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enable replicate to work with local ptrs

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This commit is contained in:
Steve Plimpton
2019-12-18 08:56:03 -07:00
parent db6d272303
commit b6374bacfb
47 changed files with 686 additions and 480 deletions
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61
src/atom_vec_ellipsoid.cpp
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@ -75,6 +75,17 @@ AtomVecEllipsoid::~AtomVecEllipsoid()
memory->sfree(bonus);
}
/* ----------------------------------------------------------------------
set local copies of all grow ptrs used by this class, except defaults
needed in replicate when 2 atom classes exist and it calls pack_restart()
------------------------------------------------------------------------- */
void AtomVecEllipsoid::grow_pointers()
{
ellipsoid = atom->ellipsoid;
rmass = atom->rmass;
}
/* ----------------------------------------------------------------------
grow bonus data structure
------------------------------------------------------------------------- */
@ -95,8 +106,6 @@ void AtomVecEllipsoid::grow_bonus()
void AtomVecEllipsoid::copy_bonus(int i, int j, int delflag)
{
int *ellipsoid = atom->ellipsoid;
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && ellipsoid[j] >= 0) {
@ -118,7 +127,7 @@ void AtomVecEllipsoid::copy_bonus(int i, int j, int delflag)
void AtomVecEllipsoid::copy_bonus_all(int i, int j)
{
atom->ellipsoid[bonus[i].ilocal] = j;
ellipsoid[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
}
@ -143,8 +152,6 @@ int AtomVecEllipsoid::pack_comm_bonus(int n, int *list, double *buf)
int i,j,m;
double *quat;
int *ellipsoid = atom->ellipsoid;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@ -167,8 +174,6 @@ void AtomVecEllipsoid::unpack_comm_bonus(int n, int first, double *buf)
int i,m,last;
double *quat;
int *ellipsoid = atom->ellipsoid;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@ -190,8 +195,6 @@ int AtomVecEllipsoid::pack_border_bonus(int n, int *list, double *buf)
double dx,dy,dz;
double *shape,*quat;
int *ellipsoid = atom->ellipsoid;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@ -220,8 +223,6 @@ int AtomVecEllipsoid::unpack_border_bonus(int n, int first, double *buf)
int i,j,m,last;
double *shape,*quat;
int *ellipsoid = atom->ellipsoid;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@ -257,8 +258,6 @@ int AtomVecEllipsoid::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
int *ellipsoid = atom->ellipsoid;
if (ellipsoid[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -283,8 +282,6 @@ int AtomVecEllipsoid::unpack_exchange_bonus(int ilocal, double *buf)
{
int m = 0;
int *ellipsoid = atom->ellipsoid;
ellipsoid[ilocal] = (int) ubuf(buf[m++]).i;
if (ellipsoid[ilocal] == 0) ellipsoid[ilocal] = -1;
else {
@ -314,8 +311,6 @@ int AtomVecEllipsoid::size_restart_bonus()
{
int i;
int *ellipsoid = atom->ellipsoid;
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
@ -336,8 +331,6 @@ int AtomVecEllipsoid::pack_restart_bonus(int i, double *buf)
{
int m = 0;
int *ellipsoid = atom->ellipsoid;
if (ellipsoid[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -362,8 +355,6 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
{
int m = 0;
int *ellipsoid = atom->ellipsoid;
ellipsoid[ilocal] = (int) ubuf(buf[m++]).i;
if (ellipsoid[ilocal] == 0) ellipsoid[ilocal] = -1;
else {
@ -390,8 +381,6 @@ int AtomVecEllipsoid::unpack_restart_bonus(int ilocal, double *buf)
void AtomVecEllipsoid::data_atom_bonus(int m, char **values)
{
int *ellipsoid = atom->ellipsoid;
if (ellipsoid[m])
error->one(FLERR,"Assigning ellipsoid parameters to non-ellipsoid atom");
@ -414,7 +403,7 @@ void AtomVecEllipsoid::data_atom_bonus(int m, char **values)
// reset ellipsoid mass
// previously stored density in rmass
atom->rmass[m] *= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
rmass[m] *= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
bonus[nlocal_bonus].ilocal = m;
ellipsoid[m] = nlocal_bonus++;
@ -437,8 +426,8 @@ bigint AtomVecEllipsoid::memory_usage_bonus()
void AtomVecEllipsoid::create_atom_post(int ilocal)
{
atom->rmass[ilocal] = 1.0;
atom->ellipsoid[ilocal] = -1;
rmass[ilocal] = 1.0;
ellipsoid[ilocal] = -1;
}
/* ----------------------------------------------------------------------
@ -448,13 +437,13 @@ void AtomVecEllipsoid::create_atom_post(int ilocal)
void AtomVecEllipsoid::data_atom_post(int ilocal)
{
ellipsoid_flag = atom->ellipsoid[ilocal];
ellipsoid_flag = ellipsoid[ilocal];
if (ellipsoid_flag == 0) ellipsoid_flag = -1;
else if (ellipsoid_flag == 1) ellipsoid_flag = 0;
else error->one(FLERR,"Invalid ellipsoid flag in Atoms section of data file");
atom->ellipsoid[ilocal] = ellipsoid_flag;
ellipsoid[ilocal] = ellipsoid_flag;
if (atom->rmass[ilocal] <= 0.0)
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
}
@ -467,14 +456,14 @@ void AtomVecEllipsoid::pack_data_pre(int ilocal)
double *shape;
ellipsoid_flag = atom->ellipsoid[ilocal];
rmass = atom->rmass[ilocal];
rmass_one = atom->rmass[ilocal];
if (ellipsoid_flag < 0) atom->ellipsoid[ilocal] = 0;
else atom->ellipsoid[ilocal] = 1;
if (ellipsoid_flag < 0) ellipsoid[ilocal] = 0;
else ellipsoid[ilocal] = 1;
if (ellipsoid_flag >= 0) {
shape = bonus[ellipsoid_flag].shape;
atom->rmass[ilocal] /= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
rmass[ilocal] /= 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2];
}
}
@ -484,8 +473,8 @@ void AtomVecEllipsoid::pack_data_pre(int ilocal)
void AtomVecEllipsoid::pack_data_post(int ilocal)
{
atom->ellipsoid[ilocal] = ellipsoid_flag;
atom->rmass[ilocal] = rmass;
ellipsoid[ilocal] = ellipsoid_flag;
rmass[ilocal] = rmass_one;
}
/* ----------------------------------------------------------------------
@ -497,8 +486,6 @@ void AtomVecEllipsoid::pack_data_post(int ilocal)
void AtomVecEllipsoid::
set_shape(int i, double shapex, double shapey, double shapez)
{
int *ellipsoid = atom->ellipsoid;
if (ellipsoid[i] < 0) {
if (shapex == 0.0 && shapey == 0.0 && shapez == 0.0) return;
if (nlocal_bonus == nmax_bonus) grow_bonus();