ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

apply clang-format

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

264
src/MISC/pair_tracker.cpp
View File

@ -12,6 +12,7 @@
------------------------------------------------------------------------- */
#include "pair_tracker.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
@ -22,9 +23,9 @@
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "update.h"
using namespace LAMMPS_NS;
@ -38,9 +39,9 @@ PairTracker::PairTracker(LAMMPS *lmp) : Pair(lmp)
neighprev = 0;
history = 1;
size_history = 4;
size_history = 4;
nondefault_history_transfer = 1;
finitecutflag = 0;
// create dummy fix as placeholder for FixNeighHistory
@ -48,25 +49,27 @@ PairTracker::PairTracker(LAMMPS *lmp) : Pair(lmp)
fix_history = nullptr;
modify->add_fix("NEIGH_HISTORY_TRACK_DUMMY all DUMMY");
fix_dummy = (FixDummy *) modify->fix[modify->nfix-1];
fix_dummy = (FixDummy *) modify->fix[modify->nfix - 1];
}
/* ---------------------------------------------------------------------- */
PairTracker::~PairTracker()
{
if (!fix_history) modify->delete_fix("NEIGH_HISTORY_TRACK_DUMMY");
else modify->delete_fix("NEIGH_HISTORY_TRACK");
if (!fix_history)
modify->delete_fix("NEIGH_HISTORY_TRACK_DUMMY");
else
modify->delete_fix("NEIGH_HISTORY_TRACK");
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
delete [] onerad_dynamic;
delete [] onerad_frozen;
delete [] maxrad_dynamic;
delete [] maxrad_frozen;
delete[] onerad_dynamic;
delete[] onerad_frozen;
delete[] maxrad_dynamic;
delete[] maxrad_frozen;
}
}
@ -74,16 +77,16 @@ 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 radi,radj,radsum,rsq,r;
int *ilist,*jlist,*numneigh,**firstneigh;
int *touch,**firsttouch;
double *data,*alldata,**firstdata;
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, time;
double radi, radj, radsum, rsq, r;
int *ilist, *jlist, *numneigh, **firstneigh;
int *touch, **firsttouch;
double *data, *alldata, **firstdata;
int updateflag = 1;
if (update->setupflag) updateflag = 0;
ev_init(eflag,vflag);
ev_init(eflag, vflag);
double **x = atom->x;
double *radius = atom->radius;
@ -119,67 +122,67 @@ void PairTracker::compute(int eflag, int vflag)
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
r = sqrt(rsq);
if (finitecutflag) {
radj = radius[j];
radsum = radi + radj;
if (rsq >= radsum*radsum) {
data = &alldata[size_history*jj];
if(touch[jj] == 1) {
if (rsq >= radsum * radsum) {
data = &alldata[size_history * jj];
if (touch[jj] == 1) {
fix_pair_tracker->lost_contact(i, j, data[0], data[1], data[2], data[3]);
}
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
} else {
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 = &alldata[size_history*jj];
} else {
data = &alldata[size_history * jj];
if (touch[jj] == 0) {
time = update->atime + (update->ntimestep-update->atimestep)*update->dt;
time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
data[0] = time;
data[1] = (double) update->ntimestep;
data[2] = r;
data[3] = r;
} else if (updateflag) {
data[2] += r;
if(data[3] > r) data[3] = r;
if (data[3] > r) data[3] = r;
}
touch[jj] = 1;
}
} else {
jtype = type[j];
} else {
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) {
data = &alldata[size_history*jj];
if(touch[jj] == 1) {
data = &alldata[size_history * jj];
if (touch[jj] == 1) {
fix_pair_tracker->lost_contact(i, j, data[0], data[1], data[2], data[3]);
}
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
} else {
data = &alldata[size_history*jj];
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
} else {
data = &alldata[size_history * jj];
if (touch[jj] == 0) {
time = update->atime + (update->ntimestep-update->atimestep)*update->dt;
time = update->atime + (update->ntimestep - update->atimestep) * update->dt;
data[0] = time;
data[1] = (double) update->ntimestep;
data[2] = r;
data[3] = r;
} else if (updateflag) {
data[2] += r;
if(data[3] > r) data[3] = r;
if (data[3] > r) data[3] = r;
}
touch[jj] = 1;
}
@ -197,18 +200,17 @@ void PairTracker::allocate()
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(setflag, n + 1, n + 1, "pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
for (int j = i; j <= n; j++) setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
memory->create(cut, n + 1, n + 1, "pair:cut");
onerad_dynamic = new double[n+1];
onerad_frozen = new double[n+1];
maxrad_dynamic = new double[n+1];
maxrad_frozen = new double[n+1];
onerad_dynamic = new double[n + 1];
onerad_frozen = new double[n + 1];
maxrad_dynamic = new double[n + 1];
maxrad_frozen = new double[n + 1];
}
/* ----------------------------------------------------------------------
@ -217,11 +219,13 @@ void PairTracker::allocate()
void PairTracker::settings(int narg, char **arg)
{
if (narg != 0 && narg != 1) error->all(FLERR,"Illegal pair_style command");
if (narg != 0 && narg != 1) error->all(FLERR, "Illegal pair_style command");
if (narg == 1) {
if (strcmp(arg[0], "finite") == 0) finitecutflag = 1;
else error->all(FLERR,"Illegal pair_style command");
if (strcmp(arg[0], "finite") == 0)
finitecutflag = 1;
else
error->all(FLERR, "Illegal pair_style command");
}
}
@ -231,27 +235,27 @@ void PairTracker::settings(int narg, char **arg)
void PairTracker::coeff(int narg, char **arg)
{
if (narg > 2 && finitecutflag) error->all(FLERR,"Incorrect args for pair coefficients");
if (narg != 3 && !finitecutflag) error->all(FLERR,"Incorrect args for pair coefficients");
if (narg > 2 && finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients");
if (narg != 3 && !finitecutflag) error->all(FLERR, "Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
int ilo, ihi, jlo, jhi;
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
double cut_one = 0.0;
if (!finitecutflag) cut_one = utils::numeric(FLERR,arg[2],false,lmp);
if (!finitecutflag) cut_one = utils::numeric(FLERR, arg[2], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
setflag[i][j] = 1;
cut[i][j] = cut_one;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
@ -265,15 +269,15 @@ void PairTracker::init_style()
// error and warning checks
if (!atom->radius_flag && finitecutflag)
error->all(FLERR,"Pair tracker requires atom attribute radius for finite cutoffs");
error->all(FLERR, "Pair tracker requires atom attribute radius for finite cutoffs");
// need a history neigh list
int irequest = neighbor->request(this,instance_me);
int irequest = neighbor->request(this, instance_me);
if (finitecutflag) {
neighbor->requests[irequest]->size = 1;
neighbor->requests[irequest]->history = 1;
// history flag won't affect results, but match granular pairstyles
// history flag won't affect results, but match granular pairstyles
// so neighborlist can be copied to reduce overhead
}
@ -283,14 +287,14 @@ void PairTracker::init_style()
if (fix_history == nullptr) {
char dnumstr[16];
sprintf(dnumstr,"%d",size_history);
char **fixarg = new char*[4];
sprintf(dnumstr, "%d", size_history);
char **fixarg = new char *[4];
fixarg[0] = (char *) "NEIGH_HISTORY_TRACK";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "NEIGH_HISTORY";
fixarg[3] = dnumstr;
modify->replace_fix("NEIGH_HISTORY_TRACK_DUMMY",4,fixarg,1);
delete [] fixarg;
modify->replace_fix("NEIGH_HISTORY_TRACK_DUMMY", 4, fixarg, 1);
delete[] fixarg;
int ifix = modify->find_fix("NEIGH_HISTORY_TRACK");
fix_history = (FixNeighHistory *) modify->fix[ifix];
fix_history->pair = this;
@ -298,63 +302,60 @@ void PairTracker::init_style()
}
if (finitecutflag) {
if(force->pair->beyond_contact)
error->all(FLERR, "Pair tracker incompatible with granular pairstyles that extend beyond contact");
if (force->pair->beyond_contact)
error->all(FLERR,
"Pair tracker incompatible with granular pairstyles that extend beyond contact");
// check for FixPour and FixDeposit so can extract particle radii
int ipour;
for (ipour = 0; ipour < modify->nfix; ipour++)
if (strcmp(modify->fix[ipour]->style,"pour") == 0) break;
if (strcmp(modify->fix[ipour]->style, "pour") == 0) break;
if (ipour == modify->nfix) ipour = -1;
int idep;
for (idep = 0; idep < modify->nfix; idep++)
if (strcmp(modify->fix[idep]->style,"deposit") == 0) break;
if (strcmp(modify->fix[idep]->style, "deposit") == 0) break;
if (idep == modify->nfix) idep = -1;
// set maxrad_dynamic and maxrad_frozen for each type
// include future FixPour and FixDeposit particles as dynamic
int itype;
for (i = 1; i <= atom->ntypes; i++) {
onerad_dynamic[i] = onerad_frozen[i] = 0.0;
if (ipour >= 0) {
itype = i;
onerad_dynamic[i] =
*((double *) modify->fix[ipour]->extract("radius",itype));
onerad_dynamic[i] = *((double *) modify->fix[ipour]->extract("radius", itype));
}
if (idep >= 0) {
itype = i;
onerad_dynamic[i] =
*((double *) modify->fix[idep]->extract("radius",itype));
onerad_dynamic[i] = *((double *) modify->fix[idep]->extract("radius", itype));
}
}
double *radius = atom->radius;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & freeze_group_bit)
onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]],radius[i]);
onerad_frozen[type[i]] = MAX(onerad_frozen[type[i]], radius[i]);
else
onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]],radius[i]);
MPI_Allreduce(&onerad_dynamic[1],&maxrad_dynamic[1],atom->ntypes,
MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(&onerad_frozen[1],&maxrad_frozen[1],atom->ntypes,
MPI_DOUBLE,MPI_MAX,world);
onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
}
int ifix = modify->find_fix("NEIGH_HISTORY_TRACK");
if (ifix < 0) error->all(FLERR,"Could not find pair fix neigh history ID");
if (ifix < 0) error->all(FLERR, "Could not find pair fix neigh history ID");
fix_history = (FixNeighHistory *) modify->fix[ifix];
ifix = modify->find_fix_by_style("pair/tracker");
if(ifix < 0) error->all(FLERR,"Cannot use pair tracker without fix pair/tracker");
fix_pair_tracker = (FixPairTracker *) modify->fix[ifix];
if (ifix < 0) error->all(FLERR, "Cannot use pair tracker without fix pair/tracker");
fix_pair_tracker = (FixPairTracker *) modify->fix[ifix];
}
/* ----------------------------------------------------------------------
@ -367,20 +368,18 @@ double PairTracker::init_one(int i, int j)
// always mix prefactors geometrically
if (setflag[i][j] == 0) {
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
if (setflag[i][j] == 0) { cut[i][j] = mix_distance(cut[i][i], cut[j][j]); }
cut[j][i] = cut[i][j];
// if finite, cutoff = sum of max I,J radii for
// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
double cutoff;
double cutoff;
if (finitecutflag) {
cutoff = maxrad_dynamic[i]+maxrad_dynamic[j];
cutoff = MAX(cutoff,maxrad_frozen[i]+maxrad_dynamic[j]);
cutoff = MAX(cutoff,maxrad_dynamic[i]+maxrad_frozen[j]);
} else {
cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
} else {
cutoff = cut[i][j];
}
return cutoff;
@ -394,13 +393,11 @@ void PairTracker::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
int i, j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&cut[i][j],sizeof(double),1,fp);
}
fwrite(&setflag[i][j], sizeof(int), 1, fp);
if (setflag[i][j]) { fwrite(&cut[i][j], sizeof(double), 1, fp); }
}
}
@ -413,18 +410,16 @@ void PairTracker::read_restart(FILE *fp)
read_restart_settings(fp);
allocate();
int i,j;
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
}
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
if (me == 0) { utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); }
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
}
}
}
@ -434,7 +429,7 @@ void PairTracker::read_restart(FILE *fp)
void PairTracker::write_restart_settings(FILE *fp)
{
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
@ -443,18 +438,14 @@ void PairTracker::write_restart_settings(FILE *fp)
void PairTracker::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
}
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
if (comm->me == 0) { utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); }
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
}
/* ---------------------------------------------------------------------- */
double PairTracker::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
double PairTracker::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
double /*factor_coul*/, double /*factor_lj*/, double &fforce)
{
return 0.0;
}
@ -464,20 +455,18 @@ double PairTracker::single(int i, int j, int /*itype*/, int /*jtype*/,
only needed if any history entries i-j are not just negative of j-i entries
------------------------------------------------------------------------- */
void PairTracker::transfer_history(double* source, double* target)
void PairTracker::transfer_history(double *source, double *target)
{
for (int i = 0; i < size_history; i++)
target[i] = source[i];
for (int i = 0; i < size_history; i++) target[i] = source[i];
}
/* ----------------------------------------------------------------------
self-interaction range of particle if finite particles
------------------------------------------------------------------------- */
double PairTracker::atom2cut(int i)
{
double cut = atom->radius[i]*2;
double cut = atom->radius[i] * 2;
return cut;
}
@ -487,7 +476,6 @@ double PairTracker::atom2cut(int i)
double PairTracker::radii2cut(double r1, double r2)
{
double cut = r1+r2;
double cut = r1 + r2;
return cut;
}