From owner-chemistry@ccl.net Fri Oct 6 10:22:00 2017 From: "Visvaldas K. coyote_v2002(a)yahoo.com" To: CCL Subject: CCL: Point charges Message-Id: <-53031-171006035804-2950-1iJvv1j9FPGvfoONVQZ6Zg++server.ccl.net> X-Original-From: "Visvaldas K." Content-Type: multipart/alternative; boundary="----=_Part_2612896_781782668.1507276675907" Date: Fri, 6 Oct 2017 07:57:55 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: "Visvaldas K." [coyote_v2002#%#yahoo.com] ------=_Part_2612896_781782668.1507276675907 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable in GAMESS, one has to use "monopoles" in the effective fragment potential (= EFP) section. The problem is, EFPs have to have >=3D3 points, so one has to= use dummy zero charges for other points, if only one charge is added. Below, one charge of -0.4 is added as PT1. PT2 and PT3 are dummy points, an= d their coordinates in $EFRAG and also in $MYCHAR ($MYCHAR could be replace= d with $WHATEWERYOUWANT) also need to be scrambled (so that they are not li= nearly dependent). The coordinates in $EFRAG are the ones which matter, the= coords from $MYCHAR are superposed onto $EFRAG coordinates using some rule= s. Please let me know if you need further help. If you need more point charges= , easiest way is to add additional FRAGNAME=3DMYCHAR sections in $EFRAG, wi= th other coordinates for the three points PT1, PT2, PT3. ($EFRAG just needs= three first points from $MYCHAR; point names are arbitrary. Without further ado, the example >>>begin -cut here ! example of using efp as point charges =C2=A0$BASIS GBASIS=3DSTO NGAUSS=3D3 $END =C2=A0$CONTRL SCFTYP=3DRHF RUNTYP=3DENERGY $END =C2=A0$DATA=20 Title C1 H=C2=A0=C2=A0=C2=A0=C2=A0 1.0=C2=A0=C2=A0=C2=A0=C2=A0 0.63109=C2=A0=C2=A0= =C2=A0 -0.02651=C2=A0=C2=A0=C2=A0=C2=A0 0.47485 O=C2=A0=C2=A0=C2=A0=C2=A0 8.0=C2=A0=C2=A0=C2=A0=C2=A0 0.14793=C2=A0=C2=A0= =C2=A0=C2=A0 0.02998=C2=A0=C2=A0=C2=A0 -0.34219 H=C2=A0=C2=A0=C2=A0=C2=A0 1.0=C2=A0=C2=A0=C2=A0 -0.77901=C2=A0=C2=A0=C2=A0 = -0.00348=C2=A0=C2=A0=C2=A0 -0.13266 =C2=A0$END =C2=A0$EFRAG =C2=A0POSITION=3DFIXED=20 =C2=A0FRAGNAME=3DMYCHAR PT1=C2=A0=C2=A0=C2=A0=C2=A0 -3.3377044155=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 .6773716468=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 .4511861323 PT2=C2=A0=C2=A0=C2=A0=C2=A0 -6.0377044155=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 .6773716468=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 .4511861323 PT3=C2=A0=C2=A0=C2=A0=C2=A0 -3.3377044155=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 1.6773716=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 .6511861323 =C2=A0$END =C2=A0$MYCHAR =C2=A0arbitrary point PT1 q=3D-0.4, note that coords in $EFRAG are the real= ones =C2=A0COORDINATES PT1=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.0=C2=A0 0.0=C2=A0 0.0=C2=A0= 0.0=C2=A0 0.0 PT2=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -1.0=C2=A0 0.0=C2=A0 0.0=C2= =A0 0.0=C2=A0 0.0 PT3=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.0=C2=A0 1.0=C2=A0 0.0=C2=A0= 0.5=C2=A0 0.0 =C2=A0STOP =C2=A0MONOPOLES PT1=C2=A0=C2=A0 -0.4=C2=A0 0.0 PT2=C2=A0=C2=A0=C2=A0 0.0=C2=A0 0.0 PT3=C2=A0=C2=A0=C2=A0 0.0=C2=A0 0.0 =C2=A0STOP =C2=A0$END >>>>>end--cut here Lastly, be careful when optimizing molecules with point charges, or even us= ing energy calculations: electrons could be sucked by the positive charge. From: "David Shobe shobedavid],[gmail.com" To: "Kairys, Visvaldas " =20 Sent: Thursday, October 5, 2017 1:58 AM Subject: CCL: Point charges =20 IIRC Gamess uses floating-point nuclear charges. I don't know if it will le= t you have an 'atom' without a basis though. Regards,--David Shobe On Oct 3, 2017 5:07 AM, "Yuri A sospiro9^-^gmail.com" wrote: Sent to CCL by: "Yuri=C2=A0 A" [sospiro9[-]gmail.com] Sorry, I forgot to say that I am using GAMESS. > "Yuri A sospiro9*o*gmail.com"=C2=A0 wrote: > > Sent to CCL by: "Yuri=C2=A0 A" [sospiro9::gmail.com] > Hi, I would to simulate the effect of point charges on molecules, I've > found some topics about this in this forum but none of them provide > examples. Is there an example to show me how I can insert point charges > using fragments or any other alternative approach? > > Thank you, > Yuri > > -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY!^!ccl.net or use: =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST!^!ccl.net or use =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ ccl/send_ccl_message=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/ sub_unsub.shtmlConferences: http://server.ccl.net/ chemistry/announcements/ conferences/ Search Messages: http://www.ccl.net/chemistry/ searchccl/index.shtml =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers. txt RTFI: http://www.ccl.net/chemistry/ aboutccl/instructions/ =20 ------=_Part_2612896_781782668.1507276675907 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
in GAMESS, one has to use "= monopoles" in the effective fragment potential (EFP) section. The problem i= s, EFPs have to have >=3D3 points, so one has to use dummy zero charges = for other points, if only one charge is added.

Below, one charge of -0.4 is added as PT1. PT2 and PT3 are dummy points, = and their coordinates in $EFRAG and also in $MYCHAR ($MYCHAR could be repla= ced with $WHATEWERYOUWANT) also need to be scrambled (so that they are not = linearly dependent). The coordinates in $EFRAG are the ones which matter, t= he coords from $MYCHAR are superposed onto $EFRAG coordinates using some ru= les.

Please let me know if you need further help.= If you need more point charges, easiest way is to add additional FRAGNAME= =3DMYCHAR sections in $EFRAG, with other coordinates for the three points P= T1, PT2, PT3. ($EF= RAG just needs three first points from $MYCHAR; point names are arbitrary.<= br>

Without further ado, the example
=

>>>begin -cut here
! example of using efp as point charges
 $BASIS GBASIS=3DSTO NGAUSS=3D3 $END $CONTRL SCFTYP=3DRHF RUN= TYP=3DENERGY $END
 $DAT= A
Title
C1
H     1.0     0.63109  = ;  -0.02651     0.47485
O     8.0     = 0.14793     0.02998    -0.34219
H     1.0 &= nbsp;  -0.77901    -0.00348    -0.13266<= br id=3D"yui_3_16_0_ym19_1_1507275906064_3494"> $END
 $EFRAG
 POSITION=3DFIXED
 FRAGNAME=3DMYCHAR
PT1     -3.3377044155    &nb= sp;  .6773716468       .4511861323
PT2     -6.03= 77044155       .6773716468   &= nbsp;   .4511861323
PT3     -3.3377044155     &n= bsp; 1.6773716         .6511861323<= br id=3D"yui_3_16_0_ym19_1_1507275906064_3501"> $END
 $MYCHAR
 arbitrary point PT1 q=3D-0.4, note that coords in $EF= RAG are the real ones
 = COORDINATES
PT1  &= nbsp;     0.0  0.0  0.0  0.0  0.0PT2    &n= bsp;   -1.0  0.0  0.0  0.0  0.0
PT3      &n= bsp; 0.0  1.0  0.0  0.5  0.0
 STOP
 MONOPOLES
PT1 = ;  -0.4  0.0
PT2&n= bsp;   0.0  0.0
PT3    0.0  0.0
 STOP
 = $END
>>>>>end= --cut here
L= astly, be careful when optimizing molecules with point charges, or even usi= ng energy calculations: electrons could be sucked by the positive charge.
From: "David Shobe shobedavid],[gmail.com" <owner-chemistry_-_ccl.net&g= t;
To: "Kairys, Visval= das " <coyote_v2002_-_yahoo.com>
Sent: Thursday, October 5, 2017 1:58 AM
Subject: CCL: Point charges

IIRC Gamess uses floating-point nuclear charges. I don't k= now if it will let you have an 'atom' without a basis though.

Regards,
--David Shobe

<= br>
On Oct 3, 2017 5:07 AM, "Yuri A sospiro9^-^gmail.com" <owner-chemistry!^!ccl.net> wr= ote:

Sent to CCL by: "Yuri  A" [sospiro9[-]gmail.com]
Sorry, I forgot to say that I am using GAMESS.

> "Yuri A sospiro9*o*gmail.com"  wrote:
>
> Sent to CCL by: "Yuri  A" [sospiro9::gmail.com]
> Hi, I would to simulate the effect of point charges on molecules, I've=
> found some topics about this in this forum but none of them provide > examples. Is there an example to show me how I can insert point charge= s
> using fragments or any other alternative approach?
>
> Thank you,
> Yuri
>
>



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------=_Part_2612896_781782668.1507276675907-- From owner-chemistry@ccl.net Fri Oct 6 10:57:00 2017 From: "Keith Refson krefson^_^gmail.com" To: CCL Subject: CCL: Calculate amplitude & angles of vectors of vibrational modes in CASTEP Message-Id: <-53032-171006074315-14724-ToW7aZkBYRBO6a+hZLMqdQ*o*server.ccl.net> X-Original-From: Keith Refson Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Fri, 6 Oct 2017 12:43:06 +0100 MIME-Version: 1.0 Sent to CCL by: Keith Refson [krefson:_:gmail.com] Dear Shaumik, Yes, CASTEP writes the phonon eigenvectors to a separate file with a suffix ".phonon". These are in Cartesian atomic co-ordinates so you will need to write or adapt code to project onto a bond length/angle description. Keith Refson On 28/09/17 06:05, Shaumik Ray rayshau+*+gmail.com wrote: > Sent to CCL by: "Shaumik Ray" [rayshau^gmail.com] > I am simulating crystal structures of tricalcium silicate, dicalcium > silicate, etc. to obtain the IR spectra of the molecules using CASTEP. When > I do the Anaylsis of the IR spectrum, I can see all the vibrational modes. > > But, apart from only coming to conclusions via visualizations, I want to > quantify the type of modes, i.e, symmetric and asymmetric bending modes. > For this purpose, I want to know the amplitude, directions and angles of > the vectors of the motions of the atoms. All these information, I am not > being able to find in the CASTEP output file. > > Can I get all this information in any of the CASTEP files? If not, can > anyone kindly suggest what else I can do? > > Thanking you. > > Shaumik> > From owner-chemistry@ccl.net Fri Oct 6 15:13:01 2017 From: "HARSH BHATIA hb976,+,snu.edu.in" To: CCL Subject: CCL:G: TDDFT Message-Id: <-53033-171006141636-17379-0FnNboj6xPm4PDFnzvLSRw]|[server.ccl.net> X-Original-From: "HARSH BHATIA" Date: Fri, 6 Oct 2017 14:16:33 -0400 Sent to CCL by: "HARSH BHATIA" [hb976]_[snu.edu.in] I am trying to do the NTO calculations through gaussian09, but every time the jobs are getting normally terminated but at the end of the job, each time I am getting the following message: This type of calculation cannot be archived. The command given by me in the root section is: #P wB97XD/3-21G Geom=AllCheck Guess=(Read,Only) Density=(Check,Transition=44) Pop=(Minimal,NTO,SaveNTO) Please help hb976 : snu.edu.in