Re: TCL force

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Tue Sep 23 2008 - 00:43:52 CDT

Hi, peter:

     Thanks a lot for your response.
     " set force [exec "./fortran_force $variable"] ", this is what I
was doing. sorry for the typo.
     Now I think the problem is: while I was trying to run NAMD with
my script in serial, everything is fine. But for parallel running, I
always got segmentation violation. Do you have any idea about why?
     Thanks a lot.

Bin

On Sep 22, 2008, at 10:37 PM, Peter Freddolino wrote:

> Hi Bin,
> you certainly can, but you'd need to do something like
> set force [exec "./fortran_force $variable"]
> ie, properly call an external command from tcl -- you'll want to pay
> careful attention to how exec works. If you're willing to use c/c++
> instead of fortran, you can also use swig to put a tcl wrapper
> around your external force calculation functions, which is something
> I do frequently (one can always make this work in principle by
> writing a tcl wrapper for your force application function, but swig
> makes the process much easier).
> With tclforces you don't need to distribute the executable because
> tclforces only runs on the head node. With tclbc this could be a
> problem if your compute nodes don't have access to the same
> filesystem as node0; you'd need to work around this accordingly.
>
> Peter
>
> BIN ZHANG wrote:
>> Hi, All:
>>
>> I was trying to use the TCL force utility of NAMD to apply some
>> forces on the system. Since the calculation of the force is a
>> little complicated, I don't want to use TCL to calculate it. So my
>> question is : can I write a FORTRAN code and compile it as an
>> executable, then in the calforces procedure, using :
>> set force [./FORTRAN_force $variable] to get the force?(assuming
>> the FORTRAN_force is an executable compiled from source code).
>>
>> If I want to run NAMD in parallel, do I need to copy the
>> executable to each node explicitly?
>> Thanks a lot in advance.
>>
>> Bin
>>
>>
>>

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