forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2656 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
f223b4951e
commit
5dc6a9e054
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@ -16,6 +16,7 @@
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------------------------------------------------------------------------- */
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#include "mpi.h"
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#include "string.h"
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#include "compute_group_group.h"
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#include "atom.h"
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#include "update.h"
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@ -41,7 +42,11 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
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extscalar = 1;
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extvector = 1;
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jgroup = group->find(arg[3]);
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int n = strlen(arg[3]) + 1;
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group2 = new char[n];
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strcpy(group2,arg[3]);
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jgroup = group->find(group2);
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if (jgroup == -1) error->all("Compute group/group group ID does not exist");
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jgroupbit = group->bitmask[jgroup];
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@ -52,6 +57,7 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
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ComputeGroupGroup::~ComputeGroupGroup()
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{
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delete [] group2;
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delete [] vector;
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}
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@ -64,6 +70,12 @@ void ComputeGroupGroup::init()
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pair = force->pair;
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cutsq = force->pair->cutsq;
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// recheck that group 2 has not been deleted
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jgroup = group->find(group2);
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if (jgroup == -1) error->all("Compute group/group group ID does not exist");
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jgroupbit = group->bitmask[jgroup];
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// need an occasional half neighbor list
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int irequest = neighbor->request((void *) this);
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@ -28,6 +28,7 @@ class ComputeGroupGroup : public Compute {
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void compute_vector();
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private:
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char *group2;
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int jgroup,jgroupbit,othergroupbit;
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double **cutsq;
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class Pair *pair;
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@ -49,6 +49,8 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
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extscalar = 1;
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extvector = 1;
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group2 = NULL;
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if (strcmp(arg[3],"tether") == 0) {
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if (narg != 9) error->all("Illegal fix spring command");
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styleflag = TETHER;
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@ -66,12 +68,17 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
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} else if (strcmp(arg[3],"couple") == 0) {
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if (narg != 10) error->all("Illegal fix spring command");
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styleflag = COUPLE;
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int n = strlen(arg[4]) + 1;
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group2 = new char[n];
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strcpy(group2,arg[4]);
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igroup2 = group->find(arg[4]);
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if (igroup2 == -1)
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error->all("Could not find fix spring couple group ID");
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error->all("Fix spring couple group ID does not exist");
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if (igroup2 == igroup)
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error->all("Two groups cannot be the same in fix spring couple");
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group2bit = group->bitmask[igroup2];
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k_spring = atof(arg[5]);
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xflag = yflag = zflag = 1;
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if (strcmp(arg[6],"NULL") == 0) xflag = 0;
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@ -90,6 +97,13 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
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/* ---------------------------------------------------------------------- */
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FixSpring::~FixSpring()
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{
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delete [] group2;
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}
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/* ---------------------------------------------------------------------- */
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int FixSpring::setmask()
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{
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int mask = 0;
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@ -104,6 +118,15 @@ int FixSpring::setmask()
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void FixSpring::init()
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{
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// recheck that group 2 has not been deleted
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if (group2) {
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igroup2 = group->find(group2);
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if (igroup2 == -1)
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error->all("Fix spring couple group ID does not exist");
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group2bit = group->bitmask[igroup2];
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}
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masstotal = group->mass(igroup);
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if (styleflag == COUPLE) masstotal2 = group->mass(igroup2);
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@ -21,6 +21,7 @@ namespace LAMMPS_NS {
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class FixSpring : public Fix {
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public:
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FixSpring(class LAMMPS *, int, char **);
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~FixSpring();
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int setmask();
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void init();
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void setup(int);
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@ -36,6 +37,7 @@ class FixSpring : public Fix {
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double k_spring;
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int xflag,yflag,zflag;
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int styleflag;
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char *group2;
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int igroup2,group2bit;
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double masstotal,masstotal2;
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int nlevels_respa;
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103
src/group.cpp
103
src/group.cpp
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@ -21,7 +21,11 @@
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#include "atom.h"
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#include "force.h"
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#include "region.h"
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#include "memory.h"
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#include "modify.h"
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#include "fix.h"
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#include "compute.h"
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#include "output.h"
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#include "dump.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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@ -44,9 +48,11 @@ Group::Group(LAMMPS *lmp) : Pointers(lmp)
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{
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MPI_Comm_rank(world,&me);
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names = (char **) memory->smalloc(MAX_GROUP*sizeof(char *),"group:names");
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names = new char*[MAX_GROUP];
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bitmask = new int[MAX_GROUP];
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inversemask = new int[MAX_GROUP];
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for (int i = 0; i < MAX_GROUP; i++) names[i] = NULL;
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for (int i = 0; i < MAX_GROUP; i++) bitmask[i] = 1 << i;
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for (int i = 0; i < MAX_GROUP; i++) inversemask[i] = bitmask[i] ^ ~0;
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@ -54,7 +60,7 @@ Group::Group(LAMMPS *lmp) : Pointers(lmp)
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char *str = (char *) "all";
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int n = strlen(str) + 1;
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names[0] = (char *) memory->smalloc(n*sizeof(char),"group:names[]");
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names[0] = new char[n];
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strcpy(names[0],str);
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ngroup = 1;
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}
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@ -65,8 +71,8 @@ Group::Group(LAMMPS *lmp) : Pointers(lmp)
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Group::~Group()
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{
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for (int i = 0; i < ngroup; i++) memory->sfree(names[i]);
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memory->sfree(names);
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for (int i = 0; i < MAX_GROUP; i++) delete [] names[i];
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delete [] names;
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delete [] bitmask;
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delete [] inversemask;
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}
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@ -83,18 +89,49 @@ void Group::assign(int narg, char **arg)
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error->all("Group command before simulation box is defined");
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if (narg < 2) error->all("Illegal group command");
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// delete the group if not being used elsewhere
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// clear mask of each atom assigned to this group
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if (strcmp(arg[1],"delete") == 0) {
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int igroup = find(arg[0]);
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if (igroup == -1) error->all("Could not find delete group ID");
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if (igroup == 0) error->all("Cannot delete group all");
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for (i = 0; i < modify->nfix; i++)
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if (modify->fix[i]->igroup == igroup)
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error->all("Cannot delete group currently used by a fix");
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for (i = 0; i < modify->ncompute; i++)
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if (modify->compute[i]->igroup == igroup)
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error->all("Cannot delete group currently used by a compute");
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for (i = 0; i < output->ndump; i++)
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if (output->dump[i]->igroup == igroup)
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error->all("Cannot delete group currently used by a dump");
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if (atom->firstgroupname && strcmp(arg[0],atom->firstgroupname) == 0)
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error->all("Cannot delete group currently used by atom_modify first");
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int bits = inversemask[igroup];
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for (i = 0; i < nlocal; i++) mask[i] &= bits;
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delete [] names[igroup];
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names[igroup] = NULL;
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ngroup--;
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return;
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}
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// find group in existing list
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// igroup = -1 requires a new group, add it
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// add a new group if igroup = -1
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int igroup = find(arg[0]);
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if (igroup == -1) {
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if (ngroup == MAX_GROUP) error->all("Too many groups");
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igroup = ngroup;
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ngroup++;
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igroup = find_unused();
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int n = strlen(arg[0]) + 1;
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names[igroup] = (char *) memory->smalloc(n*sizeof(char),"group:names[]");
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names[igroup] = new char[n];
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strcpy(names[igroup],arg[0]);
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ngroup++;
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}
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double **x = atom->x;
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@ -329,20 +366,20 @@ void Group::create(char *name, int *flag)
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int i;
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// find group in existing list
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// igroup = -1 requires a new group, add it
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// add a new group if igroup = -1
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int igroup = find(name);
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if (igroup == -1) {
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if (ngroup == MAX_GROUP) error->all("Too many groups");
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igroup = ngroup;
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ngroup++;
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igroup = find_unused();
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int n = strlen(name) + 1;
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names[igroup] = (char *) memory->smalloc(n*sizeof(char),"group:names[]");
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names[igroup] = new char[n];
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strcpy(names[igroup],name);
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ngroup++;
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}
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// add atom to group if flag is set
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// add atoms to group whose flags are set
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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@ -358,8 +395,20 @@ void Group::create(char *name, int *flag)
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int Group::find(const char *name)
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{
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for (int igroup = 0; igroup < ngroup; igroup++)
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if (strcmp(name,names[igroup]) == 0) return igroup;
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for (int igroup = 0; igroup < MAX_GROUP; igroup++)
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if (names[igroup] && strcmp(name,names[igroup]) == 0) return igroup;
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return -1;
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}
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/* ----------------------------------------------------------------------
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return index of first available group
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should never be called when group limit has been reached
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------------------------------------------------------------------------- */
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int Group::find_unused()
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{
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for (int igroup = 0; igroup < MAX_GROUP; igroup++)
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if (names[igroup] == NULL) return igroup;
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return -1;
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}
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@ -373,10 +422,11 @@ void Group::write_restart(FILE *fp)
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fwrite(&ngroup,sizeof(int),1,fp);
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int n;
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for (int i = 0; i < ngroup; i++) {
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n = strlen(names[i]) + 1;
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for (int i = 0; i < MAX_GROUP; i++) {
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if (names[i]) n = strlen(names[i]) + 1;
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else n = 0;
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fwrite(&n,sizeof(int),1,fp);
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fwrite(names[i],sizeof(char),n,fp);
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if (n) fwrite(names[i],sizeof(char),n,fp);
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}
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}
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@ -389,17 +439,22 @@ void Group::read_restart(FILE *fp)
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{
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int i,n;
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for (i = 0; i < ngroup; i++) memory->sfree(names[i]);
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// delete existing group names
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// atom masks will be overwritten by reading of restart file
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for (i = 0; i < MAX_GROUP; i++) delete [] names[i];
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if (me == 0) fread(&ngroup,sizeof(int),1,fp);
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MPI_Bcast(&ngroup,1,MPI_INT,0,world);
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for (i = 0; i < ngroup; i++) {
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for (i = 0; i < MAX_GROUP; i++) {
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if (me == 0) fread(&n,sizeof(int),1,fp);
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MPI_Bcast(&n,1,MPI_INT,0,world);
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names[i] = (char *) memory->smalloc(n*sizeof(char),"group:names[]");
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if (me == 0) fread(names[i],sizeof(char),n,fp);
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MPI_Bcast(names[i],n,MPI_CHAR,0,world);
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if (n) {
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names[i] = new char[n];
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if (me == 0) fread(names[i],sizeof(char),n,fp);
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MPI_Bcast(names[i],n,MPI_CHAR,0,world);
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} else names[i] = NULL;
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}
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}
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10
src/group.h
10
src/group.h
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@ -21,11 +21,8 @@ namespace LAMMPS_NS {
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class Group : protected Pointers {
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public:
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int me;
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int ngroup; // # of defined groups
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char **names; // name of each group
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int *bitmask; // one-bit mask for each group
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int *inversemask; // inverse mask for each group
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Group(class LAMMPS *);
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~Group();
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@ -47,6 +44,13 @@ class Group : protected Pointers {
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void angmom(int, double *, double *); // angular momentum of group
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void inertia(int, double *, double [3][3]); // inertia tensor
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void omega(double *, double [3][3], double *); // angular velocity
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private:
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int me;
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int ngroup; // # of defined groups
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int *inversemask; // inverse mask for each group
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int find_unused();
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};
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}
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