From owner-chemistry@ccl.net Sun Feb 3 08:20:01 2008 From: "Pablo Echenique echenique.p.:.gmail.com" To: CCL Subject: CCL:G: License what you want. Open what you want. No comparison? Message-Id: <-36211-080203081409-7720-IOI/R7i+6XsUv1C5c7RWSg^_^server.ccl.net> X-Original-From: "Pablo Echenique" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 3 Feb 2008 13:44:37 +0100 MIME-Version: 1.0 Sent to CCL by: "Pablo Echenique" [echenique.p!=!gmail.com] Dear friends, I must say that the conversation is really interesting and many relevant points have been introduced but, with all due respect, I think people is taking it too personally. On the one hand, we have two options: Open Source vs. Proprietary Source. It could be interesting to discuss which one is best, whether or not a sustainable firm can be based on the first, whether or not the Proprietary Source has a place in an efficient global Science scenario, etc. But, whatever anwers each one of us finds to these question, the decision to adopt one option or the other is a free one. The Open Source movement, with which I agree in most essential points, is being increasingly infected with radical supporters which, like in Middle Age, ride every day to Jerusalem to kill the unholy Proprietary Defenders. In my opinion, all development models MUST be tried before deciding which is best. And maybe the final, not so surprising answer is that the most efficiency is obtained in a world in which all options have at least one strong representant. Moreover, if Open Source is the only answer to scientific software, we will know it when we prove it, not when we declare it. In brief, what is best for Science do not depend on ethical principles, it depends on facts. In this sense, I believe Mr. DeLano's insights are very useful for the discussion, but so are Mr. Frisch's, because Gaussian Inc. is a success history too. Regarding my own free choice, I give away all knowledge, data and code I produce, since, being paid by the government, i.e., by the people, I believe it is the most ethical choice (and probably the most efficient too). However, I do not find anything unethical in the way a private firm such as Gaussian Inc. works. In the free market, nobody forces you to buy a product. You don't like Gaussian's performance, decisions, name, colour of the CD case, etc.? Just don't buy it. You have other options. I prefer to live in a world in which Gaussian exists, so I have one more option, which I can freely choose to take or not. I use Gaussian, GAMESS, Aces and Dalton, and I consider Gaussian a good overall application. My University has voluntarily signed a contract with Gaussian Inc. in which the conditions of use are clearly stated. If I freely chose to break some of that conditions (like comparing results to other codes), it is perfectly licit that Gaussian takes the appropriate actions. It is the same that I would do. This being said, like Dominic Ryan, I do not understand that particular condition and I think that it is at the root of the disconfort many users feel about Gaussian. I am not as pretentious as to give advices to Mr. Frisch about which decisions are best for Gaussian, since it is completely obvious that they have thought much more about the topic than me, and they have a lot of relevant data that I ignore. I just express my belief that the "no-comparison" clause is the most controversial point. Not opening the source is something that a lot of developers do and they are not as fiercely criticized as Gaussian. My two cents, Pablo. --=20 Pablo Echenique Instituto de Biocomputaci=F3n y F=EDsica de los Sistemas Complejos (BIFI) Departamento de F=EDsica Te=F3rica Universidad de Zaragoza Pedro Cerbuna 12, 50009 Zaragoza Spain Tel.: +34 976761260 Fax: +34 976761264 echenique.p_-_gmail.com http://www.pabloechenique.com From owner-chemistry@ccl.net Sun Feb 3 10:52:00 2008 From: "Egon Willighagen egon.willighagen_-_gmail.com" To: CCL Subject: CCL:G: License what you want. Open what you want. No comparison? Message-Id: <-36212-080203104249-20821-BoQz8J5iIohQeFWNDFjUyg{=}server.ccl.net> X-Original-From: "Egon Willighagen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 3 Feb 2008 15:40:42 +0100 MIME-Version: 1.0 Sent to CCL by: "Egon Willighagen" [egon.willighagen .. gmail.com] On Feb 3, 2008 1:44 PM, Pablo Echenique echenique.p.:.gmail.com wrote: > The Open Source movement, with which I agree in most essential points, > is being increasingly infected with radical supporters which, like in > Middle Age, ride every day to Jerusalem to kill the unholy Proprietary > Defenders. There is no OpenSource *movement*... never existed, never will. So, it can't be infected either. However, there are many people releasing opensource software; and equally many opinions. What is a problem, is that a lot of people do not understand licensing issues. I'm sure some of you understand the difference between the GPL and the LGPL... but certainly not all. Another issue clouding the issues is the OpenSource versus ProprietarySource is *not* about FreeSource versus CommercialSource. A third issue causing trouble, particularly for science, if the difference between OpenSource and OpenProjects. One can, without trouble, dump some project as OpenSource; give it non-English comments, and no documentation whatsoever, and it is no use to science at all. It happens, really. On the other hand, a proprietary code base might simply implement a detailed description of some algorithm published in literature and discussed as such. So, there are three orthogonal axis here, and you may find projects in any corner: - open source versus proprietary source - free source versus commercial source - open projects versus closed projects Finally, radical supporters are found in any 'group' of people, if you really must create a couple of groups. I only need to say PRISM, and the things must be clear... > In my opinion, all development models MUST be tried before deciding > which is best. And maybe the final, not so surprising answer is that > the most efficiency is obtained in a world in which all options have > at least one strong representant. Umm... why one for each group? Why strong? For many people who like OpenSource, it is the freedoms are the key thing. I am not sure I like single strong representatives. > Moreover, if Open Source is the only answer to scientific software, we > will know it when we prove it, not when we declare it. Science progresses by sharing thoughts and theories. Open Source is a method of publishing what you are doing; and, I must make that clear, a superior way of publishing an implementation than a PDF document is. > However, I do not find anything unethical in the way a private firm > such as Gaussian Inc. works. In the free market, nobody forces you to > buy a product. You don't like Gaussian's performance, decisions, name, > colour of the CD case, etc.? Just don't buy it. You have other > options. Well, there's actually a fourth axis: performant code versus slow code. > I prefer to live in a world in which Gaussian exists, so I have one > more option, which I can freely choose to take or not. Exactly. That's what freedom is about. > I use Gaussian, > GAMESS, Aces and Dalton, and I consider Gaussian a good overall > application. My University has voluntarily signed a contract with > Gaussian Inc. in which the conditions of use are clearly stated. If I > freely chose to break some of that conditions (like comparing results > to other codes), it is perfectly licit that Gaussian takes the > appropriate actions. It is the same that I would do. Mind that some proprietary licenses (I have no clue about Gaussian license; not speaking about that) have know to include clauses what you may or may not do in terms of development (thus study!) alternative solutions. This is, I believe, clearly bad for science. Egon -- ---- http://chem-bla-ics.blogspot.com/ From owner-chemistry@ccl.net Sun Feb 3 22:27:00 2008 From: "Naser Eltaher Eltayeb nasertaha90*yahoo.co.uk" To: CCL Subject: CCL: ZINO/s ZINDO/1 Message-Id: <-36213-080203220929-17032-mtFPxK2BtqZhSIRTJ5gzpQ**server.ccl.net> X-Original-From: "Naser Eltaher Eltayeb" Date: Sun, 3 Feb 2008 22:09:24 -0500 Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90-#-yahoo.co.uk] Dear All I am tring to calculate UV transitions using ZINDO/S in Hyperchem, I get results have good agreement with experimental, but the problem ZINO/S in Hyperchem doesn't assign transtions with which molecular orbitals. Then I used ZINDO/1 in hyperchem, this time the agreement with experimental is bad, but ZINO/1 assign the transition with molecular orbitals. Is there anyway to get good result with assignment of molecular orbitals. below some of output files of ZINDO/s and ZINDO/1 ZINDO/s 1 (Transition) Excitation Energy 42119.0 nm 237.4 1/cm 1 -> 2 Spin S 1.00 State Dipole 7.9712 Oscillator Strength 0.0000 State Dipole Components -6.9706 -3.6308 1.3300 Transition Dipole Components -0.1342 -0.0842 0.1180 ZINO/1 1 (Transition) Excitation Energy 321.3 nm 31120.3 1/cm 1 -> 2 Spin S 1.00 State Dipole 7.0964 Oscillator Strength 0.0000 State Dipole Components -6.5340 -2.7659 0.1265 Transition Dipole Components -0.0000 -0.0000 0.0000 Spin Up : Occ. MO --> Unocc. MO Coefficients ------------------------------------------------- 75 --> 77 -0.599987 Spin Down: Occ. MO --> Unocc. MO Coefficients ------------------------------------------------- 75 --> 77 -0.599987 Thank you Naser Eltaher Universiti Sains Malaysia Penang 11800