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Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding

From: Arash Azari
Subject: Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding
Date: Wed, 3 Apr 2013 09:19:03 -0700 (PDT)

Dear Axel,

Thank you very much for your reply.
Yes, you are right; the collision_detection is a typo. 
I used the “analyze energy” to get
the energy of the bond angle potential. 
Do you think that the energy analyzing
(bond_angle) works fine in this case? Or the output for energy is not
correct (due to the bug that you mentioned). 
Thank you very much,

Best regards,
Arash Azari

----- Original Message -----
From: Axel Arnold <address@hidden>
To: Arash Azari <address@hidden>; address@hidden; Rudolf Weeber <address@hidden>
Sent: Wednesday, April 3, 2013 3:29 PM
Subject: Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic bonding


There is a mistake in the UG, it should be "on_collision", not 

@ Rudolf, can you please fix that bug in the docu asap?

The BOND_ANGLE output is indeed a bug, will be fixed. That screws up 
writing of interactions, so it can be a problem.


On 04/03/2013 03:14 PM, Arash Azari wrote:
> Dear Rudolf,
> Thank you very much for your reply. I
> checked “myconfig.h” file (location and features) and the “code_info” output 
> and
> everything is fine; all the required features are available in
> the ESPResSo, but still I have the same problems: unknown interaction for
> bond angle and “invalid command name "collision_detection"
> “ for dynamic bonding.
> I highly appreciate any suggestion or
> recommendation.
> Thank you very much,
> Best regards,
> Arash
> Arash Azari
> ----- Original Message -----
> From: Rudolf Weeber <address@hidden>
> To: Arash Azari <address@hidden>
> Cc: "address@hidden" <address@hidden>
> Sent: Monday, April 1, 2013 6:08 PM
> Subject: Re: [ESPResSo-users] BOND_ANGLE, restarting simulation, dynamic 
> bonding
> Hi,
> On Mon, Apr 01, 2013 at 08:26:19AM -0700, Arash Azari wrote:
>> I am using the nightly build of
>> - I compiled it with the BOND_ANGLE
>>      option, but inter command output recognizes all the bond angle
>>      potentials as an “unknown”. I thought it is not very important
>>      because simulation looks fine in terms of the bond angle potential
>>      behaviour. The problem is that when I am using the blockfile to
>>      create an output file, ESPResSo cannot recognize the interaction
>>      type (defined as an unknown in output file). Is it a bug?
>> -I compiled the ESPResSo with the
>>      to use the dynamic bonding, but I receive the “invalid command
>>      name "collision_detection" “ error message? I used
>>      single CPU to run this dynamic bonding simulation. Could you please
>>      point out my mistake?
> One possible reason might be, that your myconfig.h was not in the directory 
> from which you executed the configure script, and you did not specify the 
> path to myconfig.h explicitly when calling configure.
> In that case, the features mentioned above might not actually be compiled in.
> To find out, what really was compiled in, call
> code_info
> from within Espresso.
>> - Is it possible to manually delete
>>      all or some of the the bonds which are created during the dynamic
>>      bonding simulation? I mean when we restart the simulation not during
>>      the same simulation.
> That's a bit tricky, because you don't only need to remove the bond (via the 
> part command), but also the two virtual sites.
> To do it, you would have to write a loop which goes over all particles and 
> locates the virtual sites related to the particles you want to separate.
> 1. Delete the bond between the two non-virtual particles you want to separate
> 2. Loop over all particles and for each particle
>    check whether it is a virtual site and it is related to one of the 
>particles you want to separate.
>    If this is the case, delete the virtual site (using the "part delete" 
> When you do this separation, make sure that the collision_detection is turned 
> off. Otherwise, the particles will be bound again in the next time step.
> Hope that helps!
> Regards, Rudolf

JP Dr. Axel Arnold
ICP, Universität Stuttgart
Pfaffenwaldring 27
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609

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