(updated 2003/12/2)
Data structure is simple. It is made of Header and x, y, z coordinates
of each time step. The header includes time step and visualization zone size... pvutil can support several different header format and each format can be saved as ini file. The basic format is following.
[this is the default header type. When you do not 'change header type' follow this format]
Line 1 (3 integers): Molecule type, number of molecules, number of scenes
Line 2 (3 reals): x, y, z coordinate size of visualizaion zone
Line 3 (2 reals): Time of 1st scene, Time-step of scenes
NOTE: Set Molecular type to 1.
For example, c output program can be following.
fprintf(fpos,"1 %d %d\n", nmol,nrep/nwrite);
fprintf(fpos,"%lf %lf %lf\n", vlx*1.0e10,vly*1.0e10,vlz*1.0e10);
fprintf(fpos,"%lf %lf\n", stime,
dt*1.0e12*nwrite);
nmol: number of molecules, nrep: number of MD steps, nwrite:
output interval of scenes
vlx, vly, vlz: size of calculation domain (m)
NOTE: x, y, z data coordinates should be in the range of (0-vlx),
(0-vly), (0-vlz)
stime: time of 1st scene (normally 0), dt: MD time step
Coordinate data are simply x, y, z data of scene 1, scene 2,...
Line 1 (3 reals): x, y, z coordinate of Scene 1 and Atom 1
Line 2 (3 reals): x, y, z coordinate of Scene 1 and Atom 2
Line 3 (3 reals): x, y, z coordinate of Scene 1 and Atom 3
.....
Line nmol (3 reals): x, y, z coordinate of Scene 1 and Atom nmol
Line nmol+1 (3 reals): x, y, z coordinate of Scene 2 and Atom 1
Line nmol+2 (3 reals): x, y, z coordinate of Scene 2 and Atom 2
Line nmol+3 (3 reals): x, y, z coordinate of Scene 2 and Atom 3
.....
.....
Line nmol*nscene (3 reals): x, y, z coordinate of Scene nscene and Atom nmol
For example with C
for(irep=1; irep<=nrep; irep++){
stime=stime+dt;
Step();
if (irep % nwrite == 0){
for(i=1; i<=nmol; i++){
fprintf(fpos, "%lf %lf
%lf\n",
x[i]*1.0e10,y[i]*1.0e10,z[i]*1.0e10);
}
}
}
By 'Change header type' buttom, several header types can be selected or created. The original header type can be saved as ini file.
3 examples of ini files are prepared.
kimutatu.ini: similar to default pvutility.ini. But, mask file is used.
See and convert sample data files: kimutatu_pos.dat, mask.dat.
By Drag & Drop kimutatu.ini and these data files to pvutility.exe, you can makekkimutatu_pos.pv
tinoue.ini: example we used for silicon cluster simulation.
RegeonCenter(0,0,0)=true. Calculated coordinates are within (-vlx, vlx), (-vly, vly),(-vlz, vlz). Bonds are drawn for pair of atoms within 3.2A.
See example data files: tinoue_pos.dat and tinoue_pos.pv
yaya.ini: example we used for metal-carbon cluster MD simulations
Metal and carbon clusters are included.BR>
See example data files: yaya_pos.dat and yaya_pos.pv