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Re: [ESPResSo] mbtools

From: martina pannuzzo
Subject: Re: [ESPResSo] mbtools
Date: Thu, 26 Mar 2009 16:58:11 +0100

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?

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!



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?

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