diff --git a/src/special.cpp b/src/special.cpp
index 420a8388a..d2d1858cd 100644
--- a/src/special.cpp
+++ b/src/special.cpp
@@ -1,1121 +1,1129 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "stdio.h"
#include "special.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "comm.h"
#include "accelerator_kokkos.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// allocate space for static class variable
Special *Special::sptr;
/* ---------------------------------------------------------------------- */
Special::Special(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
onetwo = onethree = onefour = NULL;
}
/* ---------------------------------------------------------------------- */
Special::~Special()
{
memory->destroy(onetwo);
memory->destroy(onethree);
memory->destroy(onefour);
}
/* ----------------------------------------------------------------------
create 1-2, 1-3, 1-4 lists of topology neighbors
store in onetwo, onethree, onefour for each atom
store 3 counters in nspecial[i]
------------------------------------------------------------------------- */
void Special::build()
{
int i,j,k,size;
int max,maxall,nbuf;
tagint *buf;
MPI_Barrier(world);
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
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");
+ if (me == 0 && screen) {
+ const double * const special_lj = force->special_lj;
+ const double * const special_coul = force->special_coul;
+ fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
+ " Factors LJ: %-10g %-10g %-10g\n"
+ " Factors Coul: %-10g %-10g %-10g\n",
+ special_lj[1],special_lj[2],special_lj[3],
+ special_coul[1],special_coul[2],special_coul[3]);
+ }
// initialize nspecial counters to 0
for (i = 0; i < nlocal; i++) {
nspecial[i][0] = 0;
nspecial[i][1] = 0;
nspecial[i][2] = 0;
}
// -----------------------------------------------------
// compute nspecial[i][0] = # of 1-2 neighbors of atom i
// -----------------------------------------------------
// bond partners stored by atom itself
for (i = 0; i < nlocal; i++) nspecial[i][0] = num_bond[i];
// if newton_bond off, then done
// else only counted 1/2 of all bonds, so count other half
if (force->newton_bond) {
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = global tag of 2nd atom in each bond
nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += num_bond[i];
memory->create(buf,nbuf,"special:buf");
// fill buffer with global tags of bond partners of my atoms
size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++)
buf[size++] = bond_atom[i][j];
// cycle buffer around ring of procs back to self
// when receive buffer, scan tags for atoms I own
// when find one, increment nspecial count for that atom
sptr = this;
comm->ring(size,sizeof(tagint),buf,1,ring_one,NULL);
memory->destroy(buf);
}
// ----------------------------------------------------
// create onetwo[i] = list of 1-2 neighbors for atom i
// ----------------------------------------------------
max = 0;
for (i = 0; i < nlocal; i++) max = MAX(max,nspecial[i][0]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
if (screen) fprintf(screen," %d = max # of 1-2 neighbors\n",maxall);
if (logfile) fprintf(logfile," %d = max # of 1-2 neighbors\n",maxall);
}
memory->create(onetwo,nlocal,maxall,"special:onetwo");
// count = accumulating counter
memory->create(count,nlocal,"special:count");
for (i = 0; i < nlocal; i++) count[i] = 0;
// add bond partners stored by atom to onetwo list
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++)
onetwo[i][count[i]++] = bond_atom[i][j];
// if newton_bond off, then done
// else only stored 1/2 of all bonds, so store other half
if (force->newton_bond) {
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = 2 global tags in each bond
nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += 2*num_bond[i];
memory->create(buf,nbuf,"special:buf");
// fill buffer with global tags of both atoms in bond
size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++) {
buf[size++] = tag[i];
buf[size++] = bond_atom[i][j];
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan 2nd-atom tags for atoms I own
// when find one, add 1st-atom tag to onetwo list for 2nd atom
sptr = this;
comm->ring(size,sizeof(tagint),buf,2,ring_two,NULL);
memory->destroy(buf);
}
memory->destroy(count);
// -----------------------------------------------------
// done if special_bond weights for 1-3, 1-4 are set to 1.0
// -----------------------------------------------------
if (force->special_lj[2] == 1.0 && force->special_coul[2] == 1.0 &&
force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0) {
dedup();
combine();
return;
}
// -----------------------------------------------------
// compute nspecial[i][1] = # of 1-3 neighbors of atom i
// -----------------------------------------------------
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = 2 scalars + list of 1-2 neighbors
nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += 2 + nspecial[i][0];
memory->create(buf,nbuf,"special:buf");
// fill buffer with:
// (1) = counter for 1-3 neighbors, initialized to 0
// (2) = # of 1-2 neighbors
// (3:N) = list of 1-2 neighbors
size = 0;
for (i = 0; i < nlocal; i++) {
buf[size++] = 0;
buf[size++] = nspecial[i][0];
for (j = 0; j < nspecial[i][0]; j++) buf[size++] = onetwo[i][j];
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan list of 1-2 neighbors for atoms I own
// when find one, increment 1-3 count by # of 1-2 neighbors of my atom,
// subtracting one since my list will contain original atom
sptr = this;
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
j = 0;
for (i = 0; i < nlocal; i++) {
nspecial[i][1] = buf[j];
j += 2 + nspecial[i][0];
}
memory->destroy(buf);
// ----------------------------------------------------
// create onethree[i] = list of 1-3 neighbors for atom i
// ----------------------------------------------------
max = 0;
for (i = 0; i < nlocal; i++) max = MAX(max,nspecial[i][1]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
if (screen) fprintf(screen," %d = max # of 1-3 neighbors\n",maxall);
if (logfile) fprintf(logfile," %d = max # of 1-3 neighbors\n",maxall);
}
memory->create(onethree,nlocal,maxall,"special:onethree");
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = 4 scalars + list of 1-2 neighs + list of 1-3 neighs
nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += 4 + nspecial[i][0] + nspecial[i][1];
memory->create(buf,nbuf,"special:buf");
// fill buffer with:
// (1) = global tag of original atom
// (2) = # of 1-2 neighbors
// (3) = # of 1-3 neighbors
// (4) = counter for 1-3 neighbors, initialized to 0
// (5:N) = list of 1-2 neighbors
// (N+1:2N) space for list of 1-3 neighbors
size = 0;
for (i = 0; i < nlocal; i++) {
buf[size++] = tag[i];
buf[size++] = nspecial[i][0];
buf[size++] = nspecial[i][1];
buf[size++] = 0;
for (j = 0; j < nspecial[i][0]; j++) buf[size++] = onetwo[i][j];
size += nspecial[i][1];
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan list of 1-2 neighbors for atoms I own
// when find one, add its neighbors to 1-3 list
// increment the count in buf(i+4)
// exclude the atom whose tag = original
// this process may include duplicates but they will be culled later
sptr = this;
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
// nspecial[i][1] for each atom
j = 0;
for (i = 0; i < nlocal; i++) {
if (buf[j+3] != nspecial[i][1])
error->one(FLERR,"1-3 bond count is inconsistent");
j += 4 + nspecial[i][0];
for (k = 0; k < nspecial[i][1]; k++)
onethree[i][k] = buf[j++];
}
memory->destroy(buf);
// done if special_bond weights for 1-4 are set to 1.0
if (force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0) {
dedup();
if (force->special_angle) angle_trim();
combine();
return;
}
// -----------------------------------------------------
// compute nspecial[i][2] = # of 1-4 neighbors of atom i
// -----------------------------------------------------
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = 2 scalars + list of 1-3 neighbors
nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += 2 + nspecial[i][1];
memory->create(buf,nbuf,"special:buf");
// fill buffer with:
// (1) = counter for 1-4 neighbors, initialized to 0
// (2) = # of 1-3 neighbors
// (3:N) = list of 1-3 neighbors
size = 0;
for (i = 0; i < nlocal; i++) {
buf[size++] = 0;
buf[size++] = nspecial[i][1];
for (j = 0; j < nspecial[i][1]; j++) buf[size++] = onethree[i][j];
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan list of 1-3 neighbors for atoms I own
// when find one, increment 1-4 count by # of 1-2 neighbors of my atom
// may include duplicates and original atom but they will be culled later
sptr = this;
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
j = 0;
for (i = 0; i < nlocal; i++) {
nspecial[i][2] = buf[j];
j += 2 + nspecial[i][1];
}
memory->destroy(buf);
// ----------------------------------------------------
// create onefour[i] = list of 1-4 neighbors for atom i
// ----------------------------------------------------
max = 0;
for (i = 0; i < nlocal; i++) max = MAX(max,nspecial[i][2]);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
if (screen) fprintf(screen," %d = max # of 1-4 neighbors\n",maxall);
if (logfile) fprintf(logfile," %d = max # of 1-4 neighbors\n",maxall);
}
memory->create(onefour,nlocal,maxall,"special:onefour");
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = 3 scalars + list of 1-3 neighs + list of 1-4 neighs
nbuf = 0;
for (i = 0; i < nlocal; i++)
nbuf += 3 + nspecial[i][1] + nspecial[i][2];
memory->create(buf,nbuf,"special:buf");
// fill buffer with:
// (1) = # of 1-3 neighbors
// (2) = # of 1-4 neighbors
// (3) = counter for 1-4 neighbors, initialized to 0
// (4:N) = list of 1-3 neighbors
// (N+1:2N) space for list of 1-4 neighbors
size = 0;
for (i = 0; i < nlocal; i++) {
buf[size++] = nspecial[i][1];
buf[size++] = nspecial[i][2];
buf[size++] = 0;
for (j = 0; j < nspecial[i][1]; j++) buf[size++] = onethree[i][j];
size += nspecial[i][2];
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan list of 1-3 neighbors for atoms I own
// when find one, add its neighbors to 1-4 list
// incrementing the count in buf(i+4)
// this process may include duplicates but they will be culled later
sptr = this;
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
// nspecial[i][2] for each atom
j = 0;
for (i = 0; i < nlocal; i++) {
if (buf[j+2] != nspecial[i][2])
error->one(FLERR,"1-4 bond count is inconsistent");
j += 3 + nspecial[i][1];
for (k = 0; k < nspecial[i][2]; k++)
onefour[i][k] = buf[j++];
}
memory->destroy(buf);
dedup();
if (force->special_angle) angle_trim();
if (force->special_dihedral) dihedral_trim();
combine();
}
/* ----------------------------------------------------------------------
remove duplicates within each of onetwo, onethree, onefour individually
------------------------------------------------------------------------- */
void Special::dedup()
{
int i,j;
tagint m;
// clear map so it can be used as scratch space
atom->map_clear();
// use map to cull duplicates
// exclude original atom explicitly
// adjust onetwo, onethree, onefour values to reflect removed duplicates
// must unset map for each atom
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int unique;
for (i = 0; i < nlocal; i++) {
unique = 0;
atom->map_one(tag[i],0);
for (j = 0; j < nspecial[i][0]; j++) {
m = onetwo[i][j];
if (atom->map(m) < 0) {
onetwo[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][0] = unique;
atom->map_one(tag[i],-1);
for (j = 0; j < unique; j++) atom->map_one(onetwo[i][j],-1);
}
for (i = 0; i < nlocal; i++) {
unique = 0;
atom->map_one(tag[i],0);
for (j = 0; j < nspecial[i][1]; j++) {
m = onethree[i][j];
if (atom->map(m) < 0) {
onethree[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][1] = unique;
atom->map_one(tag[i],-1);
for (j = 0; j < unique; j++) atom->map_one(onethree[i][j],-1);
}
for (i = 0; i < nlocal; i++) {
unique = 0;
atom->map_one(tag[i],0);
for (j = 0; j < nspecial[i][2]; j++) {
m = onefour[i][j];
if (atom->map(m) < 0) {
onefour[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][2] = unique;
atom->map_one(tag[i],-1);
for (j = 0; j < unique; j++) atom->map_one(onefour[i][j],-1);
}
// re-create map
atom->nghost = 0;
atom->map_set();
}
/* ----------------------------------------------------------------------
concatenate onetwo, onethree, onefour into master atom->special list
remove duplicates between 3 lists, leave dup in first list it appears in
convert nspecial[0], nspecial[1], nspecial[2] into cumulative counters
------------------------------------------------------------------------- */
void Special::combine()
{
int i,j;
tagint m;
int me;
MPI_Comm_rank(world,&me);
int **nspecial = atom->nspecial;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// ----------------------------------------------------
// compute culled maxspecial = max # of special neighs of any atom
// ----------------------------------------------------
// clear map so it can be used as scratch space
atom->map_clear();
// unique = # of unique nspecial neighbors of one atom
// cull duplicates using map to check for them
// exclude original atom explicitly
// must unset map for each atom
int unique;
int maxspecial = 0;
for (i = 0; i < nlocal; i++) {
unique = 0;
atom->map_one(tag[i],0);
for (j = 0; j < nspecial[i][0]; j++) {
m = onetwo[i][j];
if (atom->map(m) < 0) {
unique++;
atom->map_one(m,0);
}
}
for (j = 0; j < nspecial[i][1]; j++) {
m = onethree[i][j];
if (atom->map(m) < 0) {
unique++;
atom->map_one(m,0);
}
}
for (j = 0; j < nspecial[i][2]; j++) {
m = onefour[i][j];
if (atom->map(m) < 0) {
unique++;
atom->map_one(m,0);
}
}
maxspecial = MAX(maxspecial,unique);
atom->map_one(tag[i],-1);
for (j = 0; j < nspecial[i][0]; j++) atom->map_one(onetwo[i][j],-1);
for (j = 0; j < nspecial[i][1]; j++) atom->map_one(onethree[i][j],-1);
for (j = 0; j < nspecial[i][2]; j++) atom->map_one(onefour[i][j],-1);
}
// compute global maxspecial, must be at least 1
// add in extra factor from special_bonds command
// allocate correct special array with same nmax, new maxspecial
// previously allocated one must be destroyed
// must make AtomVec class update its ptr to special
MPI_Allreduce(&maxspecial,&atom->maxspecial,1,MPI_INT,MPI_MAX,world);
atom->maxspecial += force->special_extra;
atom->maxspecial = MAX(atom->maxspecial,1);
if (me == 0) {
if (screen)
fprintf(screen," %d = max # of special neighbors\n",atom->maxspecial);
if (logfile)
fprintf(logfile," %d = max # of special neighbors\n",atom->maxspecial);
}
if (lmp->kokkos) {
AtomKokkos* atomKK = (AtomKokkos*) atom;
memory->grow_kokkos(atomKK->k_special,atom->special,
atom->nmax,atom->maxspecial,"atom:special");
} else {
memory->destroy(atom->special);
memory->create(atom->special,atom->nmax,atom->maxspecial,"atom:special");
}
atom->avec->grow_reset();
tagint **special = atom->special;
// ----------------------------------------------------
// fill special array with 1-2, 1-3, 1-4 neighs for each atom
// ----------------------------------------------------
// again use map to cull duplicates
// exclude original atom explicitly
// adjust nspecial[i] values to reflect removed duplicates
// nspecial[i][1] and nspecial[i][2] now become cumulative counters
for (i = 0; i < nlocal; i++) {
unique = 0;
atom->map_one(tag[i],0);
for (j = 0; j < nspecial[i][0]; j++) {
m = onetwo[i][j];
if (atom->map(m) < 0) {
special[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][0] = unique;
for (j = 0; j < nspecial[i][1]; j++) {
m = onethree[i][j];
if (atom->map(m) < 0) {
special[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][1] = unique;
for (j = 0; j < nspecial[i][2]; j++) {
m = onefour[i][j];
if (atom->map(m) < 0) {
special[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][2] = unique;
atom->map_one(tag[i],-1);
for (j = 0; j < nspecial[i][2]; j++) atom->map_one(special[i][j],-1);
}
// re-create map
atom->nghost = 0;
atom->map_set();
}
/* ----------------------------------------------------------------------
trim list of 1-3 neighbors by checking defined angles
delete a 1-3 neigh if they are not end atoms of a defined angle
and if they are not 1,3 or 2,4 atoms of a defined dihedral
------------------------------------------------------------------------- */
void Special::angle_trim()
{
int i,j,m,n;
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
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;
// stats on old 1-3 neighbor counts
double onethreecount = 0.0;
for (i = 0; i < nlocal; i++) onethreecount += nspecial[i][1];
double allcount;
MPI_Allreduce(&onethreecount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
" %g = # of 1-3 neighbors before angle trim\n",allcount);
if (logfile)
fprintf(logfile,
" %g = # of 1-3 neighbors before angle trim\n",allcount);
}
// if angles or dihedrals are defined,
// flag each 1-3 neigh if it appears in an angle or dihedral
if ((num_angle && atom->nangles) || (num_dihedral && atom->ndihedrals)) {
// dflag = flag for 1-3 neighs of all owned atoms
int maxcount = 0;
for (i = 0; i < nlocal; i++) maxcount = MAX(maxcount,nspecial[i][1]);
memory->create(dflag,nlocal,maxcount,"special::dflag");
for (i = 0; i < nlocal; i++) {
n = nspecial[i][1];
for (j = 0; j < n; j++) dflag[i][j] = 0;
}
// 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
// and list of 1,3 and 2,4 atoms in each dihedral stored by atom
int nbuf = 0;
for (i = 0; i < nlocal; i++) {
if (num_angle && atom->nangles) nbuf += 2*num_angle[i];
if (num_dihedral && atom->ndihedrals) nbuf += 2*2*num_dihedral[i];
}
int *buf;
memory->create(buf,nbuf,"special:buf");
// 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;
if (num_angle && atom->nangles)
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_angle[i]; j++) {
buf[size++] = angle_atom1[i][j];
buf[size++] = angle_atom3[i][j];
}
if (num_dihedral && atom->ndihedrals)
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
// when receive buffer, scan list of 1,3 atoms looking for atoms I own
// when find one, scan its 1-3 neigh list and mark I,J as in an angle
sptr = this;
comm->ring(size,sizeof(tagint),buf,7,ring_seven,NULL);
// delete 1-3 neighbors if they are not flagged in dflag
for (i = 0; i < nlocal; i++) {
m = 0;
for (j = 0; j < nspecial[i][1]; j++)
if (dflag[i][j]) onethree[i][m++] = onethree[i][j];
nspecial[i][1] = m;
}
// clean up
memory->destroy(dflag);
memory->destroy(buf);
// if no angles or dihedrals are defined, delete all 1-3 neighs
} else {
for (i = 0; i < nlocal; i++) nspecial[i][1] = 0;
}
// stats on new 1-3 neighbor counts
onethreecount = 0.0;
for (i = 0; i < nlocal; i++) onethreecount += nspecial[i][1];
MPI_Allreduce(&onethreecount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
" %g = # of 1-3 neighbors after angle trim\n",allcount);
if (logfile)
fprintf(logfile,
" %g = # of 1-3 neighbors after angle trim\n",allcount);
}
}
/* ----------------------------------------------------------------------
trim list of 1-4 neighbors by checking defined dihedrals
delete a 1-4 neigh if they are not end atoms of a defined dihedral
------------------------------------------------------------------------- */
void Special::dihedral_trim()
{
int i,j,m,n;
int *num_dihedral = atom->num_dihedral;
tagint **dihedral_atom1 = atom->dihedral_atom1;
tagint **dihedral_atom4 = atom->dihedral_atom4;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
// stats on old 1-4 neighbor counts
double onefourcount = 0.0;
for (i = 0; i < nlocal; i++) onefourcount += nspecial[i][2];
double allcount;
MPI_Allreduce(&onefourcount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
" %g = # of 1-4 neighbors before dihedral trim\n",allcount);
if (logfile)
fprintf(logfile,
" %g = # of 1-4 neighbors before dihedral trim\n",allcount);
}
// if dihedrals are defined, flag each 1-4 neigh if it appears in a dihedral
if (num_dihedral && atom->ndihedrals) {
// dflag = flag for 1-4 neighs of all owned atoms
int maxcount = 0;
for (i = 0; i < nlocal; i++) maxcount = MAX(maxcount,nspecial[i][2]);
memory->create(dflag,nlocal,maxcount,"special::dflag");
for (i = 0; i < nlocal; i++) {
n = nspecial[i][2];
for (j = 0; j < n; j++) dflag[i][j] = 0;
}
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = list of 1,4 atoms in each dihedral stored by atom
int nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += 2*num_dihedral[i];
int *buf;
memory->create(buf,nbuf,"special:buf");
// fill buffer with list of 1,4 atoms in each dihedral
int size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++) {
buf[size++] = dihedral_atom1[i][j];
buf[size++] = dihedral_atom4[i][j];
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan list of 1,4 atoms looking for atoms I own
// when find one, scan its 1-4 neigh list and mark I,J as in a dihedral
sptr = this;
comm->ring(size,sizeof(tagint),buf,8,ring_eight,NULL);
// delete 1-4 neighbors if they are not flagged in dflag
for (i = 0; i < nlocal; i++) {
m = 0;
for (j = 0; j < nspecial[i][2]; j++)
if (dflag[i][j]) onefour[i][m++] = onefour[i][j];
nspecial[i][2] = m;
}
// clean up
memory->destroy(dflag);
memory->destroy(buf);
// if no dihedrals are defined, delete all 1-4 neighs
} else {
for (i = 0; i < nlocal; i++) nspecial[i][2] = 0;
}
// stats on new 1-4 neighbor counts
onefourcount = 0.0;
for (i = 0; i < nlocal; i++) onefourcount += nspecial[i][2];
MPI_Allreduce(&onefourcount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
" %g = # of 1-4 neighbors after dihedral trim\n",allcount);
if (logfile)
fprintf(logfile,
" %g = # of 1-4 neighbors after dihedral trim\n",allcount);
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan tags for atoms I own
when find one, increment nspecial count for that atom
------------------------------------------------------------------------- */
void Special::ring_one(int ndatum, char *cbuf)
{
Atom *atom = sptr->atom;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i++) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) nspecial[m][0]++;
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan 2nd-atom tags for atoms I own
when find one, add 1st-atom tag to onetwo list for 2nd atom
------------------------------------------------------------------------- */
void Special::ring_two(int ndatum, char *cbuf)
{
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
tagint **onetwo = sptr->onetwo;
int *count = sptr->count;
tagint *buf = (tagint *) cbuf;
int m;
for (int i = 1; i < ndatum; i += 2) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) onetwo[m][count[m]++] = buf[i-1];
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan list of 1-2 neighbors for atoms I own
when find one, increment 1-3 count by # of 1-2 neighbors of my atom,
subtracting one since my list will contain original atom
------------------------------------------------------------------------- */
void Special::ring_three(int ndatum, char *cbuf)
{
Atom *atom = sptr->atom;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
tagint *buf = (tagint *) cbuf;
int i,j,m,n,num12;
i = 0;
while (i < ndatum) {
n = buf[i];
num12 = buf[i+1];
for (j = 0; j < num12; j++) {
m = atom->map(buf[i+2+j]);
if (m >= 0 && m < nlocal)
n += nspecial[m][0] - 1;
}
buf[i] = n;
i += 2 + num12;
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan list of 1-2 neighbors for atoms I own
when find one, add its neighbors to 1-3 list
increment the count in buf(i+4)
exclude the atom whose tag = original
this process may include duplicates but they will be culled later
------------------------------------------------------------------------- */
void Special::ring_four(int ndatum, char *cbuf)
{
Atom *atom = sptr->atom;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
tagint **onetwo = sptr->onetwo;
tagint *buf = (tagint *) cbuf;
tagint original;
int i,j,k,m,n,num12,num13;
i = 0;
while (i < ndatum) {
original = buf[i];
num12 = buf[i+1];
num13 = buf[i+2];
n = buf[i+3];
for (j = 0; j < num12; j++) {
m = atom->map(buf[i+4+j]);
if (m >= 0 && m < nlocal)
for (k = 0; k < nspecial[m][0]; k++)
if (onetwo[m][k] != original)
buf[i+4+num12+(n++)] = onetwo[m][k];
}
buf[i+3] = n;
i += 4 + num12 + num13;
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan list of 1-3 neighbors for atoms I own
when find one, increment 1-4 count by # of 1-2 neighbors of my atom
may include duplicates and original atom but they will be culled later
------------------------------------------------------------------------- */
void Special::ring_five(int ndatum, char *cbuf)
{
Atom *atom = sptr->atom;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
tagint *buf = (tagint *) cbuf;
int i,j,m,n,num13;
i = 0;
while (i < ndatum) {
n = buf[i];
num13 = buf[i+1];
for (j = 0; j < num13; j++) {
m = atom->map(buf[i+2+j]);
if (m >= 0 && m < nlocal) n += nspecial[m][0];
}
buf[i] = n;
i += 2 + num13;
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan list of 1-3 neighbors for atoms I own
when find one, add its neighbors to 1-4 list
incrementing the count in buf(i+4)
this process may include duplicates but they will be culled later
------------------------------------------------------------------------- */
void Special::ring_six(int ndatum, char *cbuf)
{
Atom *atom = sptr->atom;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
tagint **onetwo = sptr->onetwo;
tagint *buf = (tagint *) cbuf;
int i,j,k,m,n,num13,num14;
i = 0;
while (i < ndatum) {
num13 = buf[i];
num14 = buf[i+1];
n = buf[i+2];
for (j = 0; j < num13; j++) {
m = atom->map(buf[i+3+j]);
if (m >= 0 && m < nlocal)
for (k = 0; k < nspecial[m][0]; k++)
buf[i+3+num13+(n++)] = onetwo[m][k];
}
buf[i+2] = n;
i += 3 + num13 + num14;
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan list of 1,3 atoms looking for atoms I own
when find one, scan its 1-3 neigh list and mark I,J as in an angle
------------------------------------------------------------------------- */
void Special::ring_seven(int ndatum, char *cbuf)
{
Atom *atom = sptr->atom;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
tagint **onethree = sptr->onethree;
int **dflag = sptr->dflag;
tagint *buf = (tagint *) cbuf;
tagint iglobal,jglobal;
int i,m,ilocal,jlocal;
i = 0;
while (i < ndatum) {
iglobal = buf[i];
jglobal = buf[i+1];
ilocal = atom->map(iglobal);
jlocal = atom->map(jglobal);
if (ilocal >= 0 && ilocal < nlocal)
for (m = 0; m < nspecial[ilocal][1]; m++)
if (jglobal == onethree[ilocal][m]) {
dflag[ilocal][m] = 1;
break;
}
if (jlocal >= 0 && jlocal < nlocal)
for (m = 0; m < nspecial[jlocal][1]; m++)
if (iglobal == onethree[jlocal][m]) {
dflag[jlocal][m] = 1;
break;
}
i += 2;
}
}
/* ----------------------------------------------------------------------
when receive buffer, scan list of 1,4 atoms looking for atoms I own
when find one, scan its 1-4 neigh list and mark I,J as in a dihedral
------------------------------------------------------------------------- */
void Special::ring_eight(int ndatum, char *cbuf)
{
Atom *atom = sptr->atom;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
tagint **onefour = sptr->onefour;
int **dflag = sptr->dflag;
tagint *buf = (tagint *) cbuf;
tagint iglobal,jglobal;
int i,m,ilocal,jlocal;
i = 0;
while (i < ndatum) {
iglobal = buf[i];
jglobal = buf[i+1];
ilocal = atom->map(iglobal);
jlocal = atom->map(jglobal);
if (ilocal >= 0 && ilocal < nlocal)
for (m = 0; m < nspecial[ilocal][2]; m++)
if (jglobal == onefour[ilocal][m]) {
dflag[ilocal][m] = 1;
break;
}
if (jlocal >= 0 && jlocal < nlocal)
for (m = 0; m < nspecial[jlocal][2]; m++)
if (iglobal == onefour[jlocal][m]) {
dflag[jlocal][m] = 1;
break;
}
i += 2;
}
}
diff --git a/test-respa/dual-special/data.bnzwbox b/test-respa/dual-special/data.bnzwbox
new file mode 100644
index 000000000..407a414d1
--- /dev/null
+++ b/test-respa/dual-special/data.bnzwbox
@@ -0,0 +1,697 @@
+LAMMPS data file for default_name
+
+587 atoms
+12 bonds
+18 angles
+30 dihedrals
+0 impropers
+
+3 atom types
+2 bond types
+2 angle types
+2 dihedral types
+
+-11.3621 18.0429 xlo xhi
+-13.9039 16.0051 ylo yhi
+-13.1983 16.7857 zlo zhi
+
+Masses
+
+1 12.01
+2 1.008
+3 18.015000
+
+Bond Coeffs
+
+1 344.30000000000001 1.087
+2 478.39999999999998 1.387
+
+Angle Coeffs
+
+1 48.460000000000001 120.01005126147997
+2 67.180000000000007 119.97005135892852
+
+Dihedral Coeffs
+
+1 3.625 -1 2
+2 1.1000000000000001 -1 2
+
+Atoms
+
+1 1 2.36 1.266 2.813 0.000000 12.0 -0.13 0.00000 0.00000 0.00000 1
+2 2 1.613 1.52 3.563 0.000000 1.0 0.13 0.00000 0.00000 0.00000 1
+3 1 2.533 2.086 1.698 0.000000 12.0 -0.13 0.00000 0.00000 0.00000 1
+4 2 1.927 2.98 1.580 0.000000 1.0 0.13 0.00000 0.00000 0.00000 1
+5 1 3.488 1.758 0.736 0.000000 12.0 -0.13 0.00000 0.00000 0.00000 1
+6 2 3.626 2.397 -0.132 0.000000 1.0 0.13 0.00000 0.00000 0.00000 1
+7 1 4.27 0.61 0.887 0.000000 12.0 -0.13 0.00000 0.00000 0.00000 1
+8 2 5.009 0.355 0.137 0.000000 1.0 0.13 0.00000 0.00000 0.00000 1
+9 1 4.088 -0.21 2.002 0.000000 12.0 -0.13 0.00000 0.00000 0.00000 1
+10 2 4.694 -1.105 2.12 0.000000 1.0 0.13 0.00000 0.00000 0.00000 1
+11 1 3.134 0.118 2.964 0.000000 12.0 -0.13 0.00000 0.00000 0.00000 1
+12 2 2.996 -0.521 3.833 0.000000 1.0 0.13 0.00000 0.00000 0.00000 1
+13 3 -2.106 -4.049 4.900 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 2
+14 3 7.017 -2.905 0.217 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 3
+15 3 1.093 -8.262 0.988 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 4
+16 3 -3.268 -8.103 1.137 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 5
+17 3 8.424 2.737 -8.477 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 6
+18 3 2.505 -8.728 -6.752 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 7
+19 3 2.872 3.382 -9.423 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 8
+20 3 7.844 -10.651 -1.233 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 9
+21 3 -0.259 -3.662 -9.796 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 10
+22 3 0.867 -5.205 -7.083 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 11
+23 3 7.918 -6.103 -10.725 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 12
+24 3 4.315 2.335 -1.911 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 13
+25 3 5.040 -9.618 -0.865 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 14
+26 3 -2.753 -9.780 -1.003 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 15
+27 3 7.179 -6.748 4.580 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 16
+28 3 -9.523 1.404 -11.288 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 17
+29 3 3.013 -9.736 4.514 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 18
+30 3 5.259 -11.183 -7.701 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 19
+31 3 -1.368 -11.346 3.297 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 20
+32 3 -1.634 -7.819 6.053 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 21
+33 3 0.662 -12.148 -7.978 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 22
+34 3 -5.220 -10.591 -8.638 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 23
+35 3 0.905 -1.669 -0.657 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 24
+36 3 -0.615 -9.925 -8.942 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 25
+37 3 -1.551 3.039 5.153 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 26
+38 3 -6.713 3.723 -1.769 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 27
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+68 3 -7.680 4.231 3.580 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 57
+69 3 -5.277 0.133 -11.317 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 58
+70 3 7.805 5.500 -2.112 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 59
+71 3 8.877 -1.109 -6.016 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 60
+72 3 -7.421 0.432 -9.060 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 61
+73 3 -9.144 6.208 7.016 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 62
+74 3 -6.319 3.082 5.870 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 63
+75 3 0.803 1.401 -5.837 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 64
+76 3 -5.392 -0.443 -1.464 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 65
+77 3 -2.347 -0.609 -10.723 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 66
+78 3 -1.748 1.704 -10.420 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 67
+79 3 1.667 -7.217 5.223 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 68
+80 3 -9.646 -1.170 -8.686 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 69
+81 3 7.910 -8.482 6.540 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 70
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+85 3 -3.291 -12.446 -0.502 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 74
+86 3 -5.144 -4.321 -10.813 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 75
+87 3 4.745 -12.155 0.748 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 76
+88 3 3.852 -8.862 6.901 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 77
+89 3 -1.484 -10.817 -11.232 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 78
+90 3 5.176 -3.609 -4.649 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 79
+91 3 4.335 4.437 6.664 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 80
+92 3 -1.788 -4.977 -3.199 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 81
+93 3 -9.282 -1.430 6.736 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 82
+94 3 -1.548 1.442 1.013 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 83
+95 3 4.107 -2.620 -11.263 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 84
+96 3 -2.016 -1.281 1.377 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 85
+97 3 4.295 -0.680 5.625 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 86
+98 3 5.835 -8.595 -3.117 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 87
+99 3 -3.666 4.017 -8.175 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 88
+100 3 -4.258 1.449 4.809 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 89
+101 3 -8.903 2.357 -2.710 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 90
+102 3 3.239 5.569 -3.968 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 91
+103 3 -8.146 -12.449 -7.229 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 92
+104 3 -1.172 -8.395 3.004 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 93
+105 3 5.601 6.026 -5.504 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 94
+106 3 -3.061 -8.733 -8.532 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 95
+107 3 8.789 -8.452 -9.160 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 96
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+506 3 13.003 -1.301 5.560 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 495
+507 3 11.798 2.515 -7.616 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 496
+508 3 10.181 1.404 8.363 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 497
+509 3 14.484 -10.591 11.013 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 498
+510 3 16.655 -11.488 12.994 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 499
+511 3 9.968 -11.084 14.254 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 500
+512 3 13.988 -3.310 14.009 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 501
+513 3 9.979 -3.617 8.988 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 502
+514 3 9.989 5.367 10.248 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 503
+515 3 16.547 -9.217 14.271 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 504
+516 3 14.427 0.133 8.334 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 505
+517 3 12.283 0.432 10.591 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 506
+518 3 10.059 -1.170 10.965 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 507
+519 3 14.560 -4.321 8.838 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 508
+520 3 16.038 4.017 11.476 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 509
+521 3 11.559 -12.449 12.422 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 510
+522 3 16.643 -8.733 11.119 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 511
+523 3 9.854 -5.551 11.636 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 512
+524 3 13.867 -9.729 8.118 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 513
+525 3 13.177 -6.873 8.634 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 514
+526 3 16.338 5.938 8.885 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 515
+527 3 13.732 -0.476 12.919 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 516
+528 3 15.941 -6.715 12.826 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 517
+529 3 11.476 0.961 14.329 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 518
+530 3 11.661 -2.933 14.981 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 519
+531 3 12.713 -2.816 10.297 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 520
+532 3 10.038 4.748 15.551 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 521
+533 3 13.573 -7.595 11.188 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 522
+534 3 10.918 -10.162 8.594 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 523
+535 3 12.502 -5.269 11.984 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 524
+536 3 16.135 0.043 14.063 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 525
+537 3 14.273 5.599 13.197 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 526
+538 3 12.471 -9.864 12.764 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 527
+539 3 15.525 2.936 8.634 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 528
+540 3 11.740 -8.783 15.385 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 529
+541 3 11.798 2.515 12.036 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 530
+542 3 14.484 9.281 -8.638 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 531
+543 3 16.655 8.384 -6.657 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 532
+544 3 9.968 8.788 -5.397 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 533
+545 3 14.435 14.570 1.317 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 534
+546 3 16.547 10.655 -5.380 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 535
+547 3 16.413 7.426 -0.502 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 536
+548 3 11.559 7.423 -7.229 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 537
+549 3 16.643 11.139 -8.532 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 538
+550 3 9.854 14.321 -8.015 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 539
+551 3 15.454 8.946 -3.076 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 540
+552 3 13.867 10.143 -11.533 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 541
+553 3 14.261 10.823 4.421 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 542
+554 3 13.177 12.998 -11.017 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 543
+555 3 12.972 12.197 -0.488 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 544
+556 3 14.088 12.636 -3.179 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 545
+557 3 15.941 13.157 -6.825 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 546
+558 3 12.823 9.145 -2.699 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 547
+559 3 10.135 12.704 2.539 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 548
+560 3 13.300 9.457 0.369 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 549
+561 3 13.573 12.277 -8.463 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 550
+562 3 10.918 9.710 -11.057 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 551
+563 3 12.502 14.602 -7.667 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 552
+564 3 11.956 13.564 5.480 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 553
+565 3 11.258 7.828 4.343 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 554
+566 3 11.373 10.898 4.293 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 555
+567 3 11.325 13.284 -2.393 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 556
+568 3 12.471 10.008 -6.887 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 557
+569 3 10.064 11.436 -0.735 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 558
+570 3 15.305 13.235 5.564 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 559
+571 3 15.238 8.996 1.901 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 560
+572 3 11.740 11.089 -4.266 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 561
+573 3 14.484 9.281 11.013 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 562
+574 3 16.655 8.384 12.994 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 563
+575 3 9.968 8.788 14.254 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 564
+576 3 16.547 10.655 14.271 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 565
+577 3 11.559 7.423 12.422 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 566
+578 3 16.643 11.139 11.119 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 567
+579 3 9.854 14.321 11.636 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 568
+580 3 13.867 10.143 8.118 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 569
+581 3 13.177 12.998 8.634 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 570
+582 3 15.941 13.157 12.826 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 571
+583 3 13.573 12.277 11.188 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 572
+584 3 10.918 9.710 8.594 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 573
+585 3 12.502 14.602 11.984 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 574
+586 3 12.471 10.008 12.764 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 575
+587 3 11.740 11.089 15.385 4.080749 0.5063 0.00 0.53449 0.02447 0.08219 576
+
+Bonds
+
+1 1 11 12
+2 1 9 10
+3 2 9 11
+4 1 7 8
+5 2 7 9
+6 1 5 6
+7 2 5 7
+8 1 3 4
+9 2 3 5
+10 1 1 2
+11 2 1 3
+12 2 1 11
+
+Angles
+
+1 1 10 9 11
+2 1 9 11 12
+3 1 8 7 9
+4 1 7 9 10
+5 2 7 9 11
+6 1 6 5 7
+7 1 5 7 8
+8 2 5 7 9
+9 1 4 3 5
+10 2 3 1 11
+11 1 3 5 6
+12 2 3 5 7
+13 1 2 1 3
+14 1 2 1 11
+15 1 1 3 4
+16 2 1 3 5
+17 2 1 11 9
+18 1 1 11 12
+
+Dihedrals
+
+1 1 10 9 11 12
+2 1 8 7 9 10
+3 1 8 7 9 11
+4 1 7 9 11 12
+5 1 6 5 7 8
+6 1 6 5 7 9
+7 1 11 1 3 5
+8 1 5 7 9 10
+9 1 5 7 9 11
+10 1 11 1 3 4
+11 1 4 3 5 6
+12 1 4 3 5 7
+13 1 3 1 11 9
+14 1 3 1 11 12
+15 1 3 5 7 8
+16 1 3 5 7 9
+17 1 2 1 3 4
+18 1 2 1 3 5
+19 1 2 1 11 9
+20 1 2 1 11 12
+21 1 1 3 5 6
+22 1 1 3 5 7
+23 1 1 11 9 7
+24 1 1 11 9 10
+25 2 1 9 11 12
+26 2 7 11 9 10
+27 2 5 9 7 8
+28 2 3 7 5 6
+29 2 1 5 3 4
+30 2 2 1 11 3
+
diff --git a/test-respa/dual-special/in.verlet b/test-respa/dual-special/in.verlet
new file mode 100644
index 000000000..9aa920013
--- /dev/null
+++ b/test-respa/dual-special/in.verlet
@@ -0,0 +1,60 @@
+
+units real
+atom_style hybrid sphere dipole molecular
+
+# this is equivalent to special_bonds amber,
+# but also compatible with the per-style overrides below.
+special_bonds lj 0.0 1.0e-100 0.5 coul 0.0 1.0e-100 0.8333333333333333
+
+pair_style hybrid lj/sf/dipole/sf 12.0 lj/sf/dipole/sf 12.0 &
+ lj/charmm/coul/long 11.0 12.0
+pair_modify mix arithmetic
+pair_modify pair lj/sf/dipole/sf 1 special lj/coul 0.0 1.0 1.0
+pair_modify pair lj/sf/dipole/sf 2 special lj/coul 0.0 1.0 1.0
+
+kspace_style pppm/cg 1.0e-5
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+
+read_data data.bnzwbox
+
+# pair_coeffs:
+pair_coeff 1 1 lj/charmm/coul/long 0.0860 3.39967 0.0860 3.39967 # AA-AA
+pair_coeff 2 2 lj/charmm/coul/long 0.015000 2.59964 0.015000 2.59964 # AA-AA
+pair_coeff 3 3 lj/sf/dipole/sf 1 0.550000 3.050000 # CG-CG, this will be propagated with the longer timestep
+pair_coeff 1 2 lj/charmm/coul/long 0.0359 2.9997 0.0359 2.9997 # AA-AA
+pair_coeff 1 3 lj/sf/dipole/sf 2 0.2175 3.2248 # CG-AA, this will be propagated with the shorter timestep
+pair_coeff 2 3 lj/sf/dipole/sf 2 0.0908 2.8248 # CG-AA, this will be propagated with the shorter timestep
+
+
+# this will set individual per-atom masses - as required by
+# atom style sphere - to the same value as the per-type masses.
+set type 1 mass 12.011000
+set type 2 mass 1.008000
+set type 3 mass 40.00
+
+group solute molecule 1
+group water molecule > 1
+
+set group solute diameter 0.0
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check yes
+
+#timestep 8
+#run_style respa 2 4 hybrid 2 1 1 kspace 1 improper 2
+
+timestep 2.0
+run_style verlet
+
+fix integrateSolute solute nve
+fix integrateWater water nve/sphere update dipole
+
+fix thermostatWater water langevin 298 298 100 9 omega yes zero yes
+fix thermostatSolute solute langevin 298 298 100 9 zero yes
+
+thermo 100
+
+minimize 1.0E-4 1.0E-6 100 1000
+run 1000
diff --git a/test-respa/dual-special/log.verlet b/test-respa/dual-special/log.verlet
new file mode 100644
index 000000000..32320f704
--- /dev/null
+++ b/test-respa/dual-special/log.verlet
@@ -0,0 +1,194 @@
+LAMMPS (6 Apr 2015-ICMS)
+WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:89)
+ using 1 OpenMP thread(s) per MPI task
+
+units real
+atom_style hybrid sphere dipole molecular
+
+# this is equivalent to special_bonds amber,
+# but also compatible with the per-style overrides below.
+special_bonds lj 0.0 1.0e-100 0.5 coul 0.0 1.0e-100 0.8333333333333333
+
+pair_style hybrid lj/sf/dipole/sf 12.0 lj/sf/dipole/sf 12.0 lj/charmm/coul/long 11.0 12.0
+pair_modify mix arithmetic
+pair_modify pair lj/sf/dipole/sf 1 special lj/coul 0.0 1.0 1.0
+pair_modify pair lj/sf/dipole/sf 2 special lj/coul 0.0 1.0 1.0
+
+kspace_style pppm/cg 1.0e-5
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+
+read_data data.bnzwbox
+ orthogonal box = (-11.3621 -13.9039 -13.1983) to (18.0429 16.0051 16.7857)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 587 atoms
+ scanning bonds ...
+ 3 = max bonds/atom
+ scanning angles ...
+ 3 = max angles/atom
+ scanning dihedrals ...
+ 9 = max dihedrals/atom
+ reading bonds ...
+ 12 bonds
+ reading angles ...
+ 18 angles
+ reading dihedrals ...
+ 30 dihedrals
+ 3 = max # of 1-2 neighbors
+ 4 = max # of 1-3 neighbors
+ 8 = max # of 1-4 neighbors
+ 10 = max # of special neighbors
+
+# pair_coeffs:
+pair_coeff 1 1 lj/charmm/coul/long 0.0860 3.39967 0.0860 3.39967 # AA-AA
+pair_coeff 2 2 lj/charmm/coul/long 0.015000 2.59964 0.015000 2.59964 # AA-AA
+pair_coeff 3 3 lj/sf/dipole/sf 1 0.550000 3.050000 # CG-CG, this will be propagated with the longer timestep
+pair_coeff 1 2 lj/charmm/coul/long 0.0359 2.9997 0.0359 2.9997 # AA-AA
+pair_coeff 1 3 lj/sf/dipole/sf 2 0.2175 3.2248 # CG-AA, this will be propagated with the shorter timestep
+pair_coeff 2 3 lj/sf/dipole/sf 2 0.0908 2.8248 # CG-AA, this will be propagated with the shorter timestep
+
+
+# this will set individual per-atom masses - as required by
+# atom style sphere - to the same value as the per-type masses.
+set type 1 mass 12.011000
+ 6 settings made for mass
+set type 2 mass 1.008000
+ 6 settings made for mass
+set type 3 mass 40.00
+ 575 settings made for mass
+
+group solute molecule 1
+12 atoms in group solute
+group water molecule > 1
+575 atoms in group water
+
+set group solute diameter 0.0
+ 12 settings made for diameter
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check yes
+
+#timestep 8
+#run_style respa 2 4 hybrid 2 1 1 kspace 1 improper 2
+
+timestep 2.0
+run_style verlet
+
+fix integrateSolute solute nve
+fix integrateWater water nve/sphere update dipole
+
+fix thermostatWater water langevin 298 298 100 9 omega yes zero yes
+fix thermostatSolute solute langevin 298 298 100 9 zero yes
+
+thermo 100
+
+minimize 1.0E-4 1.0E-6 100 1000
+PPPM initialization ...
+ G vector (1/distance) = 0.107059
+ grid = 3 3 3
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.00268661
+ estimated relative force accuracy = 8.09066e-06
+ using double precision FFTs
+ 3d grid and FFT values/proc = 512 27
+Neighbor list info ...
+ 4 neighbor list requests
+ update every 1 steps, delay 0 steps, check yes
+ master list distance cutoff = 14
+ PPPM/cg optimization cutoff: 1e-05
+ Total charged atoms: 2.0%
+ Min/max charged atoms/proc: 2.0% 2.0%
+Memory usage per processor = 13.1326 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 1229.2095 0.19819566 1229.4077 33888.578
+ 100 0 -2841.678 2.1349864 -2839.543 1363.0469
+
+Loop time of 1.24367 on 1 procs for 100 steps with 587 atoms
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+ Stopping criterion = max iterations
+ Energy initial, next-to-last, final =
+ 1229.4076721 -2835.11740182 -2839.54299044
+ Force two-norm initial, final = 1311.12 92.7793
+ Force max component initial, final = 529.28 52.5897
+ Final line search alpha, max atom move = 0.00240725 0.126597
+ Iterations, force evaluations = 100 181
+
+MPI task timings breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.2039 | 1.2039 | 1.2039 | 0.0 | 96.80
+Bond | 0.0011945 | 0.0011945 | 0.0011945 | 0.0 | 0.10
+Kspace | 0.0033362 | 0.0033362 | 0.0033362 | 0.0 | 0.27
+Neigh | 0.015982 | 0.015982 | 0.015982 | 0.0 | 1.29
+Comm | 0.015237 | 0.015237 | 0.015237 | 0.0 | 1.23
+Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.003967 | | | 0.32
+
+Nlocal: 587 ave 587 max 587 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3599 ave 3599 max 3599 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 75832 ave 75832 max 75832 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 75832
+Ave neighs/atom = 129.186
+Ave special neighs/atom = 0.173765
+Neighbor list builds = 5
+Dangerous builds = 0
+run 1000
+PPPM initialization ...
+ G vector (1/distance) = 0.107059
+ grid = 3 3 3
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.00268661
+ estimated relative force accuracy = 8.09066e-06
+ using double precision FFTs
+ 3d grid and FFT values/proc = 512 27
+Memory usage per processor = 12.0076 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0 -2841.678 2.1349864 -2839.543 1363.0469
+ 200 285.39211 -2675.81 14.315456 -2162.9845 3732.8229
+ 300 291.58808 -2733.738 13.268339 -2211.1368 3040.2089
+ 400 298.44197 -2860.0383 15.480615 -2323.2528 2646.7134
+ 500 296.79448 -2966.7422 11.311007 -2437.004 1958.8059
+ 600 308.29218 -3120.7411 15.267691 -2566.9626 1558.7607
+ 700 312.67712 -3194.7043 8.7624891 -2639.7716 1212.4966
+ 800 308.86454 -3385.1928 14.905594 -2830.7766 204.85265
+ 900 296.81418 -3545.2909 13.78069 -3013.0487 528.53145
+ 1000 311.33831 -3682.4629 10.590424 -3128.0408 309.35302
+ 1100 296.60224 -3749.0433 14.01717 -3216.9347 -102.75834
+
+Loop time of 5.87081 on 1 procs for 1000 steps with 587 atoms
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 29.434 ns/day 0.815 hours/ns 170.334 timesteps/s
+
+MPI task timings breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 5.5785 | 5.5785 | 5.5785 | 0.0 | 95.02
+Bond | 0.0061142 | 0.0061142 | 0.0061142 | 0.0 | 0.10
+Kspace | 0.020182 | 0.020182 | 0.020182 | 0.0 | 0.34
+Neigh | 0.051474 | 0.051474 | 0.051474 | 0.0 | 0.88
+Comm | 0.088405 | 0.088405 | 0.088405 | 0.0 | 1.51
+Output | 0.0004251 | 0.0004251 | 0.0004251 | 0.0 | 0.01
+Modify | 0.11323 | 0.11323 | 0.11323 | 0.0 | 1.93
+Other | | 0.01249 | | | 0.21
+
+Nlocal: 587 ave 587 max 587 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3622 ave 3622 max 3622 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 75556 ave 75556 max 75556 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 75556
+Ave neighs/atom = 128.716
+Ave special neighs/atom = 0.173765
+Neighbor list builds = 15
+Dangerous builds = 0