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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10148 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-06-28 16:14:30 +00:00
parent 86cba5d3b2
commit dc119da585
6 changed files with 135 additions and 47 deletions
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32
src/GRANULAR/pair_gran_hertz_history.cpp
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@ -27,6 +27,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -60,12 +61,23 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
int shearupdate = 1;
if (update->setupflag) shearupdate = 0;
// update rigid body ptrs and values for ghost atoms if using FixRigid masses
// update rigid body info for owned & ghost atoms if using FixRigid masses
// body[i] = which body atom I is in, -1 if none
// mass_body = mass of each rigid body
if (fix_rigid && neighbor->ago == 0) {
int tmp;
body = (int *) fix_rigid->extract("body",tmp);
mass_rigid = (double *) fix_rigid->extract("masstotal",tmp);
int *body = (int *) fix_rigid->extract("body",tmp);
double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
if (atom->nmax > nmax) {
memory->destroy(mass_rigid);
nmax = atom->nmax;
memory->create(mass_rigid,nmax,"pair:mass_rigid");
}
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
else mass_rigid[i] = 0.0;
comm->forward_comm_pair(this);
}
@ -164,8 +176,8 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
mj = mass[type[j]];
}
if (fix_rigid) {
if (body[i] >= 0) mi = mass_rigid[body[i]];
if (body[j] >= 0) mj = mass_rigid[body[j]];
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi*mj / (mi+mj);
@ -374,13 +386,9 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
mj = mass[type[j]];
}
if (fix_rigid) {
// NOTE: need to make sure ghost atoms have updated body?
// depends on where single() is called from
int tmp;
body = (int *) fix_rigid->extract("body",tmp);
mass_rigid = (double *) fix_rigid->extract("masstotal",tmp);
if (body[i] >= 0) mi = mass_rigid[body[i]];
if (body[j] >= 0) mj = mass_rigid[body[j]];
// NOTE: insure mass_rigid is current for owned+ghost atoms?
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi*mj / (mi+mj);

33
src/GRANULAR/pair_gran_hooke.cpp
View File

@ -25,6 +25,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "comm.h"
#include "memory.h"
using namespace LAMMPS_NS;
@ -53,12 +54,23 @@ void PairGranHooke::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// update rigid body ptrs and values for ghost atoms if using FixRigid masses
// update rigid body info for owned & ghost atoms if using FixRigid masses
// body[i] = which body atom I is in, -1 if none
// mass_body = mass of each rigid body
if (fix_rigid && neighbor->ago == 0) {
int tmp;
body = (int *) fix_rigid->extract("body",tmp);
mass_rigid = (double *) fix_rigid->extract("masstotal",tmp);
int *body = (int *) fix_rigid->extract("body",tmp);
double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
if (atom->nmax > nmax) {
memory->destroy(mass_rigid);
nmax = atom->nmax;
memory->create(mass_rigid,nmax,"pair:mass_rigid");
}
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
else mass_rigid[i] = 0.0;
comm->forward_comm_pair(this);
}
@ -144,8 +156,8 @@ void PairGranHooke::compute(int eflag, int vflag)
mj = mass[type[j]];
}
if (fix_rigid) {
if (body[i] >= 0) mi = mass_rigid[body[i]];
if (body[j] >= 0) mj = mass_rigid[body[j]];
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi*mj / (mi+mj);
@ -290,14 +302,11 @@ double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
mi = mass[type[i]];
mj = mass[type[j]];
}
if (fix_rigid) {
// NOTE: need to make sure ghost atoms have updated body?
// depends on where single() is called from
int tmp;
body = (int *) fix_rigid->extract("body",tmp);
mass_rigid = (double *) fix_rigid->extract("masstotal",tmp);
if (body[i] >= 0) mi = mass_rigid[body[i]];
if (body[j] >= 0) mj = mass_rigid[body[j]];
// NOTE: insure mass_rigid is current for owned+ghost atoms?
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi*mj / (mi+mj);

54
src/GRANULAR/pair_gran_hooke_history.cpp
View File

@ -53,6 +53,13 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp)
computeflag = 0;
neighprev = 0;
nmax = 0;
mass_rigid = NULL;
// set comm size needed by this Pair if used with fix rigid
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
@ -72,6 +79,8 @@ PairGranHookeHistory::~PairGranHookeHistory()
delete [] maxrad_dynamic;
delete [] maxrad_frozen;
}
memory->destroy(mass_rigid);
}
/* ---------------------------------------------------------------------- */
@ -98,12 +107,23 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
int shearupdate = 1;
if (update->setupflag) shearupdate = 0;
// update rigid body ptrs and values for ghost atoms if using FixRigid masses
// update rigid body info for owned & ghost atoms if using FixRigid masses
// body[i] = which body atom I is in, -1 if none
// mass_body = mass of each rigid body
if (fix_rigid && neighbor->ago == 0) {
int tmp;
body = (int *) fix_rigid->extract("body",tmp);
mass_rigid = (double *) fix_rigid->extract("masstotal",tmp);
int *body = (int *) fix_rigid->extract("body",tmp);
double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
if (atom->nmax > nmax) {
memory->destroy(mass_rigid);
nmax = atom->nmax;
memory->create(mass_rigid,nmax,"pair:mass_rigid");
}
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
else mass_rigid[i] = 0.0;
comm->forward_comm_pair(this);
}
@ -202,8 +222,8 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
mj = mass[type[j]];
}
if (fix_rigid) {
if (body[i] >= 0) mi = mass_rigid[body[i]];
if (body[j] >= 0) mj = mass_rigid[body[j]];
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi*mj / (mi+mj);
@ -653,13 +673,9 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
mj = mass[type[j]];
}
if (fix_rigid) {
// NOTE: need to make sure ghost atoms have updated body?
// depends on where single() is called from
int tmp;
body = (int *) fix_rigid->extract("body",tmp);
mass_rigid = (double *) fix_rigid->extract("masstotal",tmp);
if (body[i] >= 0) mi = mass_rigid[body[i]];
if (body[j] >= 0) mj = mass_rigid[body[j]];
// NOTE: insure mass_rigid is current for owned+ghost atoms?
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi*mj / (mi+mj);
@ -745,7 +761,7 @@ int PairGranHookeHistory::pack_comm(int n, int *list,
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = body[j];
buf[m++] = mass_rigid[j];
}
return 1;
}
@ -759,7 +775,7 @@ void PairGranHookeHistory::unpack_comm(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++)
body[i] = static_cast<int> (buf[m++]);
mass_rigid[i] = buf[m++];
}
/* ---------------------------------------------------------------------- */
@ -770,3 +786,13 @@ void *PairGranHookeHistory::extract(const char *str, int &dim)
if (strcmp(str,"computeflag") == 0) return (void *) &computeflag;
return NULL;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairGranHookeHistory::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

10
src/GRANULAR/pair_gran_hooke_history.h
View File

@ -45,6 +45,7 @@ class PairGranHookeHistory : public Pair {
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
void *extract(const char *, int &);
double memory_usage();
protected:
double kn,kt,gamman,gammat,xmu;
@ -59,9 +60,12 @@ class PairGranHookeHistory : public Pair {
double *maxrad_dynamic,*maxrad_frozen;
class FixShearHistory *fix_history;
class Fix *fix_rigid;
int *body;
double *mass_rigid;
// storage of rigid body masses for use in granular interactions
class Fix *fix_rigid; // ptr to rigid body fix, NULL if none
double *mass_rigid; // rigid mass for owned+ghost atoms
int nmax; // allocated size of mass_rigid
void allocate();
};

47
src/RIGID/fix_rigid_small.cpp
View File

@ -151,6 +151,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
bodyown[i] = nlocal_body++;
} else bodyown[i] = -1;
// bodysize = sizeof(Body) in doubles
bodysize = sizeof(Body)/sizeof(double);
@ -217,6 +218,11 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
random = NULL;
if (langflag) random = new RanMars(lmp,seed + comm->me);
// mass vector for granular pair styles
mass_body = NULL;
nmax_mass = 0;
// firstflag = 1 triggers one-time initialization of rigid body attributes
firstflag = 1;
@ -244,6 +250,7 @@ FixRigidSmall::~FixRigidSmall()
delete random;
memory->destroy(langextra);
memory->destroy(mass_body);
}
/* ---------------------------------------------------------------------- */
@ -1289,10 +1296,7 @@ void FixRigidSmall::create_bodies()
n = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (hash->find(molecule[i]) == hash->end()) {
hash->insert(std::pair<int,int> (molecule[i],n));
n++;
}
if (hash->find(molecule[i]) == hash->end()) (*hash)[molecule[i]] = n++;
}
// bbox = bounding box of each rigid body my atoms are part of
@ -1552,7 +1556,7 @@ void FixRigidSmall::setup_bodies()
atom->tri_flag || atom->mu_flag) {
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (atom2body[i] < 0) continue;
if (bodytag[i] == 0) continue;
if (radius && radius[i] > 0.0) flag = 1;
if (ellipsoid && ellipsoid[i] >= 0) flag = 1;
if (line && line[i] >= 0) flag = 1;
@ -1577,7 +1581,7 @@ void FixRigidSmall::setup_bodies()
for (i = 0; i < nlocal; i++) {
eflags[i] = 0;
if (atom2body[i] < 0) continue;
if (bodytag[i] == 0) continue;
// set to POINT or SPHERE or ELLIPSOID or LINE
@ -2518,6 +2522,37 @@ void FixRigidSmall::reset_dt()
dtq = 0.5 * update->dt;
}
/* ---------------------------------------------------------------------- */
void *FixRigidSmall::extract(const char *str, int &dim)
{
if (strcmp(str,"body") == 0) {
dim = 1;
return atom2body;
}
// return vector of rigid body masses, for owned+ghost bodies
// used by granular pair styles, indexed by atom2body
if (strcmp(str,"masstotal") == 0) {
dim = 1;
if (nmax_mass < nmax_body) {
memory->destroy(mass_body);
nmax_mass = nmax_body;
memory->create(mass_body,nmax_mass,"rigid:mass_body");
}
int n = nlocal_body + nghost_body;
for (int i = 0; i < n; i++)
mass_body[i] = body[i].mass;
return mass_body;
}
return NULL;
}
/* ----------------------------------------------------------------------
return temperature of collection of rigid bodies
non-active DOF are removed by fflag/tflag and in tfactor

6
src/RIGID/fix_rigid_small.h
View File

@ -59,6 +59,7 @@ class FixRigidSmall : public Fix {
int dof(int);
void deform(int);
void reset_dt();
void *extract(const char*,int &);
double compute_scalar();
double memory_usage();
@ -128,6 +129,11 @@ class FixRigidSmall : public Fix {
int **counts; // counts of atom types in bodies
double **itensor; // 6 space-frame components of inertia tensor
// mass per body, accessed by granular pair styles
double *mass_body;
int nmax_mass;
// Langevin thermostatting
int langflag; // 0/1 = no/yes Langevin thermostat