From owner-chemistry@ccl.net Thu Dec 18 00:51:01 2008 From: "Mr shabbir shabbir]_[nenu.edu.cn" To: CCL Subject: CCL:G: Missing Reply about Hyperpolarizability by Finite field Message-Id: <-38329-081218004930-25509-MRROhva5d7CEKizadbssPw=server.ccl.net> X-Original-From: "Mr shabbir" Date: Thu, 18 Dec 2008 00:49:25 -0500 Sent to CCL by: "Mr shabbir" [shabbir]_[nenu.edu.cn] Dear CCL users! I sent this question but still reply is missing..... I have calculated First Hyperpolarizability (Bo) with Finite Field method. I have put following key words in rout section #P polar=Enonly b3lyp/6-31G* test I got the ten components according to G03 manual, sum up 9 of them on individual axis and took their square and square root to get Beta(Total). I read in many papers like this First hyperpolarizability is calculated using the field value of 0.0010au.,the default convergence criteria in G03 was used". or "First hyperpolarizability is calculated using the field frequency of 0.0010au.,the default convergence criteria in G03 was used Now My questions 1. what about the external electric field value in my case? Is it 0.001au or zero (I mean what is by default in G03)? 2. Is it of same intensity along all three axes? 3. How can I justify this choice of external field for my system? 4. What is the difference b/w freq dependent and field dependent hyperpolarizability from the theoretical point of view? Mr.Shabbir From owner-chemistry@ccl.net Thu Dec 18 08:20:01 2008 From: "Orlin Blajiev blajiev=-=vub.ac.be" To: CCL Subject: CCL: Gaussian-Parsing polarizability derivatives Message-Id: <-38330-081218054802-14000-0DlqCL3CwjWzN888pzCA4Q|*|server.ccl.net> X-Original-From: Orlin Blajiev Date: Thu, 18 Dec 2008 10:44:34 +0100 (CET) Sent to CCL by: Orlin Blajiev [blajiev()vub.ac.be] Hi, I will very much appreciate if someone lets me know the output ordering of the polarizability polarizability derivatives. They are in the form: Polar=64.7778232,-8.8797814,104.488336,0.,0.,31.0042386Po larDeriv=-1.1983599,4.0779373,0.063937,0.,0.,0.4152837,2.3157092,-2.27 Polar are only 6- I guess in the order Axx, Axy, Axz, Ayy, Ayz, Azz? Are the PolarDeriv 9? Seems like this, but are the low frequencies included? In general how to count them? Also how are those in the formated chk file ordered? Thanks in advance. Orlin Orlin Blajiev Electrochemistry and Surface Engineering (SURF) Faculty of Engineering Vrije Universiteit Brussel Pleinlaan 2 - 1050 Brussels - Belgium tel: ++32 2 6293538 - fax: ++32 2 6293200 From owner-chemistry@ccl.net Thu Dec 18 08:55:00 2008 From: "Antonio G. De Crisci antonio.decrisci()utoronto.ca" To: CCL Subject: CCL:G: Missing Reply about Hyperpolarizability by Finite field Message-Id: <-38331-081218084003-30492-m8lXXb/GjNTeJzAkirBL3w**server.ccl.net> X-Original-From: "Antonio G. De Crisci" Date: Thu, 18 Dec 2008 08:39:58 -0500 Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci:-:utoronto.ca] Hello Mr. Shabbir, For a custom external field or to calculate a frequecy dependent hyperpolarizability, you would need to use the CPHF method and with RdFreq to input your electromagnetic field perturbation (CPHF=RdFreq with your fields at bottom of your input file). I believe the default in Gaussian is 'static' unless you specify a input field using CPHF=ReFreq where you can input any field you wish. You may also want to look in another computational program called "PC GAMESS". I find that it a bit easier when it comes to calculating hyperpolarizability of single molecules AND it is able to calculate the second hyperpolarizability or THG directly (static and frequency dependent). The output file tabulates the results quite nicely for each tensor and totals it for you. All you need to do is just multiply by a constant to convert the values to esu units and the results are amazingly accurate for known molecules at B3LYP/6311G(d,p) levels. Sincerely, Antonio G. De Crisci > "Mr shabbir shabbir]_[nenu.edu.cn" wrote: > > Sent to CCL by: "Mr shabbir" [shabbir]_[nenu.edu.cn] > Dear CCL users! > I sent this question but still reply is missing..... > > I have calculated First Hyperpolarizability (Bo) with Finite Field method. I have put following key words in rout section > > #P polar=Enonly b3lyp/6-31G* test > > I got the ten components according to G03 manual, sum up 9 of them on individual > axis and took their square and square root to get Beta(Total). > I read in many papers like this First hyperpolarizability is calculated using > the field value of 0.0010au.,the default convergence criteria in G03 was > used". or "First hyperpolarizability is calculated using the field > frequency of 0.0010au.,the default convergence criteria in G03 was used > > Now My questions > 1. what about the external electric field value in my case? Is it 0.001au or zero (I mean what is by default in G03)? > 2. Is it of same intensity along all three axes? > 3. How can I justify this choice of external field for my system? > 4. What is the difference b/w freq dependent and field dependent > hyperpolarizability from the theoretical point of view? > Mr.Shabbir > > From owner-chemistry@ccl.net Thu Dec 18 09:30:00 2008 From: "=?ISO-8859-1?Q?Milagros_Avenda=F1o?= milaven=-=gmail.com" To: CCL Subject: CCL: share information adbout your favorite soft and web tutorials Message-Id: <-38332-081217083232-6927-LcH2UfeSkpQHojA3zoxV8w[a]server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Milagros_Avenda=F1o?=" Content-Type: multipart/alternative; boundary="----=_Part_4908_15407314.1229517569056" Date: Wed, 17 Dec 2008 07:39:28 -0500 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Milagros_Avenda=F1o?=" [milaven:+:gmail.com] ------=_Part_4908_15407314.1229517569056 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline > From Milagros Avendano (new suscriber) I attended recently to a seminar announcing a new release for the program Vega ZZ. Haven't used it yet but seems pretty cool. You may want to check the following link and if you like it you can add it to your list http://www.ddl.unimi.it/vega/ 2008/12/15 Anatoli Korkin a_korkina/yahoo.com > > Sent to CCL by: "Anatoli Korkin" [a_korkin*yahoo.com] > Dear CCLers, > > We are planning to update the links at the "software" and "education pages > at ASDN: > > http://www.asdn.net/asdn/links/software.shtml > > and > > http://www.asdn.net/asdn/links/education.shtml > > Your advice/information about your favorite software and/or web based > tutorials in the area of atomic scale (molecular, nano) science not listed > at these pages will be kindly appreciated. > > Thank you for your consideration. > > Best regards, > Anatoli Korkin> > > ------=_Part_4908_15407314.1229517569056 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
From Milagros Avendano
(new suscriber)
 

 

I attended recently to a seminar announcing a new release for the program Vega ZZ. Haven't used it yet but seems pretty cool. You may want to check the following link and if you like it you can add it to your list

 

 

http://www.ddl.unimi.it/vega/

 



 
2008/12/15 Anatoli Korkin a_korkina/yahoo.com <owner-chemistry#,#ccl.net>

Sent to CCL by: "Anatoli  Korkin" [a_korkin*yahoo.com]
Dear CCLers,

We are planning to update the links at the "software" and "education pages at ASDN:

http://www.asdn.net/asdn/links/software.shtml

and

http://www.asdn.net/asdn/links/education.shtml

Your advice/information about your favorite software and/or web based tutorials in the area of atomic scale (molecular, nano) science not listed at these pages will be kindly appreciated.

Thank you for your consideration.

Best regards,
Anatoli Korkin



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------=_Part_4908_15407314.1229517569056-- From owner-chemistry@ccl.net Thu Dec 18 10:05:01 2008 From: "Josep Cester josep.cester]![urv.cat" To: CCL Subject: CCL: SMILES to VRML or X3D Message-Id: <-38333-081218085842-8315-Fcq/xma9IdeGk+37vm1bMQ###server.ccl.net> X-Original-From: "Josep Cester" Date: Thu, 18 Dec 2008 08:58:37 -0500 Sent to CCL by: "Josep Cester" [josep.cester===urv.cat] Hello, I need to convert SMILES to VRML or X3D in a java application. Does exists any java library to do it? The only way I've found to get an X3D file from an SMILES is converting SMILES to CML (with OpenBabel) and then apply an XSL stylesheet to convert CML to X3D. The problem I have is that OpenBabel is not written in java. I have also tried JOELib2 to convert SMILES to CML, but the CML I get has not got 3D coordinates. Does anybody knows another way to get VRML or X3D file from SMILES? Thank you. Josep From owner-chemistry@ccl.net Thu Dec 18 11:34:01 2008 From: "Geoffrey Hutchison geoffh+(~)pitt.edu" To: CCL Subject: CCL: SMILES to VRML or X3D Message-Id: <-38334-081218113019-5362-3pq3f2Yh7sdBPp9bfPdpuw^-^server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: 7bit Content-type: text/plain; delsp=yes; format=flowed; charset=US-ASCII Date: Thu, 18 Dec 2008 10:49:42 -0500 MIME-version: 1.0 (Apple Message framework v929.2) Sent to CCL by: Geoffrey Hutchison [geoffh+###pitt.edu] On Dec 18, 2008, at 8:58 AM, Josep Cester josep.cester]![urv.cat wrote: > The only way I've found to get an X3D file from an SMILES is > converting SMILES to CML (with OpenBabel) and then apply an XSL > stylesheet to convert CML to X3D. The problem I have is that > OpenBabel is not written in java. I have also tried JOELib2 to > convert SMILES to CML, but the CML I get has not got 3D coordinates. Well, there are multiple ways to get what you want. One uses Open Babel, the other doesn't. I'd consider CDK, which is Java and does have coordinate generation for SMILES: http://cdk.sourceforge.net/ The other way is to use the Open Babel Java interface (which uses JNI): http://openbabel.org/wiki/Java Both CDK and Open Babel collaborate pretty closely, I'd suggest checking out both and seeing which looks easier for you. Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh^pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Thu Dec 18 12:09:00 2008 From: "Wolf-D. Ihlenfeldt wdi\a/xemistry.com" To: CCL Subject: CCL: SMILES to VRML or X3D Message-Id: <-38335-081218113328-5616-amBZuDHNuvcRrpdRNoUf0Q###server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: en-us Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 18 Dec 2008 17:32:39 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi * xemistry.com] Yes, there is, though this is again not a Java lib. Here is a minimal Cactvs toolkit script (no error checking, etc., extend = it yourself): ---- prop setparam E_VRML filename [lindex $argv 1] ens get [ens create [lindex $argv 0]] E_VRML --- Run as "csts -f script.tcl smiles vrmlfilename" With the generic interpreter of the Cactvs toolkit (www.xemistry.com/academic for free academic packages). There are quite = a number of possible modifications to the VRML output - display styles, embedded javascript functions for measuring or style switching, etc. In the academic versions, atomic 3D cords are computed by implicitly contacting http://www.chembiogrid.org/cheminfo/threed/d3/get3d. This may = not be acceptable for all users. For commercial users, this functionality is available for example as general-purpose converter program in prepackaged, supported format. W. D. Ihlenfeldt Xemistry GmbH wdi a xemistry.com --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Auf den Stieden 8, D-35094 Lahntal, Germany HR Marburg B4713 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > -----Original Message----- > From: owner-chemistry+wdi=3D=3Dxemistry.com a ccl.net [mailto:owner- > chemistry+wdi=3D=3Dxemistry.com a ccl.net] On Behalf Of Josep Cester > josep.cester]![urv.cat > Sent: Thursday, December 18, 2008 2:59 PM > To: Ihlenfeldt, Wolf D > Subject: CCL: SMILES to VRML or X3D >=20 >=20 > Sent to CCL by: "Josep Cester" [josep.cester=3D=3D=3Durv.cat] > Hello, >=20 > I need to convert SMILES to VRML or X3D in a java application. Does > exists any java library to do it? >=20 > The only way I've found to get an X3D file from an SMILES is = converting > SMILES to CML (with OpenBabel) and then apply an XSL stylesheet to > convert CML to X3D. The problem I have is that OpenBabel is not = written > in java. I have also tried JOELib2 to convert SMILES to CML, but the > CML I get has not got 3D coordinates. >=20 > Does anybody knows another way to get VRML or X3D file from SMILES? >=20 > Thank you. >=20 > Josep >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please > change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search) >=20>=20 From owner-chemistry@ccl.net Thu Dec 18 12:43:02 2008 From: "Rzepa, Henry h.rzepa|*|imperial.ac.uk" To: CCL Subject: CCL: SMILES to VRML or X3D Message-Id: <-38336-081218114432-10059-D+13QzH4MUmKID+WOpzJmA]^[server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Thu, 18 Dec 2008 15:41:29 +0000 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa~!~imperial.ac.uk] >Sent to CCL by: "Josep Cester" [josep.cester===urv.cat] >Hello, > >I need to convert SMILES to VRML or X3D in a java application. Does exists any java library to do it? > >The only way I've found to get an X3D file from an SMILES is converting SMILES to CML (with OpenBabel) and then apply an XSL stylesheet to convert CML to X3D. The problem I have is that OpenBabel is not written in java. I have also tried JOELib2 to convert SMILES to CML, but the CML I get has not got 3D coordinates. > >Does anybody knows another way to get VRML or X3D file from SMILES? SMILES is a 2D format, X3D a 3D format. the missing coordinate can be added using eg Corina, ie http://www.molecular-networks.com/online_demos/corina_demo.html -- Henry Rzepa. +44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf (FOAF) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Thu Dec 18 13:18:01 2008 From: "Rajarshi Guha rguha-$-indiana.edu" To: CCL Subject: CCL: SMILES to VRML or X3D Message-Id: <-38337-081218122330-1111-k2b1GYHLxHmFs3vb0t6ynQ#,#server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 18 Dec 2008 12:22:33 -0500 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Rajarshi Guha [rguha-x-indiana.edu] On Dec 18, 2008, at 8:58 AM, Josep Cester josep.cester]![urv.cat wrote: > > Sent to CCL by: "Josep Cester" [josep.cester===urv.cat] > Hello, > > I need to convert SMILES to VRML or X3D in a java application. > Does exists any java library to do it? > > The only way I've found to get an X3D file from an SMILES is > converting SMILES to CML (with OpenBabel) and then apply an XSL > stylesheet to convert CML to X3D. The problem I have is that > OpenBabel is not written in java. I have also tried JOELib2 to > convert SMILES to CML, but the CML I get has not got 3D coordinates. You can use the CDK to go from SMILES to CML ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- "I'd love to go out with you, but my favorite commercial is on TV." From owner-chemistry@ccl.net Thu Dec 18 13:53:00 2008 From: "Elaine Meng meng=cgl.ucsf.edu" To: CCL Subject: CCL: SMILES to VRML or X3D Message-Id: <-38338-081218125531-24239-rGpBYstNKShNqp4m6kf/3Q(a)server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 18 Dec 2008 12:55:27 -0500 Sent to CCL by: "Elaine Meng" [meng[]cgl.ucsf.edu] Hello Josep, In Chimera, you can (1) enter a SMILES string and get back a 3D structure. This uses the excellent "smi23d" web service previously announced on CCL by Rajarshi Guha. It can be done in the Build Structure dialog or with the command "open": (2) after optionally adjusting the display style and colors, you can export to X3D or VRML format. This can be done with "File... Export Scene" or the command "export": You might want to try both X3D and VRML and then decide which is most convenient and successful in your situation. Chimera is free for noncommercial use, downloads available for several platforms: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng#%#cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 18, 2008, at 5:58 AM, Josep Cester josep.cester]![urv.cat wrote: Sent to CCL by: "Josep Cester" [josep.cester===urv.cat] Hello, I need to convert SMILES to VRML or X3D in a java application. Does exists any java library to do it? The only way I've found to get an X3D file from an SMILES is converting SMILES to CML (with OpenBabel) and then apply an XSL stylesheet to convert CML to X3D. The problem I have is that OpenBabel is not written in java. I have also tried JOELib2 to convert SMILES to CML, but the CML I get has not got 3D coordinates. Does anybody knows another way to get VRML or X3D file from SMILES? Thank you. Josep From owner-chemistry@ccl.net Thu Dec 18 14:29:01 2008 From: "Oellien, F (Frank) frank.oellien::sp.intervet.com" To: CCL Subject: CCL: SMILES to VRML or X3D Message-Id: <-38339-081218120913-21841-pV/M2LmPjW+uUIdnFgtE5Q++server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 18 Dec 2008 17:29:38 +0100 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien^^^sp.intervet.com] You can use our online tool (http://cactus.nci.nih.gov/vrmlcreator/) or = the software that stands behind it - CACTVS (www.xemistry.com) With kind regards =20 Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany =20 E-Mail: frank.oellien]=[sp.intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com =20 Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 = Gesch=E4ftsf=FChrer: Dr. Peter Schmid =20 > -----Original Message----- > From: owner-chemistry+frank.oellien=3D=3Dsp.intervet.com]=[ccl.net=20 > [mailto:owner-chemistry+frank.oellien=3D=3Dsp.intervet.com]=[ccl.net ] On Behalf Of Josep Cester josep.cester]![urv.cat > Sent: Donnerstag, 18. Dezember 2008 14:59 > To: Oellien, F (Frank) > Subject: CCL: SMILES to VRML or X3D >=20 >=20 > Sent to CCL by: "Josep Cester" [josep.cester=3D=3D=3Durv.cat] Hello, >=20 > I need to convert SMILES to VRML or X3D in a java=20 > application. Does exists any java library to do it? >=20 > The only way I've found to get an X3D file from an SMILES is=20 > converting SMILES to CML (with OpenBabel) and then apply an=20 > XSL stylesheet to convert CML to X3D. The problem I have is=20 > that OpenBabel is not written in java. I have also tried=20 > JOELib2 to convert SMILES to CML, but the CML I get has not=20 > got 3D coordinates. >=20 > Does anybody knows another way to get VRML or X3D file from SMILES? >=20 > Thank you. >=20 > Josep >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing=20 > script =3D- To recover the email address of the author of the=20 > message, please change the strange characters on the top line=20 > to the ]=[ sign. You can also look up the X-Original-From: line=20 > in the mail header. >=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20> Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl,=20 > Password: search) >=20>=20>=20 >=20 >=20 -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From owner-chemistry@ccl.net Thu Dec 18 15:04:01 2008 From: "Jim Kress ccl_nospam{}kressworks.com" To: CCL Subject: CCL: Millsian 1.0 Message-Id: <-38340-081217193544-7143-KHIFoPfBwp2c13Y7XL4TnA~!~server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 17 Dec 2008 18:49:36 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam|a|kressworks.com] So, Brian, why does Millsian give such good results while being fundamentally flawed? I read the Wikipedia page you linked but it did not answer that question. Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com-.-ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com-.-ccl.net] > On Behalf Of Brian Salter-Duke brian.james.duke~~gmail.com > Sent: Tuesday, December 16, 2008 5:53 PM > To: Kress, Jim > Subject: CCL: Millsian 1.0 > > > Sent to CCL by: Brian Salter-Duke > [brian.james.duke-#-gmail.com] Nicholas Labello > label030++umn.edu wrote: > > > > Sent to CCL by: Nicholas Labello [label030[#]umn.edu] The theories > > that drive that program are not accepted by the greater scientific > > community (or any scientific community that I am aware of). > > The company (Black Light Power and/or Millsian, Inc.) posted a job > > offer on the CCL list a few months ago and I looked into it a bit. > > After some reading I became convinced that the program you > asked about > > and parent companies are in the absolute best light founded > on misguided scientific > > principles and at worst are simply fraudulent. Stay away > from it. > > Please see the "controversy" section in the following wiki: > > http://en.wikipedia.org/wiki/Hydrino > > > > Nick > > I agree that this program is "not accepted by the greater > scientific community (or any scientific community that I am > aware of)". They do appear to be misguided. Nevertheless, I > think we need to be clear why they appear to give such good > results. I have been asked on wikipedia several times why > there should not be an article on this program or a large > section on it in one of the computational chemistry articles. > There was an article but it was deleted at my suggestion. See > http://en.wikipedia.org/wiki/Wikipedia:Articles_for_deletion/Millsian > > Brian. > > > > > > > Antonio G. De Crisci antonio.decrisci ~ utoronto.ca wrote: > >> Sent to CCL by: "Antonio G. De Crisci" > >> [antonio.decrisci-.-utoronto.ca] Hello All, > >> > >> Has anybody used this program found at the link below? > >> > >> http://www.millsian.com/ > >> > >> Its still in development, but I like the idea of not using super > >> computer for large system. It doesnt use the laws of QM, > but yet is > >> able to predict properties of organic molecules quite accurately > >> using classical physics? > >> > >> Anthonyhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the -.- sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > From owner-chemistry@ccl.net Thu Dec 18 16:02:01 2008 From: "Mi yang agri_chemist(~)yahoo.com" To: CCL Subject: CCL:G: Gaussian-Parsing polarizability derivatives Message-Id: <-38341-081218113616-6623-fRfvDcYivai6ntHibP+3VA###server.ccl.net> X-Original-From: "Mi yang" Date: Thu, 18 Dec 2008 11:36:12 -0500 Sent to CCL by: "Mi yang" [agri_chemist-*-yahoo.com] Dear Orlin Blajiev !! If you are a G03 or G98 user you can find this order in G03 key words in "Freq" keyword. > "Orlin Blajiev blajiev=-=vub.ac.be" wrote: > > Sent to CCL by: Orlin Blajiev [blajiev()vub.ac.be] > Hi, > > I will very much appreciate if someone lets me know the output ordering of the polarizability polarizability derivatives. They are in the form: > > Polar=64.7778232,-8.8797814,104.488336,0.,0.,31.0042386Po > larDeriv=-1.1983599,4.0779373,0.063937,0.,0.,0.4152837,2.3157092,-2.27 > > Polar are only 6- I guess in the order Axx, Axy, Axz, Ayy, Ayz, Azz? Are the > PolarDeriv 9? Seems like this, but are the low frequencies included? In general how to count them? Also how are those in the formated chk file ordered? > > Thanks in advance. > > Orlin > > Orlin Blajiev > Electrochemistry and Surface Engineering (SURF) > Faculty of Engineering > Vrije Universiteit Brussel > Pleinlaan 2 - 1050 Brussels - Belgium > tel: ++32 2 6293538 - fax: ++32 2 6293200 > > From owner-chemistry@ccl.net Thu Dec 18 16:45:00 2008 From: "Marcel Swart marcel.swart[#]icrea.es" To: CCL Subject: CCL: Millsian 1.0 Message-Id: <-38342-081218164001-25556-fERyfjLPxPNO2qabIwzvWw.@.server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 18 Dec 2008 21:38:08 +0100 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart-,-icrea.es] More hocus-pocus can be found in the paper on the Millsian website. They do a lot of fitting, it seems. I'd be interested in seeing the Millsian program/method applied to more challenging systems such as for instance the spin-state energies of iron complexes. Quoting "Jim Kress ccl_nospam{}kressworks.com" : > > Sent to CCL by: "Jim Kress" [ccl_nospam|a|kressworks.com] > So, Brian, why does Millsian give such good results while being > fundamentally flawed? I read the Wikipedia page you linked but it did not > answer that question. > > Jim > >> -----Original Message----- >> From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com=3D-=3Dccl.net >> [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com=3D-=3Dccl.net] >> On Behalf Of Brian Salter-Duke brian.james.duke~~gmail.com >> Sent: Tuesday, December 16, 2008 5:53 PM >> To: Kress, Jim >> Subject: CCL: Millsian 1.0 >> >> >> Sent to CCL by: Brian Salter-Duke >> [brian.james.duke-#-gmail.com] Nicholas Labello >> label030++umn.edu wrote: >> > >> > Sent to CCL by: Nicholas Labello [label030[#]umn.edu] The theories >> > that drive that program are not accepted by the greater scientific >> > community (or any scientific community that I am aware of). >> > The company (Black Light Power and/or Millsian, Inc.) posted a job >> > offer on the CCL list a few months ago and I looked into it a bit. >> > After some reading I became convinced that the program you >> asked about >> > and parent companies are in the absolute best light founded >> on misguided scientific >> > principles and at worst are simply fraudulent. Stay away >> from it. >> > Please see the "controversy" section in the following wiki: >> > http://en.wikipedia.org/wiki/Hydrino >> > >> > Nick >> >> I agree that this program is "not accepted by the greater >> scientific community (or any scientific community that I am >> aware of)". They do appear to be misguided. Nevertheless, I >> think we need to be clear why they appear to give such good >> results. I have been asked on wikipedia several times why >> there should not be an article on this program or a large >> section on it in one of the computational chemistry articles. >> There was an article but it was deleted at my suggestion. See >> http://en.wikipedia.org/wiki/Wikipedia:Articles_for_deletion/Millsian >> >> Brian. >> >> > >> > >> > Antonio G. De Crisci antonio.decrisci ~ utoronto.ca wrote: >> >> Sent to CCL by: "Antonio G. De Crisci" >> >> [antonio.decrisci-.-utoronto.ca] Hello All, >> >> >> >> Has anybody used this program found at the link below? >> >> >> >> http://www.millsian.com/ >> >> >> >> Its still in development, but I like the idea of not using super >> >> computer for large system. It doesnt use the laws of QM, >> but yet is >> >> able to predict properties of organic molecules quite accurately >> >> using classical physics? >> >> >> >> Anthonyhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> > http://server.ccl.net/chemistry/announcements/conferences/> >> > >> > >> >> >> >> -=3D This is automatically added to each message by the mailing >> script =3D- To recover the email address of the author of the >> message, please change the strange characters on the top line >> to the =3D-=3D sign. You can also look up the X-Original-From: line >> in the mail header.> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> >> > > > > -=3D This is automatically added to each message by the mailing script =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=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart(!)icrea.es marcel.swart(!)udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =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=3D=3D From owner-chemistry@ccl.net Thu Dec 18 17:19:01 2008 From: "Brian Salter-Duke brian.james.duke!^!gmail.com" To: CCL Subject: CCL: Millsian 1.0 Message-Id: <-38343-081218165328-2212-8R0vzyMIAvO9UmJlNINFOg^^^server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 19 Dec 2008 08:53:00 +1100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke^-^gmail.com] Jim Kress ccl_nospam{}kressworks.com wrote: > Sent to CCL by: "Jim Kress" [ccl_nospam|a|kressworks.com] > So, Brian, why does Millsian give such good results while being > fundamentally flawed? I read the Wikipedia page you linked but it did not > answer that question. I do not know. That is the point. The equations are complex and certainly not standard science. They appear to ignore the 3-body problem, so they should not work. Nevertheless the numbers look good. The comparison with small basis set Hartree-Fock results however is just nonsense. It is the comparison with experiment that has to be explained. Brian > Jim > >> -----Original Message----- >> From: owner-chemistry+ccl_nospam==kressworks.com=-=ccl.net >> [mailto:owner-chemistry+ccl_nospam==kressworks.com=-=ccl.net] >> On Behalf Of Brian Salter-Duke brian.james.duke~~gmail.com >> Sent: Tuesday, December 16, 2008 5:53 PM >> To: Kress, Jim >> Subject: CCL: Millsian 1.0 >> >> >> Sent to CCL by: Brian Salter-Duke >> [brian.james.duke-#-gmail.com] Nicholas Labello >> label030++umn.edu wrote: >>> Sent to CCL by: Nicholas Labello [label030[#]umn.edu] The theories >>> that drive that program are not accepted by the greater scientific >>> community (or any scientific community that I am aware of). >>> The company (Black Light Power and/or Millsian, Inc.) posted a job >>> offer on the CCL list a few months ago and I looked into it a bit. >>> After some reading I became convinced that the program you >> asked about >>> and parent companies are in the absolute best light founded >> on misguided scientific >>> principles and at worst are simply fraudulent. Stay away >> from it. >>> Please see the "controversy" section in the following wiki: >>> http://en.wikipedia.org/wiki/Hydrino >>> >>> Nick >> I agree that this program is "not accepted by the greater >> scientific community (or any scientific community that I am >> aware of)". They do appear to be misguided. Nevertheless, I >> think we need to be clear why they appear to give such good >> results. I have been asked on wikipedia several times why >> there should not be an article on this program or a large >> section on it in one of the computational chemistry articles. >> There was an article but it was deleted at my suggestion. See >> http://en.wikipedia.org/wiki/Wikipedia:Articles_for_deletion/Millsian >> >> Brian. >> >>> >>> Antonio G. De Crisci antonio.decrisci ~ utoronto.ca wrote: >>>> Sent to CCL by: "Antonio G. De Crisci" >>>> [antonio.decrisci-.-utoronto.ca] Hello All, >>>> >>>> Has anybody used this program found at the link below? >>>> >>>> http://www.millsian.com/ >>>> >>>> Its still in development, but I like the idea of not using super >>>> computer for large system. It doesnt use the laws of QM, >> but yet is >>>> able to predict properties of organic molecules quite accurately >>>> using classical physics? >>>> >>>> Anthonyhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >>> http://server.ccl.net/chemistry/announcements/conferences/> >>> >>> >> >> >> -= This is automatically added to each message by the mailing >> script =- To recover the email address of the author of the >> message, please change the strange characters on the top line >> to the =-= sign. You can also look up the X-Original-From: line >> in the mail header.> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> > >