From owner-chemistry@ccl.net Fri Sep 8 16:55:01 2017 From: "Lufeng Zou g09gv5_+_gmail.com" To: CCL Subject: CCL:G: Gaussian SCRF error "No solvent atoms in DisRep" Message-Id: <-52976-170908155912-25607-APXAUPT2ISiNCRvfz8GO2A]^[server.ccl.net> X-Original-From: Lufeng Zou Content-Type: multipart/alternative; boundary="001a113eb604519d480558b3028b" Date: Fri, 8 Sep 2017 15:59:04 -0400 MIME-Version: 1.0 Sent to CCL by: Lufeng Zou [g09gv5++gmail.com] --001a113eb604519d480558b3028b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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 Thu, Sep 7, 2017 at 10:14 AM, Igors Mihailovs igorsm|a|cfi.lu.lv < owner-chemistry##ccl.net> wrote: > Hi Zhiqiang, > > Yes, I got that, but notice Dr. Zou writes about *G03* PCM models. It > definitely means Gaussian, Inc. people are considering manual definition = of > Dis Rep Cav as something truly outdated, so that they did not update the > list for G09 and G16. Whereas both epsilons and SMD parameters are there > for all solvents listed in the manual. > > So we can probably look for the list of changes between G03 and G09 to > check if the solvent we need has these parameters defined. In G03 > Reference, only 24 solvents are listed as parametrized ones (neither DMFA= , > nor AcOH is there), whereas in G09 Reference there are 184 ones, with tho= se > 24 going as first. I consider therefore that all those 160 solvents canno= t > be used with Dis Rep Cav=E2=80=A6 I checked for CarbonDiSulfide and Nitro= Benzene =E2=80=93 > they both produce the same error, *No solvent atoms in DisRep*. > Some of these solvents quite obviously are not augmentable with > non-electrostatics (e.g., Xylene-mixture), though :) > > With best wishes, > Igors Mihailovs > ISSP UL > > On 06/09/17 23:45, Zhiqiang Zhang zqzhang2101-$-gmail.com wrote: > > Hi Igors, > > > > Thank you for sharing this comment. In my understanding, the comment from > Gaussian, Inc. staff means not all the solvents available in their databa= se > (like n,n-DiMethylFormamide in your case) are defined for =E2=80=9CDis Re= p Cav=E2=80=9D > calculation. This is information is not very clear in the G09 manual on > their website. Maybe this is an obsolete method as you mentioned and we c= an > use SMD to get the results. > > > > Best, > > Zhiqiang Zhang > > > > *From: *Igors Mihailovs igorsm^^^cfi.lu.lv > *Sent: *Wednesday, September 6, 2017 12:07 PM > *To: *Zhang, Zhiqiang > *Subject: *CCL:G: Gaussian SCRF error "No solvent atoms in DisRep" > > > > Dear all, > > I got the answer from *Gaussian, Inc.*, and it is below. > > Hello Igors, > Thank you for giving us a chance to comment. > > The problem is that you have "Dis Rep Cav", which are non-electrostatic > terms included in the G03 PCM models for the final energy. However, only > limited number of solvents are defined (as in G03) and limited number of > elements are available. For example, n,n-DiMethylFormamide is not availab= le > in G03. > > Please remove "Dis Rep Cav" and it should be fine. > > Lufeng Zou, Ph.D. > > Technical Support > > Gaussian, Inc. > > help,,gaussian.com > > If we read between the lines, this probably means "please use *SMD* and > not obsolete methods, if You care about non-electrostatic interactions". > For me, the reason to use Dis Rep Cav was so that I can use the low-cost > CPCM instead of presumably high-cost IEFPCM mentioned as the basis for SM= D > in *G09 Reference* (these considerations were based on previous > experience by the senior lab staff). However, I did not manage to note th= at > "SMD" is in fact "an option to PCM calculations", so now I did *p*-nitroa= niline > in DCM solution with SCRF=3D(CPCM,SMD,Solvent=3D=E2=80=A6), as well as wi= th > SCRF=3D(IEFPCM,SMD,Solvent=3D=E2=80=A6), with the following results: > 1. Both route sections did not bring about any errors > 2. IEFPCM calculation actually lasted almost a minute less than CPCM one > (2:7 vs. 2:53 minutes). > 3. Error on polarization charges was 0.016 for IEFPCM and 0.306 for CPCM. > > So now I at least understand why CPCM is not suggested by *Gaussian, Inc.= * > staff. Thanks to Dr. Zou for the comment and to > Zhiqiang Zhang for raising the issue! > > With best regards, > Igors Mihailovs > ISSP UL > > On 03/09/17 19:16, Igors Mihailovs igorsm|*|cfi.lu.lv wrote: > > Dear all, > > > I have encountered the same problem when trying to use DMFA with SCRF=3DR= ead > (in my case, also Dis Rep, along with Cav and Surface=3DSAS). Also *Gauss= ian > 09*, rev. D.01. It seems to me that N,N-DMFA is not completely defined in > this version? I postponed writing to *Gaussian, Inc.*, but I will do it > now as other people have the same issue, if nobody reports here today. > > Using the following non-standard input for PCM: > Surface=3DSAS Dis Rep Cav NonEq=3DWrite RSolv=3D2.647 > --- end of non-standard input. > ----------------------------------------------------------- > ------------------- > Polarizable Continuum Model (PCM) > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D > Model : C-PCM. > Atomic radii : UFF (Universal Force Field). > Polarization charges : Total charges. > Charge compensation : None. > Solution method : On-the-fly selection. > Cavity type : SAS (Solvent Accessible Surface) (Alpha=3D1.000). > Cavity algorithm : GePol (No added spheres) > Default sphere list used, NSphG=3D 52. > Lebedev-Laikov grids with approx. 5.0 points / > Ang**2. > Smoothing algorithm: Karplus/York (Gamma=3D1.0000= ). > Polarization charges: spherical gaussians, with > point-specific exponents > (IZeta=3D 3). > Self-potential: point-specific (ISelfS=3D 7). > Self-field : sphere-specific E.n sum rule > (ISelfD=3D 2). > Solvent : n,n-DiMethylFormamide, Eps=3D 37.219000 Eps(inf)= =3D > 2.046330 > RSolv=3D 2.647000 Ang. > ----------------------------------------------------------- > ------------------- > Warning! Inconsistent VMol and RSolv for this solvent, using VMol=3D > 77.69 Ang**3. > No solvent atoms in DisRep. > Error termination via Lnk1e in /home/igors/g09/l301.exe at Wed May 24 > 20:48:59 2017. > Job cpu time: 0 days 0 hours 0 minutes 8.5 seconds. > File lengths (MBytes): RWF=3D 610 Int=3D 0 D2E=3D 0 Chk=3D= 25 > Scr=3D 1 > > If there is no manual definition of RSolv, the following is printed: > > Solvent : n,n-DiMethylFormamide, Eps=3D 37.219000 Eps(inf)= =3D > 2.046330 > RSolv=3D 0.000000 Ang. > ----------------------------------------------------------- > ------------------- > Warning! Inconsistent VMol and RSolv for this solvent, using VMol=3D > 0.00 Ang**3. > No solvent atoms in DisRep. > Error termination via Lnk1e in /home/igors/g09/l301.exe at Fri May 19 > 02:16:27 2017 > > With best regards, > Igors Mihailovs > ISSP UL > > On 03/09/17 01:37, Zhiqiang Zhang zhangzq/./udel.edu wrote: > > Sent to CCL by: "Zhiqiang Zhang" [zhangzq{=3D}udel.edu] > > Hi all, > > I am doing calculation with solvent and get the error "No solvent atoms i= n DisRep" at the end. I am trying > > to include the dispersion and repulsion correction in my calculation. > > My input file: > > > > # opt() freq m062x/6-311G(2df,p) SCRF(CPCM, solvent=3DAceticAcid, read) > > > > Title Card Required > > > > 0 1 > > O 0.00000000 0.00000000 0.11813800 > > H 0.00000000 0.75681000 -0.47255200 > > H 0.00000000 -0.75681000 -0.47255200 > > > > dis > > rep > > cav > > > > /*End of my input file*/ > > The last two lines of the log files: > > No solvent atoms in DisRep. > > Error termination via Lnk1e in /opt/shared/gaussian/g09d01/g09/l301.exe = at Sat Sep 2 17:24:24 2017. > > > > Does anybody know how to resolve this issue? > > > > > > > ------------------------------ > [image: Avast logo] > > This email has been checked for viruses by Avast antivirus software. > www.avast.com > > <#m_3808432364363391079_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > -- > Ar cie=C5=86u, > Igors Mihailovs > Organisko materi=C4=81lu laboratorija > LU CFI > --001a113eb604519d480558b3028b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Igors,

One thing to ad= d is that SMD is a solvation model (IEFPCM using SMD radii for electrostati= c part, plus nonelectrostatic terms), so please do not combine SMD with oth= er solvation models. The program should have recognized this error and abor= t, 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 Thu, Sep 7, 2017 at 10:14 AM, Igors Mihai= lovs igorsm|a|cfi.lu.lv = <owner-chem= istry##ccl.net> wrote:
=20 =20 =20
Hi Zhiqiang,

Yes, I got that, but notice Dr. Zou writes about G03 PCM models. It definitely means Gaussian, Inc. people are considering manual definition of Dis Rep Cav as something truly outdated, so that they did not update the list for G09 and G16. Whereas both epsilons and SMD parameters are there for all solvents listed in the manual.

So we can probably look for the list of changes between G03 and G09 to check if the solvent we need has these parameters defined. In G03 Reference, only 24 solvents are listed as parametrized ones (neither DMFA, nor AcOH is there), whereas in G09 Reference there are 184 ones, with those 24 going as first. I consider therefore that all those 160 solvents cannot be used with Dis Rep Cav=E2=80=A6 = I checked for CarbonDiSulfide and NitroBenzene =E2=80=93 they both prod= uce the same error, No solvent atoms in DisRep.
Some of these solvents quite obviously are not augmentable with non-electrostatics (e.g., Xylene-mixture), though :)

With best wishes,
Igors Mihailovs
ISSP UL
On 06/09/17 23:45, = Zhiqiang Zhang zqzhang2101-$-gmail.co= m wrote:
=20 =20 =20

Hi Igors,

=C2=A0

Thank you for sharing this comment. In my understanding, the comment from Gaussian, Inc. staff means not all the solvents available in their database (like n,n-DiMethylFormamide in your case) are defined for =E2=80=9CDis = Rep Cav=E2=80=9D calculation. This is information is not very clear i= n the G09 manual on their website. Maybe this is an obsolete method as you mentioned and we can use SMD to get the results.

=C2=A0

Best,

Zhiqiang =C2=A0Zhang

=C2=A0

From: Igors Mihailovs igorsm^^^cfi.lu.lv
Sent: Wednesday, September 6, 2017 12:07 PM
To: Zhang, Zhiqiang
Subject: CCL:G: Gaussian SCRF error "No solv= ent atoms in DisRep"

=C2=A0

Dear all,

I got the answer from Gaussian, Inc., and it is below.

Hello Igors,
T= hank you for giving us a chance to comment.

T= he problem is that you have "Dis Rep Cav", which are non-electrostatic terms included in the G03 PCM models for the final energy. However, only limited number of solvents are defined (as in G03) and limited number of elements are available. For example, n,n-DiMethylFormamide is not available in G03.

P= lease remove "Dis Rep Cav" and it should be fine.<= br> 

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

If we read between the lines, this probably means "please use SMD and not obsolete methods, if You care about non-electrostatic interactions".
For me, the reason to use Dis Rep Cav was so that I can use the low-cost CPCM instead of presumably high-cost IEFPCM mentioned as the basis for SMD in G09 Reference (these considerations were based on previous experience by the senior lab staff). However, I did not manage to note that "SMD" is in fact "an option to PCM calculations", so now I did= p-nitroaniline in DCM solution with SCRF=3D(CPCM,SMD,Solvent=3D=E2=80=A6), as well as with SCRF= =3D(IEFPCM,SMD,Solvent=3D=E2=80=A6), with the following results:
1. Both route sections did not bring about any errors
2. IEFPCM calculation actually lasted almost a minute less than CPCM one (2:7 vs. 2:53 minutes).
3. Error on polarization charges was 0.016 for IEFPCM and 0.306 for CPCM.

So now I at least understand why CPCM is not suggested by Ga= ussian, Inc. staff. Thanks to Dr. Zou for the comment and to
Zhi= qiang Zhang for raising the issue!

With best regards,
Igo= rs Mihailovs
ISSP UL

On 03/09/17 19:16, Igors Mihailovs igorsm|*|cfi.lu.= lv wrote:

Dear all,


I have encountered the same problem when trying to use DMFA with SCRF=3DRead (in my case, also Dis Rep, along with Cav and Surface=3DSAS). Also Gaussian 09, rev. D.01. It seems to me that N,N-DMFA is not completely defined in this version? I postponed writing to Gaussian, Inc., but I will do it now as other people have the same issue, if nobody reports here today.

Using the following non-standard input for PCM:
=C2=A0Surface=3DSAS Dis Rep Cav NonEq=3DWrite RSolv=3D2.647=
=C2=A0--- end of non-standard input.
=C2=A0-----------------------------------------------------------= -------------------
=C2=A0Polarizable Continuum Model (PCM)
=C2=A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
=C2=A0Model=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 : C-PCM.
=C2=A0Atomic radii=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 : UFF (Universal Force Field).
=C2=A0Polarization charges : Total charges.
=C2=A0Charge compensation=C2=A0 : None.
=C2=A0Solution method=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 : On-th= e-fly selection.
=C2=A0Cavity type=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 : SAS (Solvent Accessible Surface) (Alpha=3D1.000).
=C2=A0Cavity algorithm=C2=A0=C2=A0=C2=A0=C2=A0 : GePol (No = added spheres)
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 Default sphere list used, NSphG=3D=C2=A0=C2=A0 52.
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 Lebedev-Laikov grids with approx.=C2=A0 5.0 points / Ang**2.
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 Smoothing algorithm: Karplus/York (Gamma=3D1.0000).
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 Polarization charges: spherical gaussians, with
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 point-specific exponents (IZeta=3D 3).
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 Self-potential: point-specific (ISelfS=3D 7).
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 Self-field=C2=A0=C2=A0=C2=A0 : sphere-specific E.n sum rule (ISelfD=3D 2).
=C2=A0Solvent=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 : n,n-DiMethylFormamide, Eps=3D=C2=A0 37.219000 Eps(inf)=3D=C2=A0=C2=A0 2.046330
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 RSolv=3D=C2=A0=C2=A0 2.647000 Ang.
=C2=A0-----------------------------------------------------------= -------------------
=C2=A0Warning! Inconsistent VMol and RSolv for this solvent= , using VMol=3D=C2=A0=C2=A0 77.69 Ang**3.
=C2=A0No solvent atoms in DisRep.
=C2=A0Error termination via Lnk1e in /home/igors/g09/l301.e= xe at Wed May 24 20:48:59 2017.
=C2=A0Job cpu time:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0 d= ays=C2=A0 0 hours=C2=A0 0 minutes=C2=A0 8.5 seconds.
=C2=A0File lengths (MBytes):=C2=A0 RWF=3D=C2=A0=C2=A0=C2=A0= 610 Int=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0 D2E=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0 Chk=3D=C2=A0=C2=A0= =C2=A0=C2=A0 25 Scr=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1

If there is no manual definition of RSolv, the following is printed:

Solvent=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 : n,n-DiMethylFormamide, Eps=3D=C2=A0 37.219000 Eps(inf)=3D= =C2=A0=C2=A0 2.046330
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 RSolv=3D=C2=A0=C2=A0 0.000000 Ang.
=C2=A0-----------------------------------------------------------= -------------------
=C2=A0Warning! Inconsistent VMol and RSolv for this solvent= , using VMol=3D=C2=A0=C2=A0=C2=A0 0.00 Ang**3.
=C2=A0No solvent atoms in DisRep.
=C2=A0Error termination via Lnk1e in /home/igors/g09/l301.e= xe at Fri May 19 02:16:27 2017

With best regards,
Igors Mihailovs
ISSP UL

On 03/09/17 01:37, Zhiqiang Zhang zhangzq/./udel.edu wrote:

Sent to CCL by: "Zhiqiang=C2=A0 Zhang" [zhangz=
q{=3D}udel.edu]
Hi all,
I am doing calculation with solvent and get the error &q=
uot;No solvent atoms in DisRep" at the end. I am trying 
to include the dispersion and repulsion correction in my=
 calculation.
My input file:
=C2=A0
# opt() freq m062x/6-311G(2df,p) SCRF(CPCM, solvent=3DAc=
eticAcid, read)
=C2=A0
Title Card Required
=C2=A0
0 1
 O=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00000000=C2=A0=C2=A0=C2=
=A0 0.00000000=C2=A0=C2=A0=C2=A0 0.11813800
 H=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00000000=C2=A0=C2=A0=C2=
=A0 0.75681000=C2=A0=C2=A0 -0.47255200
 H=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00000000=C2=A0=C2=A0 -0.=
75681000=C2=A0=C2=A0 -0.47255200
=C2=A0
dis
rep
cav
=C2=A0
/*End of my input file*/
The last two lines of the log files:
No solvent atoms in DisRep.
 Error termination via Lnk1e in /opt/shared/gaussian/g09=
d01/g09/l301.exe at Sat Sep=C2=A0 2 17:24:24 2017.
=C2=A0
Does anybody know how to resolve this issue?
=C2=A0

=C2=A0



3D"Avast

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Ar cie=C5=86u,
Igors Mihailovs
Organisko materi=C4=81lu laboratorija
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--001a113eb604519d480558b3028b--