Thank you so much for kindly response. On 3 February 2015 at 12:47, Chih-Chien Wang <[email protected]> wrote:
> In that case, the easiest way might be find the coordinate of the - say > 500th step, and just copy that into your new .fdf file. > > Unfortunately, .XV file, according to the webpage, would be renewed each > step. So you probably wouldn't be able to use it unless it is the last step. > > http://departments.icmab.es/leem/siesta/Documentation/Manuals/manual-2.0/node23.html > > I am not exactly certain about the DM file, but my understanding is that > .DM file is refreshed each step, too. > > > Chih-Chien Wang > Research Assistance > Institute of Atomic and Molecular Science, > Academia Sinica, Taipei, Taiwan > [email protected] > > ----- Original Message ----- > *From:* Ting Zheng <[email protected]> > *To:* [email protected] > *Sent:* Tuesday, February 03, 2015 4:46 AM > *Subject:* Re: [SIESTA-L] restarting a job > > Thanks for your reply. In my way, I just want to restart the job at > special point (not the end of the MD run). So I need the .DM, .XV (easy to > get it) and .MD file to restart it. So how do I get the .DM and .MD file at > special time point? Thanks > > Ting > > 2015-02-02 2:52 GMT-06:00 Chih-Chien Wang <[email protected]>: > >> According to the webpage, it seems to me that MD file would only have >> the coordinate and velocity of atoms. And since .MD is unformatted, one >> might consider to use fortran/C to convert the MD file. Is velocity very >> important in this case? If not, there are much easier ways to get around >> with only atomic coordinates. >> >> Chih-Chien Wang >> Research Assistance >> Institute of Atomic and Molecular Science, >> Academia Sinica, Taipei, Taiwan >> [email protected] >> >> ----- Original Message ----- >> *From:* Ting Zheng <[email protected]> >> *To:* [email protected] >> *Sent:* Sunday, February 01, 2015 4:29 AM >> *Subject:* [SIESTA-L] restarting a job >> >> Dear siesta users, >> >> I have a problem with restarting a job. As known to all, we need .XV, >> .DM, .MD files to restart a siesta MD job. It seems that the .MD file seems >> to have all the messages during the whole Molecular dynamics procedure >> since the size of that file just increasing all the time. But know I have a >> special problem that I have to restart the job from a point which is not >> the final one. Let me free my question as an example. >> >> If I have conducted a molecular dynamics job that lasted 1000 steps. >> After analyzing the data, I want to rerun the job from s special point, say >> step=500. >> >> I can make the special XV file from the out file, but how should I make >> the special MD file which start at step=500? >> >> Thanks >> Ting >> >> > -- Your Sincerely Shiba Subedi Central Department of Physics, Tribhuvan University Kathmandu, Nepal
