Re: [ESPResSo] mbtools

[martina pannuzzo]

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
> >
> >
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>

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Chiavette USB. addio! Attiva SkyDrive!

config.log
Description: Binary data