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enable and apply clang-format,

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This commit is contained in:
Axel Kohlmeyer
2022-10-18 14:34:23 -04:00
parent 3520584109
commit d7b436f833
2 changed files with 196 additions and 255 deletions
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430
src/ASPHERE/pair_ylz.cpp
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@ -13,39 +13,46 @@
/* ----------------------------------------------------------------------
Contributing author: Mehdi Baghaee (SUSTech)
------------------------------------------------------------------------- */
#include "pair_ylz.h"
#include <cmath>
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "citeme.h"
#include "memory.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS;
using MathConst::MY_4PI;
using MathConst::MY_PI2;
using MathConst::MY_TWOBYSIXTH;
static const char cite_pair_ylz[] =
"pair ylz command:\n\n"
"@Article{Yuan10,\n"
" author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},\n"
" title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},\n"
" journal = {Phys. Rev. E},\n"
" year = 2010,\n"
" volume = 82,\n"
" pages = {011905}\n"
"}\n\n";
"pair ylz command:\n\n"
"@Article{Yuan10,\n"
" author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},\n"
" title = {One-particle-thick, solvent-free, coarse-grained model for biological and "
"biomimetic fluid membranes},\n"
" journal = {Phys. Rev. E},\n"
" year = 2010,\n"
" volume = 82,\n"
" pages = {011905}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairYLZ::PairYLZ(LAMMPS *lmp) : Pair(lmp)
PairYLZ::PairYLZ(LAMMPS *lmp) :
Pair(lmp), epsilon(nullptr), sigma(nullptr), cut(nullptr), zeta(nullptr), mu(nullptr),
beta(nullptr)
{
if (lmp->citeme) lmp->citeme->add(cite_pair_ylz);
@ -69,7 +76,6 @@ PairYLZ::~PairYLZ()
memory->destroy(zeta);
memory->destroy(mu);
memory->destroy(beta);
}
}
@ -77,15 +83,15 @@ PairYLZ::~PairYLZ()
void PairYLZ::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl,one_eng,rsq,forcelj,factor_lj;
double fforce[3],ttor[3],rtor[3],r12[3];
double a1[3][3],a2[3][3];
int *ilist,*jlist,*numneigh,**firstneigh;
double *iquat,*jquat;
int i, j, ii, jj, inum, jnum, itype, jtype;
double evdwl, one_eng, rsq, factor_lj;
double fforce[3], ttor[3], rtor[3], r12[3];
double a1[3][3], a2[3][3];
int *ilist, *jlist, *numneigh, **firstneigh;
double *iquat, *jquat;
evdwl = 0.0;
ev_init(eflag , vflag);
ev_init(eflag, vflag);
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
@ -109,8 +115,7 @@ void PairYLZ::compute(int eflag, int vflag)
itype = type[i];
iquat = bonus[ellipsoid[i]].quat;
MathExtra::quat_to_mat_trans(iquat,a1);
MathExtra::quat_to_mat_trans(iquat, a1);
jlist = firstneigh[i];
jnum = numneigh[i];
@ -122,10 +127,10 @@ void PairYLZ::compute(int eflag, int vflag)
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
rsq = MathExtra::dot3(r12,r12);
r12[0] = x[j][0] - x[i][0];
r12[1] = x[j][1] - x[i][1];
r12[2] = x[j][2] - x[i][2];
rsq = MathExtra::dot3(r12, r12);
jtype = type[j];
// compute if less than cutoff
@ -133,8 +138,8 @@ void PairYLZ::compute(int eflag, int vflag)
if (rsq < cutsq[itype][jtype]) {
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
one_eng = ylz_analytic(i,j,a1,a2,r12,rsq,fforce,ttor,rtor);
MathExtra::quat_to_mat_trans(jquat, a2);
one_eng = ylz_analytic(i, j, a1, a2, r12, rsq, fforce, ttor, rtor);
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
@ -162,18 +167,16 @@ void PairYLZ::compute(int eflag, int vflag)
tor[j][2] += rtor[2];
}
if (eflag) evdwl = factor_lj*one_eng;
if (eflag) evdwl = factor_lj * one_eng;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
if (evflag)
ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0.0, fforce[0], fforce[1], fforce[2],
-r12[0], -r12[1], -r12[2]);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
@ -183,21 +186,19 @@ void PairYLZ::compute(int eflag, int vflag)
void PairYLZ::allocate()
{
allocated = 1;
int n = atom->ntypes;
int np1 = atom->ntypes + 1;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(zeta,n+1,n+1,"pair:zeta");
memory->create(mu,n+1,n+1,"pair:mu");
memory->create(beta,n+1,n+1,"pair:beta");
memory->create(setflag, np1, np1, "pair:setflag");
for (int i = 1; i < np1; i++)
for (int j = i; j < np1; j++) setflag[i][j] = 0;
memory->create(cutsq, np1, np1, "pair:cutsq");
memory->create(epsilon, np1, np1, "pair:epsilon");
memory->create(sigma, np1, np1, "pair:sigma");
memory->create(cut, np1, np1, "pair:cut");
memory->create(zeta, np1, np1, "pair:zeta");
memory->create(mu, np1, np1, "pair:mu");
memory->create(beta, np1, np1, "pair:beta");
}
/* ----------------------------------------------------------------------
@ -206,10 +207,9 @@ void PairYLZ::allocate()
void PairYLZ::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = utils::numeric(FLERR,arg[0],false, lmp);
if (narg != 1) error->all(FLERR, "Illegal pair_style command");
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
}
/* ----------------------------------------------------------------------
@ -218,24 +218,23 @@ void PairYLZ::settings(int narg, char **arg)
void PairYLZ::coeff(int narg, char **arg)
{
if (narg < 8 || narg > 8)
error->all(FLERR,"Incorrect args for pair coefficients");
if (narg < 8 || narg > 8) error->all(FLERR, "Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR, arg[0],1,atom->ntypes,ilo,ihi, error);
utils::bounds(FLERR, arg[1],1,atom->ntypes,jlo,jhi, error);
int ilo, ihi, jlo, jhi;
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
double epsilon_one = utils::numeric(FLERR,arg[2], false, lmp);
double sigma_one = utils::numeric(FLERR,arg[3], false, lmp);
double zeta_one = utils::numeric(FLERR,arg[4], false, lmp);
double mu_one = utils::numeric(FLERR,arg[5], false, lmp);
double beta_one = utils::numeric(FLERR,arg[6], false, lmp);
double cut_one = utils::numeric(FLERR,arg[7], false, lmp);
double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp);
double sigma_one = utils::numeric(FLERR, arg[3], false, lmp);
double zeta_one = utils::numeric(FLERR, arg[4], false, lmp);
double mu_one = utils::numeric(FLERR, arg[5], false, lmp);
double beta_one = utils::numeric(FLERR, arg[6], false, lmp);
double cut_one = utils::numeric(FLERR, arg[7], false, lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
cut[i][j] = cut_one;
@ -248,10 +247,9 @@ void PairYLZ::coeff(int narg, char **arg)
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
@ -259,9 +257,10 @@ void PairYLZ::coeff(int narg, char **arg)
void PairYLZ::init_style()
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec) error->all(FLERR,"Pair YLZ requires atom style ellipsoid");
if (!avec) error->all(FLERR, "Pair style ylz requires atom style ellipsoid");
neighbor->request(this, instance_me);
neighbor->request(this,instance_me);
}
@ -271,20 +270,17 @@ void PairYLZ::init_style()
double PairYLZ::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
}
epsilon[j][i] = epsilon[i][j];
sigma[j][i] = sigma[i][j];
zeta[j][i] = zeta[i][j];
mu[j][i] = mu[i][j];
beta[j][i] = beta[i][j];
beta[j][i] = beta[i][j];
return cut[i][j];
}
@ -297,18 +293,16 @@ void PairYLZ::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j], sizeof(int), 1, fp);
if (setflag[i][j]) {
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&zeta[i][j],sizeof(double),1,fp);
fwrite(&mu[i][j],sizeof(double),1,fp);
fwrite(&beta[i][j],sizeof(double),1,fp);
fwrite(&epsilon[i][j], sizeof(double), 1, fp);
fwrite(&sigma[i][j], sizeof(double), 1, fp);
fwrite(&cut[i][j], sizeof(double), 1, fp);
fwrite(&zeta[i][j], sizeof(double), 1, fp);
fwrite(&mu[i][j], sizeof(double), 1, fp);
fwrite(&beta[i][j], sizeof(double), 1, fp);
}
}
}
@ -323,34 +317,26 @@ void PairYLZ::read_restart(FILE *fp)
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) utils::sfread(FLERR, &setflag[i][j],sizeof(int),1,fp, nullptr, error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (comm->me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR, &epsilon[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &sigma[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &zeta[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &mu[i][j],sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &beta[i][j],sizeof(double),1,fp, nullptr, error);
if (comm->me == 0) {
utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &zeta[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &mu[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &beta[i][j], sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&zeta[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&mu[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&beta[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&zeta[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&mu[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&beta[i][j], 1, MPI_DOUBLE, 0, world);
}
}
}
@ -362,10 +348,9 @@ void PairYLZ::read_restart(FILE *fp)
void PairYLZ::write_restart_settings(FILE *fp)
{
//fwrite(&model_type,sizeof(int),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&cut_global, sizeof(double), 1, fp);
fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
@ -374,19 +359,16 @@ void PairYLZ::write_restart_settings(FILE *fp)
void PairYLZ::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
if (comm->me == 0) {
// utils::sfread(FLERR, &model_type,sizeof(int),1,fp, nullptr, error);
utils::sfread(FLERR, &cut_global,sizeof(double),1,fp, nullptr, error);
utils::sfread(FLERR, &offset_flag,sizeof(int),1,fp, nullptr, error);
utils::sfread(FLERR, &mix_flag,sizeof(int),1,fp, nullptr, error);
utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
}
//MPI_Bcast(&model_type,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
}
/* ----------------------------------------------------------------------
@ -396,8 +378,8 @@ void PairYLZ::read_restart_settings(FILE *fp)
void PairYLZ::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g\n",i,
epsilon[i][i],sigma[i][i],cut[i][i],zeta[i][i],mu[i][i], beta[i][i]);
fprintf(fp, "%d %g %g %g %g %g %g\n", i, epsilon[i][i], sigma[i][i], cut[i][i], zeta[i][i],
mu[i][i], beta[i][i]);
}
/* ----------------------------------------------------------------------
@ -408,144 +390,112 @@ void PairYLZ::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g %g %g %g %g\n",i,j,
epsilon[i][i],sigma[i][i],cut[i][j],zeta[i][j],mu[i][j], beta[i][j]);
fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][i], sigma[i][i], cut[i][j],
zeta[i][j], mu[i][j], beta[i][j]);
}
/* ----------------------------------------------------------------------
compute analytic energy, force (fforce), and torque (ttor & rtor)
based on rotation matrices a
if newton is off, rtor is not calculated for ghost atoms
------------------------------------------------------------------------- */
double PairYLZ::ylz_analytic(const int i,const int j,double a1[3][3],
double a2[3][3], double *r12,
const double rsq, double *fforce,
double *ttor, double *rtor)
double PairYLZ::ylz_analytic(const int i, const int j, double a1[3][3], double a2[3][3],
double *r12, const double rsq, double *fforce, double *ttor,
double *rtor)
{
int *type = atom->type;
int newton_pair = force->newton_pair;
int nlocal = atom->nlocal;
int *type = atom->type;
int newton_pair = force->newton_pair;
int nlocal = atom->nlocal;
double r12hat[3];
MathExtra::normalize3(r12,r12hat);
double r = sqrt(rsq);
double r12hat[3];
MathExtra::normalize3(r12, r12hat);
double r = sqrt(rsq);
double ni1[3], nj1[3], dphi_drhat[3], dUdrhat[3], dUdni1[3], dUdnj1[3];
double dphi_dni1[3], dphi_dnj1[3];
double t, t1, t2, t4, cos_t, U, uR, uA, dUdr, dUdphi;
const double energy_well = epsilon[type[i]][type[j]];
const double rmin = MY_TWOBYSIXTH * sigma[type[i]][type[j]];
const double rcut = cut[type[i]][type[j]];
const double zt = zeta[type[i]][type[j]];
const double muu = mu[type[i]][type[j]];
const double sint = beta[type[i]][type[j]];
double ni1[3],nj1[3],dphi_drhat[3],dUdrhat[3],dUdni1[3],dUdnj1[3],dphi_dni1[3],dphi_dnj1[3] ;
double t,t1,t2,t4,cos_t,U,uR,uA,dUdr,dUdphi;
double pi = 3.141592653589793, pow2_1by6 = 1.122462048309373;
ni1[0] = a1[0][0];
ni1[1] = a1[0][1];
ni1[2] = a1[0][2];
double energy_well = epsilon[type[i]][type[j]];
double rmin = pow2_1by6*sigma[type[i]][type[j]];
double rcut = cut[type[i]][type[j]];
double zt = zeta[type[i]][type[j]];
double muu = mu[type[i]][type[j]];
double sint = beta[type[i]][type[j]];
nj1[0] = a2[0][0];
nj1[1] = a2[0][1];
nj1[2] = a2[0][2];
ni1[0]=a1[0][0];
ni1[1]=a1[0][1];
ni1[2]=a1[0][2];
const double ninj = MathExtra::dot3(ni1, nj1);
const double ni1rhat = MathExtra::dot3(ni1, r12hat);
const double nj1rhat = MathExtra::dot3(nj1, r12hat);
nj1[0]=a2[0][0];
nj1[1]=a2[0][1];
nj1[2]=a2[0][2];
const double a = ninj + (sint - ni1rhat) * (sint + nj1rhat) - 2.0 * sint * sint;
const double phi = 1.0 + (a - 1.0) * muu;
double ninj = MathExtra::dot3(ni1,nj1);
double ni1rhat = MathExtra::dot3(ni1,r12hat);
double nj1rhat = MathExtra::dot3(nj1,r12hat);
dphi_drhat[0] = muu * ((sint - ni1rhat) * nj1[0] - ni1[0] * (sint + nj1rhat));
dphi_drhat[1] = muu * ((sint - ni1rhat) * nj1[1] - ni1[1] * (sint + nj1rhat));
dphi_drhat[2] = muu * ((sint - ni1rhat) * nj1[2] - ni1[2] * (sint + nj1rhat));
double a = ninj + (sint-ni1rhat)*(sint+nj1rhat) - 2.0*sint*sint;
double phi = 1.0 + (a-1.0)*muu;
dphi_dni1[0] = muu * (nj1[0] - r12hat[0] * (sint + nj1rhat));
dphi_dni1[1] = muu * (nj1[1] - r12hat[1] * (sint + nj1rhat));
dphi_dni1[2] = muu * (nj1[2] - r12hat[2] * (sint + nj1rhat));
dphi_drhat[0] = muu*( (sint-ni1rhat)*nj1[0]-ni1[0]*(sint+nj1rhat) );
dphi_drhat[1] = muu*( (sint-ni1rhat)*nj1[1]-ni1[1]*(sint+nj1rhat) );
dphi_drhat[2] = muu*( (sint-ni1rhat)*nj1[2]-ni1[2]*(sint+nj1rhat) );
dphi_dnj1[0] = muu * (ni1[0] + r12hat[0] * (sint - ni1rhat));
dphi_dnj1[1] = muu * (ni1[1] + r12hat[1] * (sint - ni1rhat));
dphi_dnj1[2] = muu * (ni1[2] + r12hat[2] * (sint - ni1rhat));
dphi_dni1[0] = muu*(nj1[0]-r12hat[0]*(sint+nj1rhat));
dphi_dni1[1] = muu*(nj1[1]-r12hat[1]*(sint+nj1rhat));
dphi_dni1[2] = muu*(nj1[2]-r12hat[2]*(sint+nj1rhat));
if (r < rmin) {
t = rmin / r;
t2 = t * t;
t4 = t2 * t2;
uR = (t4 - 2.0 * t2) * energy_well;
U = uR + (1.0 - phi) * energy_well;
dUdr = 4.0 * (t2 - t4) / r * energy_well;
dUdphi = -energy_well;
} else {
t = MY_PI2 * (r - rmin) / (rcut - rmin);
cos_t = cos(t);
t1 = cos_t;
dphi_dnj1[0] = muu*(ni1[0]+r12hat[0]*(sint-ni1rhat));
dphi_dnj1[1] = muu*(ni1[1]+r12hat[1]*(sint-ni1rhat));
dphi_dnj1[2] = muu*(ni1[2]+r12hat[2]*(sint-ni1rhat));
for (int k = 1; k <= 2 * zt - 2; k++) t1 *= cos_t; // get cos()^(2zt-1)
if (r < rmin)
{
t = rmin/r;
t2=t*t;
t4=t2*t2;
uR = (t4 - 2.0*t2)*energy_well;
uA = -energy_well * t1 * cos_t;
U = uA * phi;
dUdr = MY_4PI / (rcut - rmin) * (t1) *sin(t) * phi * energy_well;
dUdphi = uA;
}
U = uR +(1.0 - phi)*energy_well;
dUdrhat[0] = dUdphi * dphi_drhat[0];
dUdrhat[1] = dUdphi * dphi_drhat[1];
dUdrhat[2] = dUdphi * dphi_drhat[2];
dUdr = 4.0*(t2-t4)/r*energy_well;
double dUdrhatrhat = MathExtra::dot3(dUdrhat, r12hat);
dUdphi = -energy_well;
}
fforce[0] = dUdr * r12hat[0] + (dUdrhat[0] - dUdrhatrhat * r12hat[0]) / r;
fforce[1] = dUdr * r12hat[1] + (dUdrhat[1] - dUdrhatrhat * r12hat[1]) / r;
fforce[2] = dUdr * r12hat[2] + (dUdrhat[2] - dUdrhatrhat * r12hat[2]) / r;
// torque i
else
{
dUdni1[0] = dUdphi * dphi_dni1[0];
dUdni1[1] = dUdphi * dphi_dni1[1];
dUdni1[2] = dUdphi * dphi_dni1[2];
t = pi/2.0*(r-rmin)/(rcut-rmin);
cos_t = cos(t);
t1=cos_t;
MathExtra::cross3(dUdni1, ni1, ttor); //minus sign is replace by swapping ni1 and dUdni1
for (int k = 1; k <= 2*zt-2; k++) {t1 *= cos_t;} // get cos()^(2zt-1)
if (newton_pair || j < nlocal) {
uA = -energy_well*t1*cos_t;
U = uA*phi;
dUdr = 4.0*pi/(rcut-rmin)*(t1)*sin(t)*phi*energy_well;
dUdphi = uA;
}
dUdrhat[0] = dUdphi*dphi_drhat[0];
dUdrhat[1] = dUdphi*dphi_drhat[1];
dUdrhat[2] = dUdphi*dphi_drhat[2];
double dUdrhatrhat = MathExtra::dot3(dUdrhat,r12hat);
fforce[0] = dUdr*r12hat[0] + (dUdrhat[0]-dUdrhatrhat*r12hat[0])/r;
fforce[1] = dUdr*r12hat[1] + (dUdrhat[1]-dUdrhatrhat*r12hat[1])/r;
fforce[2] = dUdr*r12hat[2] + (dUdrhat[2]-dUdrhatrhat*r12hat[2])/r;
// torque i
dUdni1[0] = dUdphi*dphi_dni1[0];
dUdni1[1] = dUdphi*dphi_dni1[1];
dUdni1[2] = dUdphi*dphi_dni1[2];
MathExtra::cross3(dUdni1,ni1,ttor); //minus sign is replace by swapping ni1 and dUdni1
if (newton_pair || j < nlocal) {
dUdnj1[0] = dUdphi*dphi_dnj1[0];
dUdnj1[1] = dUdphi*dphi_dnj1[1];
dUdnj1[2] = dUdphi*dphi_dnj1[2];
MathExtra::cross3(dUdnj1,nj1,rtor); //minus sign is replace by swapping ni1 and dUdni1
}
// output energy, force, torque, only for the in_two_particles input file, for checking the model implementation
/*
fprintf(screen,"energy = %f \n",U);
fprintf(screen,"force_i = %f %f %f \n",fforce[0],fforce[1],fforce[2]);
fprintf(screen,"torque_i = %f %f %f \n",ttor[0],ttor[1],ttor[2]);
fprintf(screen,"torque_j = %f %f %f \n",rtor[0],rtor[1],rtor[2]);
*/
return U;
dUdnj1[0] = dUdphi * dphi_dnj1[0];
dUdnj1[1] = dUdphi * dphi_dnj1[1];
dUdnj1[2] = dUdphi * dphi_dnj1[2];
MathExtra::cross3(dUdnj1, nj1, rtor); //minus sign is replace by swapping ni1 and dUdni1
}
return U;
}

21
src/ASPHERE/pair_ylz.h
View File

@ -12,9 +12,9 @@
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(ylz,PairYLZ);
// clang-format on
#else
@ -41,25 +41,16 @@ class PairYLZ : public Pair {
void write_data(FILE *);
void write_data_all(FILE *);
protected:
double cut_global;
double **epsilon,**sigma,**cut,**zeta,**mu,**beta; // model parameter values for atom-type pairs
double **epsilon, **sigma, **cut, **zeta, **mu, **beta;
class AtomVecEllipsoid *avec;
void allocate();
double ylz_analytic(const int i, const int j, double a1[3][3],
double a2[3][3], double *r12,
const double rsq, double *fforce, double *ttor,
double *rtor);
double ylz_analytic(const int i, const int j, double a1[3][3], double a2[3][3], double *r12,
const double rsq, double *fforce, double *ttor, double *rtor);
};
}
} // namespace LAMMPS_NS
#endif
#endif