From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Tue Jan 26 2010 - 01:32:50 CST
Thanks a lot for your reply. Now everything makes more sense to me.
> There is a fix coming up on CVS to solve this issue entirely,
> together with several other bugfixes.
For my purpose, the code you posted should be enough for now. I'm only
using the simple harmonic bias.
But could you be a little bit more specific about these bugfixes? I'm
planning on using the colvar module to run some productive long
trajectories, and would like to know whether they are going to affect
my result or not.
> In the meantime, depending on what you're doing, you can try by
> replacing the function colvarmodule::finalise() at line 499 of
> colvarmodule.C with what follows.
> void colvarmodule::finalise()
> std::string const out_name =
> (output_prefix.size() ?
> std::string (output_prefix+".colvars.state") :
> std::string ("colvars.state"));
> cvm::log ("Saving collective variables state to \""+out_name+"\".
> proxy->backup_file (out_name.c_str());
> std::ofstream out (out_name.c_str());
> out.setf (std::ios::scientific, std::ios::floatfield);
> this->write_restart (out);
> This function (as opposed to the one you currently have) will write
> the state file, synchronize the buffer of the trajectory file, but
> not deallocate anything.
> This fix will work assuming that you don't need output files written
> by the bias (such as the ".pmf" files written by ABF and
> metadynamics) at the end of each "run" statement. If you do need
> them, then I can send you all the updated sources privately.
> ---- ----
> Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science
> Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> work phone: (+1)-215-204-4216
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_at_gmail.com
> ---- ----
> On Mon, Jan 25, 2010 at 4:09 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
> Dear All:
> I have experienced an interesting behavior of the colvar module. It
> seems to me that this module does not work properly with the command
> "run". Say, if I have the following in my config file
> run 100
> output ./folder/outfile
> run 100
> Then the colvar module will be only initialized correctly in the
> first 100 step. For the next 100 steps, no collective variables are
> written in either the traj, or state file. It seems the colvar
> definition are completely uninitialized. This won't cause too much
> problem, but if you happen to know how to fix it, I would be very
> happy to listen.
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