From owner-nwchem-users@emsl.pnl.gov Fri May 4 08:18:07 2007 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id l44FI6qu006812 for ; Fri, 4 May 2007 08:18:07 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l44FI6o2006811 for nwchem-users-outgoing-0915; Fri, 4 May 2007 08:18:06 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Possible-Spoof: True X-IronPort-AV: i="4.14,492,1170662400"; d="scan'208"; a="30541292:sNHT53271680" X-MimeOLE: Produced By Microsoft Exchange V6.5 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: RE: [NWCHEM] Energy doesn't continue from last value after restarting Date: Fri, 4 May 2007 08:18:18 -0700 Message-ID: <1692FA5FE0EBFD40B2B4097DAFEA887C01B95140@EMAIL02.pnl.gov> In-Reply-To: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [NWCHEM] Energy doesn't continue from last value after restarting Thread-Index: AceOUdtD/nVhO7lIRFm5Z8M7ly9scwADRDCQ References: <37275E1A43F1EC4C938AEFA1CFFAA0E301D2D9B0@EMAIL02.pnl.gov> From: "DeJong, Wibe A" To: "Vasiliy S. Znamenskiy" , "Vorpagel, Erich R" , X-OriginalArrivalTime: 04 May 2007 15:18:03.0872 (UTC) FILETIME=[690B1600:01C78E5F] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by odyssey.emsl.pnl.gov id l44FI626006808 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Vasiliy, When a calculation starts it reads info from the input file and stores it on the runtime database. In addition, while running calculations store addition (restart type) info on the database. On restart, the runtime database is not cleaned (as would be the case for a clean start). However, anything in the input deck before a task WILL override/overwrite the information that is on the runtime database. I.e., if you do a restart and your input deck contains a geometry, it will overwrite the database and use this input geometry, ect. Bert de Jong NWChem developer -----Original Message----- From: owner-nwchem-developers@emsl.pnl.gov [mailto:owner-nwchem-developers@emsl.pnl.gov] On Behalf Of Vasiliy S. Znamenskiy Sent: Friday, May 04, 2007 6:28 AM To: Vorpagel, Erich R; Vasiliy S. Znamenskiy ; nwchem-users@emsl.pnl.gov Subject: Re: [NWCHEM] Energy doesn't continue from last value after restarting Erich, according to logic of your description, the repeating calculations with directive "Restart" must do the same as previous calculation if contents of input file (*.nw) file doesn't changed. Calculations don't take from database (*.db) file anything because all data are in input file (*.nw). Is it true? Thank you, Vasiliy On Thu, 3 May 2007 13:14:03 -0700 "Vorpagel, Erich R" wrote: >Greetings Vasiliy, > >The Restart directive does restart using the data in the run time >database (*.db) file. >Addition information in the input file (*.nw) file over ride values in >the run time database, however. >This is useful so that the number of SCF iterations can be increased, >for example. If there is a geometry block, that will over ride the >runtime database. > > >Erich > >-----Original Message----- >From: Vasiliy S. Znamenskiy >[mailto:znamensk@sci.ccny.cuny.edu] >Sent: Thursday, May 03, 2007 11:21 AM >To: Vorpagel, Erich R; nwchem-users@emsl.pnl.gov >Subject: Re: [NWCHEM] Energy doesn't continue from last value after >restarting > >I have Restart directive in *.nw file. >I thought, Restart directive do force to take last geometry and NWChem >don't use geometry from *.nw file. >Is it wrong? >What is function of the Restart directive if geometry in *.nw file >exists too ? > >On Thu, 3 May 2007 09:57:26 -0700 > "Vorpagel, Erich R" wrote: >>Greetings Vasiliy, >> >>This will happen if you still have the original geometry in the input >>file. You need to either remove it, or what I do is comment it out >>with the # sign as first character for each in the geometry block. >> >>Also the "Start" directive needs to be changed to "restart" >> >>Regards, >> >>Erich R. Vorpagel, Ph.D. Technical Group Leader >>Manager Computational Grand-Challenge and Pilot Projects MSCF >>Visualization and User Services Group Environmental Molecular Sciences >>Laboratory Pacific Northwest National Laboratory P. O. >>Box 999, MS: >>K8-91 >>3335 Q Ave. Phone: >> 509-376-0751 >>Richland, WA 99352 FAX: >> 509-376-0420 >>Email: erich.vorpagel@pnl.gov >>Web: http://mscf.emsl.pnl.gov/ >> >> >> >>-----Original Message----- >>From: owner-nwchem-users@emsl.pnl.gov >>[mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Vasiliy S. >>Znamenskiy >>Sent: Thursday, May 03, 2007 9:38 AM >>To: nwchem-users@emsl.pnl.gov >>Subject: [NWCHEM] Energy doesn't continue from last value after >>restarting >> >>Hi: >> >>Why during optimization the energy doesn't continue from >>last value >>after a Job restarted ? >> >>See, please, an example: >> >>Last step of 1-st Job: >> >>p3w03.output.416462:@ 128 -229.49176596 >>p3w03.output.416462:@ 128 -229.49176596 >> >>Restarted Job: >> >>p3w03.output.416532:@ Step Energy >>p3w03.output.416532:@ ---- ---------------- >>p3w03.output.416532:@ 0 -229.48497070 >>p3w03.output.416532:@ 1 -229.48506901 >>p3w03.output.416532:@ 2 -229.48520619 Dear Sir / Madam: I am looking for a teaching, research or IT position in New York City or around. Sincerely, Dr. Vasiliy S. Znamenskiy http://www.znamenskiy.com Resume: http://web.sci.ccny.cuny.edu/~znamensk/VZnamenskiy_resume.doc http://web.sci.ccny.cuny.edu/~znamensk/VZnamenskiy_resume.pdf http://web.sci.ccny.cuny.edu/~znamensk/VZnamenskiy_resume.txt http://web.sci.ccny.cuny.edu/~znamensk/VZnamenskiy_resume.htm znamensk@sci.ccny.cuny.edu Home Phone: 1(718)238-0957 Cell Phone: 1(917)532-4377 Lab Phone: 1(212)650-6034 ___________ VASILIY S. ZNAMENSKIY 52 92nd St Apt 6C, Brooklyn, NY 11209, USA Cell phone: (917)532-4377 Home phone: (718)238-0957 znamensk@sci.ccny.cuny.edu http://www.znamenskiy.com/ SUMMARY More than 20 years working experience in software development and simulation of the various chemical, physical and technical processes and computer aided systems. Expertise in computer modeling of complicated engineering and scientific problems. Over 10 years of teaching experience in Computer Science. SKILLS Analyzing Information ; Problem Solving; Attention to Detail; Software Design; Software Debugging; Software Development Fundamentals; Software Documentation; Software Testing; Software Requirements; Software Development Process; Innovation; Quick Study; Written Communication; Database Design Languages: Unix C, Borland C++, UNIX shell scripts, HTML, JavaScript, SDL-scripts, Fortran, FORTRAN, PL/I, ALGOL Software: CHARMM, DL_POLY, PC Spartan, Gaussian, AIM2000, NWChem, gOpenMol, Microcal Origin, Microsoft Excel, Access, Golden Software Surfer, Photoshop Operating Systems: SunOS, DOS/Windows NT 4.0/2000, Linux, IBM PC, Silicon Graphics, Beowulf PC cluster Hardware: Sun workstation, Beowulf PC cluster, Silicon Graphics workstation, High-performance parallel supercomputer EXPERIENCE 6/2003 - Present. City University of New York, New York, NY Research Associate * Develop C/C++ programs; and Piton and UNIX scripts to perform data processing, data analysis, and computer-aided data conversion in a complex system of remote high-performance parallel supercomputer, two PC clusters and PC workstations * Engineer tools to assist in finding solutions to complex issues involving biophysical, biochemical systems * Perform computations of the molecular system by using modeling and simulation techniques * Use computational software such as NWChem, Gaussian, AIM2000, gOpenMol, Microcal Origin, Golden Software Surfer to perform complex molecular modeling and analysis tasks in networked, high-performance computers and PC clusters * Utilize data mining techniques to maximize the use of the computational results 09/2006 - 12/2006. Hostos Community College, New York, NY Adjunct Professor * Taught a course of General Physics II * Develop a WEB-Page to improve Professor-Students interaction (http://www.geocities.com/hostosphysics/) 05/2002 - 05/2003. Brooklyn College, Brooklyn, NY Research Associate * Computer simulation study of the solvatochromism of betaine-30 in an ionic liquid * Program development for data processing using C, C++. Provided System Administration * Use computational software such as DL_POLY, gOpenMol, Microcal Origin, Microsoft Excel, Golden Software Surfer to perform complex molecular modeling and analysis tasks in PC cluster environment 01/2001 - 04/2002. The George Washington University, Washington, DC Research Associate * Computer simulation study of the evaporation of protein ions from water nanodroplet * Used: Silicon Graphics Indigo workstations, IP22, IRIX; SUNW, Ultra-Enterprise, SunOS * Program development for data processing utilizing C, C++ Builder. Provided PC workstation administration 09/1997 - 01/2001. Kabardino-Balkaria State University, Nalchik, Russia Associate Professor * Developed the Interned based electronic library of resources on the information defense * Develop WEB-pages and computer programs to improve educational technologies * Taught courses: - Modern high-level languages (C, C++, Java Script, HTML) - Algorithmic languages and programming - Real-time systems (Petri Nets, SDL scripts) - Probability Theory and Mathematical Statistics - Introduction to Computer Science (Pascal, Basic) - Introduction to Advanced Mathematics - Chemical Computer Science 12/1981 - 09/1997. Kabardino-Balkaria State University, Nalchik, Russia Senior Researcher, Assistant Professor * Software development of computer-aided methods for designing of new polymers using C, C++ * Developed the web-pages for the small research businesses * Development of molecular-dynamics simulation software utilizing Turbo C, Borland C++, FORTRAN, Pascal * Performed various software conversions from FORTRAN to C * Modeled Computer-aided Production Analysis Systems. Used: dBase, FoxBASE * Performed simulation of inertial flight control systems for airframe aeronautics * Developed software of some hydrodynamic problems for a computer-aided system of Ministry of Melioration and Water Management. Wrote documentation and training guidelines * INMARSAT communication (C, Pascal, SDL-scripts) * Software development for simulation of the computer-aided control system of urban buses (PL/I) * Performed optimization of the signal processing algorithms 10/1978 - 11/1981. Research Institute of Chemical Technology, Biysk, Russia Engineer * Provided Software support for calculation of two-dimensional supersonic flows of heterogeneous systems in regions with complex boundaries using Godunov methods for compressible hydrodynamics 09/1977 - 09/1978. Lavrentyev Institute of Hydrodynamics, RAS. Novosibirsk, Russia Research Assistant * Investigated the parameters of shock-compressed materials utilizing detectors in magnetic chamber EDUCATION 1994 Ph.D. in Physical & Mathematical Sciences Thesis: Investigation of Contact-Melting Phenomenon by Method of Molecular-Dynamics Simulation Kabardino-Balkaria University, Russia 1978 M.S. in Physics. Specialization: Physics of High-Speed processes Physics Department, Novosibirsk State University, Russia PUBLICATIONS: 60 AWARDS & ACTIVITIES 1999 The coach of the University's team in the Quarter-Final of Northeastern European Regional Collegiate Programming Contest 1995 - 1996. Research Grant of Russian Foundation for Basic Research 1996 Grant of Scientific Affairs Division NATO 1995 Scholarship of the European Physical Society 1994 Grant of the International Science Foundation REFERENCES: Available upon request