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more additions to USER atom styles and bug fixes

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This commit is contained in:
Steve Plimpton
2019-12-13 13:54:12 -07:00
parent 9af08f2d54
commit db6d272303
29 changed files with 218 additions and 1289 deletions
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45
src/atom_vec_body.cpp
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@ -40,8 +40,8 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
// size_data_bonus is not used by Atom class for body style
size_forward_bonus = 4;
size_border_bonus = 9;
size_restart_bonus_one = 9;
size_border_bonus = 10;
size_restart_bonus_one = 10;
size_data_bonus = 0;
atom->body_flag = 1;
@ -72,11 +72,9 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
fields_border_vel = (char *) "radius rmass angmom";
fields_exchange = (char *) "radius rmass angmom";
fields_restart = (char *) "radius rmass angmom";
fields_create = (char *) "radius rmass angmom tri";
fields_create = (char *) "radius rmass angmom body";
fields_data_atom = (char *) "id type body rmass x";
fields_data_vel = (char *) "id v angmom";
setup_fields();
}
/* ---------------------------------------------------------------------- */
@ -127,6 +125,20 @@ void AtomVecBody::process_args(int narg, char **arg)
size_forward_bonus += bptr->size_forward;
size_border_bonus += bptr->size_border;
setup_fields();
}
/* ----------------------------------------------------------------------
grow atom arrays
must set local copy of body ptr
needed in replicate when 2 atom classes exist and pack_restart() is called
------------------------------------------------------------------------- */
void AtomVecBody::grow(int n)
{
AtomVec::grow(n);
body = atom->body;
}
/* ----------------------------------------------------------------------
@ -150,8 +162,6 @@ void AtomVecBody::grow_bonus()
void AtomVecBody::copy_bonus(int i, int j, int delflag)
{
int *body = atom->body;
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && body[j] >= 0) {
@ -206,8 +216,6 @@ int AtomVecBody::pack_comm_bonus(int n, int *list, double *buf)
int i,j,m;
double *quat;
int *body = atom->body;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@ -231,8 +239,6 @@ void AtomVecBody::unpack_comm_bonus(int n, int first, double *buf)
int i,m,last;
double *quat;
int *body = atom->body;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@ -254,8 +260,6 @@ int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
int i,j,m;
double *quat,*inertia;
int *body = atom->body;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@ -287,8 +291,6 @@ int AtomVecBody::unpack_border_bonus(int n, int first, double *buf)
int i,j,m,last;
double *quat,*inertia;
int *body = atom->body;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@ -330,8 +332,6 @@ int AtomVecBody::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
int *body = atom->body;
if (body[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -363,8 +363,6 @@ int AtomVecBody::unpack_exchange_bonus(int ilocal, double *buf)
{
int m = 0;
int *body = atom->body;
body[ilocal] = (int) ubuf(buf[m++]).i;
if (body[ilocal] == 0) body[ilocal] = -1;
else {
@ -408,8 +406,6 @@ int AtomVecBody::size_restart_bonus()
{
int i;
int *body = atom->body;
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
@ -418,8 +414,7 @@ int AtomVecBody::size_restart_bonus()
if (intdoubleratio == 1) n += bonus[body[i]].ninteger;
else n += (bonus[body[i]].ninteger+1)/2;
n += bonus[body[i]].ndouble;
}
n++;
} else n++;
}
return n;
@ -435,8 +430,6 @@ int AtomVecBody::pack_restart_bonus(int i, double *buf)
{
int m = 0;
int *body = atom->body;
if (body[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -470,8 +463,6 @@ int AtomVecBody::unpack_restart_bonus(int ilocal, double *buf)
{
int m = 0;
int *body = atom->body;
body[ilocal] = (int) ubuf(buf[m++]).i;
if (body[ilocal] == 0) body[ilocal] = -1;
else {