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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11250 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-17 18:43:09 +00:00
parent 961be6ee48
commit bad19033d0
172 changed files with 2523 additions and 2184 deletions
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85
src/special.cpp
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@ -56,15 +56,15 @@ void Special::build()
{
int i,j,k,size;
int max,maxall,nbuf;
int *buf;
tagint *buf;
MPI_Barrier(world);
int nlocal = atom->nlocal;
int *tag = atom->tag;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
int **bond_atom = atom->bond_atom;
tagint **bond_atom = atom->bond_atom;
int **nspecial = atom->nspecial;
if (me == 0 && screen) fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n");
@ -109,7 +109,7 @@ void Special::build()
// when find one, increment nspecial count for that atom
sptr = this;
comm->ring(size,sizeof(int),buf,1,ring_one,NULL);
comm->ring(size,sizeof(tagint),buf,1,ring_one,NULL);
memory->destroy(buf);
}
@ -167,7 +167,7 @@ void Special::build()
// when find one, add 1st-atom tag to onetwo list for 2nd atom
sptr = this;
comm->ring(size,sizeof(int),buf,2,ring_two,NULL);
comm->ring(size,sizeof(tagint),buf,2,ring_two,NULL);
memory->destroy(buf);
}
@ -214,7 +214,7 @@ void Special::build()
// subtracting one since my list will contain original atom
sptr = this;
comm->ring(size,sizeof(int),buf,3,ring_three,buf);
comm->ring(size,sizeof(tagint),buf,3,ring_three,buf);
// extract count from buffer that has cycled back to me
// nspecial[i][1] = # of 1-3 neighbors of atom i
@ -275,7 +275,7 @@ void Special::build()
// this process may include duplicates but they will be culled later
sptr = this;
comm->ring(size,sizeof(int),buf,4,ring_four,buf);
comm->ring(size,sizeof(tagint),buf,4,ring_four,buf);
// fill onethree with buffer values that have been returned to me
// sanity check: accumulated buf[i+3] count should equal
@ -330,7 +330,7 @@ void Special::build()
// may include duplicates and original atom but they will be culled later
sptr = this;
comm->ring(size,sizeof(int),buf,5,ring_five,buf);
comm->ring(size,sizeof(tagint),buf,5,ring_five,buf);
// extract count from buffer that has cycled back to me
// nspecial[i][2] = # of 1-4 neighbors of atom i
@ -389,7 +389,7 @@ void Special::build()
// this process may include duplicates but they will be culled later
sptr = this;
comm->ring(size,sizeof(int),buf,6,ring_six,buf);
comm->ring(size,sizeof(tagint),buf,6,ring_six,buf);
// fill onefour with buffer values that have been returned to me
// sanity check: accumulated buf[i+2] count should equal
@ -418,7 +418,8 @@ void Special::build()
void Special::dedup()
{
int i,j,m;
int i,j;
tagint m;
// clear map so it can be used as scratch space
@ -430,7 +431,7 @@ void Special::dedup()
// must unset map for each atom
int **nspecial = atom->nspecial;
int *tag = atom->tag;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int unique;
@ -494,13 +495,14 @@ void Special::dedup()
void Special::combine()
{
int i,j,m;
int i,j;
tagint m;
int me;
MPI_Comm_rank(world,&me);
int **nspecial = atom->nspecial;
int *tag = atom->tag;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// ----------------------------------------------------
@ -574,7 +576,7 @@ void Special::combine()
memory->create(atom->special,atom->nmax,atom->maxspecial,"atom:special");
atom->avec->grow_reset();
int **special = atom->special;
tagint **special = atom->special;
// ----------------------------------------------------
// fill special array with 1-2, 1-3, 1-4 neighs for each atom
@ -638,12 +640,12 @@ void Special::angle_trim()
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom3 = atom->angle_atom3;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom2 = atom->dihedral_atom2;
int **dihedral_atom3 = atom->dihedral_atom3;
int **dihedral_atom4 = atom->dihedral_atom4;
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom3 = atom->angle_atom3;
tagint **dihedral_atom1 = atom->dihedral_atom1;
tagint **dihedral_atom2 = atom->dihedral_atom2;
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_atom4;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
@ -716,7 +718,7 @@ void Special::angle_trim()
// when find one, scan its 1-3 neigh list and mark I,J as in an angle
sptr = this;
comm->ring(size,sizeof(int),buf,7,ring_seven,NULL);
comm->ring(size,sizeof(tagint),buf,7,ring_seven,NULL);
// delete 1-3 neighbors if they are not flagged in dflag
@ -764,8 +766,8 @@ void Special::dihedral_trim()
int i,j,m,n;
int *num_dihedral = atom->num_dihedral;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom4 = atom->dihedral_atom4;
tagint **dihedral_atom1 = atom->dihedral_atom1;
tagint **dihedral_atom4 = atom->dihedral_atom4;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
@ -822,7 +824,7 @@ void Special::dihedral_trim()
// when find one, scan its 1-4 neigh list and mark I,J as in a dihedral
sptr = this;
comm->ring(size,sizeof(int),buf,8,ring_eight,NULL);
comm->ring(size,sizeof(tagint),buf,8,ring_eight,NULL);
// delete 1-4 neighbors if they are not flagged in dflag
@ -871,7 +873,7 @@ void Special::ring_one(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int *buf = (int *) cbuf;
tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i++) {
@ -890,10 +892,10 @@ void Special::ring_two(int ndatum, char *cbuf)
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int **onetwo = sptr->onetwo;
tagint **onetwo = sptr->onetwo;
int *count = sptr->count;
int *buf = (int *) cbuf;
tagint *buf = (tagint *) cbuf;
int m;
for (int i = 1; i < ndatum; i += 2) {
@ -914,7 +916,7 @@ void Special::ring_three(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int *buf = (int *) cbuf;
tagint *buf = (tagint *) cbuf;
int i,j,m,n,num12;
i = 0;
@ -945,10 +947,11 @@ void Special::ring_four(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int **onetwo = sptr->onetwo;
tagint **onetwo = sptr->onetwo;
int *buf = (int *) cbuf;
int i,j,k,m,n,original,num12,num13;
tagint *buf = (tagint *) cbuf;
tagint original;
int i,j,k,m,n,num12,num13;
i = 0;
while (i < ndatum) {
@ -980,7 +983,7 @@ void Special::ring_five(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int *buf = (int *) cbuf;
tagint *buf = (tagint *) cbuf;
int i,j,m,n,num13;
i = 0;
@ -1009,9 +1012,9 @@ void Special::ring_six(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int **onetwo = sptr->onetwo;
tagint **onetwo = sptr->onetwo;
int *buf = (int *) cbuf;
tagint *buf = (tagint *) cbuf;
int i,j,k,m,n,num13,num14;
i = 0;
@ -1041,11 +1044,12 @@ void Special::ring_seven(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int **onethree = sptr->onethree;
tagint **onethree = sptr->onethree;
int **dflag = sptr->dflag;
int *buf = (int *) cbuf;
int i,m,iglobal,jglobal,ilocal,jlocal;
tagint *buf = (tagint *) cbuf;
tagint iglobal,jglobal;
int i,m,ilocal,jlocal;
i = 0;
while (i < ndatum) {
@ -1080,11 +1084,12 @@ void Special::ring_eight(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int **onefour = sptr->onefour;
tagint **onefour = sptr->onefour;
int **dflag = sptr->dflag;
int *buf = (int *) cbuf;
int i,m,iglobal,jglobal,ilocal,jlocal;
tagint *buf = (tagint *) cbuf;
tagint iglobal,jglobal;
int i,m,ilocal,jlocal;
i = 0;
while (i < ndatum) {