On 27/07/2012 7:14 PM, prithvi raj pandey wrote:
Message: 2
Date: Thu, 26 Jul 2012 20:56:00 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Writing velocity of particles using
template.c
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <50112240.5000...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 26/07/2012 8:22 PM, prithvi raj pandey wrote:
Dear gmx users,
I am using template.c of gromacs 4.0.7 for writing my own analysis
tool. When I am using the fr.x[i][XX], it writes the coordinates of
the particles (i crosschecked it with the coordinates written by the
trjconv command). But the problem arises when I use fr.v[i][XX] for
writing the velocities of the particles or fr.f[i][XX] for writing the
force. The program compiles fine by using make command. But finally
the template stops showing segmentation fault. The main loop is as
follows -
do {
fprintf(fp,"BOX %f %f %f %f
\n",fr.time,fr.box[XX][XX],fr.box[YY][YY],fr.box[ZZ][ZZ]);
for (i=0; i<top.atoms.nr; i++)
{
fprintf(fp,"Velocity at t=%8.3f : %f %f
%f\n",fr.time,fr.v[i][XX],fr.v[i][YY],fr.v[i][ZZ]);
}
} while(read_next_frame(status,&fr));
Am I using the variable used for writing velocity/force wrongly?
Did you verify that the trajectory has velocities, and that you read
them, and that they're found in fr.v? Look at the code for a tool that
reads velocities (g_velacc, I guess).
Mark
Dear Mark,
I ran the g_velacc command, it works fine and writes the output .xvg
file. Also i generated a .gro containing both positions and velocity
using the trjconv command.
By this time I could wirte the velocity using template.c by changing
TRX_READ_X toTRX_READ_V and by adding *vtop in rvec in the following
section of template.c
t_topology top;
int ePBC;
char title[STRLEN];
t_trxframe fr;
rvec *xtop,*vtop;
matrix box;
int status;
int flags = TRX_READ_V;
But the problem now is it only writes velocity using the variable
fr.v[i][XX], but the coordinates are not being written by the variable
fr.x[i][XX]. I intend to use both coordinates and velocity for my
program.
It seems to that the "flags =" can only take one value. This is
because I tried to write both TRX_READ_X and TRX_READ_V under the same
flags variable, but it did not compile.
If you'd looked up the header file where these are defined, or grepped
the source code for how they are used (if you're in a git tree, git grep
makes this easy!), you might have seen that they are designed to be
combined with a bitwise-or.
Mark
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