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This commit is contained in:
Axel Kohlmeyer
2021-06-04 00:43:45 -04:00
parent edf734ed59
commit d17b49a894
4 changed files with 272 additions and 292 deletions
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243
src/MISC/fix_pair_tracker.cpp
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@ -31,92 +31,88 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixPairTracker::FixPairTracker(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
nvalues(0),
array(NULL), vector(NULL), pack_choice(NULL)
Fix(lmp, narg, arg), nvalues(0), array(NULL), vector(NULL), pack_choice(NULL)
{
if (narg < 3) error->all(FLERR,"Illegal fix pair/tracker command");
if (narg < 3) error->all(FLERR, "Illegal fix pair/tracker command");
local_flag = 1;
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix pair/tracker command");
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
if (nevery <= 0) error->all(FLERR, "Illegal fix pair/tracker command");
local_freq = nevery;
// If optional arguments included, this will be oversized
nvalues = narg - 4;
nvalues = narg - 4;
pack_choice = new FnPtrPack[nvalues];
tmin = -1;
type_filter = nullptr;
type_filter = nullptr;
int iarg = 4;
nvalues = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"id1") == 0) {
if (strcmp(arg[iarg], "id1") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_id1;
} else if (strcmp(arg[iarg],"id2") == 0) {
} else if (strcmp(arg[iarg], "id2") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_id2;
} else if (strcmp(arg[iarg],"time/created") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_time_created;
} else if (strcmp(arg[iarg],"time/broken") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_time_broken;
} else if (strcmp(arg[iarg],"time/total") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_time_total;
} else if (strcmp(arg[iarg],"x") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_x;
} else if (strcmp(arg[iarg],"y") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_y;
} else if (strcmp(arg[iarg],"z") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_z;
} else if (strcmp(arg[iarg],"r/min") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_rmin;
} else if (strcmp(arg[iarg],"r/ave") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_rave;
} else if (strcmp(arg[iarg],"time/min") == 0) {
} else if (strcmp(arg[iarg], "time/created") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_time_created;
} else if (strcmp(arg[iarg], "time/broken") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_time_broken;
} else if (strcmp(arg[iarg], "time/total") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_time_total;
} else if (strcmp(arg[iarg], "x") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_x;
} else if (strcmp(arg[iarg], "y") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_y;
} else if (strcmp(arg[iarg], "z") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_z;
} else if (strcmp(arg[iarg], "r/min") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_rmin;
} else if (strcmp(arg[iarg], "r/ave") == 0) {
pack_choice[nvalues++] = &FixPairTracker::pack_rave;
} else if (strcmp(arg[iarg], "time/min") == 0) {
if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in fix pair/tracker command");
tmin = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg ++;
} else if (strcmp(arg[iarg],"type/include") == 0) {
tmin = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg++;
} else if (strcmp(arg[iarg], "type/include") == 0) {
if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in fix pair/tracker command");
int ntypes = atom->ntypes;
int i, j, itype, jtype, in, jn, infield, jnfield;
int inlo, inhi, jnlo, jnhi;
char *istr, *jstr;
if (! type_filter) {
memory->create(type_filter,ntypes+1,ntypes+1,"fix/pair/tracker:type_filter");
if (!type_filter) {
memory->create(type_filter, ntypes + 1, ntypes + 1, "fix/pair/tracker:type_filter");
for (i = 0; i <= ntypes; i ++) {
for (j = 0; j <= ntypes; j ++) {
type_filter[i][j] = 0;
}
for (i = 0; i <= ntypes; i++) {
for (j = 0; j <= ntypes; j++) { type_filter[i][j] = 0; }
}
}
in = strlen(arg[iarg+1]) + 1;
in = strlen(arg[iarg + 1]) + 1;
istr = new char[in];
strcpy(istr,arg[iarg+1]);
strcpy(istr, arg[iarg + 1]);
std::vector<std::string> iwords = Tokenizer(istr, ",").as_vector();
infield = iwords.size();
jn = strlen(arg[iarg+2]) + 1;
jn = strlen(arg[iarg + 2]) + 1;
jstr = new char[jn];
strcpy(jstr,arg[iarg+2]);
strcpy(jstr, arg[iarg + 2]);
std::vector<std::string> jwords = Tokenizer(jstr, ",").as_vector();
jnfield = jwords.size();
for (i = 0; i < infield; i++) {
const char * ifield = iwords[i].c_str();
utils::bounds(FLERR,ifield,1,ntypes,inlo,inhi,error);
const char *ifield = iwords[i].c_str();
utils::bounds(FLERR, ifield, 1, ntypes, inlo, inhi, error);
for (j = 0; j < jnfield; j++) {
const char * jfield = jwords[j].c_str();
utils::bounds(FLERR,jfield,1,ntypes,jnlo,jnhi,error);
const char *jfield = jwords[j].c_str();
utils::bounds(FLERR, jfield, 1, ntypes, jnlo, jnhi, error);
for (itype = inlo; itype <= inhi; itype++) {
for (jtype = jnlo; jtype <= jnhi; jtype++) {
type_filter[itype][jtype] = 1;
@ -126,18 +122,21 @@ FixPairTracker::FixPairTracker(LAMMPS *lmp, int narg, char **arg) :
}
}
delete [] istr;
delete [] jstr;
delete[] istr;
delete[] jstr;
iarg += 2;
} else error->all(FLERR, "Invalid keyword in fix pair/tracker command");
iarg ++;
} else
error->all(FLERR, "Invalid keyword in fix pair/tracker command");
iarg++;
}
if (nvalues == 1) size_local_cols = 0;
else size_local_cols = nvalues;
if (nvalues == 1)
size_local_cols = 0;
else
size_local_cols = nvalues;
nmax = 0;
ncount = 0;
@ -148,10 +147,10 @@ FixPairTracker::FixPairTracker(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
FixPairTracker::~FixPairTracker()
{
delete [] pack_choice;
{
delete[] pack_choice;
memory->destroy(vector);
memory->destroy(vector);
memory->destroy(array);
memory->destroy(type_filter);
}
@ -171,75 +170,72 @@ void FixPairTracker::init()
{
// Set size of array/vector
ncount = 0;
if (ncount > nmax)
reallocate(ncount);
if (ncount > nmax) reallocate(ncount);
size_local_rows = ncount;
}
/* ---------------------------------------------------------------------- */
void FixPairTracker::lost_contact(int i, int j, double time_tmp, double nstep_tmp, double rsum_tmp, double rmin_tmp)
{
double time = update->atime + (update->ntimestep-update->atimestep)*update->dt;
if ((time-time_tmp) < tmin) return;
void FixPairTracker::lost_contact(int i, int j, double time_tmp, double nstep_tmp, double rsum_tmp,
double rmin_tmp)
{
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
if ((time - time_tmp) < tmin) return;
if (type_filter) {
int *type = atom->type;
if (type_filter[type[i]][type[j]] == 0) return;
if (type_filter[type[i]][type[j]] == 0) return;
}
int *mask = atom->mask;
if (!(mask[i] & groupbit)) return;
if (!(mask[j] & groupbit)) return;
if (ncount == nmax) reallocate(ncount);
index_i = i;
index_j = j;
rmin = rmin_tmp;
rsum = rsum_tmp;
time_initial = time_tmp;
nstep_initial = nstep_tmp;
// fill vector or array with local values
if (nvalues == 1) {
(this->*pack_choice[0])(0);
} else {
for (int k = 0; k < nvalues; k++) {
(this->*pack_choice[k])(k);
}
}
ncount += 1;
for (int k = 0; k < nvalues; k++) { (this->*pack_choice[k])(k); }
}
ncount += 1;
}
/* ---------------------------------------------------------------------- */
void FixPairTracker::post_force(int /*vflag*/)
{
void FixPairTracker::post_force(int /*vflag*/)
{
if (update->ntimestep % nevery == 0) {
size_local_rows = ncount;
ncount = 0;
ncount = 0;
}
}
/* ---------------------------------------------------------------------- */
void FixPairTracker::reallocate(int n)
{
// grow vector or array
// grow vector or array
while (nmax <= n) nmax += DELTA;
if (nvalues == 1) {
memory->grow(vector,nmax,"fix_pair_tracker:vector");
memory->grow(vector, nmax, "fix_pair_tracker:vector");
vector_local = vector;
} else {
memory->grow(array,nmax,nvalues,"fix_pair_tracker:array");
memory->grow(array, nmax, nvalues, "fix_pair_tracker:array");
array_local = array;
}
}
@ -250,8 +246,8 @@ void FixPairTracker::reallocate(int n)
double FixPairTracker::memory_usage()
{
double bytes = nmax*nvalues * sizeof(double);
bytes += nmax*2 * sizeof(int);
double bytes = nmax * nvalues * sizeof(double);
bytes += nmax * 2 * sizeof(int);
return bytes;
}
@ -262,7 +258,7 @@ double FixPairTracker::memory_usage()
/* ---------------------------------------------------------------------- */
void FixPairTracker::pack_time_created(int n)
void FixPairTracker::pack_time_created(int n)
{
if (nvalues == 1)
vector[ncount] = time_initial;
@ -272,9 +268,9 @@ void FixPairTracker::pack_time_created(int n)
/* ---------------------------------------------------------------------- */
void FixPairTracker::pack_time_broken(int n)
void FixPairTracker::pack_time_broken(int n)
{
double time = update->atime + (update->ntimestep-update->atimestep)*update->dt;
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
if (nvalues == 1)
vector[ncount] = time;
else
@ -283,22 +279,21 @@ void FixPairTracker::pack_time_broken(int n)
/* ---------------------------------------------------------------------- */
void FixPairTracker::pack_time_total(int n)
void FixPairTracker::pack_time_total(int n)
{
double time = update->atime + (update->ntimestep-update->atimestep)*update->dt;
double time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
if (nvalues == 1)
vector[ncount] = time-time_initial;
vector[ncount] = time - time_initial;
else
array[ncount][n] = time-time_initial;
array[ncount][n] = time - time_initial;
}
/* ---------------------------------------------------------------------- */
void FixPairTracker::pack_id1(int n)
void FixPairTracker::pack_id1(int n)
{
tagint *tag = atom->tag;
if (nvalues == 1)
vector[ncount] = tag[index_i];
else
@ -321,38 +316,36 @@ void FixPairTracker::pack_id2(int n)
void FixPairTracker::pack_x(int n)
{
double **x = atom->x;
if (nvalues == 1)
vector[ncount] = (x[index_i][0] + x[index_j][0])/2;
else
array[ncount][n] = (x[index_i][0] + x[index_j][0])/2;
}
double **x = atom->x;
if (nvalues == 1)
vector[ncount] = (x[index_i][0] + x[index_j][0]) / 2;
else
array[ncount][n] = (x[index_i][0] + x[index_j][0]) / 2;
}
/* ---------------------------------------------------------------------- */
void FixPairTracker::pack_y(int n)
{
double **x = atom->x;
if (nvalues == 1)
vector[ncount] = (x[index_i][1] + x[index_j][1])/2;
else
array[ncount][n] = (x[index_i][1] + x[index_j][1])/2;
}
double **x = atom->x;
if (nvalues == 1)
vector[ncount] = (x[index_i][1] + x[index_j][1]) / 2;
else
array[ncount][n] = (x[index_i][1] + x[index_j][1]) / 2;
}
/* ---------------------------------------------------------------------- */
void FixPairTracker::pack_z(int n)
{
double **x = atom->x;
double **x = atom->x;
if (nvalues == 1)
vector[ncount] = (x[index_i][2] + x[index_j][2])/2;
vector[ncount] = (x[index_i][2] + x[index_j][2]) / 2;
else
array[ncount][n] = (x[index_i][2] + x[index_j][2])/2;
array[ncount][n] = (x[index_i][2] + x[index_j][2]) / 2;
}
/* ---------------------------------------------------------------------- */
@ -370,7 +363,7 @@ void FixPairTracker::pack_rmin(int n)
void FixPairTracker::pack_rave(int n)
{
if (nvalues == 1)
vector[ncount] = rsum/(update->ntimestep-nstep_initial);
vector[ncount] = rsum / (update->ntimestep - nstep_initial);
else
array[ncount][n] = rsum/(update->ntimestep-nstep_initial);
array[ncount][n] = rsum / (update->ntimestep - nstep_initial);
}