Re: [ESPResSo] mbtools

[Tristan Bereau]

Dear Martina,

It seems like fftw was well incorporated in ESPResSo. Are you sure your 
'myconfig-sample.h' or 'myconfig.h' file has the MODES feature *uncommented*? 
Again, the line should look like this
#define MODES
recompiling Espresso should activate the MODES feature.

I can't see anything else right now...

Best,

Tristan


> 

> 
> Dear Tristan,
> 
> i send you config.log file;
> 
> When I start Espresso  with the command code_info, it return me : {
> Compilation status { MPI fake } { FFTW3 } { PARTIAL_PERIODIC } {
> ELECTROSTATICS } { ROTATION } { MASS } { EXTERNAL_FORCES } { CONSTRAINTS
> } { EXCLUSIONS } { COMFORCE } { COMFIXED } { TABULATED } { LENNARD_JONES
> } { LENNARD_JONES_GENERIC } { MORSE } { BUCKINGHAM } { SOFT_SPHERE } {
> LJCOS } { LJCOS2 } { BOND_ANGLE_COSINE } { NPT } } { Debug status {
> MPI_CORE FORCE_CORE } }
> 
> 
> 
> 
> what's wrong!?
> 
> yor are very gentle;
> 
> Martina
> 
> 
>> 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/
>> 
> 
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