Writing custom fix to apply tangential force on a 'bead-spring' polymer

LAMMPS LAMMPS Development
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1

Hello,
I am trying to write a custom fix that calculates unit tangent vector for every interior bead in a linear polymer. The tangent on ith bead is defined as r[i+1] - r[i-1]. The force thus calculated should be added to the main force array in POST_FORCE.
The fix takes three arguments, fp = magnitude of the tagential force, t_start = timestep when application of tangential force is started, t_stop = the force is stopped. Something likefix ID group-ID tanactiveforce fp t_start t_stop. Here is a snippet from the fix -

void FixTanactiveforce::post_force(int vflag)
{
  bigint step = update->ntimestep; 
  if (step < t_start || step > t_stop) return;//runs fix b/w t_start and t_stop

  double **x = atom->x;
  double **f = atom->f;
  int *mask  = atom->mask;

  int **bond_atom = atom->bond_atom;
  int *num_bond   = atom->num_bond;

  int nlocal = atom->nlocal;

  for (int i = 0; i < nlocal; i++) {
    // Apply only to group atoms and atoms with 2 bonds (skips beads at ends)
    if ((mask[i] & groupbit) && num_bond[i]==2) {

      int la = atom->map(bond_atom[i][0]);
      int lb = atom->map(bond_atom[i][1]);
      if (la == -1 || lb == -1) continue; // neighbor not on this proc

      // Tangent vector = pos(a) - pos(b)
      double t[3];
      t[0] = x[la][0] - x[lb][0];
      t[1] = x[la][1] - x[lb][1];
      t[2] = x[la][2] - x[lb][2];

      double mag = sqrt(t[0]*t[0] + t[1]*t[1] + t[2]*t[2]);
      if (mag > 0.0) {
        t[0] /= mag;
        t[1] /= mag;
        t[2] /= mag;
        }

      //printf("Step %lld: Atom %d, Tangent = (%g, %g, %g), Mag = %g\n", update->ntimestep, i, t[0], t[1], t[2], mag);
      // Add tangential force to this bead
      f[i][0] += fp * t[0];
      f[i][1] += fp * t[1];
      f[i][2] += fp * t[2];
    }
  }
}

The problem is that I am not seeing the effects of active force in the animation. I have confirmed that the fix is being compiled. I am using atom_style angle
Below is a portion of my script.

fix 1 all langevin 1.0 1.5 1.0 904297
fix 2 all tanactiveforce 10.0 1 5000
fix 3 all nve

timestep 0.005

thermo 500
thermo_style custom step

dump 1 all custom 50 dump.polymer3d.lammpstrj.cusfix.100b.5fp id type xu yu zu

run 5000

I am following the LAMMPS developer guide and this project for reference.

2

Visualization is a very insensitive and indirect way of monitoring the impact of changes made to the code. It is at best qualitative.

Why not just create some simple test inputs and use regular debugging tools or simply adding print statements to check on whether the code is doing what it is supposed to do and computing the exact force that it is supposed to compute and apply?

3

Hello, thank you for your input.
I was able to find this repository with a fix that uses neighbour->anglelist to apply tangential force.