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pair.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "float.h"
#include "limits.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair.h"
#include "pair_soft.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER};
enum{R,RSQ,BMP};
/* ---------------------------------------------------------------------- */
Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
{
THIRD = 1.0/3.0;
eng_vdwl = eng_coul = 0.0;
comm_forward = comm_reverse = 0;
single_enable = 1;
respa_enable = 0;
one_coeff = 0;
no_virial_compute = 0;
// pair_modify settings
offset_flag = 0;
mix_flag = GEOMETRIC;
tail_flag = 0;
etail = ptail = etail_ij = ptail_ij = 0.0;
ncoultablebits = 12;
tabinner = sqrt(2.0);
allocated = 0;
maxeatom = maxvatom = 0;
eatom = NULL;
vatom = NULL;
}
/* ---------------------------------------------------------------------- */
Pair::~Pair()
{
memory->sfree(eatom);
memory->destroy_2d_double_array(vatom);
}
/* ----------------------------------------------------------------------
modify parameters of the pair style
pair_hybrid has its own version of this routine for its sub-styles
------------------------------------------------------------------------- */
void Pair::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal pair_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"mix") == 0) {
if (iarg+2 > narg) error->all("Illegal pair_modify command");
if (strcmp(arg[iarg+1],"geometric") == 0) mix_flag = GEOMETRIC;
else if (strcmp(arg[iarg+1],"arithmetic") == 0) mix_flag = ARITHMETIC;
else if (strcmp(arg[iarg+1],"sixthpower") == 0) mix_flag = SIXTHPOWER;
else error->all("Illegal pair_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"shift") == 0) {
if (iarg+2 > narg) error->all("Illegal pair_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) offset_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) offset_flag = 0;
else error->all("Illegal pair_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"table") == 0) {
if (iarg+2 > narg) error->all("Illegal pair_modify command");
ncoultablebits = atoi(arg[iarg+1]);
if (ncoultablebits > sizeof(float)*CHAR_BIT)
error->all("Too many total bits for bitmapped lookup table");
iarg += 2;
} else if (strcmp(arg[iarg],"tabinner") == 0) {
if (iarg+2 > narg) error->all("Illegal pair_modify command");
tabinner = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"tail") == 0) {
if (iarg+2 > narg) error->all("Illegal pair_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) tail_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) tail_flag = 0;
else error->all("Illegal pair_modify command");
iarg += 2;
} else error->all("Illegal pair_modify command");
}
}
/* ---------------------------------------------------------------------- */
void Pair::init()
{
int i,j;
if (offset_flag && tail_flag)
error->all("Cannot have both pair_modify shift and tail set to yes");
if (tail_flag && domain->dimension == 2)
error->all("Cannot use pair tail corrections with 2d simulations");
if (tail_flag && domain->nonperiodic && comm->me == 0)
error->warning("Using pair tail corrections with nonperiodic system");
if (!allocated) error->all("All pair coeffs are not set");
// I,I coeffs must be set
// init_one() will check if I,J is set explicitly or inferred by mixing
for (i = 1; i <= atom->ntypes; i++)
if (setflag[i][i] == 0) error->all("All pair coeffs are not set");
// style-specific initialization
init_style();
// call init_one() for each I,J
// set cutsq for each I,J, used to neighbor
// cutforce = max of all I,J cutoffs
double cut;
cutforce = 0.0;
etail = ptail = 0.0;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
cut = init_one(i,j);
cutsq[i][j] = cutsq[j][i] = cut*cut;
cutforce = MAX(cutforce,cut);
if (tail_flag) {
etail += etail_ij;
ptail += ptail_ij;
if (i != j) {
etail += etail_ij;
ptail += ptail_ij;
}
}
}
}
/* ----------------------------------------------------------------------
init specific to a pair style
specific pair style can override this function
if needs its own error checks
if needs another kind of neighbor list
request default neighbor list = half list
------------------------------------------------------------------------- */
void Pair::init_style()
{
int irequest = neighbor->request(this);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
specific pair style can override this function
------------------------------------------------------------------------- */
void Pair::init_list(int which, NeighList *ptr)
{
list = ptr;
}
/* ----------------------------------------------------------------------
mixing of pair potential prefactors (epsilon)
------------------------------------------------------------------------- */
double Pair::mix_energy(double eps1, double eps2, double sig1, double sig2)
{
double value;
if (mix_flag == GEOMETRIC)
value = sqrt(eps1*eps2);
else if (mix_flag == ARITHMETIC)
value = sqrt(eps1*eps2);
else if (mix_flag == SIXTHPOWER)
value = 2.0 * sqrt(eps1*eps2) *
pow(sig1,3.0) * pow(sig2,3.0) / (pow(sig1,6.0) * pow(sig2,6.0));
return value;
}
/* ----------------------------------------------------------------------
mixing of pair potential distances (sigma, cutoff)
------------------------------------------------------------------------- */
double Pair::mix_distance(double sig1, double sig2)
{
double value;
if (mix_flag == GEOMETRIC)
value = sqrt(sig1*sig2);
else if (mix_flag == ARITHMETIC)
value = 0.5 * (sig1+sig2);
else if (mix_flag == SIXTHPOWER)
value = pow((0.5 * (pow(sig1,6.0) + pow(sig2,6.0))),1.0/6.0);
return value;
}
/* ----------------------------------------------------------------------
setup for energy, virial computation
see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */
void Pair::ev_setup(int eflag, int vflag)
{
int i,n;
evflag = 1;
eflag_either = eflag;
eflag_global = eflag % 2;
eflag_atom = eflag / 2;
vflag_either = vflag;
vflag_global = vflag % 4;
vflag_atom = vflag / 4;
// reallocate per-atom arrays if necessary
if (eflag_atom && atom->nmax > maxeatom) {
maxeatom = atom->nmax;
memory->sfree(eatom);
eatom = (double *) memory->smalloc(maxeatom*sizeof(double),"pair:eatom");
}
if (vflag_atom && atom->nmax > maxvatom) {
maxvatom = atom->nmax;
memory->destroy_2d_double_array(vatom);
vatom = memory->create_2d_double_array(maxvatom,6,"pair:vatom");
}
// zero accumulators
// use force->newton instead of newton_pair
// b/c some bonds/dihedrals call pair::ev_tally with pairwise info
if (eflag_global) eng_vdwl = eng_coul = 0.0;
if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (eflag_atom) {
n = atom->nlocal;
if (force->newton) n += atom->nghost;
for (i = 0; i < n; i++) eatom[i] = 0.0;
}
if (vflag_atom) {
n = atom->nlocal;
if (force->newton) n += atom->nghost;
for (i = 0; i < n; i++) {
vatom[i][0] = 0.0;
vatom[i][1] = 0.0;
vatom[i][2] = 0.0;
vatom[i][3] = 0.0;
vatom[i][4] = 0.0;
vatom[i][5] = 0.0;
}
}
// if vflag_global = 2 and pair::compute() calls virial_compute()
// compute global virial via (F dot r) instead of via pairwise summation
// unset other flags as appropriate
if (vflag_global == 2 && no_virial_compute == 0) {
vflag_fdotr = 1;
vflag_global = 0;
if (vflag_atom == 0) vflag_either = 0;
if (vflag_either == 0 && eflag_either == 0) evflag = 0;
} else vflag_fdotr = 0;
}
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
need i < nlocal test since called by bond_quartic and dihedral_charmm
------------------------------------------------------------------------- */
void Pair::ev_tally(int i, int j, int nlocal, int newton_pair,
double evdwl, double ecoul, double fpair,
double delx, double dely, double delz)
{
double evdwlhalf,ecoulhalf,epairhalf,v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_pair) {
eng_vdwl += evdwl;
eng_coul += ecoul;
} else {
evdwlhalf = 0.5*evdwl;
ecoulhalf = 0.5*ecoul;
if (i < nlocal) {
eng_vdwl += evdwlhalf;
eng_coul += ecoulhalf;
}
if (j < nlocal) {
eng_vdwl += evdwlhalf;
eng_coul += ecoulhalf;
}
}
}
if (eflag_atom) {
epairhalf = 0.5 * (evdwl + ecoul);
if (newton_pair || i < nlocal) eatom[i] += epairhalf;
if (newton_pair || j < nlocal) eatom[j] += epairhalf;
}
}
if (vflag_either) {
v[0] = delx*delx*fpair;
v[1] = dely*dely*fpair;
v[2] = delz*delz*fpair;
v[3] = delx*dely*fpair;
v[4] = delx*delz*fpair;
v[5] = dely*delz*fpair;
if (vflag_global) {
if (newton_pair) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
} else {
if (i < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
if (j < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
}
}
if (vflag_atom) {
if (newton_pair || i < nlocal) {
vatom[i][0] += 0.5*v[0];
vatom[i][1] += 0.5*v[1];
vatom[i][2] += 0.5*v[2];
vatom[i][3] += 0.5*v[3];
vatom[i][4] += 0.5*v[4];
vatom[i][5] += 0.5*v[5];
}
if (newton_pair || j < nlocal) {
vatom[j][0] += 0.5*v[0];
vatom[j][1] += 0.5*v[1];
vatom[j][2] += 0.5*v[2];
vatom[j][3] += 0.5*v[3];
vatom[j][4] += 0.5*v[4];
vatom[j][5] += 0.5*v[5];
}
}
}
}
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
can use this version with full neighbor lists
------------------------------------------------------------------------- */
void Pair::ev_tally_full(int i, double evdwl, double ecoul, double fpair,
double delx, double dely, double delz)
{
if (eflag_either) {
if (eflag_global) {
eng_vdwl += 0.5*evdwl;
eng_coul += 0.5*ecoul;
}
if (eflag_atom) eatom[i] += 0.5 * (evdwl + ecoul);
}
if (vflag_either) {
if (vflag_global) {
virial[0] += 0.5*delx*delx*fpair;
virial[1] += 0.5*dely*dely*fpair;
virial[2] += 0.5*delz*delz*fpair;
virial[3] += 0.5*delx*dely*fpair;
virial[4] += 0.5*delx*delz*fpair;
virial[5] += 0.5*dely*delz*fpair;
}
}
if (vflag_atom) {
vatom[i][0] += 0.5*delx*delx*fpair;
vatom[i][1] += 0.5*dely*dely*fpair;
vatom[i][2] += 0.5*delz*delz*fpair;
vatom[i][3] += 0.5*delx*dely*fpair;
vatom[i][4] += 0.5*delx*delz*fpair;
vatom[i][5] += 0.5*dely*delz*fpair;
}
}
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
for virial, have delx,dely,delz and fx,fy,fz
------------------------------------------------------------------------- */
void Pair::ev_tally_xyz(int i, int j, int nlocal, int newton_pair,
double evdwl, double ecoul,
double fx, double fy, double fz,
double delx, double dely, double delz)
{
double evdwlhalf,ecoulhalf,epairhalf,v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_pair) {
eng_vdwl += evdwl;
eng_coul += ecoul;
} else {
evdwlhalf = 0.5*evdwl;
ecoulhalf = 0.5*ecoul;
if (i < nlocal) {
eng_vdwl += evdwlhalf;
eng_coul += ecoulhalf;
}
if (j < nlocal) {
eng_vdwl += evdwlhalf;
eng_coul += ecoulhalf;
}
}
}
if (eflag_atom) {
epairhalf = 0.5 * (evdwl + ecoul);
if (newton_pair || i < nlocal) eatom[i] += epairhalf;
if (newton_pair || j < nlocal) eatom[j] += epairhalf;
}
}
if (vflag_either) {
v[0] = delx*fx;
v[1] = dely*fy;
v[2] = delz*fz;
v[3] = delx*fy;
v[4] = delx*fz;
v[5] = dely*fz;
if (vflag_global) {
if (newton_pair) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
} else {
if (i < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
if (j < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
}
}
if (vflag_atom) {
if (newton_pair || i < nlocal) {
vatom[i][0] += 0.5*v[0];
vatom[i][1] += 0.5*v[1];
vatom[i][2] += 0.5*v[2];
vatom[i][3] += 0.5*v[3];
vatom[i][4] += 0.5*v[4];
vatom[i][5] += 0.5*v[5];
}
if (newton_pair || j < nlocal) {
vatom[j][0] += 0.5*v[0];
vatom[j][1] += 0.5*v[1];
vatom[j][2] += 0.5*v[2];
vatom[j][3] += 0.5*v[3];
vatom[j][4] += 0.5*v[4];
vatom[j][5] += 0.5*v[5];
}
}
}
}
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
called by SW potential, newton_pair is always on
virial = riFi + rjFj + rkFk = (rj-ri) Fj + (rk-ri) Fk = drji*fj + drki*fk
------------------------------------------------------------------------- */
void Pair::ev_tally3(int i, int j, int k, double evdwl, double ecoul,
double *fj, double *fk, double *drji, double *drki)
{
double epairthird,v[6];
if (eflag_either) {
if (eflag_global) {
eng_vdwl += evdwl;
eng_coul += ecoul;
}
if (eflag_atom) {
epairthird = THIRD * (evdwl + ecoul);
eatom[i] += epairthird;
eatom[j] += epairthird;
eatom[k] += epairthird;
}
}
if (vflag_atom) {
v[0] = THIRD * (drji[0]*fj[0] + drki[0]*fk[0]);
v[1] = THIRD * (drji[1]*fj[1] + drki[1]*fk[1]);
v[2] = THIRD * (drji[2]*fj[2] + drki[2]*fk[2]);
v[3] = THIRD * (drji[0]*fj[1] + drki[0]*fk[1]);
v[4] = THIRD * (drji[0]*fj[2] + drki[0]*fk[2]);
v[5] = THIRD * (drji[1]*fj[2] + drki[1]*fk[2]);
vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2];
vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5];
vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2];
vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5];
vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2];
vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5];
}
}
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
called by AIREBO potential, newton_pair is always on
------------------------------------------------------------------------- */
void Pair::ev_tally4(int i, int j, int k, int m, double evdwl,
double *fi, double *fj, double *fk,
double *drim, double *drjm, double *drkm)
{
double epairfourth,v[6];
if (eflag_either) {
if (eflag_global) eng_vdwl += evdwl;
if (eflag_atom) {
epairfourth = 0.25 * evdwl;
eatom[i] += epairfourth;
eatom[j] += epairfourth;
eatom[k] += epairfourth;
eatom[m] += epairfourth;
}
}
if (vflag_atom) {
v[0] = 0.25 * (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]);
v[1] = 0.25 * (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]);
v[2] = 0.25 * (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]);
v[3] = 0.25 * (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]);
v[4] = 0.25 * (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]);
v[5] = 0.25 * (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]);
vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2];
vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5];
vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2];
vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5];
vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2];
vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5];
vatom[m][0] += v[0]; vatom[m][1] += v[1]; vatom[m][2] += v[2];
vatom[m][3] += v[3]; vatom[m][4] += v[4]; vatom[m][5] += v[5];
}
}
/* ----------------------------------------------------------------------
tally ecoul and virial into each of n atoms in list
called by TIP4P potential, newton_pair is always on
changes v values by dividing by n
------------------------------------------------------------------------- */
void Pair::ev_tally_list(int n, int *list, double ecoul, double *v)
{
int i,j;
if (eflag_either) {
if (eflag_global) eng_coul += ecoul;
if (eflag_atom) {
double epairatom = ecoul/n;
for (i = 0; i < n; i++) eatom[list[i]] += epairatom;
}
}
if (vflag_either) {
if (vflag_global) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
}
if (vflag_atom) {
v[0] /= n;
v[1] /= n;
v[2] /= n;
v[3] /= n;
v[4] /= n;
v[5] /= n;
for (i = 0; i < n; i++) {
j = list[i];
vatom[j][0] += v[0];
vatom[j][1] += v[1];
vatom[j][2] += v[2];
vatom[j][3] += v[3];
vatom[j][4] += v[4];
vatom[j][5] += v[5];
}
}
}
}
/* ----------------------------------------------------------------------
tally virial into per-atom accumulators
called by AIREBO potential, newton_pair is always on
fpair is magnitude of force on atom I
------------------------------------------------------------------------- */
void Pair::v_tally2(int i, int j, double fpair, double *drij)
{
double v[6];
v[0] = 0.5 * drij[0]*drij[0]*fpair;
v[1] = 0.5 * drij[1]*drij[1]*fpair;
v[2] = 0.5 * drij[2]*drij[2]*fpair;
v[3] = 0.5 * drij[0]*drij[1]*fpair;
v[4] = 0.5 * drij[0]*drij[2]*fpair;
v[5] = 0.5 * drij[1]*drij[2]*fpair;
vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2];
vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5];
vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2];
vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5];
}
/* ----------------------------------------------------------------------
tally virial into per-atom accumulators
called by AIREBO and Tersoff potential, newton_pair is always on
------------------------------------------------------------------------- */
void Pair::v_tally3(int i, int j, int k,
double *fi, double *fj, double *drik, double *drjk)
{
double v[6];
v[0] = THIRD * (drik[0]*fi[0] + drjk[0]*fj[0]);
v[1] = THIRD * (drik[1]*fi[1] + drjk[1]*fj[1]);
v[2] = THIRD * (drik[2]*fi[2] + drjk[2]*fj[2]);
v[3] = THIRD * (drik[0]*fi[1] + drjk[0]*fj[1]);
v[4] = THIRD * (drik[0]*fi[2] + drjk[0]*fj[2]);
v[5] = THIRD * (drik[1]*fi[2] + drjk[1]*fj[2]);
vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2];
vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5];
vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2];
vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5];
vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2];
vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5];
}
/* ----------------------------------------------------------------------
tally virial into per-atom accumulators
called by AIREBO potential, newton_pair is always on
------------------------------------------------------------------------- */
void Pair::v_tally4(int i, int j, int k, int m,
double *fi, double *fj, double *fk,
double *drim, double *drjm, double *drkm)
{
double v[6];
v[0] = 0.25 * (drim[0]*fi[0] + drjm[0]*fj[0] + drkm[0]*fk[0]);
v[1] = 0.25 * (drim[1]*fi[1] + drjm[1]*fj[1] + drkm[1]*fk[1]);
v[2] = 0.25 * (drim[2]*fi[2] + drjm[2]*fj[2] + drkm[2]*fk[2]);
v[3] = 0.25 * (drim[0]*fi[1] + drjm[0]*fj[1] + drkm[0]*fk[1]);
v[4] = 0.25 * (drim[0]*fi[2] + drjm[0]*fj[2] + drkm[0]*fk[2]);
v[5] = 0.25 * (drim[1]*fi[2] + drjm[1]*fj[2] + drkm[1]*fk[2]);
vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2];
vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5];
vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2];
vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5];
vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2];
vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5];
vatom[m][0] += v[0]; vatom[m][1] += v[1]; vatom[m][2] += v[2];
vatom[m][3] += v[3]; vatom[m][4] += v[4]; vatom[m][5] += v[5];
}
/* ----------------------------------------------------------------------
tally virial into global and per-atom accumulators
called by pair lubricate potential with 6 tensor components
------------------------------------------------------------------------- */
void Pair::v_tally_tensor(int i, int j, int nlocal, int newton_pair,
double vxx, double vyy, double vzz,
double vxy, double vxz, double vyz)
{
double v[6];
v[0] = vxx;
v[1] = vyy;
v[2] = vzz;
v[3] = vxy;
v[4] = vxz;
v[5] = vyz;
if (vflag_global) {
if (newton_pair) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
} else {
if (i < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
if (j < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
}
}
if (vflag_atom) {
if (newton_pair || i < nlocal) {
vatom[i][0] += 0.5*v[0];
vatom[i][1] += 0.5*v[1];
vatom[i][2] += 0.5*v[2];
vatom[i][3] += 0.5*v[3];
vatom[i][4] += 0.5*v[4];
vatom[i][5] += 0.5*v[5];
}
if (newton_pair || j < nlocal) {
vatom[j][0] += 0.5*v[0];
vatom[j][1] += 0.5*v[1];
vatom[j][2] += 0.5*v[2];
vatom[j][3] += 0.5*v[3];
vatom[j][4] += 0.5*v[4];
vatom[j][5] += 0.5*v[5];
}
}
}
/* ----------------------------------------------------------------------
compute global pair virial via summing F dot r over own & ghost atoms
at this point, only pairwise forces have been accumulated in atom->f
------------------------------------------------------------------------- */
void Pair::virial_compute()
{
double **x = atom->x;
double **f = atom->f;
// sum over force on all particles including ghosts
if (neighbor->includegroup == 0) {
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < nall; i++) {
virial[0] += f[i][0]*x[i][0];
virial[1] += f[i][1]*x[i][1];
virial[2] += f[i][2]*x[i][2];
virial[3] += f[i][1]*x[i][0];
virial[4] += f[i][2]*x[i][0];
virial[5] += f[i][2]*x[i][1];
}
// neighbor includegroup flag is set
// sum over force on initial nfirst particles and ghosts
} else {
int nall = atom->nfirst;
for (int i = 0; i < nall; i++) {
virial[0] += f[i][0]*x[i][0];
virial[1] += f[i][1]*x[i][1];
virial[2] += f[i][2]*x[i][2];
virial[3] += f[i][1]*x[i][0];
virial[4] += f[i][2]*x[i][0];
virial[5] += f[i][2]*x[i][1];
}
nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; i++) {
virial[0] += f[i][0]*x[i][0];
virial[1] += f[i][1]*x[i][1];
virial[2] += f[i][2]*x[i][2];
virial[3] += f[i][1]*x[i][0];
virial[4] += f[i][2]*x[i][0];
virial[5] += f[i][2]*x[i][1];
}
}
}
/* ----------------------------------------------------------------------
write a table of pair potential energy/force vs distance to a file
------------------------------------------------------------------------- */
void Pair::write_file(int narg, char **arg)
{
if (narg < 8) error->all("Illegal pair_write command");
if (single_enable == 0) error->all("Pair style does not support pair_write");
// parse arguments
int itype = atoi(arg[0]);
int jtype = atoi(arg[1]);
if (itype < 1 || itype > atom->ntypes || jtype < 1 || jtype > atom->ntypes)
error->all("Invalid atom types in pair_write command");
int n = atoi(arg[2]);
int style;
if (strcmp(arg[3],"r") == 0) style = R;
else if (strcmp(arg[3],"rsq") == 0) style = RSQ;
else if (strcmp(arg[3],"bitmap") == 0) style = BMP;
else error->all("Invalid style in pair_write command");
double inner = atof(arg[4]);
double outer = atof(arg[5]);
if (inner <= 0.0 || inner >= outer)
error->all("Invalid cutoffs in pair_write command");
// open file in append mode
// print header in format used by pair_style table
int me;
MPI_Comm_rank(world,&me);
FILE *fp;
if (me == 0) {
fp = fopen(arg[6],"a");
if (fp == NULL) error->one("Cannot open pair_write file");
fprintf(fp,"# Pair potential %s for atom types %d %d: i,r,energy,force\n",
force->pair_style,itype,jtype);
if (style == R)
fprintf(fp,"\n%s\nN %d R %g %g\n\n",arg[7],n,inner,outer);
if (style == RSQ)
fprintf(fp,"\n%s\nN %d RSQ %g %g\n\n",arg[7],n,inner,outer);
}
// initialize potentials before evaluating pair potential
// insures all pair coeffs are set and force constants
force->init();
// if pair style = soft, set prefactor to final value
Pair *spair = force->pair_match("soft",1);
if (spair)
((PairSoft *) spair)->prefactor[itype][jtype] =
((PairSoft *) spair)->prestop[itype][jtype];
// if pair style = any of EAM, swap in dummy fp vector
double eamfp[2];
eamfp[0] = eamfp[1] = 0.0;
double *eamfp_hold;
Pair *epair = force->pair_match("eam",0);
if (epair) epair->swap_eam(eamfp,&eamfp_hold);
// if atom style defines charge, swap in dummy q vec
double q[2];
q[0] = q[1] = 1.0;
if (narg == 10) {
q[0] = atof(arg[8]);
q[1] = atof(arg[9]);
}
double *q_hold;
if (atom->q) {
q_hold = atom->q;
atom->q = q;
}
// evaluate energy and force at each of N distances
int masklo,maskhi,nmask,nshiftbits;
if (style == BMP) {
init_bitmap(inner,outer,n,masklo,maskhi,nmask,nshiftbits);
int ntable = 1 << n;
if (me == 0)
fprintf(fp,"\n%s\nN %d BITMAP %g %g\n\n",arg[7],ntable,inner,outer);
n = ntable;
}
double r,e,f,rsq;
union_int_float_t rsq_lookup;
for (int i = 0; i < n; i++) {
if (style == R) {
r = inner + (outer-inner) * i/(n-1);
rsq = r*r;
} else if (style == RSQ) {
rsq = inner*inner + (outer*outer - inner*inner) * i/(n-1);
r = sqrt(rsq);
} else if (style == BMP) {
rsq_lookup.i = i << nshiftbits;
rsq_lookup.i |= masklo;
if (rsq_lookup.f < inner*inner) {
rsq_lookup.i = i << nshiftbits;
rsq_lookup.i |= maskhi;
}
rsq = rsq_lookup.f;
r = sqrt(rsq);
}
if (rsq < cutsq[itype][jtype]) {
e = single(0,1,itype,jtype,rsq,1.0,1.0,f);
f *= r;
} else e = f = 0.0;
if (me == 0) fprintf(fp,"%d %g %g %g\n",i+1,r,e,f);
}
// restore original vecs that were swapped in for
double *tmp;
if (epair) epair->swap_eam(eamfp_hold,&tmp);
if (atom->q) atom->q = q_hold;
if (me == 0) fclose(fp);
}
/* ----------------------------------------------------------------------
define bitmap parameters based on inner and outer cutoffs
------------------------------------------------------------------------- */
void Pair::init_bitmap(double inner, double outer, int ntablebits,
int &masklo, int &maskhi, int &nmask, int &nshiftbits)
{
if (sizeof(int) != sizeof(float))
error->all("Bitmapped lookup tables require int/float be same size");
if (ntablebits > sizeof(float)*CHAR_BIT)
error->all("Too many total bits for bitmapped lookup table");
if (inner >= outer) error->warning("Table inner cutoff >= outer cutoff");
int nlowermin = 1;
while (!((pow(double(2),nlowermin) <= inner*inner) &&
(pow(double(2),nlowermin+1) > inner*inner))) {
if (pow(double(2),nlowermin) <= inner*inner) nlowermin++;
else nlowermin--;
}
int nexpbits = 0;
double required_range = outer*outer / pow(double(2),nlowermin);
double available_range = 2.0;
while (available_range < required_range) {
nexpbits++;
available_range = pow(double(2),pow(double(2),nexpbits));
}
int nmantbits = ntablebits - nexpbits;
if (nexpbits > sizeof(float)*CHAR_BIT - FLT_MANT_DIG)
error->all("Too many exponent bits for lookup table");
if (nmantbits+1 > FLT_MANT_DIG)
error->all("Too many mantissa bits for lookup table");
if (nmantbits < 3) error->all("Too few bits for lookup table");
nshiftbits = FLT_MANT_DIG - (nmantbits+1);
nmask = 1;
for (int j = 0; j < ntablebits+nshiftbits; j++) nmask *= 2;
nmask -= 1;
union_int_float_t rsq_lookup;
rsq_lookup.f = outer*outer;
maskhi = rsq_lookup.i & ~(nmask);
rsq_lookup.f = inner*inner;
masklo = rsq_lookup.i & ~(nmask);
}
/* ---------------------------------------------------------------------- */
double Pair::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
return bytes;
}

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