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503
src/CORESHELL/compute_temp_cs.cpp Normal file
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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: Hendrik Heenen (Technical University of Munich)
(hendrik.heenen at mytum.com)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "math.h"
#include "compute_temp_cs.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "fix_store.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 5) error->all(FLERR,"Illegal compute temp/cs command");
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Compute temp/cs used when bonds are not allowed");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
extarray = 0;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// find and define groupbits for core and shell groups
cgroup = group->find(arg[3]);
if (cgroup == -1)
error->all(FLERR,"Could not find specified group ID for core particles");
groupbit_c = group->bitmask[cgroup];
sgroup = group->find(arg[4]);
if (sgroup == -1)
error->all(FLERR,"Could not find specified group ID for shell particles");
groupbit_s = group->bitmask[sgroup];
// create a new fix STORE style
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
char **newarg = new char*[5];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "0";
newarg[4] = (char *) "1";
modify->add_fix(5,newarg);
fix = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
// set fix store values = 0 for now
// fill them in via setup() once Comm::borders() has been called
// skip if resetting from restart file
if (fix->restart_reset) {
fix->restart_reset = 0;
firstflag = 0;
} else {
double *partner = fix->vstore;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) partner[i] = ubuf(0).d;
firstflag = 1;
}
// allocate memory
vector = new double[6];
maxatom = 0;
vint = NULL;
// set comm size needed by this Compute
comm_reverse = 1;
}
/* ---------------------------------------------------------------------- */
ComputeTempCS::~ComputeTempCS()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
delete [] vector;
memory->destroy(vint);
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::init()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Compute temp/cs requires ghost atoms store velocity");
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::setup()
{
if (firstflag) {
firstflag = 0;
// insure # of core atoms = # of shell atoms
int ncores = group->count(cgroup);
nshells = group->count(sgroup);
if (ncores != nshells)
error->all(FLERR,"Number of core atoms != number of shell atoms");
// for each C/S pair:
// set partner IDs of both atoms if this atom stores bond between them
// will set partner IDs for ghost atoms if needed by another proc
// nall loop insures all ghost atom partner IDs are set before reverse comm
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *partner = fix->vstore;
tagint partnerID;
int nall = nlocal + atom->nghost;
for (int i = nlocal; i < nall; i++) partner[i] = ubuf(0).d;
int i,j,m,match;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
for (m = 0; m < num_bond[i]; m++) {
partnerID = bond_atom[i][m];
j = atom->map(partnerID);
if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
match = 0;
if (mask[i] & groupbit_c && mask[j] & groupbit_s) match = 1;
if (mask[i] & groupbit_s && mask[j] & groupbit_c) match = 1;
if (match) {
partner[i] = ubuf(partnerID).d;
partner[j] = ubuf(tag[i]).d;
}
}
}
}
// reverse comm to acquire unknown partner IDs from ghost atoms
// only needed if newton_bond = on
if (force->newton_bond) comm->reverse_comm_compute(this);
// check that all C/S partners were found
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
partnerID = (tagint) ubuf(partner[i]).i;
if (partnerID == 0) flag = 1;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"Core/shell partners were not all found");
}
// calculate DOF for temperature
fix_dof = -1;
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::dof_compute()
{
if (fix_dof) adjust_dof_fix();
int nper = domain->dimension;
double natoms = group->count(igroup);
dof = nper * natoms;
dof -= nper * nshells;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempCS::compute_scalar()
{
int i;
double vthermal[3];
invoked_scalar = update->ntimestep;
vcm_pairs();
// calculate thermal scalar in respect to atom velocities as center-of-mass
// velocities of its according core/shell pairs
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double t = 0.0;
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit) {
vthermal[0] = v[i][0] - vint[i][0];
vthermal[1] = v[i][1] - vint[i][1];
vthermal[2] = v[i][2] - vint[i][2];
if (rmass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
}
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::compute_vector()
{
double vthermal[3];
invoked_vector = update->ntimestep;
vcm_pairs();
// calculate thermal vector in respect to atom velocities as center-of-mass
// velocities of its according C/S pairs
double **v = atom->v;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double massone;
double t[6];
for (int i = 0; i < 6; i++) t[i] = 0.0;
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit) {
vthermal[0] = v[i][0] - vint[i][0];
vthermal[1] = v[i][1] - vint[i][1];
vthermal[2] = v[i][2] - vint[i][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
t[0] += massone * vthermal[0]*vthermal[0];
t[1] += massone * vthermal[1]*vthermal[1];
t[2] += massone * vthermal[2]*vthermal[2];
t[3] += massone * vthermal[0]*vthermal[1];
t[4] += massone * vthermal[0]*vthermal[2];
t[5] += massone * vthermal[1]*vthermal[2];
}
}
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::vcm_pairs()
{
int i,j;
double massone,masstwo;
double vcm[3];
// reallocate vint if necessary
int nlocal = atom->nlocal;
if (nlocal > maxatom) {
memory->destroy(vint);
maxatom = atom->nmax;
memory->create(vint,maxatom,3,"temp/cs:vint");
}
// vcm = COM velocity of each CS pair
// vint = internal velocity of each C/S atom, used as bias
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double *partner = fix->vstore;
tagint partnerID;
for (int i = 0; i < nlocal; i++) {
if ((mask[i] & groupbit) &&
(mask[i] & groupbit_c || mask[i] & groupbit_s)) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vcm[0] = v[i][0]*massone;
vcm[1] = v[i][1]*massone;
vcm[2] = v[i][2]*massone;
partnerID = (tagint) ubuf(partner[i]).i;
j = atom->map(partnerID);
if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
if (rmass) masstwo = rmass[j];
else masstwo = mass[type[j]];
vcm[0] += v[j][0]*masstwo;
vcm[1] += v[j][1]*masstwo;
vcm[2] += v[j][2]*masstwo;
vcm[0] /= (massone + masstwo);
vcm[1] /= (massone + masstwo);
vcm[2] /= (massone + masstwo);
vint[i][0] = v[i][0] - vcm[0];
vint[i][1] = v[i][1] - vcm[1];
vint[i][2] = v[i][2] - vcm[2];
} else vint[i][0] = vint[i][1] = vint[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
thermal velocity in this case is COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::remove_bias(int i, double *v)
{
v[0] -= vint[i][0];
v[1] -= vint[i][1];
v[2] -= vint[i][2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
thermal velocity in this case is COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::remove_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vint[i][0];
v[i][1] -= vint[i][1];
v[i][2] -= vint[i][2];
}
}
/* ----------------------------------------------------------------------
reset thermal velocity of all atoms to be consistent with bias
called from velocity command after it creates thermal velocities
this resets each atom's velocity to COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::reapply_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// recalculate current COM velocities
vcm_pairs();
// zero vint after using ti so that Velocity call to restore_bias_all()
// will not further alter the velocities within a C/S pair
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vint[i][0];
v[i][1] -= vint[i][1];
v[i][2] -= vint[i][2];
vint[i][0] = 0.0;
vint[i][1] = 0.0;
vint[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempCS::restore_bias(int i, double *v)
{
v[0] += vint[i][0];
v[1] += vint[i][1];
v[2] += vint[i][2];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempCS::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vint[i][0];
v[i][1] += vint[i][1];
v[i][2] += vint[i][2];
}
}
/* ---------------------------------------------------------------------- */
int ComputeTempCS::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
double *partner = fix->vstore;
m = 0;
last = first + n;
for (i = first; i < last; i++) buf[m++] = partner[i];
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
double *partner = fix->vstore;
tagint partnerID;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
partnerID = (tagint) ubuf(buf[m++]).i;
if (partnerID) partner[j] = ubuf(partnerID).d;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeTempCS::memory_usage()
{
double bytes = (bigint) maxatom * 3 * sizeof(double);
return bytes;
}

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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.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(temp/cs,ComputeTempCS)
#else
#ifndef LMP_COMPUTE_TEMP_CS_H
#define LMP_COMPUTE_TEMP_CS_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeTempCS : public Compute {
public:
ComputeTempCS(class LAMMPS *, int, char **);
~ComputeTempCS();
void init();
void setup();
double compute_scalar();
void compute_vector();
double memory_usage();
void remove_bias(int, double *);
void remove_bias_all();
void reapply_bias_all();
void restore_bias(int, double *);
void restore_bias_all();
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
private:
int groupbit_c,groupbit_s;
int nshells;
int firstflag;
int maxatom;
int cgroup,sgroup;
int fix_dof;
double tfactor;
double **vint;
char *id_fix;
class FixStore *fix;
void dof_compute();
void vcm_pairs();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Option mol of compute temp/vcm requires molecular atom style
Self-explanatory.
E: Option prop of compute temp/vcm requires one set of parameters
added by the property/atom fix
Self-explanatory.
E: Fix property/atom vector must contain only intergers to assign
sub-ID property
Self-explanatory.
E: Specified sub-ID property does not exist or has not been created
by the property/atom fix
Self-explanatory. Usually this means that the specified fix
property/atom ID does not match the ID stated in the compute temp/vcm.
E: Molecule count changed in compute com/temp/molecule
Number of molecules must remain constant over time.
E: Sub-ID count changed in compute vcm/temp
Number of Sub-ID groups must remain constant over time.
W: Atom with sub-ID = 0 included in compute group
Self-explanatory. A sub-ID with value 0 will be counted as a normal sub-ID
and not left out of by the compute treatment. Therefore a sub-ID of 0 is to
be avoided.
E: Too many sub-ID groups for compute
Self-explanatory.
W: More than 2 atoms specified with the same sub-ID, in the case
of a core-shell model simulation only core and shell should share the same ID
Self-explanatory.
*/

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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: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_born_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
#define EPSILON 1.0e-20
#define EPS_EWALD 1.0e-6
#define EPS_EWALD_SQR 1.0e-12
/* ---------------------------------------------------------------------- */
PairBornCoulLongCS::PairBornCoulLongCS(LAMMPS *lmp) : PairBornCoulLong(lmp)
{
ewaldflag = pppmflag = 1;
ftable = NULL;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
void PairBornCoulLongCS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itable,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double r,rexp;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j];
if (factor_coul < 1.0) {
// When bonded parts are being calculated a minimal distance (EPS_EWALD)
// has to be added to the prefactor and erfc in order to make the
// used approximation functions valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor /= (r+EPS_EWALD);
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - (1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = 1.0/(rsq + EPS_EWALD_SQR);
} else {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor /= r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r = sqrt(rsq);
r6inv = r2inv*r2inv*r2inv;
rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ born3[itype][jtype]*r2inv*r6inv;
} else forceborn = 0.0;
fpair = (forcecoul + factor_lj*forceborn) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}

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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: Hendrik Heenen (hendrik.heenen@mytum.com)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(born/coul/long/cs,PairBornCoulLongCS)
#else
#ifndef LMP_PAIR_BORN_COUL_LONG_CS_H
#define LMP_PAIR_BORN_COUL_LONG_CS_H
#include "pair_born_coul_long.h"
namespace LAMMPS_NS {
class PairBornCoulLongCS : public PairBornCoulLong {
public:
PairBornCoulLongCS(class LAMMPS *);
virtual void compute(int, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style born/coul/long requires atom attribute q
An atom style that defines this attribute must be used.
E: Pair style requires a KSpace style
No kspace style is defined.
*/

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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: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_buck_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
#define EPSILON 1.0e-20
#define EPS_EWALD 1.0e-6
#define EPS_EWALD_SQR 1.0e-12
/* ---------------------------------------------------------------------- */
PairBuckCoulLongCS::PairBuckCoulLongCS(LAMMPS *lmp) : PairBuckCoulLong(lmp)
{
ewaldflag = pppmflag = 1;
writedata = 1;
ftable = NULL;
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongCS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itable,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double rsq,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double r,rexp;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j];
if (factor_coul < 1.0) {
// When bonded parts are being calculated a minimal distance (EPS_EWALD)
// has to be added to the prefactor and erfc in order to make the
// used approximation functions for the Ewald correction valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor /= (r+EPS_EWALD);
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - (1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = 1.0/(rsq + EPS_EWALD_SQR);
} else {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor /= r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r = sqrt(rsq);
r6inv = r2inv*r2inv*r2inv;
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}

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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: Hendrik Heenen (hendrik.heenen@mytum.com)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(buck/coul/long/cs,PairBuckCoulLongCS)
#else
#ifndef LMP_PAIR_BUCK_COUL_LONG_CS_H
#define LMP_PAIR_BUCK_COUL_LONG_CS_H
#include "pair_buck_coul_long.h"
namespace LAMMPS_NS {
class PairBuckCoulLongCS : public PairBuckCoulLong {
public:
PairBuckCoulLongCS(class LAMMPS *);
virtual void compute(int, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style buck/coul/long requires atom attribute q
The atom style defined does not have these attributes.
E: Pair style requires a KSpace style
No kspace style is defined.
*/