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special.cpp
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/* ----------------------------------------------------------------------
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 "modify.h"
#include "fix.h"
#include "accelerator_kokkos.h"
#include "memory.h"
#include "error.h"
#include "atom_masks.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) {
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"
" special bond factors lj: %-10g %-10g %-10g\n"
" special bond 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();
fix_alteration();
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();
fix_alteration();
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();
fix_alteration();
}
/* ----------------------------------------------------------------------
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->map_init(0);
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;
atomKK->modified(Host,SPECIAL_MASK);
atomKK->sync(Device,SPECIAL_MASK);
memory->grow_kokkos(atomKK->k_special,atom->special,
atom->nmax,atom->maxspecial,"atom:special");
atomKK->modified(Device,SPECIAL_MASK);
atomKK->sync(Host,SPECIAL_MASK);
} 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->map_init(0);
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;
}
}
/* ----------------------------------------------------------------------
allow fixes to alter special list
currently, only fix drude does this
so that both the Drude core and electron are same level of neighbor
------------------------------------------------------------------------- */
void Special::fix_alteration()
{
for (int ifix = 0; ifix < modify->nfix; ifix++)
if (modify->fix[ifix]->special_alter_flag)
modify->fix[ifix]->rebuild_special();
}
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