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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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58
src/atom_vec_body.cpp
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@ -100,6 +100,7 @@ AtomVecBody::~AtomVecBody()
void AtomVecBody::process_args(int narg, char **arg)
{
// suppress unused parameter warning dependent on style_body.h
(void)(arg);
if (narg < 1) error->all(FLERR,"Invalid atom_style body command");
@ -120,11 +121,12 @@ void AtomVecBody::process_args(int narg, char **arg)
icp = bptr->icp;
dcp = bptr->dcp;
// max size of forward/border comm
// max size of forward/border and exchange comm
// bptr values = max number of additional ivalues/dvalues from Body class
size_forward_bonus += bptr->size_forward;
size_border_bonus += bptr->size_border;
maxexchange = bptr->maxexchange;
setup_fields();
}
@ -138,7 +140,11 @@ void AtomVecBody::process_args(int narg, char **arg)
void AtomVecBody::grow(int n)
{
AtomVec::grow(n);
body = atom->body;
rmass = atom->rmass;
radius = atom->radius;
angmom = atom->angmom;
}
/* ----------------------------------------------------------------------
@ -186,7 +192,7 @@ void AtomVecBody::copy_bonus(int i, int j, int delflag)
void AtomVecBody::copy_bonus_all(int i, int j)
{
atom->body[bonus[i].ilocal] = j;
body[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
}
@ -503,9 +509,9 @@ int AtomVecBody::unpack_restart_bonus(int ilocal, double *buf)
void AtomVecBody::create_atom_post(int ilocal)
{
atom->radius[ilocal] = 0.5;
atom->rmass[ilocal] = 1.0;
atom->body[ilocal] = -1;
radius[ilocal] = 0.5;
rmass[ilocal] = 1.0;
body[ilocal] = -1;
}
/* ----------------------------------------------------------------------
@ -515,19 +521,19 @@ void AtomVecBody::create_atom_post(int ilocal)
void AtomVecBody::data_atom_post(int ilocal)
{
body_flag = atom->body[ilocal];
body_flag = body[ilocal];
if (body_flag == 0) body_flag = -1;
else if (body_flag == 1) body_flag = 0;
else error->one(FLERR,"Invalid body flag in Atoms section of data file");
atom->body[ilocal] = body_flag;
body[ilocal] = body_flag;
if (atom->rmass[ilocal] <= 0.0)
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
atom->radius[ilocal] = 0.5;
atom->angmom[ilocal][0] = 0.0;
atom->angmom[ilocal][1] = 0.0;
atom->angmom[ilocal][2] = 0.0;
radius[ilocal] = 0.5;
angmom[ilocal][0] = 0.0;
angmom[ilocal][1] = 0.0;
angmom[ilocal][2] = 0.0;
}
/* ----------------------------------------------------------------------
@ -537,12 +543,12 @@ void AtomVecBody::data_atom_post(int ilocal)
void AtomVecBody::data_body(int m, int ninteger, int ndouble,
int *ivalues, double *dvalues)
{
if (atom->body[m])
if (body[m])
error->one(FLERR,"Assigning body parameters to non-body atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
bonus[nlocal_bonus].ilocal = m;
bptr->data_body(nlocal_bonus,ninteger,ndouble,ivalues,dvalues);
atom->body[m] = nlocal_bonus++;
body[m] = nlocal_bonus++;
}
/* ----------------------------------------------------------------------
@ -570,10 +576,10 @@ bigint AtomVecBody::memory_usage_bonus()
void AtomVecBody::pack_data_pre(int ilocal)
{
body_flag = atom->body[ilocal];
body_flag = body[ilocal];
if (body_flag < 0) atom->body[ilocal] = 0;
else atom->body[ilocal] = 1;
if (body_flag < 0) body[ilocal] = 0;
else body[ilocal] = 1;
}
/* ----------------------------------------------------------------------
@ -582,7 +588,7 @@ void AtomVecBody::pack_data_pre(int ilocal)
void AtomVecBody::pack_data_post(int ilocal)
{
atom->body[ilocal] = body_flag;
body[ilocal] = body_flag;
}
/* ----------------------------------------------------------------------
@ -602,8 +608,8 @@ double AtomVecBody::radius_body(int ninteger, int ndouble,
void AtomVecBody::set_quat(int m, double *quat_external)
{
if (atom->body[m] < 0) error->one(FLERR,"Assigning quat to non-body atom");
double *quat = bonus[atom->body[m]].quat;
if (body[m] < 0) error->one(FLERR,"Assigning quat to non-body atom");
double *quat = bonus[body[m]].quat;
quat[0] = quat_external[0]; quat[1] = quat_external[1];
quat[2] = quat_external[2]; quat[3] = quat_external[3];
}
@ -616,15 +622,15 @@ void AtomVecBody::set_quat(int m, double *quat_external)
void AtomVecBody::check(int flag)
{
for (int i = 0; i < atom->nlocal; i++) {
if (atom->body[i] >= 0 && atom->body[i] >= nlocal_bonus) {
if (body[i] >= 0 && body[i] >= nlocal_bonus) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD AAA");
}
}
for (int i = atom->nlocal; i < atom->nlocal+atom->nghost; i++) {
if (atom->body[i] >= 0 &&
(atom->body[i] < nlocal_bonus ||
atom->body[i] >= nlocal_bonus+nghost_bonus)) {
if (body[i] >= 0 &&
(body[i] < nlocal_bonus ||
body[i] >= nlocal_bonus+nghost_bonus)) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD BBB");
}
@ -636,7 +642,7 @@ void AtomVecBody::check(int flag)
}
}
for (int i = 0; i < nlocal_bonus; i++) {
if (atom->body[bonus[i].ilocal] != i) {
if (body[bonus[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD DDD");
}
@ -649,7 +655,7 @@ void AtomVecBody::check(int flag)
}
}
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
if (atom->body[bonus[i].ilocal] != i) {
if (body[bonus[i].ilocal] != i) {
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
errorx->one(FLERR,"BAD FFF");
}