation from unit magnitude is 3.33D-15 >> for 317. >> Iteration 1 A^-1*A deviation from orthogonality is 2.19D-15 >> for 545 224. >> Error on total polarization charges = 0.01601 >> SCF Done: E(RB3LYP) = -492.138961313 A.U. after 13 cycles >> NFock= 13 Conv=0.35D-08 -V/T= 2.0086 >> SMD-CDS (non-electrostatic) energy (kcal/mol) = -1.55 >> >> >> Yours sincerely, >> Igors Mihailovs >> ISSP UL >> >> On 08/09/17 22:59, Lufeng Zou g09gv5_+_gmail.com wrote: >>> Hello Igors, >>> >>> One thing to add is that SMD is a solvation model (IEFPCM using SMD >>> radii for electrostatic part, plus nonelectrostatic terms), so >>> please do not combine SMD with other solvation models. The program >>> should have recognized this error and abort, thank you for catching >>> the bug. >>> >>> As for the cost, please rest assured that difference between IEFPCM >>> and CPCM will be minor for most calculations. The only exception is >>> that for very large molecules with hundreds of atoms, more MEMORY >>> (RAM) is required for IEFPCM than CPCM. >>> >>> Lufeng Zou, Ph.D. >>> Technical Support >>> Gaussian, Inc. >>> help . gaussian.com >> >> >> On 09/09/17 04:16, Andreas Klamt klamt#cosmologic.de wrote: >>> For the differences of IEFPCM and CPCM see >>> Comprehensive Comparison of the IEFPCM and SS(V)PE Continuum >>> Solvation Methods with the COSMO Approach >>> http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00601?src=recsys&journalCode=jctcce >>> >>> They are indeed essentially identical. Hence I do not really >>> understand why the more complicated IEFPCM is so much in use. >>> >>> Andreas > > > -- > -------------------------------------------------- > > Prof. Dr. Andreas Klamt > CEO / Geschäftsführer > COSMOlogic GmbH & Co. KG > Imbacher Weg 46 > D-51379 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt+/-cosmologic.de > web www.cosmologic.de > > [University address: Inst. of Physical and > Theoretical Chemistry, University of Regensburg] > > HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt > --------------2A3D99DFE872EA0B49E737C0 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear Dr. Klamt,

Actually, this was just p-nitroaniline (C6H6N2O2).

But this was CPCM + SMD calculation. As Dr. Zou said, SMD is constructed over IEFPCM (if I use the right words), at least in Gaussian.

I actually got to check it without SMD option (same molecule), and in this case

1) the "error on total polarization charges" is 0.00492 for CPCM and 0.00493 for IEFPCM, so, seems to me, it's all right with CPCM in Gaussian, for all that.
I also checked some archived files, in which a molecule of 71 atom has this number -0.00015 for CPCM; another one is 88 atoms and the error value is 0.01296 (but here it was a 'generic' solvent; similar case has 0.01106 for 92 atoms); and I also found a rather big molecule with 258 atoms, for which CPCM "error on total polarization charges" is 0.01800 for one conformer and 0.02019 for another one.

2) yes, escaped charge is not reported now also for CPCM, so it is probably due to a threshold.

So, in fact, Dr. Zou told all I needed at the moment. It's just that SMD is a model which was not build with CPCM. And CPCM alone is as good (from that "error" side) as IEFPCM.

3) there is an IOp option (3/70=20000) to "Do COSMO style CPCM: Klamt radii, iterative (implies g03defaults)", and it does not return any "error on total polarization charges" (maybe this is why You were confused by this message). The corresponding part of output is (same molecule/solvent):

Gaussian default C-PCM:
 No special actions if energy rises.
 Inv3:  Mode=1 IEnd=     6203532.
 Iteration    1 A*A^-1 deviation from unit magnitude is 3.55D-15 for    771.
 Iteration    1 A*A^-1 deviation from orthogonality  is 2.58D-15 for    583    203.
 Iteration    1 A^-1*A deviation from unit magnitude is 3.55D-15 for    771.
 Iteration    1 A^-1*A deviation from orthogonality  is 1.56D-15 for   1219     49.
 Error on total polarization charges =  0.00492
 SCF Done:  E(RB3LYP) =  -492.131647316     A.U. after   13 cycles
            NFock= 13  Conv=0.26D-08     -V/T= 2.0086
           
Gaussian "COSMO-style C-PCM":
 No special actions if energy rises.
 Integral accuracy reduced to 1.0D-05 until final iterations.
 Initial convergence to 1.0D-05 achieved.  Increase integral accuracy.
 SCF Done:  E(RB3LYP) =  -492.120662663     A.U. after   15 cycles
            NFock= 15  Conv=0.48D-08     -V/T= 2.0086

Seems to be two quite different algorithms – and there actually are two different algorithms, as IOp(3/140) possible values suggest:
Override PCM solution method.
0 Leave unchanged.
1 Force inversion.
2 Force iterative.
3 Force simultaneous in L502. (Gaussian 09 IOp Reference, 2nd ed., p. 72).

Looks like that "error on total polarization charges" appears only for the inversion method of solving PCM (the first case, as I can guess).

I am starting to feel uneasy if this discussion does not fall under 'reverse engineering' or something else which is not permitted under Gaussian license...

Yours sincerely,
Igors Mihailovs
ISSP UL

On 10/09/17 14:25, Andreas Klamt klamt_-_cosmologic.de wrote:
Dear Igors,

Can you tell me how big the molecule with escaped charge of  0.46 e is?
This either means, that too small radii have been used somewhere, or that the molecule is very big, so that even with COSMO (C-PCM) the error is that large. By the way, this error does not depend on epsilon.

And what does the
"Error on total polarization charges =  0.30616 "mean?
It is claimed to be only 0.01 for IEFPCM.

Andreas


Am 09.09.2017 um 21:24 schrieb Igors Mihailovs igorsm###cfi.lu.lv:
Dear Dr. Zou,

Thank You for the further clarification!

One another thing I am a little curious about -- only in CPCM+SMD calculation the escaped charge is reported (in my case, enormous 0.46984). Is that because of some threshold for things to appear in output, or due to a different algorithm in use (for IEFPCM, even with #P there is no sign of escaped charge)?

Dear Dr. Klamt,

That's why I was surprised by the results I had got, because I have read before, well, at least the abstract of the article You cited (due to the lack of access) and Your article of 2011 (DOI: 10.1002/wcms.56) where You argued that, although it was proven that the best value of x in the equation for COSMO is 0.5, "[u]nfortunately, several reimplementations of COSMO, including C-PCM, set the value of x to zero either by default or fixed." Can this be the reason? Or is it simply because SMD model in Gaussian is optimized for IEFPCM, not CPCM? (Maybe Dr. Zou can comment on that.)
You also mention that "in the literature the COSMO approximation is often claimed to be applicable only to polar solvents, it needs to be emphasized that for neutral compounds the COSMO approximation with x = 0.5 provides very accurate results down to ε = 2". Maybe this is why COSMO is not that popular? On the other hand, if, as Dr. Zou said, the differences in computational cost arise only in really large molecules, maybe software developers just feel it is not that urgent to implement COSMO if they already have another methods implemented…

By "the equation" I mean the equation of COSMO scaling factor for unscreened charge density,

f (ε) = (ε – 1) / (ε + x)

---------------------------------------------------------------------------

To mention some other details, the differing part in the output is the following:

***** CPCM_SMD.out
 No special actions if energy rises.
 Using charges instead of weights in PCMQM.
 Inv3:  Mode=1 IEnd=     5838075.
 Iteration    1 A*A^-1 deviation from unit magnitude is 2.78D-15 for    865.
 Iteration    1 A*A^-1 deviation from orthogonality  is 1.65D-15 for    711    187.
 Iteration    1 A^-1*A deviation from unit magnitude is 3.11D-15 for    813.
 Iteration    1 A^-1*A deviation from orthogonality  is 1.65D-15 for   1142     64.
 Escaped charge =  0.46984
 Error on total polarization charges =  0.30616
 SCF Done:  E(RB3LYP) =  -492.141763479     A.U. after   13 cycles
            NFock= 13  Conv=0.34D-08     -V/T= 2.0086
 SMD-CDS (non-electrostatic) energy       (kcal/mol) =      -1.55

***** IEFPCM_SMD.OUT
 No special actions if energy rises.
 Inv3:  Mode=1 IEnd=     5838075.
 Iteration    1 A*A^-1 deviation from unit magnitude is 3.55D-15 for    317.
 Iteration    1 A*A^-1 deviation from orthogonality  is 2.67D-15 for    629    474.
 Iteration    1 A^-1*A deviation from unit magnitude is 3.33D-15 for    317.
 Iteration    1 A^-1*A deviation from orthogonality  is 2.19D-15 for    545    224.
 Error on total polarization charges =  0.01601
 SCF Done:  E(RB3LYP) =  -492.138961313     A.U. after   13 cycles
            NFock= 13  Conv=0.35D-08     -V/T= 2.0086
 SMD-CDS (non-electrostatic) energy       (kcal/mol) =      -1.55


Yours sincerely,
Igors Mihailovs
ISSP UL

On 08/09/17 22:59, Lufeng Zou g09gv5_+_gmail.com wrote:
Hello Igors,

One thing to add is that SMD is a solvation model (IEFPCM using SMD radii for electrostatic part, plus nonelectrostatic terms), so please do not combine SMD with other solvation models. The program should have recognized this error and abort, thank you for catching the bug.

As for the cost, please rest assured that difference between IEFPCM and CPCM will be minor for most calculations. The only exception is that for very large molecules with hundreds of atoms, more MEMORY (RAM) is required for IEFPCM than CPCM.

Lufeng Zou, Ph.D.
Technical Support
Gaussian, Inc.
help . gaussian.com


On 09/09/17 04:16, Andreas Klamt klamt#cosmologic.de wrote:
For the differences of IEFPCM and CPCM see
 Comprehensive Comparison of the IEFPCM and SS(V)PE Continuum Solvation Methods with the COSMO Approach
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00601?src=recsys&journalCode=jctcce

They are indeed essentially identical. Hence I do not really understand why the more complicated IEFPCM is so much in use.

Andreas


-- 
--------------------------------------------------

Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt+/-cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
--------------2A3D99DFE872EA0B49E737C0--