From owner-chemistry@ccl.net Mon May 11 07:11:01 2015 From: "Renier Dreyer renier.dreyer[A]crunchyard.com" To: CCL Subject: CCL: Remote access to high performance computing Message-Id: <-51366-150511044436-29999-IODrV15LJNXEhZ9yv+qDFQ{=}server.ccl.net> X-Original-From: Renier Dreyer Content-Type: multipart/alternative; boundary=089e01538ab4b54b220515ca6290 Date: Mon, 11 May 2015 10:44:27 +0200 MIME-Version: 1.0 Sent to CCL by: Renier Dreyer [renier.dreyer__crunchyard.com] --089e01538ab4b54b220515ca6290 Content-Type: text/plain; charset=UTF-8 Hi All As mentioned there are numerous online providers. There are however some differences that I would like to point out: 1) Some cloud based providers such as Amazon and Google virtualize their environment through a hypervisor. This means that you are sharing the actual hardware with other users as well as the extra overhead of the hypervisor. 2) Network speeds are 10GbE for these providers across their entire netowrk. 3) I would agree that for small simulations (4 cores) it is better to invest in a good desktop or server. For large simulation that require many cores, this means that simulation will run between 7 and 10 times slower than running on a dedicated HPC system. HPC systems also provide immediate access to 100's or thousands of cores. The cost per simulation would then also be much more expensive. For example: Running a 64 water molecule CP2K simulation on a 32 core compute instance on AWS take 45 minutes. Running the same simulation on CrunchYard takes 7 minutes using 4 cores. AWS cost: US$1.12 CrunchYard cost commercial: US$ 0.2 CrunchYard cost academic: US$ 0.02 Additionally there is no setup and management needed for CrunchYard as all submissions are through the website portal with packages pre-installed (for advanced users there is a scripting option :) Kind Regards Renier On Sun, May 10, 2015 at 2:21 AM, Brian Skinn bskinn#,#alum.mit.edu < owner-chemistry]^[ccl.net> wrote: > All, > > I utilized the free trial offer for Google Cloud Compute to evaluate its > cost structure for computational chemistry applications (ORCA quantum > calculations, to be exact). It ended up being far more economical to just > buy a refurbished server to run at home, rather than rent the CPU time from > somewhere else. Of course, this is in large part because I have sufficient > familiarity with Linux to configure, administer and maintain such a > server. If that expertise is not available to you, renting the CPU time > may well be the better deal. If CrunchYard does not support the > computational software you require, you should be able to install just > about anything onto a G Cloud Instance. > > Google Compute tracks the free trial by giving a $300 account credit and > then just billing normally. For my own records, I tracked the decrease in > funds over my testing period. I've laid that data into a Google > Spreadsheet; it can be viewed here > . > I've enabled comments for all viewers, so if anyone has questions feel free > to either email me at bskinn-AT-alum-DOT-mit-DOT-edu, or to tag comments > into the sheet. > > Amazon Web Services is another big player for cloud computing. I surveyed > their pricing briefly; I think Google's services would end up being less > expensive, but in large part I went with Google's trial offer because it > was much easier to get it started & I think the terms were less restrictive. > > > Good luck, > Brian > > > On Sat, May 9, 2015 at 5:40 PM, Computational Chemist > computationalchemist++ymail.com wrote: > >> >> Thank you Sergio, Victor, Chris and Wojciech for replying. >> >> I am doing this research at Alexandriah University, Egypt. I want to do >> comparable molecular dynamics simulations on three HCV protease genotypes. >> For each simulation, I need 4 processors with 2GB RAM for each processor. >> I expect the calculations to take 6-8 months. I can use AMBER or Gomacs or >> NAMD. >> >> Thank you, >> >> Dina >> >> >> >> On Saturday, May 9, 2015 10:35 PM, Wojciech Kolodziejczyk dziecial** >> icnanotox.org wrote: >> >> >> The answer is YES they are. >> >> 2015-05-09 13:45 GMT-05:00 Jim Kress jimkress35=gmail.com < >> owner-chemistry###ccl.net>: >> >> I recommend (and use) CrunchYard: >> >> https://www.crunchyard.com/default.aspx >> >> Jim >> >> *> From:* owner-chemistry+jimkress35==gmail.com(!)ccl.net [mailto: >> owner-chemistry+jimkress35==gmail.com(!)ccl.net] *On Behalf Of *Computational >> Chemist computationalchemist * ymail.com >> *Sent:* Saturday, May 09, 2015 11:03 AM >> *To:* Kress, Jim >> *Subject:* CCL: Remote access to high performance computing >> >> Dear All, >> >> I need more computer resources so that I can do large scale molecular >> dynamics simulations. Are there any high performance computing centers that >> provide international access for users through application, proposals, >> fees...etc >> >> Thank you so much. >> >> Dina >> >> >> >> >> > --089e01538ab4b54b220515ca6290 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi All

As mentioned there are numerous = online providers.
There are however some differences that I would= like to point out:

1) Some cloud based providers = such as Amazon and Google virtualize their environment through a hypervisor= . This means that you are sharing the actual hardware with other users as w= ell as the extra overhead of the hypervisor.

2) Ne= twork speeds are 10GbE for these providers across their entire netowrk.

3) I would agree that for small simulations (4 cores)= it is better to invest in a good desktop or server.

For large simulation that require many cores, this means that simulation= will run between 7 and 10 times slower than running on a dedicated HPC sys= tem. HPC systems also provide immediate access to 100's or thousands of= cores.

The cost per simulation would then als= o be much more expensive.
For example:

R= unning a 64 water molecule CP2K simulation on a 32 core compute instance on= AWS take 45 minutes. Running the same simulation on CrunchYard takes 7 min= utes using 4 cores.

AWS cost: US$1.12
Cr= unchYard cost commercial: US$ 0.2
CrunchYard cost academic: US$ 0= .02

Additionally there is no setup and managem= ent needed for CrunchYard as all submissions are through the website portal= with packages pre-installed (for advanced users there is a scripting optio= n :)

Kind Regards
Renier

<= /div>

On Sun, May = 10, 2015 at 2:21 AM, Brian Skinn bskinn#,#a= lum.mit.edu <owner-chemistry]^[ccl.net> wrote:
All,

I uti= lized the free trial offer for Google Cloud Compute to evaluate its cost st= ructure for computational chemistry applications (ORCA quantum calculations= , to be exact). =C2=A0 It ended up being far more economical to just buy a = refurbished server to run at home, rather than rent the CPU time from somew= here else.=C2=A0 Of course, this is in large part because I have sufficient= familiarity with Linux to configure, administer and maintain such a server= .=C2=A0 If that expertise is not available to you, renting the CPU time may= well be the better deal.=C2=A0 If CrunchYard does not support the computat= ional software you require, you should be able to install just about anythi= ng onto a G Cloud Instance.

Google Compute tracks = the free trial by giving a $300 account credit and then just billing normal= ly.=C2=A0 For my own records, I tracked the decrease in funds over my testi= ng period.=C2=A0 I've laid that data into a Google Spreadsheet; it can = be viewed here.=C2=A0 I've enabled comments for all viewers, so if anyone has questi= ons feel free to either email me at bskinn-AT-alum-DOT-mit-DOT-edu, or to t= ag comments into the sheet.




On Sat, May 9, 2015 at 5:40 PM, Computati= onal Chemist computationalchemist++ymail.com <owner-chemistry(-)ccl.net> wro= te:

Thank you Sergio,= Victor, Chris and Wojciech for replying.

I am doing this research at Alexandriah University, Egypt. I want to do= comparable molecular dynamics simulations on three HCV protease genotypes.= For each simulation, I need 4 processors with =C2=A02GB RAM for each proce= ssor. I expect the calculations to take 6-8 months. I can use AMBER or Goma= cs or NAMD.

=C2=A0Thank you,

<= div>Dina



On Saturday, May 9,= 2015 10:35 PM, Wojciech Kolodziejczyk dziecial**icnanotox.org <owner-chemistry**ccl.net> wrote:
=

The answer is YES they are.
=

2015-05-09 13:45 GMT-05:00 Jim Kress jimkress35=3Dgmail.com <owner-chemistry###ccl.net>:
I recommend (and use) CrunchYard:

https://www.crunc= hyard.com/default.aspx
=C2=A0
Jim
= =C2=A0<= /div>
> From: owner-chemistry+jimkress35=3D=3Dgmail.com= (!)ccl.net [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com(!)ccl.net] On Behalf = Of Computational Chemist computationalchemist * ymail.com
Sent: Sat= urday, May 09, 2015 11:03 AM
To: Kress, Jim
Subject: C= CL: Remote access to high performance computing
<= /div>
=C2=A0
Dear All,
= =C2=A0
I need more computer resources so that I can d= o large scale molecular dynamics simulations. Are there any high performanc= e computing centers that provide international access for users through app= lication, proposals, fees...etc
=C2=A0<= /span>
Thank you so much.
=C2=A0<= /u>
Dina





--089e01538ab4b54b220515ca6290-- From owner-chemistry@ccl.net Mon May 11 12:59:00 2015 From: "Wirawan Purwanto wirawan0%yahoo.com" To: CCL Subject: CCL: Making symmetry equivalence atomic orbitals Message-Id: <-51367-150511125738-16626-VhNmGboHLN930wKmeW9Pfg::server.ccl.net> X-Original-From: "Wirawan Purwanto" Date: Mon, 11 May 2015 12:57:37 -0400 Sent to CCL by: "Wirawan Purwanto" [wirawan0{}yahoo.com] Hi, Can someone give me a pointer to how to make "symmetry equivalenced" orbitals? I am not that familiar with this terminology, and in some papers this is mentioned without any citation. This is my limited understanding of it: in the context of Hartree-Fock calculation of an isolated atom (say, ROHF calculation of Co atom), the five 3d orbitals ended up not having the same shape and energy because of the symmetry-broken configuration (3d7 4s2). The symmetry equivalenced 3d orbitals would then be obtained by somehow restoring the degenerate nature of these orbitals (which would raise the variational energy by a little bit). I think this can also be done for e.g. diatomic molecule where the pix-piy degeneracy could be broken due to open shell nature of the HF solution. Here are my questions: 1. Is this understanding correct? 2. What are the step-by-step way to make the symmetry equivalenced orbitals from the usual ROHF or UHF orbitals? Any reference or program that can do this from a MO output given by a quantum chemistry program (e.g. GAMESS, molpro...whatever you like), assuming that I know the composition of the underlying AO basis (i.e. which function is 1s, ...2px,... 3dxy, and so on). Thanks, Wirawan From owner-chemistry@ccl.net Mon May 11 15:01:01 2015 From: "Igors Mihailovs igors.mihailovs0!^!gmail.com" To: CCL Subject: CCL:G: I want to solve the error termination g09/l703 Message-Id: <-51368-150511145958-18855-pzT5OgVGz/sw5S9TD+XpSQ-$-server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=001a113f5e92a981e70515d2fb95 Date: Mon, 11 May 2015 21:59:32 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0[#]gmail.com] --001a113f5e92a981e70515d2fb95 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear di Wang, "Allocation failure" looks like a message of no space left on Your drive... My question in connection with this is =E2=80=93 as far as I can see by now= , are You placing four separate RWF files on the same drive and in the same directory? Was it how You intended that? Because, if You do not mention explicit path for each of Your (really tremendous in size) RWFs, they all will be placed in the default Scratch directory. Or do You have some alternate configuration stored in Your Default.Route file? With best wishes, Igors Mihailovs (engineer) Institute of Solid State Physics University of Latvia 2015-05-08 4:58 GMT+03:00 di Wang 271855335=3D-=3Dqq.com < owner-chemistry{=}ccl.net>: > > Sent to CCL by: "di Wang" [271855335^-^qq.com] > TO dear CCL Subscribers: > I have met a problem when I used DFT with the b3lyp exchange-correlati= on > functional and the sto-3g basis set in the gas phase using the Gaussian 0= 9 > suite of programs to optimize full geometries and vibrational frequencies > and > provid the disperison energy. > The input file is " > %chk=3Da.chk > %mem=3D4GB > %NProcShared=3D12 > %rwf=3D1,19900000mb,2,19900000mb,3,19900000mb,4,19900000mb > #p opt freq b3lyp/STO-3G EmpiricalDispersion=3DGD3BJ scf=3Dxqc > geom=3Dconnectivity > test " > The output file shows that "Allocation failure for numerical > quadrature.Error > termination via Lnk1e in/share/apps/g09.D01/g09/l703 ." > I do not kown how to solve this problem .I wish dear CCL Subscribers ca= n > help me with it! > > > > > > > > > From: di Wang > > Email address: 271855335^^ > qq.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a113f5e92a981e70515d2fb95 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear di Wang,

"Allocation failure&q= uot; looks like a message of no space left on Your drive...
My question = in connection with this is =E2=80=93 as far as I can see by now, are You pl= acing four separate RWF files on the same drive and in the same directory? = Was it how You intended that? Because, if You do not mention explicit path = for each of Your (really tremendous in size) RWFs, they all will be placed = in the default Scratch directory. Or do You have some alternate configurati= on stored in Your Default.Route file?

Wit= h best wishes,
Igors Mihailovs (engineer)
Institute of Solid State Physics<= br>
University of Latvia


2015-05-08 4:58 GMT+03:00 di Wang 271855335= =3D-=3Dqq.com <owner-chemistry{=}ccl.n= et>:

Sent to CCL by: "di=C2=A0 Wang" [271855335^-^qq.com]
TO dear CCL Subscribers:
=C2=A0 =C2=A0I have met a problem when I used DFT with the b3lyp exchange-c= orrelation
functional and the sto-3g basis set in the gas phase using the Gaussian 09<= br> suite of programs to optimize full geometries and vibrational frequencies a= nd
provid the disperison energy.
The input file is "
%chk=3Da.chk
%mem=3D4GB
%NProcShared=3D12
%rwf=3D1,19900000mb,2,19900000mb,3,19900000mb,4,19900000mb
#p opt freq b3lyp/STO-3G EmpiricalDispersion=3DGD3BJ scf=3Dxqc geom=3Dconne= ctivity
test "
The output file shows that "Allocation failure for numerical quadratur= e.Error
termination via Lnk1e in/share/apps/g09.D01/g09/l703 ."
=C2=A0 I do not kown how to solve this problem .I wish dear CCL Subscribers= can
help me with it!








=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 From: di Wang

=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=A0Email address: 271855335^^qq.com



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY{=}ccl.n= et or use:
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RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--001a113f5e92a981e70515d2fb95-- From owner-chemistry@ccl.net Mon May 11 15:36:01 2015 From: "Kirk Peterson kipeters##wsu.edu" To: CCL Subject: CCL: Making symmetry equivalence atomic orbitals Message-Id: <-51369-150511151436-23690-DAM2+wkGMI76wjuX4i/UQw-$-server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Mon, 11 May 2015 12:14:23 -0700 Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2098\)) Sent to CCL by: Kirk Peterson [kipeters]=[wsu.edu] Dear Wirawan, yes, I believe you have the general understanding of the situation correct below. If codes would use full atomic symmetry this presumably wouldn't be an issue, but generally you’re stuck with calculating one component of a degenerate atomic state in the highest abelian group, hence for example px will be ‘different’ than py or pz. I usually use the MCSCF program in Molpro for symmetry equivalencing. In this case you just state-average the various HF states corresponding to the different open shells. This is not a black-box procedure though. best, -Kirk > On May 11, 2015, at 9:57 AM, Wirawan Purwanto wirawan0%yahoo.com wrote: > > > Sent to CCL by: "Wirawan Purwanto" [wirawan0{}yahoo.com] > Hi, > > Can someone give me a pointer to how to make "symmetry equivalenced" orbitals? I am not that familiar with this terminology, and in some papers this is mentioned without any citation. > > > This is my limited understanding of it: in the context of Hartree-Fock calculation of an isolated atom (say, ROHF calculation of Co atom), the five 3d orbitals ended up not having the same shape and energy because of the symmetry-broken configuration (3d7 4s2). The symmetry equivalenced 3d orbitals would then be obtained by somehow restoring the degenerate nature of these orbitals (which would raise the variational energy by a little bit). I think this can also be done for e.g. diatomic molecule where the pix-piy degeneracy could be broken due to open shell nature of the HF solution. > > > Here are my questions: > > 1. Is this understanding correct? > > 2. What are the step-by-step way to make the symmetry equivalenced orbitals from the usual ROHF or UHF orbitals? Any reference or program that can do this from a MO output given by a quantum chemistry program (e.g. GAMESS, molpro...whatever you like), assuming that I know the composition of the underlying AO basis (i.e. which function is 1s, ...2px,... 3dxy, and so on). > > > Thanks, > Wirawan> https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/cgi-bin/ccl/send_ccl_message&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=54de310d7862582eda966c6d2c71d66bde1c6e3fea01c4f40b19982b538b7872> https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/cgi-bin/ccl/send_ccl_message&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=54de310d7862582eda966c6d2c71d66bde1c6e3fea01c4f40b19982b538b7872> https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/chemistry/sub_unsub.shtml&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=1380054a1d4769a76447e2182c3504eb82028b1817887e8224886b3a9204e41a > > Before posting, check wait time at: https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=54d6471eed733b463ec2b43d12a25ddd9afb5d4361dd059371501a36415c05d8 > > Job: https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/jobs&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=c3ad93570c6221ea91e9c72209a730935d2630b74f13525cdbdde234b018c90d > Conferences: https://urldefense.proofpoint.com/v1/url?u=http://server.ccl.net/chemistry/announcements/conferences/&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=6abb77aeef4fd4cc86270aa36ec0a56ebd5847c2f44bdd26f89fa8f559a3a158 > > Search Messages: https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/chemistry/searchccl/index.shtml&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=dcfe1ae566f45531cba9239027bd6873e6c207e4497a468a9c7a4d2857b4d906> https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/spammers.txt&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=63d56e0721834b46dfd5afd37d4b9a04067aac191c6e8131b4d75f560a055b11 > > RTFI: https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/chemistry/aboutccl/instructions/&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=f072ce5d9c9ac77d5f59959b010d70c233783b21fc79cf724bbcb99e9126b391 > > From owner-chemistry@ccl.net Mon May 11 16:11:00 2015 From: "Tymofii Nikolaienko tim_mail||ukr.net" To: CCL Subject: CCL: Making symmetry equivalence atomic orbitals Message-Id: <-51370-150511150309-19766-bc1bjNqLwMKZRKrdtZQG6w]|[server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Type: multipart/alternative; boundary="------------090403080807080808060706" Date: Mon, 11 May 2015 22:02:58 +0300 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail%ukr.net] This is a multi-part message in MIME format. --------------090403080807080808060706 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit Dear Wirawan, I'm not sure whether this might be helpful for you, but in our recent paper [T.Y.Nikolaienko, L.A.Bulavin, D.M.Hovorun, Comput. Theor. Chem. (2014), V.1050, P.15-22, DOI: 10.1016/j.comptc.2014.10.002 ] we have mentioned and proved a theorem (see Appendix B) which states that the eigenfunctions of reduced one-particle density matrix (i.e., natural orbitals, which in case of Hartree-Fock approximation coincide with the Hartree-Fock orbitals) can always be selected such as to be the eigenfunctions of l^2 (the squared single-particle angular momentum operator) and l_z (its projection onto z axis) operators, i.e., as to be representable in the form of psi (x,y,z) = f(r) *  Y_{lm}(theta, phi) (where Y_{lm} is the spherical harmonic). The key words here in the context of your question are '_*can *_always be selected', since when orbital occupancy is exactly 2.0 (as it is in the Hartree-Fock case), it is possible to make a linear combination of occupied orbitals and consider them as new, equally good orbitals, since these it is possible for these linear combinations to be build in such a way that the Slater determinant build from them will give the same wavefunction as the one build > from 'old' orbitals. Tymofii On 11.05.2015 19:57, Wirawan Purwanto wirawan0%yahoo.com wrote: > Sent to CCL by: "Wirawan Purwanto" [wirawan0{}yahoo.com] > Hi, > > Can someone give me a pointer to how to make "symmetry equivalenced" orbitals? I am not that familiar with this terminology, and in some papers this is mentioned without any citation. > > > This is my limited understanding of it: in the context of Hartree-Fock calculation of an isolated atom (say, ROHF calculation of Co atom), the five 3d orbitals ended up not having the same shape and energy because of the symmetry-broken configuration (3d7 4s2). The symmetry equivalenced 3d orbitals would then be obtained by somehow restoring the degenerate nature of these orbitals (which would raise the variational energy by a little bit). I think this can also be done for e.g. diatomic molecule where the pix-piy degeneracy could be broken due to open shell nature of the HF solution. > > > Here are my questions: > > 1. Is this understanding correct? > > 2. What are the step-by-step way to make the symmetry equivalenced orbitals from the usual ROHF or UHF orbitals? Any reference or program that can do this from a MO output given by a quantum chemistry program (e.g. GAMESS, molpro...whatever you like), assuming that I know the composition of the underlying AO basis (i.e. which function is 1s, ...2px,... 3dxy, and so on). > > > Thanks, > Wirawan> > > --------------090403080807080808060706 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: 8bit Dear Wirawan,

I'm not sure whether this might be helpful for you, but in our recent paper [T.Y.Nikolaienko, L.A.Bulavin, D.M.Hovorun, Comput. Theor. Chem. (2014), V.1050, P.15-22,
DOI: 10.1016/j.comptc.2014.10.002 ] we have mentioned and proved a theorem (see Appendix B) which states that the eigenfunctions of reduced one-particle density
matrix (i.e., natural orbitals, which in case of Hartree-Fock approximation coincide with the Hartree-Fock orbitals) can always be selected such as to
be the eigenfunctions of l^2 (the squared single-particle angular momentum operator) and l_z (its projection onto z axis) operators, i.e., as to be representable
in the form of psi (x,y,z) = f(r) *  Y_{lm}(theta, phi)  (where Y_{lm} is the spherical harmonic).
The key words here in the context of your question are 'can always be selected', since when orbital occupancy is exactly 2.0 (as it is in the Hartree-Fock case),
it is possible to make a linear combination of occupied orbitals and consider them as new, equally good orbitals, since these it is possible
for these linear combinations to be build in such a way that the Slater determinant build from them will give the same wavefunction as the one build
from 'old' orbitals.

Tymofii




On 11.05.2015 19:57, Wirawan Purwanto wirawan0%yahoo.com wrote:
Sent to CCL by: "Wirawan  Purwanto" [wirawan0{}yahoo.com]
Hi,

Can someone give me a pointer to how to make "symmetry equivalenced" orbitals? I am not that familiar with this terminology, and in some papers this is mentioned without any citation.


This is my limited understanding of it: in the context of Hartree-Fock calculation of an isolated atom (say, ROHF calculation of Co atom), the five 3d orbitals ended up not having the same shape and energy because of the symmetry-broken configuration (3d7 4s2). The symmetry equivalenced 3d orbitals would then be obtained by somehow restoring the degenerate nature of these orbitals (which would raise the variational energy by a little bit). I think this can also be done for e.g. diatomic molecule where the pix-piy degeneracy could be broken due to open shell nature of the HF solution.


Here are my questions:

1. Is this understanding correct?

2. What are the step-by-step way to make the symmetry equivalenced orbitals from the usual ROHF or UHF orbitals? Any reference or program that can do this from a MO output given by a quantum chemistry program (e.g. GAMESS, molpro...whatever you like), assuming that I know the composition of the underlying AO basis (i.e. which function is 1s, ...2px,... 3dxy, and so on).


Thanks,
WirawanE-mail to subscribers: CHEMISTRY]![ccl.net or use:
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--------------090403080807080808060706-- From owner-chemistry@ccl.net Mon May 11 16:46:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor[A]fluor.quimica.uniovi.es" To: CCL Subject: CCL: Making symmetry equivalence atomic orbitals Message-Id: <-51371-150511150618-20865-QlbAE0VdIWvL1uzbkJXZog .. server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Mon, 11 May 2015 20:57:03 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor++fluor.quimica.uniovi.es] On Mon, May 11, 2015 at 12:57:37PM -0400, Wirawan Purwanto wirawan0%yahoo.com wrote: > > Sent to CCL by: "Wirawan Purwanto" [wirawan0{}yahoo.com] > Hi, > > Can someone give me a pointer to how to make "symmetry equivalenced" > orbitals? I am not that familiar with this terminology, and in some > papers this is mentioned without any citation. Wirawan: The concept corresponds to group theory. Depending on the local symmetry of the center (atom) you are considering the initial energetic degeneration of the atomic arbitals breaks down, but not complitely. Let us take a particular case: an atom in the center of a molecule with octahedral (O_h) symmetry. In the isolated M atom the five components of the 3d orbitals are degenerated in energy, because the isolated atom corresponds to the rotation group of the sphere (O3, let's say). In the octahedral ML_6 molecule the five 3d orbitals of M will transform either as t_{2g} (three) or e_g (two) symmetry-adapted orbitals (SAO), each type having a different orbital energy. A simple reference is the symmetry book by Cotton. A more complex but lovely book on the subject is Hammermesh, for instance. Cotton: Chemical Applications of Group Theory, 3rd Edition Hammermesh: Group Theory and Its Application to Physical Problems (Dover Books on Physics) Enjoy, Dr: Víctor Luaña -- . . "Research is to see what everybody else has seen, and to / `' \ think what nobody else has thought"-- Albert Szent-Gyorgi /(o)(o)\ /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor .. fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Mon May 11 18:20:00 2015 From: "Salter-Duke, Brian James - brian.james.duke],[gmail.com" To: CCL Subject: CCL: Making symmetry equivalence atomic orbitals Message-Id: <-51372-150511171505-30927-DwQaxMTwncMsBh9JRKJ74Q::server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Tue, 12 May 2015 07:14:48 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke++gmail.com] I think you could use any MCSCF code to do this, but as Kirk says, it is not black-box. 40 years ago I could have done it black-box with the ATMOL program. Maybe it is in GAMESS(UK) which sort-of grew out of ATMOL. Some times progress goes backwards. Brian. On Mon, May 11, 2015 at 12:14:23PM -0700, Kirk Peterson kipeters##wsu.edu wrote: > > Sent to CCL by: Kirk Peterson [kipeters]=[wsu.edu] > Dear Wirawan, > > yes, I believe you have the general understanding of the situation correct below. If codes would use full atomic symmetry this presumably wouldn't be an issue, but generally you’re stuck with calculating one component of a degenerate atomic state in the highest abelian group, hence for example px will be ‘different’ than py or pz. > > I usually use the MCSCF program in Molpro for symmetry equivalencing. In this case you just state-average the various HF states corresponding to the different open shells. This is not a black-box procedure though. > > best, > > -Kirk > > > On May 11, 2015, at 9:57 AM, Wirawan Purwanto wirawan0%yahoo.com wrote: > > > > > > Sent to CCL by: "Wirawan Purwanto" [wirawan0{}yahoo.com] > > Hi, > > > > Can someone give me a pointer to how to make "symmetry equivalenced" orbitals? I am not that familiar with this terminology, and in some papers this is mentioned without any citation. > > > > > > This is my limited understanding of it: in the context of Hartree-Fock calculation of an isolated atom (say, ROHF calculation of Co atom), the five 3d orbitals ended up not having the same shape and energy because of the symmetry-broken configuration (3d7 4s2). The symmetry equivalenced 3d orbitals would then be obtained by somehow restoring the degenerate nature of these orbitals (which would raise the variational energy by a little bit). I think this can also be done for e.g. diatomic molecule where the pix-piy degeneracy could be broken due to open shell nature of the HF solution. > > > > > > Here are my questions: > > > > 1. Is this understanding correct? > > > > 2. What are the step-by-step way to make the symmetry equivalenced orbitals from the usual ROHF or UHF orbitals? Any reference or program that can do this from a MO output given by a quantum chemistry program (e.g. GAMESS, molpro...whatever you like), assuming that I know the composition of the underlying AO basis (i.e. which function is 1s, ...2px,... 3dxy, and so on). > > > > > > Thanks, > > Wirawan> https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/cgi-bin/ccl/send_ccl_message&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=54de310d7862582eda966c6d2c71d66bde1c6e3fea01c4f40b19982b538b7872> https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/cgi-bin/ccl/send_ccl_message&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=54de310d7862582eda966c6d2c71d66bde1c6e3fea01c4f40b19982b538b7872> https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/chemistry/sub_unsub.shtml&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=1380054a1d4769a76447e2182c3504eb82028b1817887e8224886b3a9204e41a > > > > Before posting, check wait time at: https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=54d6471eed733b463ec2b43d12a25ddd9afb5d4361dd059371501a36415c05d8 > > > > Job: https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/jobs&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=c3ad93570c6221ea91e9c72209a730935d2630b74f13525cdbdde234b018c90d > > Conferences: https://urldefense.proofpoint.com/v1/url?u=http://server.ccl.net/chemistry/announcements/conferences/&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=6abb77aeef4fd4cc86270aa36ec0a56ebd5847c2f44bdd26f89fa8f559a3a158 > > > > Search Messages: https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/chemistry/searchccl/index.shtml&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=dcfe1ae566f45531cba9239027bd6873e6c207e4497a468a9c7a4d2857b4d906> https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/spammers.txt&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=63d56e0721834b46dfd5afd37d4b9a04067aac191c6e8131b4d75f560a055b11 > > > > RTFI: https://urldefense.proofpoint.com/v1/url?u=http://www.ccl.net/chemistry/aboutccl/instructions/&k=EWEYHnIvm0nsSxnW5y9VIw%3D%3D%0A&r=ndj2Vta%2FisUMMOFOMobgvg%3D%3D%0A&m=MoY4K2vo2Vt6auAeG3H1BHQ%2BbZg6M4vlbxitj1iUZPo%3D%0A&s=f072ce5d9c9ac77d5f59959b010d70c233783b21fc79cf724bbcb99e9126b391> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke..monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia