From owner-chemistry@ccl.net Wed Oct 29 07:33:00 2014 From: "Pierre Archirel pierre.archirel/a\u-psud.fr" To: CCL Subject: CCL: symmetry in molpro Message-Id: <-50656-141029072804-11236-PfkhTbAtwIz5NqbE9j6DVw ~ server.ccl.net> X-Original-From: "Pierre Archirel" Date: Wed, 29 Oct 2014 07:28:02 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel..u-psud.fr] Dear colleagues, I use molpro only rarely, could you help me with this symmetry issue? My molpro version is the following: Version 2010.1 linked 21 Dec 2010 10:58:30 My system is a doublet anion with a C2v symmetry (4 symmetries a1, b1, b2, a2) I want to calculate the energies of the 4 states, A1, B1, B2, A2. > From the molpro manual I build the following data: set,nelec=85,sym=1,spin=1,charge=-1 geometry={ A, C, 2.996448 1.730000 0.000000; .. A, O, 3.070926 -1.773000 0.000000;} basis=aug-cc-pvdz int rhf and get the following lines in the output: SETTING SYM = 1.00000000 and then Initial alpha occupancy: 22 15 4 2 Initial beta occupancy: 22 14 4 2 Wave function symmetry: 2 so that sym=1 is not operating and consequently I get the same rhf energy with sym=1,2,3,4 (that of symmetry 2). If now I give the alternative data: {rhf; wf,85,1,1; closed,22,14,4,2; open , 1,0,0,0 } (also asking for symmetry 1) I get the following error: SYMMETRIES FROM ORBITAL RESTRICTIONS AND WF CARD NOT CONSISTENT: 1 2 MS2= 1 NOPEN= 1 GLOBAL ERROR fehler on processor 0 So, how shall I ask for a given symmetry? Many thanks in advance, Pierre Archirel LCP, universite Paris-11 Orsay, France pierre.archirel::u-psud.fr From owner-chemistry@ccl.net Wed Oct 29 13:17:01 2014 From: "Peterson, Kirk kipeters(!)wsu.edu" To: CCL Subject: CCL: symmetry in molpro Message-Id: <-50657-141029131400-18512-tMaeQ+eMC+ua/6Ci1lVwoA{=}server.ccl.net> X-Original-From: "Peterson, Kirk" Content-ID: <60A31697507AA042A88FCA1487F78D8F{=}ad.wsu.edu> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 29 Oct 2014 17:13:52 +0000 MIME-Version: 1.0 Sent to CCL by: "Peterson, Kirk" [kipeters\a/wsu.edu] Dear Pierre, I'm not sure why the first syntax doesn't work, but in the 2nd case you need to add your extra electron to your total number of electrons, i.e., if your molecule really does have a negative charge then the total number of electrons is 86, not 85, i.e., wf,86,1,1 best regards, -Kirk > On Oct 29, 2014, at 4:28 AM, Pierre Archirel pierre.archirel/au-psud.fr wrote: > > > Sent to CCL by: "Pierre Archirel" [pierre.archirel..u-psud.fr] > Dear colleagues, > I use molpro only rarely, could you help me with this symmetry issue? > My molpro version is the following: > > Version 2010.1 linked 21 Dec 2010 10:58:30 > > My system is a doublet anion with a C2v symmetry > (4 symmetries a1, b1, b2, a2) > I want to calculate the energies of the 4 states, A1, B1, B2, A2. > >> From the molpro manual I build the following data: > > set,nelec=85,sym=1,spin=1,charge=-1 > > geometry={ > A, C, 2.996448 1.730000 0.000000; > .. > A, O, 3.070926 -1.773000 0.000000;} > > basis=aug-cc-pvdz > int > rhf > > and get the following lines in the output: > SETTING SYM = 1.00000000 > and then > Initial alpha occupancy: 22 15 4 2 > Initial beta occupancy: 22 14 4 2 > Wave function symmetry: 2 > > so that sym=1 is not operating and consequently I get the same rhf energy with sym=1,2,3,4 (that of symmetry 2). > > If now I give the alternative data: > {rhf; > > wf,85,1,1; > closed,22,14,4,2; > open , 1,0,0,0 } > > (also asking for symmetry 1) I get the following error: > > SYMMETRIES FROM ORBITAL RESTRICTIONS AND WF CARD NOT CONSISTENT: 1 2 MS2= 1 NOPEN= 1 > > GLOBAL ERROR fehler on processor 0 > > So, how shall I ask for a given symmetry? > Many thanks in advance, > Pierre Archirel > LCP, universite Paris-11 Orsay, France > pierre.archirel::u-psud.fr> > From owner-chemistry@ccl.net Wed Oct 29 13:52:01 2014 From: "Partha Sengupta anapspsmo^^gmail.com" To: CCL Subject: CCL: IR peak in DFT Message-Id: <-50658-141026144559-16324-JDVd0JHCfojLP2/l1hGGVA#,#server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=001a113481e4e4392c050657d201 Date: Mon, 27 Oct 2014 00:15:53 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo a gmail.com] --001a113481e4e4392c050657d201 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Friends, I am synthesized a octahedral Zn =E2=80=93water complex (hexa aqua) comple= x. The Experimental IR spectra shows a number of peaks within the range 3500-300 c= m -.1. One strong intensity peak was observed in 2835, 2461, 2369 and high intensity peak at 2089 cm-.1.. I perform Density Functional calculation of the same complex with B3LYP/6-31g(d) method with freq keyword. But I found a gross discrepancy of spectral data in the region 2900- 1900 cm-1, The computed peak does not show any peak within the range from 3000 cm-1 10 1750 cm-1. Please explain the fact. Thanking you in advance Partha S. Sengupta --=20 Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --001a113481e4e4392c050657d201 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Friends,

=C2=A0I am synthesized a octahedral Zn =E2=80=93water complex (hexa aqua) complex. The Experimental = IR spectra shows a number of peaks within the range 3500-300 cm-.1. One strong intensity peak was observed in 2835, 2461, 2369 and high intensity peak at = 2089 =C2=A0=C2=A0cm-.1.. =C2=A0I perform Density Functional calculation of the same complex with B3LYP/6-31g(d) method with freq keywor= d. =C2=A0But I found a gross discrepancy of spectral data in the region 2900- 1900 cm-1, The computed peak does not s= how any peak within the range from 3000 cm-1 10 1750 cm-1= .

Please explain the fact.

Thanking you in advance

Partha S. Sengupta



--
Dr. Partha Sarathi Sengupta
Associate Profe= ssor
Vivekananda Mahavidyalaya, Burdwan
--001a113481e4e4392c050657d201-- From owner-chemistry@ccl.net Wed Oct 29 16:16:00 2014 From: "Mehboob Alam mehboob.cu(_)gmail.com" To: CCL Subject: CCL: IR peak in DFT Message-Id: <-50659-141029151112-27170-/U4zO9Z7t+sfBGToymCDgQ{}server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=001a113ebb0e9c615505069486fc Date: Wed, 29 Oct 2014 20:11:06 +0100 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu#,#gmail.com] --001a113ebb0e9c615505069486fc Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Did you optimize the geometry? You need to perform both the geometry optimization as well as frequency calculation. Apart from that I don't think you should trust the result of 6-31g(d) basis set. Use some larger basis set. Hope it will help.. Best of Luck, Mehboob Dr. Md. Mehboob Alam Post-Doctoral Researcher Institut de Chimie de Strasbourg Laboratoire de Chimie Quantique Universit=E9 de Strasbourg PostDoc Supervisor - Dr. Emmanuel Fromager On Sun, Oct 26, 2014 at 7:45 PM, Partha Sengupta anapspsmo^^gmail.com < owner-chemistry_+_ccl.net> wrote: > Friends, > > I am synthesized a octahedral Zn -water complex (hexa aqua) complex. The > Experimental IR spectra shows a number of peaks within the range 3500-300= cm > -.1. One strong intensity peak was observed in 2835, 2461, 2369 and high > intensity peak at 2089 cm-.1.. I perform Density Functional > calculation of the same complex with B3LYP/6-31g(d) method with freq > keyword. But I found a gross discrepancy of spectral data in the region > 2900- 1900 cm-1, The computed peak does not show any peak within the > range from 3000 cm-1 10 1750 cm-1. > > Please explain the fact. > > Thanking you in advance > > Partha S. Sengupta > > > -- > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan > --001a113ebb0e9c615505069486fc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,

Did you optimize the geometry= ? You need to perform both the geometry optimization as well as frequency c= alculation. Apart from that I don't think you should trust the result o= f 6-31g(d) basis set. Use some larger basis set.

Hope it= will help..

Best of Luck,
Mehboob
=

<= div>
Dr. Md. Mehboob Alam
Post-Doctoral Researcher
Institut de Chimie de Strasbourg
Laboratoire de Chimie Quantiq= ue
Universit=E9 de Strasbourg
PostDoc Supervisor - Dr. Em= manuel Fromager

On Sun, Oct 26, 2014 at 7:45 PM, Partha Seng= upta anapspsmo^^gmail.com <owner-ch= emistry_+_ccl.net> wrote:

Friends,

 I am synthesized a octahedral Zn –water complex (hexa aqua) complex. The Experimental IR= spectra shows a number of peaks within the range 3500-300 cm-.1. One strong intensity peak was observed in 2835, 2461, 2369 and high intensity peak at = 2089   cm-.1..  I perform Density Functional calculation of the same complex with B3LYP/6-31g(d) method with freq keywor= d.  But I found a gross discrepancy of spectral data in the region 2900- 1900 cm-1, The computed peak does not s= how any peak within the range from 3000 cm-1 10 1750 cm-1= .

Please explain the fact.

Thanking you in advance

Partha S. Sengupta



--
Dr. Partha Sarathi Sengupta
Associate Profe= ssor
Vivekananda Mahavidyalaya, Burdwan

--001a113ebb0e9c615505069486fc-- From owner-chemistry@ccl.net Wed Oct 29 23:58:00 2014 From: "Thomas Manz tmanz~~nmsu.edu" To: CCL Subject: CCL: use of research ideas without citation Message-Id: <-50660-141029224048-5709-n8wt7cEuNgfDMtna2vqdeQ*o*server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a11c13e4a77a8c605069acefc Date: Wed, 29 Oct 2014 20:40:42 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [tmanz::nmsu.edu] --001a11c13e4a77a8c605069acefc Content-Type: text/plain; charset=UTF-8 Dear Colleagues, I've had difficulties recently with some researchers using my research ideas in their publications without citing me. Given the very tight funding environment, this has become an especially serious problem, because the denial of credit for my work is impacting the funding I can receive to continue my research program. I would like to point out the following recent cases: 1) T. Bucko, S. Lebegue, J. G. Angyan, and J. Hafner, "Extending the applicability of the Tkatchenko-Scheffler dispersion correction via iterative Hirshfeld partitioning," J. Chem. Phys. 141 (2014) 034114. These researchers used an idea I was the first to propose and use. Specifically, I was the first to propose and use charge compensated reference atomic ions in stockholder-type charge partitioning methods such as Density Derived Electrostatic and Chemical (DDEC) and Iterative Hirshfeld charge partitioning (T. A. Manz and D. S. Sholl, "Chemically Meaningful Atomic Charges that Reproduce the Electrostatic Potential in Periodic and Nonperiodic Materials," J. Chem. Theory Comput. 6 (2010) 2455-2468.). Even though these researchers used this idea, which I was the first to develop and use, they did not cite any of my work in their journal article. 2) A. J. Misquitta, A. J. Stone, and Farhang Fazeli, "Distributed multipoles from a robust basis-space implementation of the iterated stockholder atoms procedure," ArXiv manuscript 1409.5875v1, 2014. These researchers used an idea I was the first to propose and use. Specifically, I was the first to propose and use a constraint that enforces exponential decay of atomic weighting factors for atom tails in stockholder-type charge partitioning methods such as Iterated Stockholder Atoms (ISA) and Density Derived Electrostatic and Chemical (DDEC) charge partitioning ((a) T. A. Manz and D. S. Sholl, "Methods for Computing Accurate Atomic Spin Moments for Collinear and Noncollinear Magnetism in Periodic and Nonperiodic Materials," J. Chem. Theory Comput. 7 (2011) 4146-4164, (b) T. A. Manz and D. S. Sholl, "Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Nonperiodic Materials," J. Chem. Theory Comput. 8 (2012) 2844-2867). Even though these researchers used this idea, which I was the first to develop and use, they did not cite any of my work in their ArXiv manuscript. It is important that we as a scientific community reward those who are honest and punish those who are dishonest. Sincerely, Tom Manz assistant professor Chemical & Materials Engineering New Mexico State University --001a11c13e4a77a8c605069acefc Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

I've had difficult= ies recently with some researchers using my research ideas in their publica= tions without citing me. Given the very tight funding environment, this has= become an especially serious problem, because the denial of credit for my = work is impacting the funding I can receive to continue my research program= .

I would like to point out the following recent c= ases:

1) T. Bucko, S. Lebegue, J. G. Angyan, and J= . Hafner, "Extending the applicability of the Tkatchenko-Scheffler dis= persion correction via iterative Hirshfeld partitioning," J. Chem. Phy= s. 141 (2014) 034114. These researchers used an idea I was the first to pro= pose and use. Specifically, I was the first to propose and use charge compe= nsated reference atomic ions in stockholder-type charge partitioning method= s such as Density Derived Electrostatic and Chemical (DDEC) and Iterative H= irshfeld charge partitioning (T. A. Manz and D. S. Sholl, "Chemically = Meaningful Atomic Charges that Reproduce the Electrostatic Potential in Per= iodic and Nonperiodic Materials," J. Chem. Theory Comput. 6 (2010) 245= 5-2468.). Even though these researchers used this idea, which I was the fir= st to develop and use, they did not cite any of my work in their journal ar= ticle.

2)=C2=A0A. J. Misquitta, A. J. Stone, and F= arhang Fazeli, "Distributed multipoles from a robust basis-space imple= mentation of the iterated stockholder atoms procedure,"=C2=A0ArXiv manuscript 1409.58= 75v1, 2014. These researchers used an idea I was the first to propose and u= se.=C2=A0Specifically, I was the first to propose and use a constrai= nt that enforces exponential decay of atomic weighting factors for atom tai= ls in stockholder-type charge partitioning methods such as Iterated Stockho= lder Atoms (ISA) and Density Derived Electrostatic and Chemical (DDEC) char= ge partitioning=C2=A0((a) T. A. Manz and D. S. Sholl, "Methods for Com= puting Accurate Atomic Spin Moments for Collinear and Noncollinear Magnetis= m in Periodic and Nonperiodic Materials," J. Chem. Theory Comput. 7 (2= 011) 4146-4164, (b) T. A. Manz and D. S. Sholl, "Improved Atoms-in-Mol= ecule Charge Partitioning Functional for Simultaneously Reproducing the Ele= ctrostatic Potential and Chemical States in Periodic and Nonperiodic Materi= als," J. Chem. Theory Comput. 8 (2012) 2844-2867). Even though these r= esearchers used this idea, which I was the first to develop and use, they d= id not cite any of my work in their ArXiv manuscript.

It i= s important that we as a scientific community reward those who are honest a= nd punish those who are dishonest.

Sincerely,<= /div>

Tom Manz
assistant professor
C= hemical & Materials Engineering
New Mexico State University

--001a11c13e4a77a8c605069acefc--