From owner-chemistry@ccl.net Wed Sep 6 08:25:00 2017 From: "Giuseppe Mallia g.mallia(~)imperial.ac.uk" To: CCL Subject: CCL:G: MSSC2017 - Ab initio Modelling in Solid State Chemistry - LAST CALL Message-Id: <-52971-170906073619-29994-w2VHyip38H3es961d9Inrw^server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Wed, 6 Sep 2017 07:36:17 -0400 Sent to CCL by: "Giuseppe Mallia" [g.mallia a imperial.ac.uk] This is the last call and if you register before Friday the 8th of September you will be added to the reduced fee list. ### MSSC2017 Ab initio Modelling in Solid State Chemistry Discovering quantum-mechanical simulations with CRYSTAL www.imperial.ac.uk/mssc2017 London Edition (New Users): London (UK), 18 - 22 September 2017 Directors: L. Bernasconi - N.M. Harrison - G. Mallia ### The Department of Chemistry and the Thomas Young Centre at Imperial College London and the Computational Materials Science Group of the Science and Technology Facilities Council (STFC), in collaboration with the Theoretical Chemistry Group of the University of Torino, are organizing the 2017 MSSC Summer School on the "ab initio modelling of crystalline and defective solids with the CRYSTAL code". The week long school is designed for new users of CRYSTAL, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide an introduction to the capabilities of quantum mechanical simulations and to the practical use of CRYSTAL. CRYSTAL is a general-purpose program for the study of periodic solids. It uses a local basis set comprised of Gaussian type functions and can be used to perform calculations at the Hartree-Fock, density functional or global and range-separated hybrid functionals (e.g. B3LYP, HSE06), double hybrid levels of theory. Analytical first derivatives with respect to the nuclear coordinates and cell parameters and analytical derivatives, up to fourth order, with respect to an applied electric field (CPHF/CPKS) are available. The list of lecturers, registration details and general information can be found at the official School web site (see link above). From owner-chemistry@ccl.net Wed Sep 6 09:33:00 2017 From: "Carlos Simmerling carlos.simmerling:+:stonybrook.edu" To: CCL Subject: CCL: Oct 2 deadline for awards application, Computers in Chemistry Division Message-Id: <-52972-170906082907-1226-7dEOzJQdGKgvyo6QHzLjTg[A]server.ccl.net> X-Original-From: "Carlos Simmerling" Date: Wed, 6 Sep 2017 08:29:06 -0400 Sent to CCL by: "Carlos Simmerling" [carlos.simmerling+*+stonybrook.edu] Dear Students, PostDocs and Junior Faculty COMP Members: On behalf of the Division of Computers in Chemistry (COMP) of the American Chemical Society, we are soliciting nominations for the 2018 COMP awards for the Spring 2018 National American Chemical Society Meeting (March 18- 22 New Orleans, LA). Please note most of the awards have a October 2nd deadline. To find out more information about all COMP awards please visit our website http://www.acscomp.org CCG-sponsored award for grad students: http://www.acscomp.org/awards/chemical-computing-group-excellence-award Wiley-sponsored award for postdocs: http://www.acscomp.org/awards/the-comp-acs-outstanding-postdoc-award Openeye-sponsored outstanding junior faculty award: http://www.acscomp.org/awards/the-comp-acs-outstanding-junior-faculty- award Nvidia-sponsored GPU computing award: http://www.acscomp.org/awards/nvidia-gpu-award COMP also provides a select number of undergraduate poster awards at the meeting. No special application is needed other than the normal abstract submission to the ACS MAPS system. Application materials for many of these awards are due October 2nd! Please contact Carlos Simmerling if you have any questions. Prof. Carlos Simmerling Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 carlos.simmerling]*[stonybrook.edu From owner-chemistry@ccl.net Wed Sep 6 10:08:01 2017 From: "Igors Mihailovs igorsm^^^cfi.lu.lv" To: CCL Subject: CCL:G: Gaussian SCRF error "No solvent atoms in DisRep" Message-Id: <-52973-170906083843-4440-5w+s0xifrfNnE3Dm1cPUYw : server.ccl.net> X-Original-From: Igors Mihailovs Content-Language: en-US Content-Type: multipart/alternative; boundary="------------1F69AFCAB09F8256FBB13593" Date: Wed, 6 Sep 2017 15:41:00 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm(0)cfi.lu.lv] This is a multi-part message in MIME format. --------------1F69AFCAB09F8256FBB13593 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit 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 available 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 Cavwas 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=(CPCM,SMD,Solvent=…), as well as withSCRF=(IEFPCM,SMD,Solvent=…), 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=Read (in my case, also Dis Rep, along with Cav and Surface=SAS). > 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: > Surface=SAS Dis Rep Cav NonEq=Write RSolv=2.647 > --- end of non-standard input. > ------------------------------------------------------------------------------ > Polarizable Continuum Model (PCM) > ================================= > 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=1.000). > Cavity algorithm : GePol (No added spheres) > Default sphere list used, NSphG= 52. > Lebedev-Laikov grids with approx. 5.0 points / > Ang**2. > Smoothing algorithm: Karplus/York (Gamma=1.0000). > Polarization charges: spherical gaussians, with > point-specific exponents > (IZeta= 3). > Self-potential: point-specific (ISelfS= 7). > Self-field : sphere-specific E.n sum rule > (ISelfD= 2). > Solvent : n,n-DiMethylFormamide, Eps= 37.219000 > Eps(inf)= 2.046330 > RSolv= 2.647000 Ang. > ------------------------------------------------------------------------------ > Warning! Inconsistent VMol and RSolv for this solvent, using VMol= > 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= 610 Int= 0 D2E= 0 Chk= > 25 Scr= 1 > > If there is no manual definitionof RSolv, the following is printed: > > Solvent : n,n-DiMethylFormamide, Eps= 37.219000 > Eps(inf)= 2.046330 > RSolv= 0.000000 Ang. > ------------------------------------------------------------------------------ > Warning! Inconsistent VMol and RSolv for this solvent, using VMol= > 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{=}udel.edu] >> Hi all, >> I am doing calculation with solvent and get the error "No solvent atoms in 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=AceticAcid, 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? >> --------------1F69AFCAB09F8256FBB13593 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit 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 available 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 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=(CPCM,SMD,Solvent=…), as well as with SCRF=(IEFPCM,SMD,Solvent=…), 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=Read (in my case, also Dis Rep, along with Cav and Surface=SAS). 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:
 Surface=SAS Dis Rep Cav NonEq=Write RSolv=2.647
 --- end of non-standard input.
 ------------------------------------------------------------------------------
 Polarizable Continuum Model (PCM)
 =================================
 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=1.000).
 Cavity algorithm     : GePol (No added spheres)
                        Default sphere list used, NSphG=   52.
                        Lebedev-Laikov grids with approx.  5.0 points / Ang**2.
                        Smoothing algorithm: Karplus/York (Gamma=1.0000).
                        Polarization charges: spherical gaussians, with
                                              point-specific exponents (IZeta= 3).
                        Self-potential: point-specific (ISelfS= 7).
                        Self-field    : sphere-specific E.n sum rule (ISelfD= 2).
 Solvent              : n,n-DiMethylFormamide, Eps=  37.219000 Eps(inf)=   2.046330
                        RSolv=   2.647000 Ang.
 ------------------------------------------------------------------------------
 Warning! Inconsistent VMol and RSolv for this solvent, using VMol=   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=    610 Int=      0 D2E=      0 Chk=     25 Scr=      1

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

Solvent              : n,n-DiMethylFormamide, Eps=  37.219000 Eps(inf)=   2.046330
                        RSolv=   0.000000 Ang.
 ------------------------------------------------------------------------------
 Warning! Inconsistent VMol and RSolv for this solvent, using VMol=    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{=}udel.edu]
Hi all,
I am doing calculation with solvent and get the error "No solvent atoms in 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=AceticAcid, 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?
--------------1F69AFCAB09F8256FBB13593-- From owner-chemistry@ccl.net Wed Sep 6 17:49:00 2017 From: "Zhiqiang Zhang zqzhang2101-$-gmail.com" To: CCL Subject: CCL:G: Gaussian SCRF error "No solvent atoms in DisRep" Message-Id: <-52974-170906164539-16174-uMiKdLrfvHsri3Zq8xG7TQ---server.ccl.net> X-Original-From: Zhiqiang Zhang Content-Type: multipart/alternative; boundary="_5E5868C6-B423-46B7-8DD1-08A63F058AB3_" Date: Wed, 6 Sep 2017 16:45:32 -0400 MIME-Version: 1.0 Sent to CCL by: Zhiqiang Zhang [zqzhang2101]~[gmail.com] --_5E5868C6-B423-46B7-8DD1-08A63F058AB3_ Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="utf-8" SGkgSWdvcnMsDQoNClRoYW5rIHlvdSBmb3Igc2hhcmluZyB0aGlzIGNvbW1lbnQuIEluIG15IHVu ZGVyc3RhbmRpbmcsIHRoZSBjb21tZW50IGZyb20gR2F1c3NpYW4sIEluYy4gc3RhZmYgbWVhbnMg bm90IGFsbCB0aGUgc29sdmVudHMgYXZhaWxhYmxlIGluIHRoZWlyIGRhdGFiYXNlIChsaWtlIG4s bi1EaU1ldGh5bEZvcm1hbWlkZSBpbiB5b3VyIGNhc2UpIGFyZSBkZWZpbmVkIGZvciDigJxEaXMg 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Hi Igors,

 

Thank you for sharing this comment.= In my understanding, the comment from Gaussian, Inc. staff means not all t= he 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 i= nformation is not very clear in the G09 manual on their website. Maybe this= is an obsolete method as you mentioned and we can use SMD to get the resul= ts.

 

Best,=

Zhiqiang =C2=A0Zhang

=  

From: Igors Mihailovs igorsm^^^cfi.lu.lv
Sent: Wednes= day, 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 prob= lem is that you have "Dis Rep Cav", which are non-electrostatic t= erms included in the G03 PCM models for the final energy. However, only lim= ited number of solvents are defined (as in G03) and limited number of eleme= nts are available. For example, n,n-DiMethylFormamide is not available in G= 03.

Plea= se remove "Dis Rep Cav" and it should be fine.

Lufeng Zou, Ph.D.
Technical Support
Gau=
ssian, 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&= quot;, so now I did p-nitroaniline in DCM solution with <= span style=3D'font-size:10.0pt'>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 th= an 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 w= hy 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,<= /span>
Igors Mihailo= vs
ISSP UL

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

Dear all,


I have encountered the same pr= oblem 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 se= ems to me that N,N-DMFA is not completely defined in this version? I postpo= ned writing to Gaussian, Inc., but I will do it now as other people = have the same issue, if nobody reports here today.

Using the follow= ing non-standard input for PCM:
 Surface=3DSAS Dis Rep Cav NonEq=3D= Write 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  &n= bsp;      : UFF (Universal Force Field).
 = Polarization charges : Total charges.
 Charge compensation  : = None.
 Solution method      : On-the-fly s= election.
 Cavity type       &nb= sp;  : SAS (Solvent Accessible Surface) (Alpha=3D1.000).
 Cavi= ty algorithm     : GePol (No added spheres)
 &n= bsp;            = ;          Default sphere list= used, NSphG=3D   52.
      &nbs= p;            &= nbsp;    Lebedev-Laikov grids with approx.  5.0 points = / Ang**2.
          &n= bsp;            = ; Smoothing algorithm: Karplus/York (Gamma=3D1.0000).
   =             &nb= sp;        Polarization charges: spheric= al gaussians, with
         = ;            &n= bsp;            = ;            point-s= pecific exponents (IZeta=3D 3).
      &nbs= p;            &= nbsp;    Self-potential: point-specific (ISelfS=3D 7).
&n= bsp;            = ;           Self-field&nb= sp;   : sphere-specific E.n sum rule (ISelfD=3D 2).
 Solv= ent            =   : n,n-DiMethylFormamide, Eps=3D  37.219000 Eps(inf)=3D &nb= sp; 2.046330
          = ;            &n= bsp; RSolv=3D   2.647000 Ang.
 --------------------------= ----------------------------------------------------
 Warning! Inco= nsistent VMol and RSolv for this solvent, using VMol=3D   77.69 A= ng**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&nb= sp;   610 Int=3D      0 D2E=3D &nbs= p;    0 Chk=3D     25 Scr=3D  =     1

If there is no manual definition of RSolv, the following is printed:
With best regards,
Igors Mihailovs
ISSP UL

On 03/09/17 01:37, Zhiqiang Zhang zhangzq/./udel.edu wrote:<= /o:p>

<= pre>Sent to CCL by: "Zhiqiang=C2=A0 Zhang" [zhangzq{=3D}udel.edu]= 
Hi all,
I am doing calculation with solvent and get th=
e error "No solvent atoms in DisRep" at the end. I am trying 
to include the dispersion and repulsion correction in my calculation=
=2E
My input file:
 
# opt() =
freq m062x/6-311G(2df,p) SCRF(CPCM, solvent=3DAceticAcid, read)
<=
o:p> 
Title Card Required
 <=
/pre>
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 -0.4725=
5200
 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 -0.756=
81000=C2=A0=C2=A0 -0.47255200
 
dis
rep
cav
 
/*End of my =
input file*/
The last two lines of the log files:
No so=
lvent atoms in DisRep.
 Error termination via Lnk1e in /opt/share=
d/gaussian/g09d01/g09/l301.exe at Sat Sep=C2=A0 2 17:24:24 2017.
=
 
Does anybody know how to resolve this issue?
 
 








	

		
			
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