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Adding Steve's edits in documenation + associated changes in files

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This commit is contained in:
Joel Thomas Clemmer
2021-12-03 16:12:31 -07:00
parent 7113334f99
commit 40258f8b9a
33 changed files with 745 additions and 732 deletions
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59
src/MISC/pair_tracker.cpp
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@ -44,7 +44,7 @@ PairTracker::PairTracker(LAMMPS *lmp) :
neighprev = 0;
history = 1;
size_history = 4;
size_history = 3;
nondefault_history_transfer = 1;
finitecutflag = 0;
@ -96,7 +96,7 @@ PairTracker::~PairTracker()
void PairTracker::compute(int eflag, int vflag)
{
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, time;
double xtmp, ytmp, ztmp, delx, dely, delz;
double radi, radj, radsum, rsq, r;
int *ilist, *jlist, *numneigh, **firstneigh;
int *touch, **firsttouch;
@ -152,23 +152,20 @@ void PairTracker::compute(int eflag, int vflag)
}
touch[jj] = 0;
data[0] = 0.0; // initial time
data[1] = 0.0; // initial timestep
data[2] = 0.0; // sum of r, may overflow
data[3] = 0.0; // min of r
data[0] = 0.0; // initial timestep
data[1] = 0.0; // sum of r, may be inaccurate over long times
data[2] = 0.0; // min of r
} else {
data = &alldata[size_history * jj];
if (touch[jj] == 0) {
time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
data[0] = time;
data[1] = (double) update->ntimestep;
data[0] = (double) update->ntimestep;
data[1] = r;
data[2] = r;
data[3] = r;
} else if (updateflag) {
data[2] += r;
if (data[3] > r) data[3] = r;
data[1] += r;
if (data[2] > r) data[2] = r;
}
touch[jj] = 1;
}
@ -182,23 +179,20 @@ void PairTracker::compute(int eflag, int vflag)
}
touch[jj] = 0;
data[0] = 0.0; // initial time
data[1] = 0.0; // initial timestep
data[2] = 0.0; // sum of r, may overflow
data[3] = 0.0; // min of r
data[0] = 0.0; // initial timestep
data[1] = 0.0; // sum of r, may be inaccurate over long times
data[2] = 0.0; // min of r
} else {
data = &alldata[size_history * jj];
if (touch[jj] == 0) {
time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
data[0] = time;
data[1] = (double) update->ntimestep;
data[0] = (double) update->ntimestep;
data[1] = r;
data[2] = r;
data[3] = r;
} else if (updateflag) {
data[2] += r;
if (data[3] > r) data[3] = r;
data[1] += r;
if (data[2] > r) data[2] = r;
}
touch[jj] = 1;
}
@ -570,9 +564,7 @@ double PairTracker::radii2cut(double r1, double r2)
void PairTracker::process_data(int i, int j, double * input_data)
{
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
int time_initial = (int) input_data[0];
if ((time - time_initial) < tmin) return;
if ((update->ntimestep - input_data[0]) < tmin) return;
if (type_filter) {
int *type = atom->type;
@ -590,25 +582,21 @@ void PairTracker::process_data(int i, int j, double * input_data)
void PairTracker::pack_time_created(int n, int i, int j, double * data)
{
double time_initial = data[0];
output_data[n] = time_initial;
output_data[n] = data[0];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_time_broken(int n, int i, int j, double * data)
{
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
output_data[n] = time;
output_data[n] = update->ntimestep;
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_time_total(int n, int i, int j, double * data)
{
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
double time_initial = data[0];
output_data[n] = time - time_initial;
output_data[n] = update->ntimestep - data[0];
}
/* ---------------------------------------------------------------------- */
@ -655,15 +643,12 @@ void PairTracker::pack_z(int n, int i, int j, double * data)
void PairTracker::pack_rmin(int n, int i, int j, double * data)
{
double rmin = data[3];
output_data[n] = rmin;
output_data[n] = data[2];
}
/* ---------------------------------------------------------------------- */
void PairTracker::pack_rave(int n, int i, int j, double * data)
{
double rsum = data[2];
double nstep_initial = data[1];
output_data[n] = rsum / (update->ntimestep - nstep_initial);
output_data[n] = data[1] / (update->ntimestep - data[0]);
}