Hi,<div><br></div><div>You don't need to do any of this manually. You can use AnalysisDataPlotModule to create the output, which will write the output on-the-fly, without extra memory requirements. Similarly, you can compute the average and std.dev. using an AnalysisDataAverage module without coding any of that explicitly. Both of these also make them <span></span>work with the future plans for parallelization without any changes. Can't say much more without seeing the rest of the code, but hopefully this helps.</div>
<div><br></div><div>Best regards,</div>Teemu<br><div><br>torstai, 28. maaliskuuta 2013 David van der Spoel kirjoitti:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I'm working my way through the documentation trying to find out some stuff needed to finish my new analysis tool, to compute the free volume in a box. Most of it works, but when trying to get a time series I am apparently missing something.<br>
<br>
My final writing routine looks like:<br>
<br>
Freevolume::writeOutput()<br>
{<br>
AnalysisDataFrameRef ref;<br>
FILE *fp;<br>
int i;<br>
double faver = fractot_/nframes_;<br>
double fsigma = sqrt(frac2tot_/nframes_-faver*<u></u>faver);<br>
printf("Free volume %.2f +/- %.2f %%\n",100*faver,100*fsigma);<br>
printf("Number of frames %d\n",data_.frameCount());<br>
fp = fopen("koko.xvg","w");<br>
for(i=0; (i<data_.frameCount()); i++)<br>
{<br>
ref = data_.getDataFrame(i);<br>
fprintf(fp,"%g %g\n",ref.x(),ref.y(0));<br>
}<br>
fclose(fp);<br>
}<br>
<br>
however, despite frameCount() yielding 101 frames, getDataFrame() fails with an API error. I suspect that either I have selected the wrong data type for storing the numbers (<u></u>AnalysisDataFrameAverageModule<u></u>) or I have to call a routine to actually get storage for frames (bool gmx::AbstractAnalysisData::<u></u>requestStorage)<br>
<br>
Any clues?<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a>spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
-- <br>
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</blockquote></div><br><br>-- <br>Teemu Murtola<br><<a href="mailto:teemu.murtola@iki.fi" target="_blank">teemu.murtola@iki.fi</a>><br>+358 50 362 6829<br>