From owner-chemistry@ccl.net Tue Oct 23 04:25:00 2012 From: "Jean Jules FIFEN julesfifen-.-gmail.com" To: CCL Subject: CCL: problem in frequency calculation Message-Id: <-47792-121023035416-29745-1b0gFmq+9LKAduNV6os+8g%x%server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=e89a8fb201ca78ec1204ccb546d9 Date: Tue, 23 Oct 2012 08:54:10 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen^gmail.com] --e89a8fb201ca78ec1204ccb546d9 Content-Type: text/plain; charset=ISO-8859-1 Hi, You can solve this problem by spliting the rwf files. You can achieved this by: %rwf=/tmp/file1.rwf,1998MB,/tmp/file2.rwf,1998MB,/tmp/file3.rwf,1998MB,/tmp/file4.rwf,1998MB,... filen is name of the rwf file n. You can split at least on 10 parts of 1998MB. If you running on Windows, remind to change the slash onto the anti-slash. Best regards, ---------------------------------------- Jean Jules FIFEN, PhD Department of Physics Faculty of Science University of Ngaoundere, Cameroon --e89a8fb201ca78ec1204ccb546d9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
You can solve this problem by spliting the rwf files. You can ac= hieved this by:
%rwf=3D/tmp/file1.rwf,1998MB,/tmp/file2.rwf,1998MB,/tmp/file3.rwf,1998= MB,/tmp/file4.rwf,1998MB,...
filen is name of the rwf file n. You can split a= t least on 10 parts of 1998MB. If you running on Windows, remind to change = the slash onto the anti-slash.
Best regards,
=A0
----------------------------------------
Jean Jules FIFEN, PhD
Department of Physics
Faculty of Science
University of Ngaoundere, Cameroon
=A0
=A0
=A0
--e89a8fb201ca78ec1204ccb546d9-- From owner-chemistry@ccl.net Tue Oct 23 07:58:00 2012 From: "Emilio Xavier Esposito emilio.esposito]_[gmail.com" To: CCL Subject: CCL: COMP abstract submissions for the New Orleans ACS meeting (spring 2013) Message-Id: <-47793-121023075344-12877-jnlS4A+kGAABFwyLtFuLwg_._server.ccl.net> X-Original-From: Emilio Xavier Esposito Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 23 Oct 2012 07:53:16 -0400 MIME-Version: 1.0 Sent to CCL by: Emilio Xavier Esposito [emilio.esposito/./gmail.com] Hi On the morning of Monday, October 22 the abstract submission server at the ACS failed. The ACS is working to put the server back online and is continually informing the COMP Programming Board -- and the Programming Board of other ACS Divisions -- of their progress. More information, when it becomes available, will be posted on the COMP website ( http://www.acsCOMP.org ) and on Twitter ( http://twitter.com/acsCOMPprog ). Thank you for your patience Emilio Xavier Esposito From owner-chemistry@ccl.net Tue Oct 23 08:32:01 2012 From: "Johannes Johansson johjo76%gmail.com" To: CCL Subject: CCL: S^2 for a antiferromagnetic system of 6 Fe(III) Message-Id: <-47794-121023044906-9166-jlCNHhPLLUBN0I/SaY1DHQ(~)server.ccl.net> X-Original-From: Johannes Johansson Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 23 Oct 2012 10:49:01 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76{:}gmail.com] Dear Walter, it depends on the electronic state/structure of the system. Maybe you have some information on this (could be from Mössbauer spectroscopy)? But I'll make two examples just to show how it works. Let's assume that all 6 Fe(III) ions are high-spin (depends on the ligand field), meaning that each ion (d5) has five unpaired electrons and thus a spin of 5/2. If the system is ferromagnetically coupled (30 d-electrons spin up), then the total spin is 6*5/2=15 and the eigenvalue of the S^2 operator is S(S+1) (in units of squared reduced Plancks constant), thus =240. If, on the hand, the system is totally antiferromagnetically coupled, 3 Fe(III) ions (15 d-electrons) are spin up and 3 Fe(III) ions (15 e) are spin down, meaning that the total spin equals S=0. According to the formula given above for the eigenvalue of the S^2 operator, a singlet state should have =0. Now there are two things more to say: 1) You need to know more about the electronic configuration of the ions. Are all six ligand fields identical? Are the ions low spin (S=1/2), high spin (5/2), intermediate (3/2) spin? It is possible that the system is not "completely" antiferromagnetic, e.g. one Fe(III) could be antiferromagnetically coupled to the remaining five ions, giving S=(20/2)=10 if each ion is high spin. 2) Since you are probably using DFT, formally a single determinant method, the antiferromagnetically coupled states are not properly described (they are referred to as "broken-symmetry" or for the specific case of a singlet "open-shell singlet state") and it will be "contaminated" by ferromagnetic configurations, meaning that is higher than it should be (e.g. it should be zero for a singlet state but an unrestricted DFT calculation will show that an open shell singlet has roughly =1, i.e. intermediate of closed-shell singlet and triplet). This contamination will not only affect the value but also the energy of the system. There is a way to correct the energy for this contamination provided that you have the energy for the corresponding ferromagnetic state, if you are interested I could send you some papers on this issue. Good luck with your work! / Johannes -- Adam Johannes Johansson Ph.D., M.Sc. Linkedin: http://se.linkedin.com/pub/adam-johannes-johansson/22/209/395 ************************************************************************************** Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swedish Pharmacist, Humanist and Pioneer Quantum Chemist: http://pubs.acs.org/doi/abs/10.1021/ed300024g ************************************************************************************** From owner-chemistry@ccl.net Tue Oct 23 15:43:01 2012 From: "Devang Sachdev dsachdev+/-nvidia.com" To: CCL Subject: CCL: New Molecular Dynamics Benchmark Reports Oct 2012 Message-Id: <-47795-121023154100-4621-9lH8Vxz7UkPdIV5BTNGMvg(~)server.ccl.net> X-Original-From: "Devang Sachdev" Date: Tue, 23 Oct 2012 15:40:59 -0400 Sent to CCL by: "Devang Sachdev" [dsachdev%%nvidia.com] Hi Folks, New Molecular Dynamics Benchmark Reports Oct 2012 are now available to compare CPU vs GPU & NVIDIAs New Kepler GPU Performance. These reports are intended to assist computational chemistry researchers and IT managers to discover acceleration achieved by running MD applications on GPU based computing solutions. Download Benchmark Reports - www.nvidia.com/GPUTestDrive AMBER, GROMACS, LAMMPS, NAMD reports provide: a. Benchmark data on latest GPU architectures b. Hardware recommendations Also, if you are looking to try GPUs: Sign up for a FREE GPU Test Drive on a remote cluster with AMBER, GROMACS, LAMMPS and NAMD preinstalled - www.nvidia.com/GPUTestDrive Thanks Devang Sachdev Sr. Product Manager, GPU Computing NVIDIA From owner-chemistry@ccl.net Tue Oct 23 21:05:00 2012 From: "MarkG gates.mark,+,gmail.com" To: CCL Subject: CCL: S^2 for a antiferromagnetic system of 6 Fe(III) Message-Id: <-47796-121023172221-16034-0bBT1S5j/0UI39OvtaVgXQ!^!server.ccl.net> X-Original-From: MarkG Content-Type: multipart/alternative; boundary=20cf303b3afd57fd8f04ccc090eb Date: Tue, 23 Oct 2012 15:21:54 -0600 MIME-Version: 1.0 Sent to CCL by: MarkG [gates.mark{=}gmail.com] --20cf303b3afd57fd8f04ccc090eb Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Johannes, I would be interested in reading those papers you refer to on correcting the singlet state energy from the broken symmetry calculation. Thanks, MarkG On Tue, Oct 23, 2012 at 2:49 AM, Johannes Johansson johjo76%gmail.com < owner-chemistry*ccl.net> wrote: > > Sent to CCL by: Johannes Johansson [johjo76{:}gmail.com] > Dear Walter, > > it depends on the electronic state/structure of the system. Maybe you > have some information on this (could be from M=C3=B6ssbauer spectroscopy)= ? > But I'll make two examples just to show how it works. > > Let's assume that all 6 Fe(III) ions are high-spin (depends on the > ligand field), meaning that each ion (d5) has five unpaired electrons > and thus a spin of 5/2. If the system is ferromagnetically coupled (30 > d-electrons spin up), then the total spin is 6*5/2=3D15 and the > eigenvalue of the S^2 operator is S(S+1) (in units of squared reduced > Plancks constant), thus =3D240. > > If, on the hand, the system is totally antiferromagnetically coupled, > 3 Fe(III) ions (15 d-electrons) are spin up and 3 Fe(III) ions (15 e) > are spin down, meaning that the total spin equals S=3D0. According to > the formula given above for the eigenvalue of the S^2 operator, a > singlet state should have =3D0. > > Now there are two things more to say: > > 1) You need to know more about the electronic configuration of the > ions. Are all six ligand fields identical? Are the ions low spin > (S=3D1/2), high spin (5/2), intermediate (3/2) spin? It is possible that > the system is not "completely" antiferromagnetic, e.g. one Fe(III) > could be antiferromagnetically coupled to the remaining five ions, > giving S=3D(20/2)=3D10 if each ion is high spin. > > 2) Since you are probably using DFT, formally a single determinant > method, the antiferromagnetically coupled states are not properly > described (they are referred to as "broken-symmetry" or for the > specific case of a singlet "open-shell singlet state") and it will be > "contaminated" by ferromagnetic configurations, meaning that is > higher than it should be (e.g. it should be zero for a singlet state > but an unrestricted DFT calculation will show that an open shell > singlet has roughly =3D1, i.e. intermediate of closed-shell singlet > and triplet). This contamination will not only affect the value > but also the energy of the system. There is a way to correct the > energy for this contamination provided that you have the energy for > the corresponding ferromagnetic state, if you are interested I could > send you some papers on this issue. > > Good luck with your work! / Johannes > > -- > Adam Johannes Johansson > Ph.D., M.Sc. > Linkedin: http://se.linkedin.com/pub/adam-johannes-johansson/22/209/395 > > *************************************************************************= ************* > Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swedish > Pharmacist, Humanist and Pioneer Quantum Chemist: > http://pubs.acs.org/doi/abs/10.1021/ed300024g > > *************************************************************************= ************* > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --20cf303b3afd57fd8f04ccc090eb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Johannes,

I would be interested in reading those papers you refe= r to on correcting the singlet state energy from the broken symmetry calcul= ation.

Thanks,
MarkG



On= Tue, Oct 23, 2012 at 2:49 AM, Johannes Johansson johjo76%gmail.com <owner-chemistry*ccl.net> wr= ote:

Sent to CCL by: Johannes Johansson [johjo76{:}gmail.com]
Dear Walter,

it depends on the electronic state/structure of the system. Maybe you
have some information on this (could be from M=C3=B6ssbauer spectroscopy)?<= br> But I'll make two examples just to show how it works.

Let's assume that all 6 Fe(III) ions are high-spin (depends on the
ligand field), meaning that each ion (d5) has five unpaired electrons
and thus a spin of 5/2. If the system is ferromagnetically coupled (30
d-electrons spin up), then the total spin is 6*5/2=3D15 and the
eigenvalue of the S^2 operator is S(S+1) (in units of squared reduced
Plancks constant), thus <S^2>=3D240.

If, on the hand, the system is totally antiferromagnetically coupled,
3 Fe(III) ions (15 d-electrons) are spin up and 3 Fe(III) ions (15 e)
are spin down, meaning that the total spin equals S=3D0. According to
the formula given above for the eigenvalue of the S^2 operator, a
singlet state should have <S^2>=3D0.

Now there are two things more to say:

1) You need to know more about the electronic configuration of the
ions. Are all six ligand fields identical? Are the ions low spin
(S=3D1/2), high spin (5/2), intermediate (3/2) spin? It is possible that the system is not "completely" antiferromagnetic, e.g. one Fe(III= )
could be antiferromagnetically coupled to the remaining five ions,
giving S=3D(20/2)=3D10 if each ion is high spin.

2) Since you are probably using DFT, formally a single determinant
method, the antiferromagnetically coupled states are not properly
described (they are referred to as "broken-symmetry" or for the specific case of a singlet "open-shell singlet state")=C2=A0and i= t will be
"contaminated" by ferromagnetic configurations, meaning that <= S^2> is
higher than it should be (e.g. it should be zero for a singlet state
but an unrestricted DFT calculation will show that an open shell
singlet has roughly <S^2>=3D1, i.e. intermediate of closed-shell sing= let
and triplet). This contamination will not only affect the <S^2> value=
but also the energy of the system. There is a way to correct the
energy for this contamination provided that you have the energy for
the corresponding ferromagnetic state, if you are interested I could
send you some papers on this issue.

Good luck with your work! / Johannes

--
Adam Johannes Johansson
Ph.D., M.Sc.
Linkedin: http://se.linkedin.com/pub/adam-johannes-johanss= on/22/209/395
***************************************************************************= ***********
Read the biography: Inga Fischer-Hjalmars (1918-2008) - Swedish
Pharmacist, Humanist and Pioneer Quantum Chemist:
http://pubs.acs.org/doi/abs/10.1021/ed300024g
***************************************************************************= ***********



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY*ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST*ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

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/



--20cf303b3afd57fd8f04ccc090eb-- From owner-chemistry@ccl.net Tue Oct 23 21:40:00 2012 From: "Mike Zhukovskiy mxa4+*+unh.edu" To: CCL Subject: CCL: POLYRATE 2008 compilation errors Message-Id: <-47797-121023191650-31994-IKE4k+9FV/l1Yp0zDj91Qw!A!server.ccl.net> X-Original-From: "Mike Zhukovskiy" Date: Tue, 23 Oct 2012 19:16:49 -0400 Sent to CCL by: "Mike Zhukovskiy" [mxa4]-[unh.edu] Dear CCLers, I am having trouble compiling the Truhalr group's POLYRATE 2008 program for transition state theory calculations with variable reaction coordinate capability, using openmpi. Here is an example of the compilation errors that I get: main_vrcmpi.o: In function `MAIN__': main_vrcmpi.F:(.text+0xc43): undefined reference to `savexrp_' main_vrcmpi.F:(.text+0xc80): undefined reference to `vrctst_' collect2: error: ld returned 1 exit status gmake[1]: *** [../exe/polyrate2008.ch5.serial.exe] Error 1 gmake: *** [CH5S] Error 2 Has anyone run into this problem before? Sincerely, Mike Zhukovskiy mxa4(-at-)unh.edu