git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@438 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
635
src/neighbor.cpp
635
src/neighbor.cpp
@ -44,7 +44,7 @@ using namespace LAMMPS_NS;
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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enum{NSQ,BIN,MULTI};
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enum{NSQ,BIN,MULTI}; // also in neigh_stencil.cpp
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/* ---------------------------------------------------------------------- */
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@ -62,8 +62,9 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
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maxlocal = 0;
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cutneigh = NULL;
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cutneighsq = NULL;
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cuttype = NULL;
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cuttypesq = NULL;
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fixchecklist = NULL;
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// last neighbor info
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@ -90,27 +91,35 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
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maxbin = 0;
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bins = NULL;
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maxstencil = 0;
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nstencil = maxstencil = 0;
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stencil = NULL;
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maxstencil_full = 0;
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nstencil_full = maxstencil_full = 0;
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stencil_full = NULL;
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//mstencil = NULL;
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maxstencil_multi = 0;
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nstencil_multi = NULL;
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stencil_multi = NULL;
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distsq_multi = NULL;
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maxstencil_full_multi = 0;
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nstencil_full_multi = NULL;
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stencil_full_multi = NULL;
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distsq_full_multi = NULL;
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// half neighbor list info
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half = half_command = 0;
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maxpage = 0;
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numneigh = NULL;
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firstneigh = NULL;
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maxpage = 0;
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pages = NULL;
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// full neighbor list info
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full = 0;
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maxpage_full = 0;
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numneigh_full = NULL;
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firstneigh_full = NULL;
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maxpage_full = 0;
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pages_full = NULL;
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// shear history neighbor list info
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@ -118,19 +127,20 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
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fix_history = NULL;
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firsttouch = NULL;
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firstshear = NULL;
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maxpage_history = 0;
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pages_touch = NULL;
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pages_shear = NULL;
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// multiple respa neighbor list info
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respa = 0;
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maxpage_inner = 0;
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maxpage_middle = 0;
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numneigh_inner = NULL;
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firstneigh_inner = NULL;
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pages_inner = NULL;
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numneigh_middle = NULL;
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firstneigh_middle = NULL;
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maxpage_inner = 0;
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maxpage_middle = 0;
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pages_inner = NULL;
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pages_middle = NULL;
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// bond list info
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@ -149,8 +159,10 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
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Neighbor::~Neighbor()
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{
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memory->destroy_2d_double_array(cutneigh);
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memory->destroy_2d_double_array(cutneighsq);
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delete [] cuttype;
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delete [] cuttypesq;
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delete [] fixchecklist;
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memory->destroy_2d_double_array(xhold);
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@ -168,9 +180,29 @@ Neighbor::~Neighbor()
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memory->sfree(binhead);
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memory->sfree(bins);
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memory->sfree(stencil);
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memory->sfree(stencil_full);
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if (nstencil_multi) {
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for (int i = 1; i <= atom->ntypes; i++) {
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memory->sfree(stencil_multi[i]);
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memory->sfree(distsq_multi[i]);
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}
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delete [] nstencil_multi;
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delete [] stencil_multi;
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delete [] distsq_multi;
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}
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if (nstencil_full_multi) {
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for (int i = 1; i <= atom->ntypes; i++) {
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memory->sfree(stencil_full_multi[i]);
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memory->sfree(distsq_full_multi[i]);
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}
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delete [] nstencil_full_multi;
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delete [] stencil_full_multi;
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delete [] distsq_full_multi;
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}
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memory->destroy_2d_int_array(bondlist);
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memory->destroy_2d_int_array(anglelist);
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memory->destroy_2d_int_array(dihedrallist);
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@ -178,33 +210,22 @@ Neighbor::~Neighbor()
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memory->sfree(numneigh);
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memory->sfree(firstneigh);
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for (int i = 0; i < maxpage; i++) memory->sfree(pages[i]);
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memory->sfree(pages);
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clear_pages();
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memory->sfree(numneigh_full);
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memory->sfree(firstneigh_full);
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for (int i = 0; i < maxpage_full; i++) memory->sfree(pages_full[i]);
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memory->sfree(pages_full);
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clear_pages_full();
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if (fix_history) {
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memory->sfree(firsttouch);
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memory->sfree(firstshear);
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for (int i = 0; i < maxpage; i++) memory->sfree(pages_touch[i]);
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for (int i = 0; i < maxpage; i++) memory->sfree(pages_shear[i]);
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memory->sfree(pages_touch);
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memory->sfree(pages_shear);
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}
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memory->sfree(firsttouch);
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memory->sfree(firstshear);
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clear_pages_history();
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if (respa) {
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memory->sfree(numneigh_inner);
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memory->sfree(firstneigh_inner);
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for (int i = 0; i < maxpage_inner; i++) memory->sfree(pages_inner[i]);
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memory->sfree(pages_inner);
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memory->sfree(numneigh_middle);
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memory->sfree(firstneigh_middle);
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for (int i = 0; i < maxpage_middle; i++) memory->sfree(pages_middle[i]);
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memory->sfree(pages_middle);
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}
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memory->sfree(numneigh_inner);
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memory->sfree(firstneigh_inner);
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memory->sfree(numneigh_middle);
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memory->sfree(firstneigh_middle);
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clear_pages_inner();
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clear_pages_middle();
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}
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/* ---------------------------------------------------------------------- */
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@ -235,31 +256,34 @@ void Neighbor::init()
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triggersq = 0.25*skin*skin;
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n = atom->ntypes;
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if (cutneigh == NULL) {
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cutneigh = memory->create_2d_double_array(n+1,n+1,"neigh:cutneigh");
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if (cutneighsq == NULL) {
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cutneighsq = memory->create_2d_double_array(n+1,n+1,"neigh:cutneighsq");
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cuttype = new double[n+1];
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cuttypesq = new double[n+1];
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}
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double cutoff,delta;
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for (i = 1; i <= n; i++)
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for (j = i; j <= n; j++) {
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double cutoff,delta,cut;
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cutneighmin = BIG;
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cutneighmax = 0.0;
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for (i = 1; i <= n; i++) {
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cuttype[i] = cuttypesq[i] = 0.0;
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for (j = 1; j <= n; j++) {
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if (force->pair) cutoff = sqrt(force->pair->cutsq[i][j]);
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else cutoff = 0.0;
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if (cutoff > 0.0) delta = skin;
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else delta = 0.0;
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cutneigh[i][j] = cutneigh[j][i] = cutoff + delta;
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cutneighsq[i][j] = cutneighsq[j][i] = (cutoff+delta) * (cutoff+delta);
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}
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cut = cutoff + delta;
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cutneighmin = BIG;
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cutneighmax = 0.0;
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cutghost = skin;
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for (i = 1; i <= n; i++)
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for (j = i; j <= n; j++) {
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cutneighmin = MIN(cutneighmin,cutneigh[i][j]);
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cutneighmax = MAX(cutneighmax,cutneigh[i][j]);
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cutghost = MAX(cutghost,cutneigh[i][j]);
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cutneighsq[i][j] = cut*cut;
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cuttype[i] = MAX(cuttype[i],cut);
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cuttypesq[i] = MAX(cuttypesq[i],cut*cut);
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cutneighmin = MIN(cutneighmin,cut);
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cutneighmax = MAX(cutneighmax,cut);
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}
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}
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cutghost = MAX(cutneighmax,skin);
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cutneighmaxsq = cutneighmax * cutneighmax;
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// check other classes that can induce reneighboring in decide()
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@ -313,6 +337,7 @@ void Neighbor::init()
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if (dist_check == 0) {
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memory->destroy_2d_double_array(xhold);
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maxhold = 0;
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xhold = NULL;
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}
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if (style == NSQ) {
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@ -321,6 +346,8 @@ void Neighbor::init()
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memory->sfree(stencil);
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memory->sfree(stencil_full);
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maxbin = maxhead = maxstencil = maxstencil_full = 0;
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binhead = NULL;
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bins = NULL;
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}
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// 1st time allocation of xhold and bins
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@ -332,7 +359,7 @@ void Neighbor::init()
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}
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}
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if (style == BIN) {
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if (style != NSQ) {
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if (maxbin == 0) {
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maxbin = atom->nmax;
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bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
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@ -384,15 +411,11 @@ void Neighbor::init()
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}
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// ------------------------------------------------------------------
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// half and full pairwise neighbor lists
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// neighbor list flags and memory allocation/deallocation
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// determine whether to build half and full lists
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// query pair,fix,compute for their requirements
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maxlocal = atom->nmax;
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int half_previous = half;
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int full_previous = full;
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half_once = full_once = 0;
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half_every = full_every = 0;
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if (force->pair) half_every = force->pair->neigh_half_every;
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@ -415,89 +438,19 @@ void Neighbor::init()
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if (full_every || full_once) full = 1;
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half = 1;
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// setup/delete memory for half and full lists
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if (half == 0 && half_previous) {
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memory->sfree(numneigh);
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memory->sfree(firstneigh);
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for (i = 0; i < maxpage; i++) memory->sfree(pages[i]);
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memory->sfree(pages);
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pages = NULL;
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maxpage = 0;
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} else if (half && half_previous == 0) {
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numneigh =
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(int *) memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh");
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firstneigh =
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(int **) memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh");
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add_pages(0);
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} else if (half && half_previous) {
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memory->sfree(numneigh);
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memory->sfree(firstneigh);
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numneigh =
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(int *) memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh");
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firstneigh =
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(int **) memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh");
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}
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if (full == 0 && full_previous) {
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memory->sfree(numneigh_full);
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memory->sfree(firstneigh_full);
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for (i = 0; i < maxpage_full; i++) memory->sfree(pages_full[i]);
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memory->sfree(pages_full);
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pages_full = NULL;
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maxpage_full = 0;
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} else if (full && full_previous == 0) {
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numneigh_full =
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(int *) memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_full");
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firstneigh_full =
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(int **) memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_full");
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add_pages_full(0);
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} else if (full && full_previous) {
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memory->sfree(numneigh_full);
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memory->sfree(firstneigh_full);
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numneigh_full =
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(int *) memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_full");
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firstneigh_full =
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(int **) memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_full");
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}
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// setup/delete memory for shear history neighbor lists
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// fix_history = granular shear history fix if it exists
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// determine whether to build granular history lists
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// fix_history = granular shear history fix
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FixShearHistory *fix_previous = fix_history;
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fix_history = NULL;
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if (force->pair_match("gran/history") || force->pair_match("gran/hertzian"))
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for (i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0)
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fix_history = (FixShearHistory *) modify->fix[i];
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if (fix_history == NULL && fix_previous) {
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memory->sfree(firsttouch);
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memory->sfree(firstshear);
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for (i = 0; i < maxpage; i++) memory->sfree(pages_touch[i]);
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for (i = 0; i < maxpage; i++) memory->sfree(pages_shear[i]);
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memory->sfree(pages_touch);
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memory->sfree(pages_shear);
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pages_touch = NULL;
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pages_shear = NULL;
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} else if (fix_history && fix_previous == NULL) {
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firsttouch = (int **) memory->smalloc(maxlocal*sizeof(int *),"firsttouch");
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firstshear = (double **)
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memory->smalloc(maxlocal*sizeof(double *),"firstshear");
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add_pages_history(0);
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} else if (fix_history && fix_previous >= 0) {
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memory->sfree(firsttouch);
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memory->sfree(firstshear);
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firsttouch = (int **) memory->smalloc(maxlocal*sizeof(int *),"firsttouch");
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firstshear = (double **)
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memory->smalloc(maxlocal*sizeof(double *),"firstshear");
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}
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// setup/delete memory for rRESPA neighbor lists
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// respa = 1 if rRESPA requires extra neighbor lists
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// determine whether to build extra rRESPA lists
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// respa = 1,2 if rRESPA requires inner,middle neighbor lists
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// set neighbor cutoffs for multiple lists
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int respa_previous = respa;
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respa = 0;
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if (update->whichflag == 0 && strcmp(update->integrate_style,"respa") == 0) {
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if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
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@ -507,51 +460,6 @@ void Neighbor::init()
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if (respa && half_every == 0)
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error->all("Cannot use rRESPA with full neighbor lists");
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if (respa == 0 && respa_previous) {
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memory->sfree(numneigh_inner);
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memory->sfree(firstneigh_inner);
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for (i = 0; i < maxpage_inner; i++) memory->sfree(pages_inner[i]);
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memory->sfree(pages_inner);
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pages_inner = NULL;
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maxpage_inner = 0;
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if (respa_previous == 2) {
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memory->sfree(numneigh_middle);
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memory->sfree(firstneigh_middle);
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for (i = 0; i < maxpage_middle; i++) memory->sfree(pages_middle[i]);
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memory->sfree(pages_middle);
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pages_middle = NULL;
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maxpage_middle = 0;
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}
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} else if (respa && respa_previous == 0) {
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numneigh_inner = (int *)
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memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_inner");
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firstneigh_inner = (int **)
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memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_inner");
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add_pages_inner(0);
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if (respa == 2) {
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numneigh_middle = (int *)
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memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_middle");
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firstneigh_middle = (int **)
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memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_middle");
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add_pages_middle(0);
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}
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} else if (respa && respa_previous) {
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memory->sfree(numneigh_inner);
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memory->sfree(firstneigh_inner);
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numneigh_inner = (int *)
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memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_inner");
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firstneigh_inner = (int **)
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memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_inner");
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if (respa == 2) {
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memory->sfree(numneigh_middle);
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memory->sfree(firstneigh_middle);
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numneigh_middle = (int *)
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memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_middle");
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firstneigh_middle = (int **)
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memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_middle");
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}
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}
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if (respa) {
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double *cut_respa = ((Respa *) update->integrate)->cutoff;
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cut_inner_sq = (cut_respa[1] + skin) * (cut_respa[1] + skin);
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@ -559,8 +467,46 @@ void Neighbor::init()
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cut_middle_inside_sq = (cut_respa[0] - skin) * (cut_respa[0] - skin);
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}
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// set ptrs to correct half, full, multi, triclinic build functions
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// cannot combine granular and rRESPA
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// zero atom-length numneigh and firstneigh arrays
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// will be (re)allocated on first build()
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maxlocal = 0;
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memory->sfree(numneigh);
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memory->sfree(firstneigh);
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memory->sfree(numneigh_full);
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memory->sfree(firstneigh_full);
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memory->sfree(firsttouch);
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memory->sfree(firstshear);
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memory->sfree(numneigh_inner);
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memory->sfree(firstneigh_inner);
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memory->sfree(numneigh_middle);
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memory->sfree(firstneigh_middle);
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numneigh = numneigh_full = numneigh_inner = numneigh_middle = NULL;
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firstneigh = firstneigh_full = NULL;
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firsttouch = NULL;
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firstshear = NULL;
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firstneigh_inner = firstneigh_middle = NULL;
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// clear old neighbor lists if no longer needed (whether exist or not)
|
||||
|
||||
if (half == 0) clear_pages();
|
||||
if (full == 0) clear_pages_full();
|
||||
if (fix_history == NULL) clear_pages_history();
|
||||
if (respa == 0) clear_pages_inner();
|
||||
if (respa == 0 || respa == 1) clear_pages_middle();
|
||||
|
||||
// setup new neighbor lists
|
||||
// only if they don't exist so memory will persist from run to run
|
||||
|
||||
if (half && pages == NULL) add_pages(0);
|
||||
if (full && pages_full == NULL) add_pages_full(0);
|
||||
if (fix_history && pages_touch == NULL) add_pages_history(0);
|
||||
if (respa >= 1 && pages_inner == NULL) add_pages_inner(0);
|
||||
if (respa == 2 && pages_middle == NULL) add_pages_middle(0);
|
||||
|
||||
// set ptrs to half/full/multi/triclinic build & stencil functions
|
||||
|
||||
if (half) {
|
||||
if (atom->check_style("granular")) {
|
||||
@ -569,24 +515,54 @@ void Neighbor::init()
|
||||
half_build = &Neighbor::granular_nsq_no_newton;
|
||||
else half_build = &Neighbor::granular_nsq_newton;
|
||||
} else if (style == BIN) {
|
||||
if (force->newton_pair == 0)
|
||||
if (force->newton_pair == 0) {
|
||||
half_build = &Neighbor::granular_bin_no_newton;
|
||||
else if (triclinic)
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_no_newton;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_no_newton;
|
||||
} else if (triclinic) {
|
||||
half_build = &Neighbor::granular_bin_newton_tri;
|
||||
else half_build = &Neighbor::granular_bin_newton;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
|
||||
} else {
|
||||
half_build = &Neighbor::granular_bin_newton;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_newton;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_newton;
|
||||
}
|
||||
} else error->all("Neighbor multi not allowed with granular");
|
||||
|
||||
} else if (respa) {
|
||||
if (style == NSQ) {
|
||||
if (force->newton_pair == 0)
|
||||
half_build = &Neighbor::respa_nsq_no_newton;
|
||||
else half_build = &Neighbor::respa_nsq_newton;
|
||||
} else if (style == BIN) {
|
||||
if (force->newton_pair == 0)
|
||||
if (force->newton_pair == 0) {
|
||||
half_build = &Neighbor::respa_bin_no_newton;
|
||||
else if (triclinic)
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_no_newton;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_no_newton;
|
||||
} else if (triclinic) {
|
||||
half_build = &Neighbor::respa_bin_newton_tri;
|
||||
else half_build = &Neighbor::respa_bin_newton;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
|
||||
} else {
|
||||
half_build = &Neighbor::respa_bin_newton;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_newton;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_newton;
|
||||
}
|
||||
} else error->all("Neighbor multi not allowed with rRESPA");
|
||||
|
||||
} else {
|
||||
if (style == NSQ) {
|
||||
if (force->newton_pair == 0) {
|
||||
@ -598,31 +574,84 @@ void Neighbor::init()
|
||||
}
|
||||
} else if (style == BIN) {
|
||||
if (force->newton_pair == 0) {
|
||||
if (full_every) half_build = &Neighbor::half_full_no_newton;
|
||||
else half_build = &Neighbor::half_bin_no_newton;
|
||||
if (full_every) {
|
||||
half_build = &Neighbor::half_full_no_newton;
|
||||
half_stencil = &Neighbor::stencil_none;
|
||||
} else {
|
||||
half_build = &Neighbor::half_bin_no_newton;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_no_newton;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_no_newton;
|
||||
}
|
||||
} else {
|
||||
if (full_every) half_build = &Neighbor::half_full_newton;
|
||||
else if (triclinic) half_build = &Neighbor::half_bin_newton_tri;
|
||||
else half_build = &Neighbor::half_bin_newton;
|
||||
if (full_every) {
|
||||
half_build = &Neighbor::half_full_newton;
|
||||
half_stencil = &Neighbor::stencil_none;
|
||||
} else if (triclinic) {
|
||||
half_build = &Neighbor::half_bin_newton_tri;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
|
||||
} else {
|
||||
half_build = &Neighbor::half_bin_newton;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_newton;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_newton;
|
||||
}
|
||||
}
|
||||
} else if (style == MULTI) {
|
||||
if (force->newton_pair == 0) {
|
||||
if (full_every) half_build = &Neighbor::half_full_no_newton;
|
||||
else half_build = &Neighbor::half_bin_no_newton_multi;
|
||||
if (full_every) {
|
||||
half_build = &Neighbor::half_full_no_newton;
|
||||
half_stencil = &Neighbor::stencil_none;
|
||||
} else {
|
||||
half_build = &Neighbor::half_bin_no_newton_multi;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_no_newton_multi;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_no_newton_multi;
|
||||
}
|
||||
} else {
|
||||
if (full_every) half_build = &Neighbor::half_full_newton;
|
||||
else if (triclinic)
|
||||
if (full_every) {
|
||||
half_build = &Neighbor::half_full_newton;
|
||||
half_stencil = &Neighbor::stencil_none;
|
||||
} else if (triclinic) {
|
||||
half_build = &Neighbor::half_bin_newton_multi_tri;
|
||||
else half_build = &Neighbor::half_bin_newton_multi;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_newton_multi_tri;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_newton_multi_tri;
|
||||
} else {
|
||||
half_build = &Neighbor::half_bin_newton_multi;
|
||||
if (force->dimension == 3)
|
||||
half_stencil = &Neighbor::stencil_half_3d_newton_multi;
|
||||
else
|
||||
half_stencil = &Neighbor::stencil_half_2d_newton_multi;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else half_build = NULL;
|
||||
|
||||
if (full) {
|
||||
if (style == NSQ) full_build = &Neighbor::full_nsq;
|
||||
else if (style == BIN) full_build = &Neighbor::full_bin;
|
||||
else error->all("Neighbor multi not allowed with full neighbor lists");
|
||||
else if (style == BIN) {
|
||||
full_build = &Neighbor::full_bin;
|
||||
if (force->dimension == 3)
|
||||
full_stencil = &Neighbor::stencil_full_3d;
|
||||
else
|
||||
full_stencil = &Neighbor::stencil_full_2d;
|
||||
} else {
|
||||
full_build = &Neighbor::full_bin_multi;
|
||||
if (force->dimension == 3)
|
||||
full_stencil = &Neighbor::stencil_full_3d_multi;
|
||||
else
|
||||
full_stencil = &Neighbor::stencil_full_2d_multi;
|
||||
}
|
||||
} else full_build = NULL;
|
||||
|
||||
// ------------------------------------------------------------------
|
||||
@ -663,7 +692,6 @@ void Neighbor::init()
|
||||
// bond_quartic sets bonds to 0
|
||||
// delete_bonds sets all interactions negative
|
||||
|
||||
|
||||
int bond_off = 0;
|
||||
int angle_off = 0;
|
||||
for (i = 0; i < modify->nfix; i++)
|
||||
@ -705,7 +733,7 @@ void Neighbor::init()
|
||||
}
|
||||
}
|
||||
|
||||
// set ptrs to correct intra-molecular build functions
|
||||
// set ptrs to intra-molecular build functions
|
||||
|
||||
if (bond_off) bond_build = &Neighbor::bond_partial;
|
||||
else bond_build = &Neighbor::bond_all;
|
||||
@ -1040,107 +1068,26 @@ void Neighbor::setup_bins()
|
||||
binhead = (int *) memory->smalloc(maxhead*sizeof(int),"neigh:binhead");
|
||||
}
|
||||
|
||||
// create stencil of bins whose closest corner to central bin
|
||||
// is within cutneighmax
|
||||
// stencil will be empty if cutneighmax = 0.0
|
||||
// next(xyz) = how far the stencil could possibly extend
|
||||
// for partial Newton (newton = 0)
|
||||
// stencil is all surrounding bins
|
||||
// stencil includes self
|
||||
// for triclinic
|
||||
// stencil is all bins in z-plane of self and above, but not below
|
||||
// in 2d is all bins in y-plane of self and above, but not below
|
||||
// stencil includes self
|
||||
// for full Newton (newton = 1)
|
||||
// stencil is bins to the "upper right" of central bin
|
||||
// stencil does not include self
|
||||
// for full neighbor list (full = 1)
|
||||
// stencil is all surrounding bins including self, regardless of Newton
|
||||
// stored in stencil_full
|
||||
// 3d creates xyz stencil, 2d is only xy
|
||||
// create stencil of bins to search over in neighbor list construction
|
||||
// sx,sy,sz = max range of stencil extent
|
||||
// stencil is empty if cutneighmax = 0.0
|
||||
|
||||
int nextx = static_cast<int> (cutneighmax*bininvx);
|
||||
if (nextx*binsizex < cutneighmax) nextx++;
|
||||
int nexty = static_cast<int> (cutneighmax*bininvy);
|
||||
if (nexty*binsizey < cutneighmax) nexty++;
|
||||
int nextz = static_cast<int> (cutneighmax*bininvz);
|
||||
if (nextz*binsizez < cutneighmax) nextz++;
|
||||
int sx = static_cast<int> (cutneighmax*bininvx);
|
||||
if (sx*binsizex < cutneighmax) sx++;
|
||||
int sy = static_cast<int> (cutneighmax*bininvy);
|
||||
if (sy*binsizey < cutneighmax) sy++;
|
||||
int sz = static_cast<int> (cutneighmax*bininvz);
|
||||
if (sz*binsizez < cutneighmax) sz++;
|
||||
|
||||
int nmax = (2*nextz+1) * (2*nexty+1) * (2*nextx+1);
|
||||
if (nmax > maxstencil) {
|
||||
maxstencil = nmax;
|
||||
memory->sfree(stencil);
|
||||
stencil = (int *) memory->smalloc(maxstencil*sizeof(int),"neigh:stencil");
|
||||
}
|
||||
// allocate stencil memory and create stencil(s)
|
||||
// check half/full instead of half_every/full_every so stencils will be
|
||||
// allocated correctly whenever build_half() and build_full() are called
|
||||
|
||||
int i,j,k;
|
||||
nstencil = 0;
|
||||
double cutneighmaxsq = cutneighmax*cutneighmax;
|
||||
|
||||
if (force->dimension == 3) {
|
||||
if (force->newton_pair == 0) {
|
||||
for (k = -nextz; k <= nextz; k++)
|
||||
for (j = -nexty; j <= nexty; j++)
|
||||
for (i = -nextx; i <= nextx; i++)
|
||||
if (bin_distance(i,j,k) < cutneighmaxsq)
|
||||
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
||||
} else if (triclinic) {
|
||||
for (k = 0; k <= nextz; k++)
|
||||
for (j = -nexty; j <= nexty; j++)
|
||||
for (i = -nextx; i <= nextx; i++)
|
||||
if (bin_distance(i,j,k) < cutneighmaxsq)
|
||||
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
||||
} else {
|
||||
for (k = 0; k <= nextz; k++)
|
||||
for (j = -nexty; j <= nexty; j++)
|
||||
for (i = -nextx; i <= nextx; i++)
|
||||
if (k > 0 || j > 0 || (j == 0 && i > 0))
|
||||
if (bin_distance(i,j,k) < cutneighmaxsq)
|
||||
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
|
||||
}
|
||||
} else {
|
||||
if (force->newton_pair == 0) {
|
||||
for (j = -nexty; j <= nexty; j++)
|
||||
for (i = -nextx; i <= nextx; i++)
|
||||
if (bin_distance(i,j,0) < cutneighmaxsq)
|
||||
stencil[nstencil++] = j*mbinx + i;
|
||||
} else if (triclinic) {
|
||||
for (j = 0; j <= nexty; j++)
|
||||
for (i = -nextx; i <= nextx; i++)
|
||||
if (bin_distance(i,j,0) < cutneighmaxsq)
|
||||
stencil[nstencil++] = j*mbinx + i;
|
||||
} else {
|
||||
for (j = 0; j <= nexty; j++)
|
||||
for (i = -nextx; i <= nextx; i++)
|
||||
if (j > 0 || (j == 0 && i > 0))
|
||||
if (bin_distance(i,j,0) < cutneighmaxsq)
|
||||
stencil[nstencil++] = j*mbinx + i;
|
||||
}
|
||||
}
|
||||
|
||||
if (full) {
|
||||
if (nmax > maxstencil_full) {
|
||||
maxstencil_full = nmax;
|
||||
memory->sfree(stencil_full);
|
||||
stencil_full = (int *) memory->smalloc(maxstencil_full*sizeof(int),
|
||||
"neigh:stencil_full");
|
||||
}
|
||||
nstencil_full = 0;
|
||||
if (force->dimension == 3) {
|
||||
for (k = -nextz; k <= nextz; k++)
|
||||
for (j = -nexty; j <= nexty; j++)
|
||||
for (i = -nextx; i <= nextx; i++)
|
||||
if (bin_distance(i,j,k) < cutneighmaxsq)
|
||||
stencil_full[nstencil_full++] = k*mbiny*mbinx + j*mbinx + i;
|
||||
} else {
|
||||
for (j = -nexty; j <= nexty; j++)
|
||||
for (i = -nextx; i <= nextx; i++)
|
||||
if (bin_distance(i,j,0) < cutneighmaxsq)
|
||||
stencil_full[nstencil_full++] = j*mbinx + i;
|
||||
}
|
||||
}
|
||||
stencil_allocate(sx,sy,sz);
|
||||
if (half) (this->*half_stencil)(sx,sy,sz);
|
||||
if (full) (this->*full_stencil)(sx,sy,sz);
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute closest distance between central bin (0,0,0) and bin (i,j,k)
|
||||
------------------------------------------------------------------------- */
|
||||
@ -1149,26 +1096,17 @@ double Neighbor::bin_distance(int i, int j, int k)
|
||||
{
|
||||
double delx,dely,delz;
|
||||
|
||||
if (i > 0)
|
||||
delx = (i-1)*binsizex;
|
||||
else if (i == 0)
|
||||
delx = 0.0;
|
||||
else
|
||||
delx = (i+1)*binsizex;
|
||||
if (i > 0) delx = (i-1)*binsizex;
|
||||
else if (i == 0) delx = 0.0;
|
||||
else delx = (i+1)*binsizex;
|
||||
|
||||
if (j > 0)
|
||||
dely = (j-1)*binsizey;
|
||||
else if (j == 0)
|
||||
dely = 0.0;
|
||||
else
|
||||
dely = (j+1)*binsizey;
|
||||
if (j > 0) dely = (j-1)*binsizey;
|
||||
else if (j == 0) dely = 0.0;
|
||||
else dely = (j+1)*binsizey;
|
||||
|
||||
if (k > 0)
|
||||
delz = (k-1)*binsizez;
|
||||
else if (k == 0)
|
||||
delz = 0.0;
|
||||
else
|
||||
delz = (k+1)*binsizez;
|
||||
if (k > 0) delz = (k-1)*binsizez;
|
||||
else if (k == 0) delz = 0.0;
|
||||
else delz = (k+1)*binsizez;
|
||||
|
||||
return (delx*delx + dely*dely + delz*delz);
|
||||
}
|
||||
@ -1317,8 +1255,8 @@ int Neighbor::memory_usage()
|
||||
if (fix_history) {
|
||||
bytes += maxlocal * sizeof(int *);
|
||||
bytes += maxlocal * sizeof(double *);
|
||||
bytes += maxpage*pgsize * sizeof(int);
|
||||
bytes += maxpage*pgsize*3 * sizeof(double);
|
||||
bytes += maxpage_history*pgsize * sizeof(int);
|
||||
bytes += maxpage_history*pgsize*3 * sizeof(double);
|
||||
}
|
||||
|
||||
if (respa) {
|
||||
@ -1341,7 +1279,7 @@ int Neighbor::memory_usage()
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add pages to half or full neighbor list, starting at npage
|
||||
add pages to half/full/granular/rRESPA neighbor lists, starting at npage
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Neighbor::add_pages(int npage)
|
||||
@ -1363,18 +1301,16 @@ void Neighbor::add_pages_full(int npage)
|
||||
(int *) memory->smalloc(pgsize*sizeof(int),"neigh:pages_full[i]");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add pages to granular neighbor list, starting at npage
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Neighbor::add_pages_history(int npage)
|
||||
{
|
||||
maxpage_history += PGDELTA;
|
||||
pages_touch = (int **)
|
||||
memory->srealloc(pages_touch,maxpage*sizeof(int *),"neigh:pages_touch");
|
||||
memory->srealloc(pages_touch,maxpage_history*sizeof(int *),
|
||||
"neigh:pages_touch");
|
||||
pages_shear = (double **)
|
||||
memory->srealloc(pages_shear,maxpage*sizeof(double *),
|
||||
memory->srealloc(pages_shear,maxpage_history*sizeof(double *),
|
||||
"neigh:pages_shear");
|
||||
for (int i = npage; i < maxpage; i++) {
|
||||
for (int i = npage; i < maxpage_history; i++) {
|
||||
pages_touch[i] = (int *)
|
||||
memory->smalloc(pgsize*sizeof(int),"neigh:pages_touch[i]");
|
||||
pages_shear[i] = (double *)
|
||||
@ -1382,10 +1318,6 @@ void Neighbor::add_pages_history(int npage)
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add pages to rRESPA inner neighbor list, starting at npage_inner
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Neighbor::add_pages_inner(int npage_inner)
|
||||
{
|
||||
maxpage_inner += PGDELTA;
|
||||
@ -1397,10 +1329,6 @@ void Neighbor::add_pages_inner(int npage_inner)
|
||||
(int *) memory->smalloc(pgsize*sizeof(int),"neigh:pages_inner[i]");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add pages to rRESPA middle neighbor list, starting at npage_middle
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Neighbor::add_pages_middle(int npage_middle)
|
||||
{
|
||||
maxpage_middle += PGDELTA;
|
||||
@ -1412,6 +1340,53 @@ void Neighbor::add_pages_middle(int npage_middle)
|
||||
(int *) memory->smalloc(pgsize*sizeof(int),"neigh:pages_middle[i]");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
clear half/full/granular/rRESPA neighbor lists
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Neighbor::clear_pages()
|
||||
{
|
||||
for (int i = 0; i < maxpage; i++) memory->sfree(pages[i]);
|
||||
memory->sfree(pages);
|
||||
pages = NULL;
|
||||
maxpage = 0;
|
||||
}
|
||||
|
||||
void Neighbor::clear_pages_full()
|
||||
{
|
||||
for (int i = 0; i < maxpage_full; i++) memory->sfree(pages_full[i]);
|
||||
memory->sfree(pages_full);
|
||||
pages_full = NULL;
|
||||
maxpage_full = 0;
|
||||
}
|
||||
|
||||
void Neighbor::clear_pages_history()
|
||||
{
|
||||
for (int i = 0; i < maxpage_history; i++) memory->sfree(pages_touch[i]);
|
||||
for (int i = 0; i < maxpage_history; i++) memory->sfree(pages_shear[i]);
|
||||
memory->sfree(pages_touch);
|
||||
memory->sfree(pages_shear);
|
||||
pages_touch = NULL;
|
||||
pages_shear = NULL;
|
||||
maxpage_history = 0;
|
||||
}
|
||||
|
||||
void Neighbor::clear_pages_inner()
|
||||
{
|
||||
for (int i = 0; i < maxpage_inner; i++) memory->sfree(pages_inner[i]);
|
||||
memory->sfree(pages_inner);
|
||||
pages_inner = NULL;
|
||||
maxpage_inner = 0;
|
||||
}
|
||||
|
||||
void Neighbor::clear_pages_middle()
|
||||
{
|
||||
for (int i = 0; i < maxpage_middle; i++) memory->sfree(pages_middle[i]);
|
||||
memory->sfree(pages_middle);
|
||||
pages_middle = NULL;
|
||||
maxpage_middle = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
determine if atom j is in special list of atom i
|
||||
if it is not, return 0
|
||||
|
||||
Reference in New Issue
Block a user