From chemistry-request@ccl.net Sun May 16 16:23:43 2004 Received: from calmail-cl.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4GLNfVC017212 for ; Sun, 16 May 2004 16:23:41 -0500 Received: from [128.32.198.91] (account shaji$at$calmail.berkeley.edu HELO berkeley.edu) by calmail-cl.berkeley.edu (CommuniGate Pro SMTP 4.1.8) with ESMTP id 28409971 for chemistry$at$ccl.net; Sun, 16 May 2004 14:26:13 -0700 Message-ID: <40A7DC75.6060208$at$berkeley.edu> Date: Sun, 16 May 2004 14:26:13 -0700 From: Shaji Chempath User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031114 X-Accept-Language: en-us, en MIME-Version: 1.0 To: ccl Subject: Summary of replies: Slab Calculations References: <40A40CDB.2060306$at$berkeley.edu> In-Reply-To: <40A40CDB.2060306$at$berkeley.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.5 required=7.5 tests=FREE_TRIAL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Here is an edited summary of replies I got for my question regarding software suitable for Slab Calculations. Thanks a lot to all those replied. Shaji ------------------------------------- Replies: --------- DMol is one of the best programs for such calculations! --------- The ADF-BAND (or simply BAND) program can perform DFT calculations for 1-, 2-, or 3-dimensional periodic structures. It uses Slater and numerical Atomic Orbitals, can handle all elements in the periodic table (relativistic methods and basis sets are available), and does not need ECP or pseudopotential approximations. BAND also has analysis options that tell you how the interaction between a molecule and a surface is built up. An advantage of BAND is that it uses the same techniques as ADF (molecular program) which makes it suitable for direct comparisons between cluster and periodic calculations. More information is available at http://www.scm.com and a free trial is available on request. --------- If you want to study slab's I suggest to use plane wave codes. If you are a beginner in this area, you should take a code where pseudopotentials are included. Our favourite code is VASP, which comes with pseudo potentials. We also use CPMD for some other problems. Please note that there is at least one group in nearly in every country developing a plane wave code, so you may choose ... VASP, CPMD, DACAPO, SISSA, FLEUR, NWCHEM, CASTEP, and many more I guess. The LCAO codes like CRYSTAL and GAUSSIAN are usally much slower than the plane wave codes. But they've got the possibility to calculate B3LYP, which is not (yet) possible with the plane wave codes (to my knowledge). -------- I am using the CASTEP code from Cambridge University (UK) for this type of calculations (adsorption of small molecules on metal surfaces (Pt, Pd, Ag, etc)), but not for oxides (see, among others, (1) Physical Review Letters, V 90, N 21, 216102 (2003) and (2) Physical Review Letters, V 92, N13, 136104 (2004)). -------- I have done the similar jobs as your plan. I recommendate CPMD or VASP because they are easy to use. And the results are very reliable. CPMD is free, VASP needs to buy lisence. CPMD, VASP, and NWCHEM are program based on pseudopotential plane-wave method. Grystal03 and Gaussian programs employ the localized wavefunction. Using plane-wave programs, you need not to choose basis set. When you study to oxide surface, please pay attention to the layer thickness. If the surface has defect, you should also notice the interaction between the defects. -------- My Question: > > Could you please tell me what are the commonly used programs for > calculating the structures of surfaces with DFT level theory. > I have seen that CPMD, VASP, NWCHEM, and CRYSTAL03 are capable of > doing such calculations, but I have not used any of those. > Specifically I want to study the adsorption of small molecules on > different surfaces of ZrO2 crystals. I will have to use > pseudopotentials for Zr. If anybody can recommend me some softwares > that will do the job that will be great. I promise to post a summary > of available softwares and their limitations. > > I notice that Gaussian (G03) has periodic (PBC) caluclations. If > anybody has experience with this and can share it with me that will be > great. > > Thanks a lot, From chemistry-request@ccl.net Mon May 17 12:01:57 2004 Received: from LaTech.edu (selene.LaTech.edu [138.47.18.25]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4HH1uvI001002 for ; Mon, 17 May 2004 12:01:56 -0500 Received: from localhost (localhost [127.0.0.1]) by LaTech.edu (Postfix) with ESMTP id BB578308E94 for ; Mon, 17 May 2004 12:04:26 -0500 (CDT) Received: from LaTech.edu ([127.0.0.1]) by localhost (selene.latech.edu [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 27864-01-24 for ; Mon, 17 May 2004 12:04:25 -0500 (CDT) Received: from helius.latech.edu (helius.LaTech.edu [138.47.18.18]) by LaTech.edu (Postfix) with ESMTP id E5073308D49 for ; Mon, 17 May 2004 12:04:25 -0500 (CDT) Received: from LAPACHA (unknown [138.47.56.165]) by helius.latech.edu (Postfix) with ESMTP id EF8E99920E for ; Mon, 17 May 2004 12:04:25 -0500 (CDT) Message-ID: <019401c43c31$003369d0$a5382f8a@LAPACHA> Reply-To: "pderosa-Latech" From: "pderosa-Latech" To: Subject: Compiling Gaussian 03 in Xeon system Date: Mon, 17 May 2004 12:04:22 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0191_01C43C07.1734F240" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Virus-Scanned: by amavisd-new at latech.edu X-Spam-Status: No, hits=5.0 required=7.5 tests=HTML_20_30,HTML_MESSAGE, NO_RDNS,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0191_01C43C07.1734F240 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all: I have compiled Gaussian 03 in a dual Xeon system running Red = Hat 9.0 where I have the Portland group compiler. After solving a few = issues the compilation went smoothly and seemingly with not error (the = make.log file is too long and probably I missed something). However I = tried to run a simple calculation (h2o) and the calculation crashes when = entering link 101, in fact the last line in the log file is " (Enter = /usr/apps/gaussian/g03/l101.exe)" Below a list of a few issues I had to solve before compilation = works and that may have been the reasons for this problem 1) when I source g03.login (some times) come back that 'gau-machine is = not known' or something like that and the variable 'x' has not value = assigned to it. I notice though that when I run bldg03 the variable x = is assigned i386. 2) bldg03 is trying to link a file f2c.make into g03.make however = f2c.make does NOT come with the package. Assuming this is an error I = copy i386.make into f2c.make and allow the system to use that file to = compile. 3) the environmental variable PGI (location of the compiler) is not = assigned any value so I assigned the value manually 4) the make file tries to use pgf77 that was not in the path, I set the = path so it would find it After these issues were solved Gaussian compile with no errors but, as I = said before, it does not work. The step I am particularly suspicious = about is when I copy i386.make into f2c.make but I assumed that if = i386.make is not the correct make file the compilation would failed. Any help will be greatly appreciated, I can forward answers I receive to = anybody with the same problem. Thanks, Pedro ------=_NextPart_000_0191_01C43C07.1734F240 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all:
 
        I = have=20 compiled Gaussian 03 in a dual Xeon system running Red Hat 9.0 where I = have the=20 Portland group compiler.  After solving a few issues the = compilation went=20 smoothly and seemingly with not error (the make.log file is too long and = probably I missed something).  However I tried to run a simple = calculation=20 (h2o) and the calculation crashes when entering link 101, in fact the = last line=20 in the log file is " (Enter = /usr/apps/gaussian/g03/l101.exe)"
 
        = Below a list=20 of a few issues I had to solve before compilation works and that may = have been=20 the reasons for this problem
 
1) when I source g03.login (some times) = come back=20 that 'gau-machine is not known' or something like that and the variable = 'x' has=20 not value assigned to it.  I notice though that when I run bldg03 = the=20 variable x is assigned i386.
 
2) bldg03 is trying to link a file = f2c.make into=20 g03.make however f2c.make does NOT come with the package.  Assuming = this is=20 an error I copy i386.make into f2c.make and allow the system to use that = file to=20 compile.
 
3) the environmental variable PGI = (location of the=20 compiler) is not assigned any value so I assigned the value=20 manually
 
4) the make file tries to use pgf77 = that was not in=20 the path, I set the path so it would find it
 
After these issues were solved Gaussian = compile=20 with no errors but, as I said before, it does not work.  The step I = am=20 particularly suspicious about is when I copy i386.make into f2c.make but = I=20 assumed that if i386.make is not the correct make file the compilation = would=20 failed.
 
Any help will be greatly appreciated, I = can forward=20 answers I receive to anybody with the same problem.
 
Thanks,
 
Pedro
 
------=_NextPart_000_0191_01C43C07.1734F240-- From chemistry-request@ccl.net Mon May 17 15:12:16 2004 Received: from netra.ksu.edu.sa (netra.ksu.edu.sa [212.138.39.67]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4HKCDvI009684; Mon, 17 May 2004 15:12:14 -0500 Received: from netra.ksu.edu.sa (localhost [127.0.0.1]) by netra.ksu.edu.sa (8.11.7+Sun/8.11.6) with ESMTP id i4LGFZl02063; Mon, 17 May 2004 23:15:35 -1700 (Mideast/Riyadh) Received: from sun1.ksu.edu.sa (sun1.ksu.edu.sa [212.138.39.68]) by netra.ksu.edu.sa (8.11.7+Sun/8.11.6) with ESMTP id i4LGFT302046; Mon, 17 May 2004 23:15:34 -1700 (Mideast/Riyadh) Received: from IBM94D5EB6CA38 (localhost [127.0.0.1]) by sun1.ksu.edu.sa (8.11.7+Sun/8.11.7) with SMTP id i4LGDGt25732; Mon, 17 May 2004 23:13:16 -1700 (Mideast/Riyadh) Message-ID: <004401c43c4b$80ddf4a0$c002c80a@IBM94D5EB6CA38> From: "muneerah" To: Cc: Subject: Structure or shapes of metal clusters Date: Mon, 17 May 2004 23:14:03 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0041_01C43C64.A4B9C250" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=1.5 required=7.5 tests=DATE_IN_PAST_12_24,HTML_60_70, HTML_FONT_BIG,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0041_01C43C64.A4B9C250 Content-Type: text/plain; charset="windows-1256" Content-Transfer-Encoding: quoted-printable Dear all: =20 I am looking for a program that can predict the different possible = structures of a given metal cluster. I really doubt that such program = exists. For example it would predict the known structure of c60. = Actually we will work on much smaller metal cluster. =20 Thanking you for your cooperation. =20 Best regards, =20 M. Mogren ------=_NextPart_000_0041_01C43C64.A4B9C250 Content-Type: text/html; charset="windows-1256" Content-Transfer-Encoding: quoted-printable

Dear all:

 

I am looking for a program that can predict the different = possible=20 structures of a given metal cluster. I really doubt that such program = exists.=20 For example it would predict the known structure of c60. Actually we = will work=20 on much smaller metal cluster.

 

Thanking you for your cooperation.

 

Best regards,

 

M. Mogren

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