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

enable replicate to work with local ptrs

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

93
src/atom_vec_line.cpp
View File

@ -86,6 +86,19 @@ void AtomVecLine::init()
error->all(FLERR,"Atom_style line can only be used in 2d simulations");
}
/* ----------------------------------------------------------------------
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 AtomVecLine::grow_pointers()
{
line = atom->line;
radius = atom->radius;
rmass = atom->rmass;
omega = atom->omega;
}
/* ----------------------------------------------------------------------
grow bonus data structure
------------------------------------------------------------------------- */
@ -106,8 +119,6 @@ void AtomVecLine::grow_bonus()
void AtomVecLine::copy_bonus(int i, int j, int delflag)
{
int *line = atom->line;
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && line[j] >= 0) {
@ -129,7 +140,7 @@ void AtomVecLine::copy_bonus(int i, int j, int delflag)
void AtomVecLine::copy_bonus_all(int i, int j)
{
atom->line[bonus[i].ilocal] = j;
line[bonus[i].ilocal] = j;
memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
}
@ -153,8 +164,6 @@ int AtomVecLine::pack_comm_bonus(int n, int *list, double *buf)
{
int i,j,m;
int *line = atom->line;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@ -170,8 +179,6 @@ void AtomVecLine::unpack_comm_bonus(int n, int first, double *buf)
{
int i,m,last;
int *line = atom->line;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@ -185,8 +192,6 @@ int AtomVecLine::pack_border_bonus(int n, int *list, double *buf)
{
int i,j,m;
int *line = atom->line;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@ -207,8 +212,6 @@ int AtomVecLine::unpack_border_bonus(int n, int first, double *buf)
{
int i,j,m,last;
int *line = atom->line;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@ -237,8 +240,6 @@ int AtomVecLine::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
int *line = atom->line;
if (line[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -256,8 +257,6 @@ int AtomVecLine::unpack_exchange_bonus(int ilocal, double *buf)
{
int m = 0;
int *line = atom->line;
line[ilocal] = (int) ubuf(buf[m++]).i;
if (line[ilocal] == 0) line[ilocal] = -1;
else {
@ -280,8 +279,6 @@ int AtomVecLine::size_restart_bonus()
{
int i;
int *line = atom->line;
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
@ -302,8 +299,6 @@ int AtomVecLine::pack_restart_bonus(int i, double *buf)
{
int m = 0;
int *line = atom->line;
if (line[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -323,8 +318,6 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
{
int m = 0;
int *line = atom->line;
line[ilocal] = (int) ubuf(buf[m++]).i;
if (line[ilocal] == 0) line[ilocal] = -1;
else {
@ -344,8 +337,6 @@ int AtomVecLine::unpack_restart_bonus(int ilocal, double *buf)
void AtomVecLine::data_atom_bonus(int m, char **values)
{
int *line = atom->line;
if (line[m]) error->one(FLERR,"Assigning line parameters to non-line atom");
if (nlocal_bonus == nmax_bonus) grow_bonus();
@ -377,8 +368,8 @@ void AtomVecLine::data_atom_bonus(int m, char **values)
// reset line radius and mass
// rmass currently holds density
atom->radius[m] = 0.5 * length;
atom->rmass[m] *= length;
radius[m] = 0.5 * length;
rmass[m] *= length;
bonus[nlocal_bonus].ilocal = m;
line[m] = nlocal_bonus++;
@ -402,10 +393,10 @@ bigint AtomVecLine::memory_usage_bonus()
void AtomVecLine::create_atom_post(int ilocal)
{
double radius = 0.5;
atom->radius[ilocal] = radius;
atom->rmass[ilocal] = 4.0*MY_PI/3.0 * radius*radius*radius;
atom->line[ilocal] = -1;
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] = 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
line[ilocal] = -1;
}
/* ----------------------------------------------------------------------
@ -415,24 +406,24 @@ void AtomVecLine::create_atom_post(int ilocal)
void AtomVecLine::data_atom_post(int ilocal)
{
line_flag = atom->line[ilocal];
line_flag = line[ilocal];
if (line_flag == 0) line_flag = -1;
else if (line_flag == 1) line_flag = 0;
else error->one(FLERR,"Invalid line flag in Atoms section of data file");
atom->line[ilocal] = line_flag;
line[ilocal] = line_flag;
if (atom->rmass[ilocal] <= 0.0)
if (rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid density in Atoms section of data file");
if (line_flag < 0) {
double radius = 0.5;
atom->radius[ilocal] = radius;
atom->rmass[ilocal] *= 4.0*MY_PI/3.0 * radius*radius*radius;
} else atom->radius[ilocal] = 0.0;
double radius_one = 0.5;
radius[ilocal] = radius_one;
rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else radius[ilocal] = 0.0;
atom->omega[ilocal][0] = 0.0;
atom->omega[ilocal][1] = 0.0;
atom->omega[ilocal][2] = 0.0;
omega[ilocal][0] = 0.0;
omega[ilocal][1] = 0.0;
omega[ilocal][2] = 0.0;
}
/* ----------------------------------------------------------------------
@ -441,16 +432,16 @@ void AtomVecLine::data_atom_post(int ilocal)
void AtomVecLine::pack_data_pre(int ilocal)
{
line_flag = atom->line[ilocal];
rmass = atom->rmass[ilocal];
line_flag = line[ilocal];
rmass_one = rmass[ilocal];
if (line_flag < 0) atom->line[ilocal] = 0;
else atom->line[ilocal] = 1;
if (line_flag < 0) line[ilocal] = 0;
else line[ilocal] = 1;
if (line_flag < 0) {
double radius = atom->radius[ilocal];
atom->rmass[ilocal] /= 4.0*MY_PI/3.0 * radius*radius*radius;
} else atom->rmass[ilocal] /= bonus[line_flag].length;
double radius_one = radius[ilocal];
rmass[ilocal] /= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
} else rmass[ilocal] /= bonus[line_flag].length;
}
/* ----------------------------------------------------------------------
@ -459,8 +450,8 @@ void AtomVecLine::pack_data_pre(int ilocal)
void AtomVecLine::pack_data_post(int ilocal)
{
atom->line[ilocal] = line_flag;
atom->rmass[ilocal] = rmass;
line[ilocal] = line_flag;
rmass[ilocal] = rmass_one;
}
/* ----------------------------------------------------------------------
@ -471,8 +462,6 @@ void AtomVecLine::pack_data_post(int ilocal)
void AtomVecLine::set_length(int i, double value)
{
int *line = atom->line;
if (line[i] < 0) {
if (value == 0.0) return;
if (nlocal_bonus == nmax_bonus) grow_bonus();
@ -489,8 +478,8 @@ void AtomVecLine::set_length(int i, double value)
// also set radius = half of length
// unless value = 0.0, then set diameter = 1.0
atom->radius[i] = 0.5 * value;
if (value == 0.0) atom->radius[i] = 0.5;
radius[i] = 0.5 * value;
if (value == 0.0) radius[i] = 0.5;
}
/* ----------------------------------------------------------------------