Hello everybody,
i am using lammps version of 24th december and trying to save atom coordinates when a condition is met and then reset the coordiantes after another condition is met at a specific timestep (only minimization is done here). I am able to store my coordinates by using a fix which adds the coordinates of the atoms to an array:
void own::addState(int currstate)
{
fix_s->add_vector(7);
double *x0;
x0 = fix_s->request_vector(currstate);
double **x = atom->x;
int *tag = atom->tag;
int *type = atom->type;
int *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = 0;
for (int i = 0; i < nlocal; i++){
x0[n] = x[i][0];
x0[n+1] = x[i][1];
x0[n+2] = x[i][2];
x0[n+3] = tag[i];
x0[n+4] = type[i];
x0[n+5] = image[i];
x0[n+6] = mask[i];
n += 7;
}
}
The problem is in MPI when i want to reset my coordinates to a specific timestep i am losing atoms:
void own::back()
{
double *x0;
x0 = fix_s->request_vector(0); // get coordinates for timestep (here 0)
double **x = atom->x;
int nlocal = atom->nlocal;
int *tag = atom->tag;
int *type = atom->type;
int *image = atom->image;
int *mask = atom->mask;
int n = 0;
int triclinic = domain->triclinic;
for (int i = 0; i < nlocal; i++){
x[i][0] = x0[n];
x[i][1] = x0[n+1];
x[i][2] = x0[n+2];
tag[i] = x0[n+3];
type[i] = x0[n+4];
image[i] = x0[n+5];
mask[i] = x0[n+6];
n += 7;
}
output->write_dump(update->ntimestep);
atom->setup();
modify->setup_pre_exchange();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
domain->image_check();
domain->box_too_small_check();
modify->setup_pre_neighbor();
neighbor->build(1);
modify->setup_post_neighbor();
neighbor->ncalls = 0;
}
Now i do understand the issue but how can i solve my problem ? Do i need to add a fix where the atom exchange between the processors happens ? I could not find a fix which does a similar thing.
Best regards