From chemistry-request@server.ccl.net Fri Nov 23 19:10:55 2001 Received: from hermes.lfc.edu ([164.68.1.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAO0AtB17113 for ; Fri, 23 Nov 2001 19:10:55 -0500 Received: from forester.lfc.edu ([164.68.1.25]) by hermes.lfc.edu (PMDF V5.2-31 #40904) with SMTP id <0GNA0035S35UBC@hermes.lfc.edu> for chemistry@ccl.net; Fri, 23 Nov 2001 18:10:42 -0600 (CST) Date: Fri, 23 Nov 2001 18:08:20 -0600 (CST) From: Lucas E Sweet Subject: compilation of g98 rev A.11 using g77 To: chemistry@ccl.net Cc: sweetle@hermes.lfc.edu Message-id: <29969683.1006560500280.JavaMail.cpadmin@forester> MIME-version: 1.0 Content-type: text/plain Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAO0AtB17114 Thanks to the help of several people I have managed to make some progress in my attempt to compile g98 rev A.11 on a AMD k6-3 running redhat linux 7.2.  I am now stuck again.  The number of errors in the bldg98.log has reduced but there are still a number of them.  I lack the knowege of how to fix these errors.  Any help would be greatly appreciated.  Here is the end of the bldg98.log file: utilam.F:95576: Integer MaxShl,MaxPrm,MaxSh1,MaxS21,JAN,ShellA,ShellN,ShellT, 1 utilam.F:95582: (continued): $Y(MaxShl),Z(MaxShl),JAN(MaxShl),ShellA(MaxShl),ShellN(MaxShl), 2 Invalid declaration of or reference to symbol `shelln' at (2) [initially seen at (1)] utilam.F:95576: Integer MaxShl,MaxPrm,MaxSh1,MaxS21,JAN,ShellA,ShellN,ShellT, 1 utilam.F:95583: (continued): $ShellT(MaxShl),ShellC(MaxShl),AOS(MaxShl),AON(MaxShl), 2 Invalid declaration of or reference to symbol `shellt' at (2) [initially seen at (1)] utilam.F:95577: $ ShellC,ShlADF,AOS,AON,NShell,MaxTyp 1 utilam.F:95583: (continued): $ShellT(MaxShl),ShellC(MaxShl),AOS(MaxShl),AON(MaxShl), 2 Invalid declaration of or reference to symbol `shellc' at (2) [initially seen at (1)] utilam.F:95577: $ ShellC,ShlADF,AOS,AON,NShell,MaxTyp 1 utilam.F:95583: (continued): $ShellT(MaxShl),ShellC(MaxShl),AOS(MaxShl),AON(MaxShl), 2 Invalid declaration of or reference to symbol `aos' at (2) [initially seen at (1)] utilam.F:95577: $ ShellC,ShlADF,AOS,AON,NShell,MaxTyp if ( 1 ) then make -f bsd/g98.make JUNK1=JUNK exe gau-cpp -I/luke/sweetle/g982/g98 -I/luke/sweetle/g982/g98s -DGAUSS_PAR -DGAUSS_THPAR -DDEFMAXSHL=20000 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFNVDIM=257 -DDEFARCREC=1024 -DMERGE_LOOPS -DUSE_ESSL -D_I386_ -DLITTLE_END -DUSING_F2C -DDEFMAXIOP=100 -DDEFMAXCHR=1024 -DDEFLMAX=13 -DDEFN3MIN=10 -DDEFMAXHEV=2000 -DDEFCACHE=64 -DDEFMAXLECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMAXINFO=200 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -D_ALIGN_CORE_ -DCA1_DGEMM -DCA2_DGEMM -DCAB_DGEMM -DLV_DSP -DO_BKSPEF -DDEFMXTS=1500 -DDEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500 dummy.F dummy.f g77 -malign-double -m486 -fexpensive-optimizations -O2 -ffast-math -funroll-loops -c dummy.f rm -f dummy.f dummy.c ld -shared -o util.so dummy.o --whole-archive util.a \ --no-whole-archive gau-fsplit -e ml0 bsd/main.F ml0.F already exists, over-written make -f bsd/g98.make OPTFLAG=' -malign-double -m486 -fexpensive-optimizations -O2 -ffast-math -funroll-loops' ml0.o make[1]: Entering directory `/luke/sweetle/g982/g98' gau-cpp -I/luke/sweetle/g982/g98 -I/luke/sweetle/g982/g98s -DGAUSS_PAR -DGAUSS_THPAR -DDEFMAXSHL=20000 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFNVDIM=257 -DDEFARCREC=1024 -DMERGE_LOOPS -DUSE_ESSL -D_I386_ -DLITTLE_END -DUSING_F2C -DDEFMAXIOP=100 -DDEFMAXCHR=1024 -DDEFLMAX=13 -DDEFN3MIN=10 -DDEFMAXHEV=2000 -DDEFCACHE=64 -DDEFMAXLECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMAXINFO=200 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -D_ALIGN_CORE_ -DCA1_DGEMM -DCA2_DGEMM -DCAB_DGEMM -DLV_DSP -DO_BKSPEF -DDEFMXTS=1500 -DDEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500 ml0.F ml0.f g77 -malign-double -m486 -fexpensive-optimizations -O2 -ffast-math -funroll-loops -c ml0.f rm -f ml0.f ml0.c make[1]: Leaving directory `/luke/sweetle/g982/g98' g77 -malign-double -m486 -fexpensive-optimizations -O2 -ffast-math -funroll-loops -o g98 ml0.o util.so util.so: undefined reference to `dspmv_' util.so: undefined reference to `dgemm_' util.so: undefined reference to `wait_' util.so: undefined reference to `fork_' collect2: ld returned 1 exit status make: *** [g98] Error 1 endif Thanks, Luke Sweet Lake Forest College sweetle@lfc.edu From chemistry-request@server.ccl.net Sat Nov 24 01:17:43 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAO6HhB30224 for ; Sat, 24 Nov 2001 01:17:43 -0500 Received: from [128.97.147.208] (ch-08.psnet.ucla.edu [128.97.147.208]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id fAO6HdC29245 for ; Fri, 23 Nov 2001 22:17:39 -0800 (PST) Mime-Version: 1.0 Message-Id: Date: Fri, 23 Nov 2001 22:17:22 -0800 To: ccl From: Eric Scerri Subject: usage of terms "ab initio" and "first principles" Content-Type: text/plain; charset="us-ascii" ; format="flowed" I am interested in discovering the origins and current usage of the terms "ab initio" and "first principles" in computational work. Am I correct in thinking that the latter was introduced relatively recently, because one can no longer claim that practically implemented DFT methods are truly ab initio given the 'fixing' of density gradients by reference to experimental data. So although in terms of translation the two terms are virtually synonymous the usage implies that "first principles" is not quite so "ab initio"? I would appreciate comments and/or references to articles which may have discussed this question or first suggested such terminology regarding "first principles" as an alternative. I will post responses. -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.wkap.nl/prod/j/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@server.ccl.net Sat Nov 24 05:05:05 2001 Received: from mail.rpi.edu (root@[128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAOA55B03891 for ; Sat, 24 Nov 2001 05:05:05 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by mail.rpi.edu (8.11.3/8.11.3) with ESMTP id fAOA50Z86280; Sat, 24 Nov 2001 05:05:00 -0500 Message-Id: <200111241005.fAOA50Z86280@mail.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: mattacf@mcmail.cis.mcmaster.ca From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: grzesb@asp.biogeo.uw.edu.pl, chemistry@ccl.net X-Originating-Ip: 128.113.21.163 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Sat, 24 Nov 2001 5:05:00 EST X-Mailer: EMUmail 4.00 Subject: Re: CCL:AIM in g98 problems - NO GOOD SOLUTION --- SUMMARY On Sat, 24 Nov 2001 01:07:29 -0500 (EST) "C.F. Matta" wrote: > > Dear Dr. Sukumar, > > > I do not agree, however, with the statement that AIM does not > discriminate > between multiple bonding: All what you have to do is to examine the > magnitude of the density at the saddle point on the bond path, > i.e. the density at the bond critical point [Rho(b)].A few examples: > > Rho(b)[ethane C-C] = 0.253 au Delta(C,C)=0.991 pair > Rho(b)[benzene C=C] = 0.327 au Delta(C,C)=1.388 pair > Rho(b)[ethylene C=C] = 0.364 au Delta(C,C)=1.890 pair > I totally agree with you here. My statement "does not discriminate between multiple bonding" was loosely worded. Of course the density carries all the info.and, in particular, the density and curvatures at the critical point provide an indication of bond order as well as bond character. Dr. N. Sukumar Rensselaer Department of Chemistry From chemistry-request@server.ccl.net Sat Nov 24 01:07:54 2001 Received: from mcmail.cis.mcmaster.ca (mattacf@[130.113.64.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAO67sB29835 for ; Sat, 24 Nov 2001 01:07:54 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.mcmaster.ca with ESMTP id BAA10681; Sat, 24 Nov 2001 01:07:29 -0500 (EST) Date: Sat, 24 Nov 2001 01:07:29 -0500 (EST) From: "C.F. Matta" To: "Dr. N. SUKUMAR" cc: , Subject: Re: CCL:AIM in g98 problems - NO GOOD SOLUTION --- SUMMARY In-Reply-To: <200111231919.fANJJVZ89848@mail.rpi.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id fAO67sB29836 Dear Dr. Sukumar, I agree totally with you that the bond order is an artificial concept, this is why I propose the physical measure of electron delocalization (DELTA) provided by integrating the fermi hole density over the atomic basins in question (see my previous CCL message distributed yesterday for details and references). DELTA recover much of the chemistry and chemical concepts by counting the number of electron pairs shared between two specific atoms in a molecule. You are correct in saying that AIM provides an all-or-none answer as to the existance of bonding (which can be very helpful in assigning a bonded structure in ambigiuous cases where distance alone can be missleading - check our Inorg.Chem.(2001),40,5603 paper. The all-or-none nature of the bond path also is important to locate points on the reaction coordinate where a change in structure happen (i.e. when bonds form or break). I do not agree, however, with the statement that AIM does not discriminate between multiple bonding: All what you have to do is to examine the magnitude of the density at the saddle point on the bond path, i.e. the density at the bond critical point [Rho(b)].A few examples: Rho(b)[ethane C-C] = 0.253 au Delta(C,C)=0.991 pair Rho(b)[benzene C=C] = 0.327 au Delta(C,C)=1.388 pair Rho(b)[ethylene C=C] = 0.364 au Delta(C,C)=1.890 pair Best wishes. Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ___________________________________________________________________________ On Fri, 23 Nov 2001, Dr. N. SUKUMAR wrote: > Aren't bond orders a somewhat arbitrary concept? > > The simplest -- and also cheapest -- way of estimating bond orders I know > of is simply to use a distance criterion and parametrize for different > bonds. Some molecular modeling software do just this. But calculating bond > orders ab initio? I'm afraid that really depends on how you define bond > orders. > > More elaborate ways have been employed in the literature to calculate bond > orders, but really it depends on whose definition you accept (see, e.g. > J.S. Murray, N.Sukumar, S.Ranganathan and P.Politzer, “A Computational > Analysis of the Electrostatic Potentials and Relative Bond Strengths of > Hydrazine and some of its 1,1-Dimethyl Derivatives” Intl. J. Quantum Chem. > 38, 611-629, 1990). I personally think that the bond order concept today > provides no more useful information than bond length or bond dissociation > energy, both of which can be unambiguously defined. > > AIM can be used to determine the existence or absence of a bond path > between atoms in a molecule. It does not distinguish multiple bonds. > > Dr. N. Sukumar > Rensselaer Department of Chemistry > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Sat Nov 24 01:13:19 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAO6DJB30095 for ; Sat, 24 Nov 2001 01:13:19 -0500 Received: from [128.97.147.208] (ch-08.psnet.ucla.edu [128.97.147.208]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id fAO6DGC29193 for ; Fri, 23 Nov 2001 22:13:16 -0800 (PST) Mime-Version: 1.0 Message-Id: Date: Fri, 23 Nov 2001 22:12:59 -0800 To: ccl From: Eric Scerri Subject: 6th ISPC meeting in DC Content-Type: multipart/alternative; boundary="============_-1205540101==_ma============" --============_-1205540101==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" Call for papers Sixth Summer Symposium of the International Society for the Philosophy of Chemistry August 4-8, 2002 Georgetown University, Washington, DC 20057 Abstracts (one half page) and/or prospectuses (up to three pages) are solicited for papers to be presented at The Sixth Annual Summer Symposium of the International Society for the Philosophy of Chemistry (ISPC) to be held August 4-8, 2002 at Georgetown University, Washington, DC 20057. As at prior ISPC symposia, both longer (50-60 minute) and shorter (15-30 minute) presentations will be scheduled. Papers dealing with chemistry-related issues raised in recent philosophical literature, especially Foundations of Chemistry (http://www.wkap.nl/prod/j/1386-4238) and Hyle (http://www.hyle.org), are preferred. Abstracts and/or prospectuses, and conference pre-registration, should be sent electronically, to the address below, by February 15, 2002. There will be no registration fee for the meeting. Accommodation will be available in air-conditioned on-campus housing (price range, including tax: $250 for four nights double or single occupancy with private bath, to $108 for four nights for shared room with floor bath) and at the Rosslyn Holiday Inn, Virginia ($99.00 plus tax per day, two double beds or king bed, transportation to Georgetown available). Please visit the ISPC website at http://www.georgetown.edu/earleyj/ISPC.html or contact J. E. Earley, Sr. (Georgetown Chemistry) for more information. E-mail: earleyj@georgetown.edu. Phone: 703-532-5238. Fax: 202-687-6209. -- -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.wkap.nl/prod/j/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html --============_-1205540101==_ma============ Content-Type: text/html; charset="us-ascii" 6th ISPC meeting in DC


Call for papers
                 
Sixth Summer Symposium
of the
International Society
 for the Philosophy of Chemistry

August 4-8, 2002

 Georgetown University, Washington, DC 20057


Abstracts (one half page) and/or prospectuses (up to three pages) are solicited for papers to be presented at The Sixth Annual Summer Symposium of the International Society for the Philosophy of Chemistry (ISPC) to be held August 4-8, 2002 at Georgetown University, Washington, DC 20057. As at prior ISPC symposia, both longer (50-60 minute) and shorter (15-30 minute) presentations will be scheduled. Papers dealing with chemistry-related issues raised in recent philosophical literature, especially Foundations of Chemistry (http://www.wkap.nl/prod/j/1386-4238) and Hyle (http://www.hyle.org), are preferred. Abstracts and/or prospectuses, and conference pre-registration, should be sent electronically, to the address below, by February 15, 2002.

There will be no registration fee for the meeting. Accommodation will be available in air-conditioned on-campus housing (price range, including tax: $250 for four nights double or single occupancy with private bath, to $108 for four nights for shared room with floor bath) and at the Rosslyn Holiday Inn, Virginia ($99.00 plus tax per day, two double beds or king bed, transportation to Georgetown available).

Please visit the ISPC website at http://www.georgetown.edu/earleyj/ISPC.html  or contact J. E. Earley, Sr. (Georgetown Chemistry) for more information.
E-mail: earleyj@georgetown.edu.
Phone:   703-532-5238.                         Fax: 202-687-6209.

--
--


Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri@chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.wkap.nl/prod/j/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html
--============_-1205540101==_ma============-- From chemistry-request@server.ccl.net Sat Nov 24 12:38:18 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAOHcHB12094 for ; Sat, 24 Nov 2001 12:38:17 -0500 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KB2ZAMUY8C004N8J@trentu.ca> for chemistry@ccl.net; Sat, 24 Nov 2001 12:37:33 EST Date: Sat, 24 Nov 2001 12:39:04 -0500 From: elewars Subject: Re: CCL:usage of terms "ab initio" and "first principles" To: chemistry@ccl.net Message-id: <3BFFDB38.31688F2@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: 2001 nov 24 Hello, Re the term _ab initio_", Dewar said: ""The term ab initio was originally applied to the Roothaan=Hall (RH) approach through an amusing accident. Parr was collaborating in some work of this kind with a group in England. In reporting one of his calculations, he described it as "ab initio", implying that the whole of that particular project had been carried out from the beginning in his laboratory. The term, unfortunately, became ..." See M. J. S. Dewar, "A Semiempirical Life", ACS, Washington, DC, 1992; p. 129 (series Profiles, Pathways and Dreams, autobiographies of eminent chemists). Dewar was the leading champion of semiempirical methods over ab initio ones, and I do not know if Robert Parr ever commented on the above account. I don't know if "first principles" was introduced to play down the claim that ab initio is purely theoretical; certainly high-accuracy methods like G2 and G3 are calibrated with experimental data, something which would have amused Dewar. E. Lewars ====== Eric Scerri wrote: > I am interested in discovering the origins and current usage of the terms > "ab initio" and "first principles" in computational work. > > Am I correct in thinking that the latter was introduced relatively > recently, because one can no longer claim that practically > implemented DFT methods are truly ab initio given the 'fixing' of > density gradients by reference to experimental data. > > So although in terms of translation the two terms are virtually > synonymous the usage implies that "first principles" is not quite so > "ab initio"? > > I would appreciate comments and/or references to articles which may > have discussed this question or first suggested such terminology > regarding "first principles" as an alternative. I will post > responses. > > -- > > Dr. Eric Scerri , > UCLA, > Department of Chemistry & Biochemistry, > 607 Charles E. Young Drive East, > Los Angeles, CA 90095-1569 > USA > > E-mail : scerri@chem.ucla.edu > tel: 310 206 7443 > fax: 310 206 2061 > Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html > > Editor of Foundations of Chemistry > http://www.wkap.nl/prod/j/1386-4238 > > Also see International Society for the Philosophy of Chemistry > http://www.georgetown.edu/earleyj/ISPC.html > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net