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

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5754 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2011-03-07 22:47:03 +00:00
parent 649ea52fbd
commit f60d2adc33
5 changed files with 85 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
src/atom_vec.h
View File

@ -40,7 +40,8 @@ class AtomVec : protected Pointers {
AtomVec(class LAMMPS *, int, char **); AtomVec(class LAMMPS *, int, char **);
virtual ~AtomVec() {} virtual ~AtomVec() {}
virtual void init() {} void init();
virtual void init_style() {}
virtual void grow(int) = 0; virtual void grow(int) = 0;
virtual void grow_reset() = 0; virtual void grow_reset() = 0;
@ -82,6 +83,9 @@ class AtomVec : protected Pointers {
protected: protected:
int nmax; // local copy of atom->nmax int nmax; // local copy of atom->nmax
int deform_vremap; // local copy of domain properties
int deform_groupbit;
double *h_rate;
}; };
} }

50
src/atom_vec_charge.cpp
View File

@ -155,7 +155,7 @@ int AtomVecCharge::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc) int pbc_flag, int *pbc)
{ {
int i,j,m; int i,j,m;
double dx,dy,dz; double dx,dy,dz,dvx,dvy,dvz;
m = 0; m = 0;
if (pbc_flag == 0) { if (pbc_flag == 0) {
@ -178,6 +178,7 @@ int AtomVecCharge::pack_comm_vel(int n, int *list, double *buf,
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd; dz = pbc[2]*domain->zprd;
} }
if (!deform_vremap) {
for (i = 0; i < n; i++) { for (i = 0; i < n; i++) {
j = list[i]; j = list[i];
buf[m++] = x[j][0] + dx; buf[m++] = x[j][0] + dx;
@ -187,6 +188,26 @@ int AtomVecCharge::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = v[j][1]; buf[m++] = v[j][1];
buf[m++] = v[j][2]; buf[m++] = v[j][2];
} }
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
}
} }
return m; return m;
} }
@ -305,7 +326,7 @@ int AtomVecCharge::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc) int pbc_flag, int *pbc)
{ {
int i,j,m; int i,j,m;
double dx,dy,dz; double dx,dy,dz,dvx,dvy,dvz;
m = 0; m = 0;
if (pbc_flag == 0) { if (pbc_flag == 0) {
@ -332,6 +353,7 @@ int AtomVecCharge::pack_border_vel(int n, int *list, double *buf,
dy = pbc[1]; dy = pbc[1];
dz = pbc[2]; dz = pbc[2];
} }
if (!deform_vremap) {
for (i = 0; i < n; i++) { for (i = 0; i < n; i++) {
j = list[i]; j = list[i];
buf[m++] = x[j][0] + dx; buf[m++] = x[j][0] + dx;
@ -345,6 +367,30 @@ int AtomVecCharge::pack_border_vel(int n, int *list, double *buf,
buf[m++] = v[j][1]; buf[m++] = v[j][1];
buf[m++] = v[j][2]; buf[m++] = v[j][2];
} }
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
}
} }
return m; return m;
} }

18
src/domain.cpp
View File

@ -107,14 +107,14 @@ void Domain::init()
// check for fix deform // check for fix deform
deform_flag = deform_remap = 0; deform_flag = deform_vremap = deform_groupbit = 0;
for (int i = 0; i < modify->nfix; i++) for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) { if (strcmp(modify->fix[i]->style,"deform") == 0) {
deform_flag = 1; deform_flag = 1;
if (((FixDeform *) modify->fix[i])->remapflag == V_REMAP) { if (((FixDeform *) modify->fix[i])->remapflag == V_REMAP) {
deform_remap = 1; deform_vremap = 1;
deform_groupbit = modify->fix[i]->groupbit; deform_groupbit = modify->fix[i]->groupbit;
} else deform_remap = 0; }
} }
// region inits // region inits
@ -384,7 +384,7 @@ void Domain::pbc()
if (xperiodic) { if (xperiodic) {
if (x[i][0] < lo[0]) { if (x[i][0] < lo[0]) {
x[i][0] += period[0]; x[i][0] += period[0];
if (deform_remap && mask[i] & deform_groupbit) v[i][0] += h_rate[0]; if (deform_vremap && mask[i] & deform_groupbit) v[i][0] += h_rate[0];
idim = image[i] & 1023; idim = image[i] & 1023;
otherdims = image[i] ^ idim; otherdims = image[i] ^ idim;
idim--; idim--;
@ -394,7 +394,7 @@ void Domain::pbc()
if (x[i][0] >= hi[0]) { if (x[i][0] >= hi[0]) {
x[i][0] -= period[0]; x[i][0] -= period[0];
x[i][0] = MAX(x[i][0],lo[0]); x[i][0] = MAX(x[i][0],lo[0]);
if (deform_remap && mask[i] & deform_groupbit) v[i][0] -= h_rate[0]; if (deform_vremap && mask[i] & deform_groupbit) v[i][0] -= h_rate[0];
idim = image[i] & 1023; idim = image[i] & 1023;
otherdims = image[i] ^ idim; otherdims = image[i] ^ idim;
idim++; idim++;
@ -406,7 +406,7 @@ void Domain::pbc()
if (yperiodic) { if (yperiodic) {
if (x[i][1] < lo[1]) { if (x[i][1] < lo[1]) {
x[i][1] += period[1]; x[i][1] += period[1];
if (deform_remap && mask[i] & deform_groupbit) { if (deform_vremap && mask[i] & deform_groupbit) {
v[i][0] += h_rate[5]; v[i][0] += h_rate[5];
v[i][1] += h_rate[1]; v[i][1] += h_rate[1];
} }
@ -419,7 +419,7 @@ void Domain::pbc()
if (x[i][1] >= hi[1]) { if (x[i][1] >= hi[1]) {
x[i][1] -= period[1]; x[i][1] -= period[1];
x[i][1] = MAX(x[i][1],lo[1]); x[i][1] = MAX(x[i][1],lo[1]);
if (deform_remap && mask[i] & deform_groupbit) { if (deform_vremap && mask[i] & deform_groupbit) {
v[i][0] -= h_rate[5]; v[i][0] -= h_rate[5];
v[i][1] -= h_rate[1]; v[i][1] -= h_rate[1];
} }
@ -434,7 +434,7 @@ void Domain::pbc()
if (zperiodic) { if (zperiodic) {
if (x[i][2] < lo[2]) { if (x[i][2] < lo[2]) {
x[i][2] += period[2]; x[i][2] += period[2];
if (deform_remap && mask[i] & deform_groupbit) { if (deform_vremap && mask[i] & deform_groupbit) {
v[i][0] += h_rate[4]; v[i][0] += h_rate[4];
v[i][1] += h_rate[3]; v[i][1] += h_rate[3];
v[i][2] += h_rate[2]; v[i][2] += h_rate[2];
@ -448,7 +448,7 @@ void Domain::pbc()
if (x[i][2] >= hi[2]) { if (x[i][2] >= hi[2]) {
x[i][2] -= period[2]; x[i][2] -= period[2];
x[i][2] = MAX(x[i][2],lo[2]); x[i][2] = MAX(x[i][2],lo[2]);
if (deform_remap && mask[i] & deform_groupbit) { if (deform_vremap && mask[i] & deform_groupbit) {
v[i][0] -= h_rate[4]; v[i][0] -= h_rate[4];
v[i][1] -= h_rate[3]; v[i][1] -= h_rate[3];
v[i][2] -= h_rate[2]; v[i][2] -= h_rate[2];

2
src/domain.h
View File

@ -75,7 +75,7 @@ class Domain : protected Pointers {
int box_change; // 1 if box bounds ever change, 0 if fixed int box_change; // 1 if box bounds ever change, 0 if fixed
int deform_flag; // 1 if fix deform exist, else 0 int deform_flag; // 1 if fix deform exist, else 0
int deform_remap; // 1 if fix deform remaps v, else 0 int deform_vremap; // 1 if fix deform remaps v, else 0
int deform_groupbit; // atom group to perform v remap for int deform_groupbit; // atom group to perform v remap for
class Lattice *lattice; // user-defined lattice class Lattice *lattice; // user-defined lattice

3
src/lammps.cpp
View File

@ -331,10 +331,11 @@ void LAMMPS::init()
update->init(); update->init();
force->init(); // pair must come after update due to minimizer force->init(); // pair must come after update due to minimizer
domain->init(); domain->init();
atom->init(); // atom must come after force: atom->init(); // atom must come after force and domain
// atom deletes extra array // atom deletes extra array
// used by fix shear_history::unpack_restart() // used by fix shear_history::unpack_restart()
// when force->pair->gran_history creates fix ?? // when force->pair->gran_history creates fix ??
// atom_vec init uses deform_vremap
modify->init(); // modify must come after update, force, atom, domain modify->init(); // modify must come after update, force, atom, domain
neighbor->init(); // neighbor must come after force, modify neighbor->init(); // neighbor must come after force, modify
comm->init(); // comm must come after force, modify, neighbor comm->init(); // comm must come after force, modify, neighbor