special.cpp
No OneTemporary
Actions

Subscribers

None

File Metadata

Created: Fri, Jul 12, 17:22

special.cpp
View Options

	/* ----------------------------------------------------------------------
	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 "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;
	int *buf;

	MPI_Barrier(world);

	int nlocal = atom->nlocal;

	int *tag = atom->tag;
	int *num_bond = atom->num_bond;
	int **bond_atom = atom->bond_atom;
	int **nspecial = atom->nspecial;

	if (me == 0 && screen) fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n");

	// 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(int),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(int),buf,2,ring_two,NULL);

	memory->destroy(buf);
	}

	memory->destroy(count);

	// -----------------------------------------------------
	// done if special_bonds 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(int),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(int),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_bonds 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(int),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(int),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,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;
	int *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,m;

	int me;
	MPI_Comm_rank(world,&me);

	int **nspecial = atom->nspecial;
	int *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);
	}

	memory->destroy(atom->special);

	memory->create(atom->special,atom->nmax,atom->maxspecial,"atom:special");
	atom->avec->grow_reset();
	int **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;
	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;
	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++) nbuf += 2num_angle[i] + 22*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;
	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];
	}
	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(int),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;
	int **dihedral_atom1 = atom->dihedral_atom1;
	int **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(int),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;

	int buf = (int ) 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;

	int **onetwo = sptr->onetwo;
	int *count = sptr->count;

	int buf = (int ) 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;

	int buf = (int ) 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;

	int **onetwo = sptr->onetwo;

	int buf = (int ) cbuf;
	int i,j,k,m,n,original,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;

	int buf = (int ) 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;

	int **onetwo = sptr->onetwo;

	int buf = (int ) 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;

	int **onethree = sptr->onethree;
	int **dflag = sptr->dflag;

	int buf = (int ) cbuf;
	int i,m,iglobal,jglobal,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;

	int **onefour = sptr->onefour;
	int **dflag = sptr->dflag;

	int buf = (int ) cbuf;
	int i,m,iglobal,jglobal,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;
	}
	}

special.cppNo OneTemporaryActions

File Metadata

special.cppView Options

Event Timeline

special.cpp
No OneTemporary
Actions

special.cpp
View Options