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From: | martina pannuzzo |
Subject: | Re: [ESPResSo] mbtools |
Date: | Thu, 26 Mar 2009 18:46:06 +0100 |
sorry... > Date: Thu, 26 Mar 2009 12:35:24 -0400 > Subject: RE: [ESPResSo] mbtools > From: address@hidden > To: address@hidden > CC: address@hidden > > Dear Martina, > > Could you provide your config.log file in your next message, in order to check that fftw was properly included in ESPResSo? > Also, can you start Espresso_bin and type in the command line: > code_info > you should get something like this: > > ESPResSo: 2.1.1q, Last Change: January 12th, 2009 > { Compilation status { MPI generic } { FFTW3 } { MODES } { PARTIAL_PERIODIC } > ... > > Does "{ MODES }" show up in the output? > > Best, > > Tristan > > > > > > > Dear Tristan, > > > > i installed FFTW, recompiled Espresso, but untill now i have the same > > problem. > > > > i installed fftw .3.2.1 on an ubuntu pc ..... > > > > please someone could help me? thanks > > > > > > CC: address@hidden From: address@hidden To: > > address@hidden 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: > > > > Dear all, i started, succesfully, all scripts in the samples folder of > > Espresso. Now i am trying to use the mbtools scripts, in particular i'm > > interested in the simplebilayer.tcl; but when i start the script i, > > allways, obtain an error message and the job crash: The operation > > "set_bilayer" you requested is not implemented. > > > > Curiously in the ug of Espresso at page 71, appear a box in the right > > side indicating a lot of not implemented command. > > > > can someone help me in launching such script? > > > > cheers Martina > > > > > > > > Chiavette USB. addio! Attiva SkyDrive! > > _______________________________________________ ESPResSo mailing list > > address@hidden > > https://fias.uni-frankfurt.de/mailman/listinfo/espresso > > > > > > _________________________________________________________________ 25 GB di > > spazio gratis online: attiva SkyDrive! > > http://clk.atdmt.com/GBL/go/136430529/direct/01/ > Chiavette USB. addio! Attiva SkyDrive! |
config.log
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