From ORG3@caos.caos.kun.nl Tue Nov 10 05:45:01 1992 Date: Tue, 10 Nov 1992 11:36:05 METDST From: CMC department Subject: PLS (partial least squares) To: CHEMISTRY@oscsunb.ccl.net Dear Netters, does anyone know whether PLS (partial least squares) code is available in public domain? I would very much appreciate to get some feedback on this. Regards Vincent van Geerestein From CFAT@DS0RUS1I.bitnet Tue Nov 10 11:44:41 1992 Date: Tue, 10 Nov 92 16:31:08 MEZ From: CFAT%DS0RUS1I.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: reliability of pseudopotentials for TM To: chemistry mailbox Concerning the accuracy of pseudopotentials for transition metals (TM), I'd like to make the following comments on the contribution of Jan Hrusak, Nov. 4, 92. In my opinion, his comments, especially the table summarizing some results for the iron metal, give a completely wrong picture concerning the reliability of the Hay-Wadt pseudopotentials. Using pseudopotentials one should keep in mind the following: 1. In order to judge the accuracy of a pseudopotential one should compare results of pseudopotential to all-electron calculations performed at a corresponding level of theory, e.g. the HF level. One should always exclude basis set effects since pseudopotentials and basis sets are different things. I suggest to do such comparisions always at the finite-difference level. In case of the iron atom one can take the numerical all-electron data (nonrelativistic and spin-orbit averaged quasirelativistic) from Martin and Hay, JCP 75, 4539 (1981). Their Cowan-Griffin results for ionisation and excitation energies agree with values calculated by us using the related Wood-Boring scheme within 0.01 eV. It is not correct to compare UHF results (which give no well-defined LS-state anyhow) to such RHF results. 2. Errors due to the valence basis sets can be checked by comparision of the corresponding results to finite difference pseudopotential results or at least pseudopotential calculations performed with very large basis sets (we used 15s15p15d before we applied the finite-difference code). 3. Correlation errors can finally be checked by comparing correlated quasirelativistic pseudopotential calculations to experimental data. One should not forget to average the experimental numbers over spin-orbit components when doing the pseudopotential calculation in LS-coupling (Gaussian). This was not done by Jan Hrusak. There is much literature on correlation effects in transition metals and MP2 is definitely not the method to be used. I suppose that the excellent results Jan Hrusak obtains with his Ar-core pseudopotential, a 6s3p8d/5s3p5d basis (how can one describe 4p or 4s2->4p2 correlation with this basis set?) in the framework of MP2 are not due to an excellent pseudopotential, but rather to an excellent error cancelation (pseudopotential error, basis set error, correlation error, error in averaging the experimental numbers). I really have no idea how Jan Hrusak can 'publish' an all-electron excitation energy for iron for 5D->3F (most likely s2d6 -> d8) of 7.53 eV, compare this to pseudopotential results for 5D->3F (most likely s2d6 -> s1d7) of 2.08 eV (error 5.45 eV) and 3.37 eV (error 4.16 eV) and state (without any doubts, that his comparison is affected by errors), that this is due to the 'ground state oriented parametrization procedure more than with the valence space'. In order to discuss this, one needs to know frozen-core results for Ne and Ar core: The frozen-core errors in excitation and ionisation energies for 13 LS states of Fe and Fe(+) are less than 0.02 eV for the Ne core and less than 0.25 eV for the Ar core in finite difference all-electron HF calculations, when this core is taken from the s2d6 5D ground state. I don't see, how 4 or 5 eV errors should arise from this in pseudopotential work. Therefore, in order to prove that Hay-Wadt pseudopotentials are quite accurate, in the following table I summarize some numbers for iron pseudopotentials of Hay and Wadt and ourselves (Dolg, Wedig, Stoll, Preuss, JCP 86, 866, 1987) in comparison to the all-electron data published by Martin and Hay: 5D -> 5F 5D -> 3F 5D -> 6D 5D -> 4F s2d6 s1d7 s2d6 d8 s2d6 s1d5 s2d6 d7 num. RHF, nonrelativistic AE,HF (Martin,Hay) 1.80 7.46 6.28 7.95 ECP (Ar, Hay,Wadt) 1.53 7.28 6.06 7.73 ECP (Ne, Hay,Wadt) 1.96 7.72 6.28 8.12 PP (Ne, Dolg,Stoll,Preuss) 1.78 7.50 6.28 7.95 with 7s6p5d/5s4p3d basis set 1.79 7.48 6.33 7.99 num. RHF, quasirelativistic AE,HF (Martin,Hay) 2.06 7.87 6.34 8.33 PP (Ne, Dolg,Stoll,Preuss) 2.06 7.94 6.35 8.36 with 7s6p5d/5s4p3d basis set 2.07 7.93 6.40 8.40 (This is the data for 4 out of 13 states I looked on in 1986; the results for the other states are of the same quality.) It is clearly seen that all pseudopotentials give reliable results at the HF or SCF level. The same is true for the pseudopotentials published by the Christiansen group or the Toulouse group (I don't have the numbers for Fe, but e.g. for Ni the Christiansen pseudopotential HF results agree with all-electron HF results within 0.1 eV). Finally, I would like to remark that it is rather a matter of a proper initial guess and not a problem of the Hay-Wadt pseudopotential, if Gaussian calculations often converge to an excited state. The message should be: Distinguish pseudopotential, basis set and computational method as well as the errors occuring at in all of these. Although the final results might be 'excellent', it could be accidential. Michael Dolg Institut fuer Theoretische Chemie Universit{t Stuttgart Pfaffenwaldring 55 W 7000 Stuttgart 80 CFAT .at. DS0RUS1I From MARYJO@northeastern.edu Tue Nov 10 07:15:00 1992 Date: Tue, 10 Nov 1992 12:15 EST From: MARYJO@northeastern.edu Subject: LaTeX doublespace format by ftp? To: chemistry@ccl.net Pardon my interruption of profound discussion with a mundane problem, but we are having a hell of a time getting LaTeX to print in doublespace format (i.e. the type of doublespace format you would use for a journal submission or proposal) 1) Does anybody have the command set which will print pages in double-space with common margins and pica type? 2) Is that command set available by ftp? 3) Do any of our journals (e.g J Chem Phys, Chem Phys Lett, and J Phys Chem, etc) have a LaTeX command set which is preferred for manuscript submission? If so, are they available by ftp? I would appreciate any help and advice on this, Thanks Mary Jo Ondrechen From dorand@rocbi.DNET.roche.com Tue Nov 10 06:18:03 1992 Date: Tue, 10 Nov 92 06:17:58 EST From: "Daniel M. Doran, PRTC, phone 88270" To: chemistry@ccl.net Subject: RE: cambridge database > > Does anyone knows if there's an ftp anonymous acces to the Cambridge database? > Cambridge wants you to pay for the data they collect and hence there is no ftp access. ------------------------------------------------------------------------------ Daniel M. Doran, Ph.D. InterNet: DoranD@Rocbi.Dnet.Roche.Com Pharmaceutical Research - Phone: +41-61-688-8270 New Technologies +41-61-688-7080 F.Hoffmann-La Roche Ltd. Fax: +41-61-688-1745 CH-4002 Basel, Switzerland X400: S=Doran,G=Daniel,O=RocheBasel,P=Roche,A=ARCOM,C=CH ------------------------------------------------------------------------------ From JOHNSON@CMCHEM.CHEM.CMU.EDU Tue Nov 10 09:31:59 1992 Date: Tue, 10 Nov 1992 14:31:59 EST From: JOHNSON@CMCHEM.CHEM.CMU.EDU (Benny Johnson) Subject: Translational invariance in DFT derivative calculations To: chemistry@ccl.net Katrina Werpetinski writes: > I've got another problem with which I'm hoping someone can help. We're > using an Xalpha LDF code to do geometry optimizations. The gradient > calculations wrt Cartesian coordinates are not conserving linear and > angular momentum; that is, there are net translational and rotational > energies. This, of course, makes it impossible to find gradients wrt > internal coordinates. Has anyone come up against this problem before > and fixed it? One possible source of loss of translational invariance in DFT gradients is in the way the numerical quadrature weights are handled. Most DFT codes use atomic weighting schemes to partition the molecular XC integrals into single-center contributions (the most popular scheme is that of Becke, JCP 88, 2547 (1988)). These weights depend on the nuclear configuration, and hence have derivatives with respect to the nuclear coordinates. Strictly speaking, in order to be consistent with the implementation of the XC energy (as a numerical sum over points and weights, not an analytic integral), when taking gradients one must include the terms involving the weight derivatives. However, none of the currently available DFT packages of which I am aware include these. Translational invariance is strictly not obeyed unless the weight derivatives are included. The magnitude of the loss of translational invariance depends on the "completeness" of the quadrature grid used. I am doing some coding of DFT methods as part of my Ph.D. work, and have looked at the effect of the weight derivatives. For fairly large grids (say, O(10000) points per atom) the effect is insignificant for practical purposes. For small grids, though (O(1000) points per atom), the errors in the nuclear forces from leaving out the weight derivatives can be significant (around 10**-4 - 10**-3 a.u.) unless the point distribution is very well-chosen. Some optimizers can indeed get confused by this inconsistency. The effect is more severe for vibrational frequencies, where both first and second derivatives of the weights contribute. Once the weight derivative terms are put in, however, e.g. the related optimization difficulties go away, regardless of the size of the grid, since one is now exactly differentiating what has been defined as the energy. We routinely include the weight derivatives in our optimization and frequency calculations. As far as the loss of rotational invariance is concerned, that is a tougher problem, and one which I have not yet considered in detail myself. However, as I implied earlier, in the case of geometry optimization the TI problem is more significant. Benny Johnson Carnegie Mellon University From sheely@cobalt.chem.uidaho.edu Tue Nov 10 04:43:13 1992 From: sheely@cobalt.chem.uidaho.edu Subject: Re: Music To: WATHELET%BNANDP11.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU (Valerie Wathelet) Date: Tue, 10 Nov 92 12:43:13 PST > > Hi, > > Does anyone have any information on the MUSIC Method and more precisely as used > in the determination of the vibration frequencies in molecules. > Recently, I have read a paper of Noid and Pfeffer : "Short Time Molecular Dynam I would sugest looking at the book "Digital Spectral Analysis With Applications" by S. Lawrence Marple, Jr. From 100012.1163@compuserve.com Sat Nov 10 10:47:47 1992 Date: 10 Nov 92 15:47:47 EST From: "100012.1163@compuserve.com (Rainer Stumpe)" <100012.1163@CompuServe.COM> To: Subject: New files on Springer's server To: >INTERNET:CHEMISTRY@oscsunb.ccl.net Dear Netters, Springer-Verlag has just made available the tables of contents of issues of "Theoretica Chimica Acta". Our intention is to make the tables of contents available at the time of publication of each issue. Similar services for other journals might follow in due time and if there is a demand. As of today the following files are available from the directory /TCA: TCA84_12.TXT ToC Vol. 84, Issue 1/2 (released Nov. 5th), TCA_V83.TXT ToC Vol. 83, 1992, TCA_V82.TXT ToC Vol. 82, 1992, TCASUBS.TXT Subscription information. Springer-Verlag's server holds many useful routines, macros for TeX and a lot of information on our products (e.g. tables of contents of the ENZYME HANDBOOK and of Landolt-Boernstein). There will soon be a demo of our molecular modelling program MOBY (Version 1.5) available in English (it is presently only in German language). SPRINGER-VERLAG Server currently understands the following commands which may be abreviated to the upper case portion in this list: CD Change directory format: CD /directory DIRALL Returns a list of ALL files available format: DIRALL DIRectory Returns a list of files available format: DIR /directory GET Synonym for SEND format: GET /directory/filename HELP Returns this list format: HELP INDex Synonym for DIRECTORY format IND /directory SEND Returns a file format: SEND /directory/filename These commands must be the body of your message (Note the blank after the command and use slash NOT backslash). For a start, I suggest you send the message HELP to: SVSERV@DHDSPRI6.BITNET DO NOT USE SVSERV FOR MESSAGES! Your comments will be most welcome. 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