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| From: | Tristan Bereau |
| Subject: | Re: [ESPResSo] mbtools |
| Date: | Thu, 26 Mar 2009 08:05:29 -0400 |
| Dear Martina, As far as I know, the set_bilayer routine creates a 2d grid in order to prepare for a modes analysis (which will be called in simplebilayer.tcl when reaching the line 'lappend analysis_flags fluctuations'). It's useful for different things, one of them being the fourier spectrum of fluctuations of your bilayer. * Easy answer #1: if you have 'fftw' on your system (calculates fast fourier transform): look into the $ESPRESSO/obj-XXX/config.log file where you can check whether Espresso had successfully found a working version of fftw on your system. Then recompile Espresso after uncommenting the following line in $ESPRESSO/myconfig-sample.h (or $ESPRESSO/myconfig.h if you have one): #define MODES * Easy answer #2: if you don't have 'fftw' and don't want to install it now: you can do a little hack by removing the command to 'set_bilayer'. This will prevent setting up the 2d grid in order to do FFTs. Here's what to do: go to $ESPRESSO/packages/mbtools/analysis/analysis.tcl look for the 'set_bilayer' command, and comment the line. HOWEVER, there will obviously be some analysis features in mbtools that will crash - because they use FFTs! As you might have discovered, analysis features are turned on/off in the simulation parameter script, aka simplebilayer.tcl. At the end of that file, you'll have to get rid of all of these analysis features: - orient_order - flipflop - stray - fluctuations - density profile These are usually placed at the end of the file, called by appending the analysis_flags variable. Hope this helps! Best, Tristan On Mar 26, 2009, at 7:30 AM, martina pannuzzo wrote: |
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