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Renaming multi nstencils to multi/old

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This commit is contained in:
Joel Clemmer
2020-12-19 17:39:20 -07:00
parent 4a85afcde2
commit 1c52ff15c3
16 changed files with 298 additions and 302 deletions
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232
src/nstencil.cpp
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@ -46,12 +46,12 @@ using namespace LAMMPS_NS;
in 2d is all bins in y-plane of self and above, but not below
stencil includes self
no versions that allow ghost on (no callers need it?)
for multi:
for multi/old:
create one stencil for each atom type
stencil follows same rules for half/full, newton on/off, triclinic
cutoff is not cutneighmaxsq, but max cutoff for that atom type
no versions that allow ghost on (any need for it?)
for multi2:
for multi:
create one stencil for each itype-jtype pairing
the full/half stencil label refers to the same-type stencil
a half list with newton on has a half same-type stencil
@ -68,16 +68,16 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
last_stencil = -1;
xyzflag = 0;
maxstencil = maxstencil_multi = 0;
maxstencil = maxstencil_multi_old = 0;
stencil = nullptr;
stencilxyz = nullptr;
nstencil_multi = nullptr;
stencil_multi = nullptr;
distsq_multi = nullptr;
nstencil_multi_old = nullptr;
stencil_multi_old = nullptr;
distsq_multi_old = nullptr;
nstencil_multi2 = nullptr;
stencil_multi2 = nullptr;
maxstencil_multi2 = nullptr;
nstencil_multi = nullptr;
stencil_multi = nullptr;
maxstencil_multi = nullptr;
stencil_half = nullptr;
stencil_skip = nullptr;
@ -93,46 +93,46 @@ NStencil::~NStencil()
memory->destroy(stencil);
memory->destroy(stencilxyz);
if (stencil_multi) {
if (stencil_multi_old) {
int n = atom->ntypes;
for (int i = 1; i <= n; i++) {
memory->destroy(stencil_multi[i]);
memory->destroy(distsq_multi[i]);
memory->destroy(stencil_multi_old[i]);
memory->destroy(distsq_multi_old[i]);
}
delete [] nstencil_multi;
delete [] stencil_multi;
delete [] distsq_multi;
delete [] nstencil_multi_old;
delete [] stencil_multi_old;
delete [] distsq_multi_old;
}
if (stencil_multi2) {
if (stencil_multi) {
int n = atom->ntypes;
memory->destroy(nstencil_multi2);
memory->destroy(nstencil_multi);
for (int i = 1; i <= n; i++) {
for (int j = 0; j <= n; j++) {
if (! stencil_skip[i][j])
memory->destroy(stencil_multi2[i][j]);
memory->destroy(stencil_multi[i][j]);
}
delete [] stencil_multi2[i];
delete [] stencil_multi[i];
}
delete [] stencil_multi2;
memory->destroy(maxstencil_multi2);
delete [] stencil_multi;
memory->destroy(maxstencil_multi);
memory->destroy(stencil_half);
memory->destroy(stencil_skip);
memory->destroy(stencil_bin_type);
memory->destroy(stencil_sx_multi2);
memory->destroy(stencil_sy_multi2);
memory->destroy(stencil_sz_multi2);
memory->destroy(stencil_sx_multi);
memory->destroy(stencil_sy_multi);
memory->destroy(stencil_sz_multi);
memory->destroy(stencil_mbinx_multi2);
memory->destroy(stencil_mbiny_multi2);
memory->destroy(stencil_mbinz_multi2);
memory->destroy(stencil_mbinx_multi);
memory->destroy(stencil_mbiny_multi);
memory->destroy(stencil_mbinz_multi);
memory->destroy(stencil_binsizex_multi2);
memory->destroy(stencil_binsizey_multi2);
memory->destroy(stencil_binsizez_multi2);
memory->destroy(stencil_binsizex_multi);
memory->destroy(stencil_binsizey_multi);
memory->destroy(stencil_binsizez_multi);
}
}
@ -183,20 +183,20 @@ void NStencil::copy_bin_info()
}
/* ----------------------------------------------------------------------
copy needed info for multi2 from NBin class to this stencil class
copy needed info for multi from NBin class to this stencil class
------------------------------------------------------------------------- */
void NStencil::copy_bin_info_multi2()
void NStencil::copy_bin_info_multi()
{
mbinx_multi2 = nb->mbinx_multi2;
mbiny_multi2 = nb->mbiny_multi2;
mbinz_multi2 = nb->mbinz_multi2;
binsizex_multi2 = nb->binsizex_multi2;
binsizey_multi2 = nb->binsizey_multi2;
binsizez_multi2 = nb->binsizez_multi2;
bininvx_multi2 = nb->bininvx_multi2;
bininvy_multi2 = nb->bininvy_multi2;
bininvz_multi2 = nb->bininvz_multi2;
mbinx_multi = nb->mbinx_multi;
mbiny_multi = nb->mbiny_multi;
mbinz_multi = nb->mbinz_multi;
binsizex_multi = nb->binsizex_multi;
binsizey_multi = nb->binsizey_multi;
binsizez_multi = nb->binsizez_multi;
bininvx_multi = nb->bininvx_multi;
bininvy_multi = nb->bininvy_multi;
bininvz_multi = nb->bininvz_multi;
}
/* ----------------------------------------------------------------------
@ -207,7 +207,7 @@ void NStencil::copy_bin_info_multi2()
void NStencil::create_setup()
{
if (neighstyle != Neighbor::MULTI2){
if (neighstyle != Neighbor::MULTI){
if (nb) copy_bin_info();
last_stencil = update->ntimestep;
@ -242,25 +242,25 @@ void NStencil::create_setup()
} else {
int i;
int n = atom->ntypes;
if (maxstencil_multi == 0) {
nstencil_multi = new int[n+1];
stencil_multi = new int*[n+1];
distsq_multi = new double*[n+1];
if (maxstencil_multi_old == 0) {
nstencil_multi_old = new int[n+1];
stencil_multi_old = new int*[n+1];
distsq_multi_old = new double*[n+1];
for (i = 1; i <= n; i++) {
nstencil_multi[i] = 0;
stencil_multi[i] = nullptr;
distsq_multi[i] = nullptr;
nstencil_multi_old[i] = 0;
stencil_multi_old[i] = nullptr;
distsq_multi_old[i] = nullptr;
}
}
if (smax > maxstencil_multi) {
maxstencil_multi = smax;
if (smax > maxstencil_multi_old) {
maxstencil_multi_old = smax;
for (i = 1; i <= n; i++) {
memory->destroy(stencil_multi[i]);
memory->destroy(distsq_multi[i]);
memory->create(stencil_multi[i],maxstencil_multi,
"neighstencil:stencil_multi");
memory->create(distsq_multi[i],maxstencil_multi,
"neighstencil:distsq_multi");
memory->destroy(stencil_multi_old[i]);
memory->destroy(distsq_multi_old[i]);
memory->create(stencil_multi_old[i],maxstencil_multi_old,
"neighstencil:stencil_multi_old");
memory->create(distsq_multi_old[i],maxstencil_multi_old,
"neighstencil:distsq_multi_old");
}
}
}
@ -269,7 +269,7 @@ void NStencil::create_setup()
double stencil_range;
int n = atom->ntypes;
if(nb) copy_bin_info_multi2();
if(nb) copy_bin_info_multi();
// Allocate arrays to store stencil information
memory->create(stencil_half, n+1, n+1,
@ -279,26 +279,26 @@ void NStencil::create_setup()
memory->create(stencil_bin_type, n+1, n+1,
"neighstencil:stencil_bin_type");
memory->create(stencil_sx_multi2, n+1, n+1,
"neighstencil:stencil_sx_multi2");
memory->create(stencil_sy_multi2, n+1, n+1,
"neighstencil:stencil_sy_multi2");
memory->create(stencil_sz_multi2, n+1, n+1,
"neighstencil:stencil_sz_multi2");
memory->create(stencil_sx_multi, n+1, n+1,
"neighstencil:stencil_sx_multi");
memory->create(stencil_sy_multi, n+1, n+1,
"neighstencil:stencil_sy_multi");
memory->create(stencil_sz_multi, n+1, n+1,
"neighstencil:stencil_sz_multi");
memory->create(stencil_binsizex_multi2, n+1, n+1,
"neighstencil:stencil_binsizex_multi2");
memory->create(stencil_binsizey_multi2, n+1, n+1,
"neighstencil:stencil_binsizey_multi2");
memory->create(stencil_binsizez_multi2, n+1, n+1,
"neighstencil:stencil_binsizez_multi2");
memory->create(stencil_binsizex_multi, n+1, n+1,
"neighstencil:stencil_binsizex_multi");
memory->create(stencil_binsizey_multi, n+1, n+1,
"neighstencil:stencil_binsizey_multi");
memory->create(stencil_binsizez_multi, n+1, n+1,
"neighstencil:stencil_binsizez_multi");
memory->create(stencil_mbinx_multi2, n+1, n+1,
"neighstencil:stencil_mbinx_multi2");
memory->create(stencil_mbiny_multi2, n+1, n+1,
"neighstencil:stencil_mbiny_multi2");
memory->create(stencil_mbinz_multi2, n+1, n+1,
"neighstencil:stencil_mbinz_multi2");
memory->create(stencil_mbinx_multi, n+1, n+1,
"neighstencil:stencil_mbinx_multi");
memory->create(stencil_mbiny_multi, n+1, n+1,
"neighstencil:stencil_mbiny_multi");
memory->create(stencil_mbinz_multi, n+1, n+1,
"neighstencil:stencil_mbinz_multi");
// Skip all stencils by default, initialize smax
for (i = 1; i <= n; i++) {
@ -312,15 +312,15 @@ void NStencil::create_setup()
// Allocate arrays to store stencils
if (!maxstencil_multi2) {
memory->create(maxstencil_multi2, n+1, n+1, "neighstencil::stencil_multi2");
memory->create(nstencil_multi2, n+1, n+1, "neighstencil::nstencil_multi2");
stencil_multi2 = new int**[n+1]();
if (!maxstencil_multi) {
memory->create(maxstencil_multi, n+1, n+1, "neighstencil::stencil_multi");
memory->create(nstencil_multi, n+1, n+1, "neighstencil::nstencil_multi");
stencil_multi = new int**[n+1]();
for (i = 1; i <= n; ++i) {
stencil_multi2[i] = new int*[n+1]();
stencil_multi[i] = new int*[n+1]();
for (j = 1; j <= n; ++j) {
maxstencil_multi2[i][j] = 0;
nstencil_multi2[i][j] = 0;
maxstencil_multi[i][j] = 0;
nstencil_multi[i][j] = 0;
}
}
}
@ -334,34 +334,34 @@ void NStencil::create_setup()
// Copy bin info for this particular pair of types
bin_type = stencil_bin_type[i][j];
stencil_binsizex_multi2[i][j] = binsizex_multi2[bin_type];
stencil_binsizey_multi2[i][j] = binsizey_multi2[bin_type];
stencil_binsizez_multi2[i][j] = binsizez_multi2[bin_type];
stencil_binsizex_multi[i][j] = binsizex_multi[bin_type];
stencil_binsizey_multi[i][j] = binsizey_multi[bin_type];
stencil_binsizez_multi[i][j] = binsizez_multi[bin_type];
stencil_mbinx_multi2[i][j] = mbinx_multi2[bin_type];
stencil_mbiny_multi2[i][j] = mbiny_multi2[bin_type];
stencil_mbinz_multi2[i][j] = mbinz_multi2[bin_type];
stencil_mbinx_multi[i][j] = mbinx_multi[bin_type];
stencil_mbiny_multi[i][j] = mbiny_multi[bin_type];
stencil_mbinz_multi[i][j] = mbinz_multi[bin_type];
stencil_range = sqrt(cutneighsq[i][j]);
sx = static_cast<int> (stencil_range*bininvx_multi2[bin_type]);
if (sx*binsizex_multi2[bin_type] < stencil_range) sx++;
sy = static_cast<int> (stencil_range*bininvy_multi2[bin_type]);
if (sy*binsizey_multi2[bin_type] < stencil_range) sy++;
sz = static_cast<int> (stencil_range*bininvz_multi2[bin_type]);
if (sz*binsizez_multi2[bin_type] < stencil_range) sz++;
sx = static_cast<int> (stencil_range*bininvx_multi[bin_type]);
if (sx*binsizex_multi[bin_type] < stencil_range) sx++;
sy = static_cast<int> (stencil_range*bininvy_multi[bin_type]);
if (sy*binsizey_multi[bin_type] < stencil_range) sy++;
sz = static_cast<int> (stencil_range*bininvz_multi[bin_type]);
if (sz*binsizez_multi[bin_type] < stencil_range) sz++;
stencil_sx_multi2[i][j] = sx;
stencil_sy_multi2[i][j] = sy;
stencil_sz_multi2[i][j] = sz;
stencil_sx_multi[i][j] = sx;
stencil_sy_multi[i][j] = sy;
stencil_sz_multi[i][j] = sz;
smax = ((2*sx+1) * (2*sy+1) * (2*sz+1));
if (smax > maxstencil_multi2[i][j]) {
maxstencil_multi2[i][j] = smax;
memory->destroy(stencil_multi2[i][j]);
memory->create(stencil_multi2[i][j], smax,
"neighstencil::stencil_multi2");
if (smax > maxstencil_multi[i][j]) {
maxstencil_multi[i][j] = smax;
memory->destroy(stencil_multi[i][j]);
memory->create(stencil_multi[i][j], smax,
"neighstencil::stencil_multi");
}
}
}
@ -396,21 +396,21 @@ double NStencil::bin_distance(int i, int j, int k)
compute closest distance for a given atom type
------------------------------------------------------------------------- */
double NStencil::bin_distance_multi2(int i, int j, int k, int type)
double NStencil::bin_distance_multi(int i, int j, int k, int type)
{
double delx,dely,delz;
if (i > 0) delx = (i-1)*binsizex_multi2[type];
if (i > 0) delx = (i-1)*binsizex_multi[type];
else if (i == 0) delx = 0.0;
else delx = (i+1)*binsizex_multi2[type];
else delx = (i+1)*binsizex_multi[type];
if (j > 0) dely = (j-1)*binsizey_multi2[type];
if (j > 0) dely = (j-1)*binsizey_multi[type];
else if (j == 0) dely = 0.0;
else dely = (j+1)*binsizey_multi2[type];
else dely = (j+1)*binsizey_multi[type];
if (k > 0) delz = (k-1)*binsizez_multi2[type];
if (k > 0) delz = (k-1)*binsizez_multi[type];
else if (k == 0) delz = 0.0;
else delz = (k+1)*binsizez_multi2[type];
else delz = (k+1)*binsizez_multi[type];
return (delx*delx + dely*dely + delz*delz);
}
@ -423,16 +423,16 @@ double NStencil::memory_usage()
if (neighstyle == Neighbor::BIN) {
bytes += memory->usage(stencil,maxstencil);
bytes += memory->usage(stencilxyz,maxstencil,3);
} else if (neighstyle == Neighbor::MULTI_OLD) {
bytes += atom->ntypes*maxstencil_multi_old * sizeof(int);
bytes += atom->ntypes*maxstencil_multi_old * sizeof(double);
} else if (neighstyle == Neighbor::MULTI) {
bytes += atom->ntypes*maxstencil_multi * sizeof(int);
bytes += atom->ntypes*maxstencil_multi * sizeof(double);
} else if (neighstyle == Neighbor::MULTI2) {
int n = atom->ntypes;
for (int i = 1; i <= n; i++) {
for (int j = 1; j <= n; j++) {
bytes += maxstencil_multi2[i][j] * sizeof(int);
bytes += maxstencil_multi2[i][j] * sizeof(int);
bytes += maxstencil_multi2[i][j] * sizeof(double);
bytes += maxstencil_multi[i][j] * sizeof(int);
bytes += maxstencil_multi[i][j] * sizeof(int);
bytes += maxstencil_multi[i][j] * sizeof(double);
}
}
bytes += 2 * n * n * sizeof(bool);