From caoch at rsi.co.jp Tue Feb 19 08:15:05 2008 From: caoch at rsi.co.jp (caoch) Date: Tue, 19 Feb 2008 16:15:05 +0900 Subject: [Tremolo-users] Stress-strain questions Message-ID: <200802190713.m1J7D9YD018473@rsigw.rsi.co.jp> Dear Tremolo developers; Thank you for opening the Tremolo MD source. I have downloaded the source code and want to do some simulations for predicting the elastic moduli of polymer. Such simulation is very similar with the work you published at INS preprint No 0503 (Molecular dynamics simulations of the influence of chemical cross-links on the elastic moduli of polymer-carbon nanotube composites). I have some questions for the simulation run. 1) According to the above paper, such simulation should be done by add a tensile load with a stress rate. I think this is a Non-equilibration MD approach. However, the simulation parameters file seems only allow equilibration setting. How can I define these parameters into the simulation parameters file? 2) According to the application tools introduction on the website. It seems there is a tool, which can be used for plot stress-strain relationship, in the Tremolo. Can you tell me which is the tool is and how to use this tool? 3) Can you send me one example file for doing stress-strain simulation, such as you did in the above paper? Because I also want to check some benchmark properties of Tremolo? 4) Is there a complete manual of Tremolo? Because I want to understand the properties of the program (including calculation algorithms, results analysis tools and so or) absolutely. Best regards ---------------------------- Caoch JST-CREST Researcher Fundamental Technology Laboratory Research and Development Division Mitsubishi Chemical Group Science and Technology Research Center, INC. 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan TEL +81-45-963-3264 caoch at rsi.co.jp ---------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From wildenhues at ins.uni-bonn.de Tue Feb 19 10:29:52 2008 From: wildenhues at ins.uni-bonn.de (Ralf Wildenhues) Date: Tue, 19 Feb 2008 10:29:52 +0100 Subject: [Tremolo-users] Stress-strain questions In-Reply-To: <200802190713.m1J7D9YD018473@rsigw.rsi.co.jp> References: <200802190713.m1J7D9YD018473@rsigw.rsi.co.jp> Message-ID: <20080219092952.GA12205@ins.uni-bonn.de> Dear Caoch, * caoch wrote on Tue, Feb 19, 2008 at 08:15:05AM CET: > > I have some questions for the simulation run. Thanks for your interest in Tremolo. We have made a package available, but not yet announced it, because there are a few known issues we'd like to still fix first. Announcement and updated package are to follow real soon now. > 1) According to the above paper, such simulation should be done by add > a tensile load with a stress rate. I think this is a Non-equilibration MD > approach. However, the simulation parameters file seems only allow > equilibration setting. How can I define these parameters into the simulation > parameters file? I'll make sure there is a non-equilibration example in the tree, and at least a bit of documentation for the add-on tools. > 4) Is there a complete manual of Tremolo? Because I want to understand > the properties of the program (including calculation algorithms, results > analysis tools and so or) absolutely. At this time, such a thing does not exist, unfortunately. Most algorithmic details are explained in the published book, and we're working on a docbook-style document for the simulation code. Best regards, Ralf -- Ralf Wildenhues University of Bonn, Department of Numerical Simulation Wegelerstrasse 6, 53115 Bonn, Germany tel: +49 228 733178 mailto:wildenhues at ins.uni-bonn.de fax: +49 228 737527 http://wissrech.ins.uni-bonn.de/people/wildenhues.html From caoch at rsi.co.jp Wed Feb 20 12:12:09 2008 From: caoch at rsi.co.jp (caoch) Date: Wed, 20 Feb 2008 20:12:09 +0900 Subject: [Tremolo-users] Stress-strain questions In-Reply-To: <20080219092952.GA12205@m-pharma.co.uk> Message-ID: <200802201110.m1KBADmi024333@rsigw.rsi.co.jp> Dear Ralf Thank you for the answer. Please inform me when you put a Non- equilibration example in the tar file. At this time, Can you tell the way of setting an external stress tensor in the simulation parameter file? For example, if I want to add 0.01Gpa/ps external stress along the second axis, say Y direction, how can I set time step(1ps), tensor(the value of XX YY ZZ XY XZ YZ) and the real stress(0.01Gpa)? Although I think these setup should be easily defined in the ensemble and propagator section of the simulation parameter file, I don't know what these keywords are. Furthermore, is it possible for setting a limitation value to the simulation system, such as the simulation will be stopped when the loaded strain reached to some value? Best regards ---------------------------- Caoch JST-CREST Researcher Fundamental Technology Laboratory Research and Development Division Mitsubishi Chemical Group Science and Technology Research Center, INC. 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan TEL +81-45-963-3264 caoch at rsi.co.jp ---------------------------- -----Original Message----- From: Ralf Wildenhues [mailto:wildenhues at ins.uni-bonn.de] Sent: Tuesday, February 19, 2008 6:30 PM To: caoch Cc: tremolo-users at ins.uni-bonn.de Subject: Re: [Tremolo-users] Stress-strain questions Dear Caoch, * caoch wrote on Tue, Feb 19, 2008 at 08:15:05AM CET: > > I have some questions for the simulation run. Thanks for your interest in Tremolo. We have made a package available, but not yet announced it, because there are a few known issues we'd like to still fix first. Announcement and updated package are to follow real soon now. > 1) According to the above paper, such simulation should be done by add > a tensile load with a stress rate. I think this is a Non-equilibration MD > approach. However, the simulation parameters file seems only allow > equilibration setting. How can I define these parameters into the simulation > parameters file? I'll make sure there is a non-equilibration example in the tree, and at least a bit of documentation for the add-on tools. > 4) Is there a complete manual of Tremolo? Because I want to understand > the properties of the program (including calculation algorithms, results > analysis tools and so or) absolutely. At this time, such a thing does not exist, unfortunately. Most algorithmic details are explained in the published book, and we're working on a docbook-style document for the simulation code. Best regards, Ralf -- Ralf Wildenhues University of Bonn, Department of Numerical Simulation Wegelerstrasse 6, 53115 Bonn, Germany tel: +49 228 733178 mailto:wildenhues at ins.uni-bonn.de fax: +49 228 737527 http://wissrech.ins.uni-bonn.de/people/wildenhues.html