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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4457 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-08-06 15:13:04 +00:00
parent 6f2be925c4
commit 334ec50bba
1 changed files with 20 additions and 4 deletions
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24
src/special.cpp
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@ -708,8 +708,13 @@ void Special::angle_trim()
MPI_Status status; MPI_Status status;
int *num_angle = atom->num_angle; int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int **angle_atom1 = atom->angle_atom1; int **angle_atom1 = atom->angle_atom1;
int **angle_atom3 = atom->angle_atom3; 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;
int **nspecial = atom->nspecial; int **nspecial = atom->nspecial;
int **special = atom->special; int **special = atom->special;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
@ -732,9 +737,10 @@ void Special::angle_trim()
" %g = # of 1-3 neighbors before angle trim\n",allcount); " %g = # of 1-3 neighbors before angle trim\n",allcount);
} }
// if angles are defined, flag each 1-3 neigh if it appears in an angle // if angles or dihedrals are defined,
// flag each 1-3 neigh if it appears in an angle or dihedral
if (num_angle && atom->nangles) { if ((num_angle && atom->nangles) || (num_dihedral && atom->ndihedrals)) {
// dflag = flag for 1-3 neighs of all owned atoms // dflag = flag for 1-3 neighs of all owned atoms
@ -751,9 +757,10 @@ void Special::angle_trim()
// nbufmax = largest buffer needed to hold info from any proc // nbufmax = largest buffer needed to hold info from any proc
// info for each atom = list of 1,3 atoms in each angle stored by atom // info for each atom = list of 1,3 atoms in each angle stored by atom
// and list of 1,3 and 2,4 atoms in each dihedral stored by atom
int nbuf = 0; int nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += 2*num_angle[i]; for (i = 0; i < nlocal; i++) nbuf += 2*num_angle[i] + 2*2*num_dihedral[i];
int nbufmax; int nbufmax;
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world); MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
@ -762,6 +769,7 @@ void Special::angle_trim()
int *bufcopy = new int[nbufmax]; int *bufcopy = new int[nbufmax];
// fill buffer with list of 1,3 atoms in each angle // fill buffer with list of 1,3 atoms in each angle
// and with list of 1,3 and 2,4 atoms in each dihedral
int size = 0; int size = 0;
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++)
@ -769,6 +777,13 @@ void Special::angle_trim()
buf[size++] = angle_atom1[i][j]; buf[size++] = angle_atom1[i][j];
buf[size++] = angle_atom3[i][j]; buf[size++] = angle_atom3[i][j];
} }
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++) {
buf[size++] = dihedral_atom1[i][j];
buf[size++] = dihedral_atom3[i][j];
buf[size++] = dihedral_atom2[i][j];
buf[size++] = dihedral_atom4[i][j];
}
// cycle buffer around ring of procs back to self // cycle buffer around ring of procs back to self
// when receive buffer, scan list of 1,3 atoms looking for atoms I own // when receive buffer, scan list of 1,3 atoms looking for atoms I own
@ -831,7 +846,8 @@ void Special::angle_trim()
delete [] buf; delete [] buf;
delete [] bufcopy; delete [] bufcopy;
// if no angles are defined, delete all 1-3 neighs, preserving 1-4 neighs // if no angles or dihedrals are defined,
// delete all 1-3 neighs, preserving 1-4 neighs
} else { } else {
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {