Re: [ESPResSo] mbtools

[Tristan Bereau]

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
> 
> 
> 
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