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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11829 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-04-18 15:25:28 +00:00
parent c62e2a91c4
commit f461504c93
60 changed files with 185 additions and 372 deletions
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2
src/ASPHERE/pair_tri_lj.cpp
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@ -515,8 +515,6 @@ double PairTriLJ::init_one(int i, int j)
void PairTriLJ::discretize(int i, double sigma,
double *c1, double *c2, double *c3)
{
double c1c2[3],c2c3[3],c1c3[3];
double centroid[3],dc1[3],dc2[3],dc3[3];
centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;

4
src/COLLOID/fix_wall_colloid.cpp
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@ -78,7 +78,7 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
{
double delta,delta2,rinv,r2inv,r4inv,r8inv,fwall;
double r2,rinv2,r2inv2,r4inv2;
double r3,rinv3,r2inv3,r4inv3,r6inv3;
double r3,rinv3,r2inv3,r4inv3;
double rad,rad2,rad4,rad8,diam,new_coeff2;
double eoffset;
@ -129,7 +129,6 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
rinv3 = 1.0/r3;
r2inv3 = rinv3*rinv3;
r4inv3 = r2inv3*r2inv3;
r6inv3 = r4inv3*r2inv3;
ewall[0] += coeff3[m]*((-3.5*diam+delta)*r4inv2*r2inv2*rinv2
+ (3.5*diam+delta)*r4inv3*r2inv3*rinv3) -
coeff4[m]*((diam*delta-r2*r3*(log(-r2)-log(r3)))*
@ -145,7 +144,6 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
rinv3 = 1.0/r3;
r2inv3 = rinv3*rinv3;
r4inv3 = r2inv3*r2inv3;
r6inv3 = r4inv3*r2inv3;
eoffset = coeff3[m]*((-3.5*diam+cutoff[m])*r4inv2*r2inv2*rinv2
+ (3.5*diam+cutoff[m])*r4inv3*r2inv3*rinv3) -
coeff4[m]*((diam*cutoff[m]-r2*r3*(log(-r2)-log(r3)))*

6
src/COLLOID/pair_yukawa_colloid.cpp
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@ -42,7 +42,7 @@ void PairYukawaColloid::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,radi,radj;
double rsq,r2inv,r,rinv,screening,forceyukawa,factor;
double rsq,r,rinv,screening,forceyukawa,factor;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
@ -87,7 +87,6 @@ void PairYukawaColloid::compute(int eflag, int vflag)
radj = radius[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*(r-(radi+radj)));
@ -166,9 +165,8 @@ double PairYukawaColloid::single(int i, int j, int itype, int jtype,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r,rinv,screening,forceyukawa,phi;
double r,rinv,screening,forceyukawa,phi;
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*(r-(rad[itype]+rad[jtype])));

4
src/FLD/pair_brownian.cpp
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@ -84,7 +84,6 @@ void PairBrownian::compute(int eflag, int vflag)
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **torque = atom->torque;
double *radius = atom->radius;
@ -464,13 +463,12 @@ void PairBrownian::init_style()
"Pair brownian needs newton pair on for "
"momentum conservation");
int irequest = neighbor->request(this);
neighbor->request(this);
// insure all particles are finite-size
// for pair hybrid, should limit test to types using the pair style
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)

2
src/FLD/pair_brownian_poly.cpp
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@ -70,7 +70,6 @@ void PairBrownianPoly::compute(int eflag, int vflag)
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **torque = atom->torque;
double *radius = atom->radius;
@ -340,7 +339,6 @@ void PairBrownianPoly::init_style()
// for pair hybrid, should limit test to types using the pair style
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)

3
src/GPU/pair_born_coul_long_gpu.cpp
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@ -210,9 +210,8 @@ void PairBornCoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,rexp,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
int *jlist;

3
src/GPU/pair_buck_coul_long_gpu.cpp
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@ -203,9 +203,8 @@ void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,rexp,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
int *jlist;

2
src/GPU/pair_dpd_tstat_gpu.cpp
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@ -338,7 +338,7 @@ double PairDPDTstatGPU::memory_usage()
void PairDPDTstatGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair;
double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
double rsq,r,rinv,dot,wd,randnum,factor_dpd;
int *jlist;

9
src/GPU/pair_eam_gpu.cpp
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@ -94,18 +94,13 @@ double PairEAMGPU::memory_usage()
void PairEAMGPU::compute(int eflag, int vflag)
{
double evdwl;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
// compute density on each atom on GPU
int nall = atom->nlocal + atom->nghost;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int inum, host_start, inum_dev;
bool success = true;

3
src/GPU/pair_lj_sdk_coul_long_gpu.cpp
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@ -214,13 +214,12 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
{
int i,j,ii,jj;
double qtmp,xtmp,ytmp,ztmp;
double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double r2inv,forcecoul,forcelj,factor_coul,factor_lj;
const double * const * const x = atom->x;
double * const * const f = atom->f;
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;

10
src/GRANULAR/fix_pour.cpp
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@ -447,13 +447,12 @@ void FixPour::pre_exchange()
int success;
double radtmp,delx,dely,delz,rsq,radsum,rn,h;
double coord[3],xcm[3];
double coord[3];
int nfix = modify->nfix;
Fix **fix = modify->fix;
AtomVec *avec = atom->avec;
double denstmp,vxtmp,vytmp,vztmp;
double denstmp;
double *sublo = domain->sublo;
double *subhi = domain->subhi;
@ -707,11 +706,6 @@ int FixPour::overlap(int i)
if (mode == ATOM) delta = atom->radius[i] + radius_max;
else delta = atom->radius[i] + onemol->molradius;
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *prd = domain->prd;
int *periodicity = domain->periodicity;
double *x = atom->x[i];
if (domain->dimension == 3) {

4
src/GRANULAR/pair_gran_hooke.cpp
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@ -41,7 +41,7 @@ PairGranHooke::PairGranHooke(LAMMPS *lmp) : PairGranHookeHistory(lmp)
void PairGranHooke::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
double radi,radj,radsum,rsq,r,rinv,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
@ -235,7 +235,7 @@ double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3,wr1,wr2,wr3;
double vtr1,vtr2,vtr3,vrel;
double mi,mj,meff,damp,ccel;
double fn,fs,ft,fs1,fs2,fs3;
double fn,fs,ft;
double *radius = atom->radius;
radi = radius[i];

3
src/GRANULAR/pair_gran_hooke_history.cpp
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@ -86,7 +86,7 @@ PairGranHookeHistory::~PairGranHookeHistory()
void PairGranHookeHistory::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
double radi,radj,radsum,rsq,r,rinv,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
@ -712,7 +712,6 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
// start from neighprev, since will typically be next neighbor
// reset neighprev to 0 as necessary
int *jlist = list->firstneigh[i];
int jnum = list->numneigh[i];
int *touch = list->listgranhistory->firstneigh[i];
double *allshear = list->listgranhistory->firstdouble[i];

5
src/KSPACE/pair_lj_cut_tip4p_long.cpp
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@ -83,11 +83,10 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double delxOM, delyOM, delzOM;
double r,r2inv,r6inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc,ddotf;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],f1[3],v[6],xH1[3],xH2[3];
double grij,expm2,prefactor,t,erfc;
double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;

5
src/KSPACE/pair_lj_long_coul_long.cpp
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@ -221,11 +221,6 @@ void PairLJLongCoulLong::coeff(int narg, char **arg)
void PairLJLongCoulLong::init_style()
{
const char *style1[] =
{"ewald", "ewald/n", "pppm", "pppm_disp", "pppm_disp/tip4p", NULL};
const char *style6[] = {"ewald/n", "pppm_disp", "pppm_disp/tip4p", NULL};
int i;
// require an atom style with charge defined
if (!atom->q_flag && (ewald_order&(1<<1)))

59
src/KSPACE/pair_lj_long_tip4p_long.cpp
View File

@ -84,9 +84,9 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double r,r2inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double factor_coul;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
@ -126,7 +126,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
inum = list->inum;
@ -172,7 +172,6 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
@ -460,13 +459,11 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
void PairLJLongTIP4PLong::compute_inner()
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int i,j,ii,jj,inum,jnum,itype,jtype;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double r,r2inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double r2inv,forcecoul,forcelj,cforce;
double fO[3],fH[3],fd[3];// f1[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq, qri;
@ -504,13 +501,12 @@ void PairLJLongTIP4PLong::compute_inner()
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
int order1 = ewald_order&(1<<1);
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double *lj1i, *lj2i;
inum = listinner->inum;
ilist = listinner->ilist;
@ -549,14 +545,11 @@ void PairLJLongTIP4PLong::compute_inner()
jlist = firstneigh[i];
jnum = numneigh[i];
offseti = offset[itype];
lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype];
lj1i = lj1[itype]; lj2i = lj2[itype];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
@ -719,13 +712,11 @@ void PairLJLongTIP4PLong::compute_inner()
void PairLJLongTIP4PLong::compute_middle()
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int i,j,ii,jj,inum,jnum,itype,jtype;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double r,r2inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double r2inv,forcecoul,forcelj,cforce;
double fO[3],fH[3],fd[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq,qri;
@ -746,8 +737,6 @@ void PairLJLongTIP4PLong::compute_middle()
// initialize hneigh[0] to -1 on steps when reneighboring occurred
// initialize hneigh[2] to 0 every step
int nlocal = atom->nlocal;
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
@ -755,14 +744,12 @@ void PairLJLongTIP4PLong::compute_middle()
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
int order1 = ewald_order&(1<<1);
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
double *lj1i, *lj2i;
inum = listmiddle->inum;
ilist = listmiddle->ilist;
@ -801,14 +788,11 @@ void PairLJLongTIP4PLong::compute_middle()
jlist = firstneigh[i];
jnum = numneigh[i];
offseti = offset[itype];
lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype];
lj1i = lj1[itype]; lj2i = lj2[itype];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
@ -979,16 +963,13 @@ void PairLJLongTIP4PLong::compute_middle()
void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int i,j,ii,jj,inum,jnum,itype,jtype;
int n,vlist[6];
int key;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double r,r2inv,forcecoul,forcelj,cforce, respa_coul, respa_lj, frespa,fvirial;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double r2inv,forcecoul,forcelj,cforce, respa_coul, respa_lj, frespa,fvirial;
double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq,qri;
@ -1030,7 +1011,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
double cut_in_off = cut_respa[2];
@ -1084,8 +1065,6 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];

13
src/KSPACE/remap.cpp
View File

@ -114,12 +114,7 @@ void remap_3d(FFT_SCALAR *in, FFT_SCALAR *out, FFT_SCALAR *buf,
} else {
if (plan->commringlen > 0) {
MPI_Status status;
int i,isend,irecv;
FFT_SCALAR *scratch;
if (plan->memory == 0) scratch = buf;
else scratch = plan->scratch;
int isend,irecv;
// create send and recv buffers for alltoallv collective
@ -180,9 +175,9 @@ void remap_3d(FFT_SCALAR *in, FFT_SCALAR *out, FFT_SCALAR *buf,
}
}
int mpirc = MPI_Alltoallv(packedSendBuffer, sendcnts, sdispls,
MPI_FFT_SCALAR, packedRecvBuffer, rcvcnts,
rdispls, MPI_FFT_SCALAR, plan->comm);
MPI_Alltoallv(packedSendBuffer, sendcnts, sdispls,
MPI_FFT_SCALAR, packedRecvBuffer, rcvcnts,
rdispls, MPI_FFT_SCALAR, plan->comm);
// unpack the data from the recv buffer into out

2
src/MANYBODY/pair_airebo.cpp
View File

@ -318,8 +318,6 @@ void PairAIREBO::REBO_neigh()
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (atom->nmax > maxlocal) {
maxlocal = atom->nmax;

15
src/MANYBODY/pair_comb.cpp
View File

@ -1844,13 +1844,12 @@ void PairComb::qfo_direct(int inty, int mr1, int mr2, int mr3,
void PairComb::qfo_field(Param *param, double rsq,double iq,double jq,
double &fqij, double &fqjj)
{
double r,r5,r6,rc,rc5,rc6;
double r,r5,rc,rc5,rc6;
double cmi1,cmi2,cmj1,cmj2,rf5;
fqij = fqjj = 0.0;
r = sqrt(rsq);
r5 = r*r*r*r*r;
r6 = r5 * r;
rc = param->lcut;
rc5 = rc*rc*rc*rc*rc;
rc6 = rc5 * rc;
@ -1871,7 +1870,7 @@ void PairComb::qfo_field(Param *param, double rsq,double iq,double jq,
void PairComb::qfo_short(Param *param, int i, int j, double rsq,
double iq, double jq, double &fqij, double &fqjj)
{
double r,tmp_fc,tmp_fc_d,tmp_exp1,tmp_exp2;
double r,tmp_fc,tmp_exp1,tmp_exp2;
double bigA,Asi,Asj,vrcs;
double romi = param->addrep,rrcs = param->bigr + param->bigd;
double qi,qj,Di,Dj,bigB,Bsi,Bsj;
@ -1881,7 +1880,7 @@ void PairComb::qfo_short(Param *param, int i, int j, double rsq,
double romie = param->romiga;
double romib = param->romigb;
double ca1,ca2,ca3,ca4;
double rslp,rslp2,rslp4,arr1,arr2,fc2j,fc3j,fcp2j,fcp3j;
double rslp,rslp2,rslp4,arr1,arr2,fc2j,fc3j;
qi = iq; qj = jq; r = sqrt(rsq);
Di = Dj = Asi = Asj = bigA = Bsi = Bsj = bigB = 0.0;
@ -1890,7 +1889,6 @@ void PairComb::qfo_short(Param *param, int i, int j, double rsq,
caj = cbj = vrcs = cfqr = cfqs = 0.0;
tmp_fc = comb_fc(r,param);
tmp_fc_d = comb_fc_d(r,param);
tmp_exp1 = exp(-param->rlm1 * r);
tmp_exp2 = exp(-param->rlm2 * r);
bij = bbij[i][j]; //comb_bij(zeta_ij,param);
@ -1898,8 +1896,6 @@ void PairComb::qfo_short(Param *param, int i, int j, double rsq,
arr1 = 2.22850; arr2 = 1.89350;
fc2j = comb_fc2(r);
fc3j = comb_fc3(r);
fcp2j = comb_fc2_d(r);
fcp3j = comb_fc3_d(r);
vrcs = 0.0;
if (romi > 0.0) {
@ -2047,14 +2043,13 @@ void PairComb::unpack_reverse_comm(int n, int *list, double *buf)
void PairComb::Short_neigh()
{
int nj,itype,jtype;
int nj;
int inum,jnum,i,j,ii,jj;
int *neighptrj,*ilist,*jlist,*numneigh;
int **firstneigh;
double xtmp,ytmp,ztmp,rsq,delrj[3];
double **x = atom->x;
int *type = atom->type;
if (atom->nmax > nmax) {
memory->sfree(sht_first);
@ -2077,7 +2072,6 @@ void PairComb::Short_neigh()
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
nj = 0;
neighptrj = ipage->vget();
@ -2092,7 +2086,6 @@ void PairComb::Short_neigh()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delrj[0] = xtmp - x[j][0];
delrj[1] = ytmp - x[j][1];

10
src/MANYBODY/pair_lcbop.cpp
View File

@ -259,8 +259,6 @@ void PairLCBOP::SR_neigh()
int *neighptr;
double **x = atom->x;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (atom->nmax > maxlocal) { // ensure ther is enough space
maxlocal = atom->nmax; // for atoms and ghosts allocated
@ -360,7 +358,7 @@ void PairLCBOP::FSR(int eflag, int vflag)
double delx,dely,delz,fpair,xtmp,ytmp,ztmp;
double r_sq,rijmag,f_c_ij,df_c_ij;
double VR,dVRdi,VA,Bij,dVAdi,dVA;
double d_f_c_ij,del[3];
double del[3];
int *ilist,*SR_neighs;
double **x = atom->x;
@ -451,7 +449,7 @@ void PairLCBOP::FSR(int eflag, int vflag)
void PairLCBOP::FLR(int eflag, int vflag)
{
int i,j,jj,m,ii;
int i,j,jj,ii;
tagint itag,jtag;
double delx,dely,delz,fpair,xtmp,ytmp,ztmp;
double r_sq,rijmag,f_c_ij,df_c_ij;
@ -556,7 +554,7 @@ void PairLCBOP::FNij( int i, int j, double factor, double **f, int vflag_atom )
if( riksq > r_1*r_1 ) { // && riksq < r_2*r_2, if second condition not fulfilled neighbor would not be in the list
double rikmag = sqrt(riksq);
double df_c_ik;
double f_c_ik = f_c( rikmag, r_1, r_2, &df_c_ik );
f_c( rikmag, r_1, r_2, &df_c_ik );
// F = factor*df_c_ik*(-grad rikmag)
// grad_i rikmag = \vec{rik} /rikmag
@ -967,7 +965,7 @@ double PairLCBOP::F_conj( double N_ij, double N_ji, double N_conj_ij, double *dF
void PairLCBOP::read_file(char *filename)
{
int i,j,k,l,limit;
int i,k,l;
char s[MAXLINE];
MPI_Comm_rank(world,&me);

4
src/MC/fix_bond_create.cpp
View File

@ -623,7 +623,7 @@ void FixBondCreate::check_ghosts()
void FixBondCreate::update_topology()
{
int i,j,k,n,influence,influenced,found;
int i,j,k,n,influence,influenced;
tagint id1,id2;
tagint *slist;
@ -887,7 +887,7 @@ void FixBondCreate::create_angles(int m)
void FixBondCreate::create_dihedrals(int m)
{
int i,j,k,n,i1local,i2local,i3local,n1,n2,n3,n4;
int i,j,k,n,i1local,i2local,i3local,n1,n2,n3;
tagint i1,i2,i3,i4;
tagint *s1list,*s2list,*s3list;

2
src/MEAM/pair_meam.cpp
View File

@ -118,11 +118,9 @@ PairMEAM::~PairMEAM()
void PairMEAM::compute(int eflag, int vflag)
{
int i,j,ii,n,inum_half,errorflag;
double evdwl;
int *ilist_half,*numneigh_half,**firstneigh_half;
int *numneigh_full,**firstneigh_full;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;

2
src/MISC/compute_ti.cpp
View File

@ -200,7 +200,7 @@ double ComputeTI::compute_scalar()
else jt = ilo[m];
for (; jt <=ihi[m];jt++) {
if ((force->pair->tail_flag)&&(force->pair->setflag[it][jt])) {
double cut = force->pair->init_one(it,jt);
force->pair->init_one(it,jt);
eng += force->pair->etail_ij;
}
if (it !=jt) eng += force->pair->etail_ij;

1
src/MOLECULE/pair_tip4p_cut.cpp
View File

@ -106,7 +106,6 @@ void PairTIP4PCut::compute(int eflag, int vflag)
tagint *tag = atom->tag;
int *type = atom->type;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;

13
src/PERI/pair_peri_eps.cpp
View File

@ -89,8 +89,8 @@ void PairPeriEPS::compute(int eflag, int vflag)
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
double rsq,r,dr,dr1,rk,rkNew,evdwl,fpair,fbond;
double ed,fbondElastoPlastic,fbondFinal;
double rsq,r,dr,rk,rkNew,evdwl,fpair,fbond;
double fbondElastoPlastic,fbondFinal;
double deltalambda,edpNp1;
int *ilist,*jlist,*numneigh,**firstneigh;
double d_ij,delta,stretch;
@ -104,7 +104,6 @@ void PairPeriEPS::compute(int eflag, int vflag)
int *type = atom->type;
int nlocal = atom->nlocal;
double timestepsize = update->dt;
double *vfrac = atom->vfrac;
double *s0 = atom->s0;
double **x0 = atom->x0;
@ -259,7 +258,7 @@ void PairPeriEPS::compute(int eflag, int vflag)
// first = true if this is first neighbor of particle i
bool first;
double omega_minus, omega_plus, omega;
double omega_minus, omega_plus;
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
@ -717,17 +716,13 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0;
double rsq,r,dr;
double delta;
double tdtrial;
double norm = 0.0;
double **x = atom->x;
int *type = atom->type;
double **x0 = atom->x0;
double *s0 = atom->s0;
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double vfrac_scale = 1.0;
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
@ -795,8 +790,6 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
double omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
double omega_minus = influence_function(delx0,dely0,delz0);
double stretch = dr / r0[i][jj];
tdtrial = ( 15 * shearmodulus[itype][itype]) *
((omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) * (ed - edPNP1);

2
src/PERI/pair_peri_ves.cpp
View File

@ -91,7 +91,7 @@ void PairPeriVES::compute(int eflag, int vflag)
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
double rsq,r,dr,dr1,rk,evdwl,fpair,fbond;
double rsq,r,dr,rk,evdwl,fpair,fbond;
double deltaed,fbondViscoElastic,fbondFinal;
double decay,betai,lambdai,edbNp1,rkNew;
int *ilist,*jlist,*numneigh,**firstneigh;

14
src/REPLICA/prd.cpp
View File

@ -58,7 +58,7 @@ PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {}
void PRD::command(int narg, char **arg)
{
int flag,ireplica;
int ireplica;
// error checks
@ -773,7 +773,7 @@ void PRD::replicate(int ireplica)
{
int nreplica = universe->nworlds;
int nprocs_universe = universe->nprocs;
int i,m,flag,commflag;
int i,m;
if (nreplica == nprocs_universe) {
MPI_Bcast(atom->image,atom->nlocal,MPI_INT,ireplica,comm_replica);
@ -856,17 +856,17 @@ void PRD::options(int narg, char **arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"min") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal prd command");
etol = atof(arg[iarg+1]);
ftol = atof(arg[iarg+2]);
maxiter = atoi(arg[iarg+3]);
maxeval = atoi(arg[iarg+4]);
etol = force->numeric(FLERR,arg[iarg+1]);
ftol = force->numeric(FLERR,arg[iarg+2]);
maxiter = force->inumeric(FLERR,arg[iarg+3]);
maxeval = force->inumeric(FLERR,arg[iarg+4]);
if (maxiter < 0) error->all(FLERR,"Illegal prd command");
iarg += 5;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal prd command");
temp_flag = 1;
temp_dephase = atof(arg[iarg+1]);
temp_dephase = force->numeric(FLERR,arg[iarg+1]);
if (temp_dephase <= 0.0) error->all(FLERR,"Illegal prd command");
iarg += 2;

2
src/RIGID/fix_shake.cpp
View File

@ -645,7 +645,7 @@ int FixShake::dof(int igroup)
void FixShake::find_clusters()
{
int i,j,m,n,imol,iatom;
int flag,flag_all,messtag,loop,nbuf,nbufmax,size;
int flag,flag_all,nbuf,size;
tagint tagprev;
double massone;
tagint *buf;

2
src/SHOCK/fix_wall_piston.cpp
View File

@ -185,7 +185,7 @@ void FixWallPiston::initial_integrate(int vflag)
void FixWallPiston::post_integrate()
{
double xlo, xhi, ylo, yhi, zlo, zhi;
double zlo;
double **x = atom->x;
double **v = atom->v;

40
src/USER-COLVARS/fix_colvars.cpp
View File

@ -75,8 +75,6 @@ static int inthash_lookup(void *tptr, int key);
static int inthash_insert(inthash_t *tptr, int key, int data);
/* delete the hash table */
static void inthash_destroy(inthash_t *tptr);
/* adapted sort for in-place sorting of map indices. */
static void id_sort(int *idmap, int left, int right);
/************************************************************************
* integer hash code:
@ -239,44 +237,6 @@ void inthash_destroy(inthash_t *tptr) {
}
}
/************************************************************************
* integer list sort code:
************************************************************************/
/* sort for integer map. initial call id_sort(idmap, 0, natoms - 1); */
static void id_sort(int *idmap, int left, int right)
{
int pivot, l_hold, r_hold;
l_hold = left;
r_hold = right;
pivot = idmap[left];
while (left < right) {
while ((idmap[right] >= pivot) && (left < right))
right--;
if (left != right) {
idmap[left] = idmap[right];
left++;
}
while ((idmap[left] <= pivot) && (left < right))
left++;
if (left != right) {
idmap[right] = idmap[left];
right--;
}
}
idmap[left] = pivot;
pivot = left;
left = l_hold;
right = r_hold;
if (left < pivot)
id_sort(idmap, left, pivot-1);
if (right > pivot)
id_sort(idmap, pivot+1, right);
}
/***************************************************************/
using namespace LAMMPS_NS;

6
src/USER-CUDA/compute_temp_partial_cuda.cpp
View File

@ -71,9 +71,9 @@ ComputeTempPartialCuda::ComputeTempPartialCuda(LAMMPS *lmp, int narg, char **arg
tempflag = 1;
tempbias = 1;
xflag = atoi(arg[3]);
yflag = atoi(arg[4]);
zflag = atoi(arg[5]);
xflag = force->inumeric(FLERR,arg[3]);
yflag = force->inumeric(FLERR,arg[4]);
zflag = force->inumeric(FLERR,arg[5]);
if (zflag && domain->dimension == 2)
error->all(FLERR,"Compute temp/partial cannot use vz for 2d systemx");

4
src/USER-EFF/pair_eff_cut.cpp
View File

@ -867,7 +867,7 @@ void PairEffCut::init_style()
// add hook to minimizer for eradius and erforce
if (update->whichflag == 2)
int ignore = update->minimize->request(this,1,0.01);
update->minimize->request(this,1,0.01);
// make sure to use the appropriate timestep when using real units
@ -878,7 +878,7 @@ void PairEffCut::init_style()
// need a half neigh list and optionally a granular history neigh list
int irequest = neighbor->request(this);
neighbor->request(this);
}
/* ----------------------------------------------------------------------

6
src/USER-EFF/pair_eff_inline.h
View File

@ -314,9 +314,6 @@ inline void ElecElecElec(double rc, double re1, double re2,
re = sqrt(re1 * re1 + re2 * re2);
double ratio;
ratio = rc / re;
/* constants: sqrt(2), 2 / sqrt(pi) */
a = coeff_a / re;
arc = a * rc;
@ -369,7 +366,7 @@ inline void ElecCoreCore(double q, double rc, double re1, double re2,
{
double a, arc, re;
double coeff_a;
double E, dEdr, f, fre, df;
double E, dEdr, f, df;
coeff_a = 1.4142135623730951;
@ -379,7 +376,6 @@ inline void ElecCoreCore(double q, double rc, double re1, double re2,
f = ierfoverx1(arc, &df);
dEdr = -q * a * a * df;
fre = q * a * (f + arc * df) / (re * re);
E = q * a * f;
*ecoul += E;

2
src/USER-MISC/fix_smd.cpp
View File

@ -205,8 +205,6 @@ void FixSMD::smd_tether()
r = sqrt(dx*dx + dy*dy + dz*dz);
if (styleflag & SMD_CVEL) {
if(r > SMALL) {
double fsign;
fsign = (v_smd<0.0) ? -1.0 : 1.0;
dr = r - r0 - r_old;
fx = k_smd*dx*dr/r;
fy = k_smd*dy*dr/r;

3
src/USER-MISC/improper_fourier.cpp
View File

@ -114,9 +114,8 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
const double &vb2x, const double &vb2y, const double &vb2z,
const double &vb3x, const double &vb3y, const double &vb3z)
{
int n;
double eimproper,f1[3],f2[3],f3[3],f4[3];
double domega,c,c2,a,s,projhfg,dhax,dhay,dhaz,dahx,dahy,dahz,cotphi;
double c,c2,a,s,projhfg,dhax,dhay,dhaz,dahx,dahy,dahz,cotphi;
double ax,ay,az,ra2,rh2,ra,rh,rar,rhr,arx,ary,arz,hrx,hry,hrz;
double **x = atom->x;

2
src/USER-MISC/pair_coul_diel.cpp
View File

@ -219,7 +219,7 @@ void PairCoulDiel::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/diel requires atom attribute q");
int irequest = neighbor->request(this);
neighbor->request(this);
}
/* ----------------------------------------------------------------------

1
src/USER-MISC/pair_lj_sf.cpp
View File

@ -73,7 +73,6 @@ void PairLJShiftedForce::compute(int eflag, int vflag)
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;

2
src/USER-OMP/fix_shear_history_omp.cpp
View File

@ -39,8 +39,6 @@ using namespace FixConst;
void FixShearHistoryOMP::pre_exchange()
{
const int nlocal = atom->nlocal;
const int nghost = atom->nghost;
const int nthreads = comm->nthreads;
maxtouch = 0;

9
src/USER-OMP/msm_omp.cpp
View File

@ -180,15 +180,13 @@ void MSMOMP::direct_eval(const int nn)
icz += nzlo_inn;
icy += nylo_inn;
icx += nxlo_inn;
const int kmax = zper ? nzhi_direct : MIN(nzhi_direct,betazn - icz);
const int jmin = yper ? nylo_direct : MAX(nylo_direct,alphan - icy);
const int jmax = yper ? nyhi_direct : MIN(nyhi_direct,betayn - icy);
const int imin = xper ? nxlo_direct : MAX(nxlo_direct,alphan - icx);
const int imax = xper ? nxhi_direct : MIN(nxhi_direct,betaxn - icx);
const double qtmp = qgridn[icz][icy][icx]; // charge on center grid point
esum = 0.0;
if (VFLAG_GLOBAL || VFLAG_ATOM)
v0sum = v1sum = v2sum = v3sum = v4sum = v5sum = 0.0;
@ -357,8 +355,7 @@ void MSMOMP::direct_peratom(const int nn)
const int yper = domain->yperiodic;
const int xper = domain->xperiodic;
const int n=nn;
int i,ifrom,ito,tid,icx,icy,icz,ix,iy,iz,k;
int i,icx,icy,icz,ix,iy,iz,k;
for (i = 0; i < inum; ++i) {
@ -371,7 +368,7 @@ void MSMOMP::direct_peratom(const int nn)
icz += nzlo_inn;
icy += nylo_inn;
icx += nxlo_inn;
const int kmax = zper ? nzhi_direct : MIN(nzhi_direct,betazn - icz);
const int jmin = yper ? nylo_direct : MAX(nylo_direct,alphan - icy);
const int jmax = yper ? nyhi_direct : MIN(nyhi_direct,betayn - icy);

5
src/USER-OMP/pair_comb_omp.cpp
View File

@ -567,12 +567,11 @@ void PairCombOMP::Short_neigh_thr()
#pragma omp parallel default(none)
#endif
{
int nj,npntj,*neighptrj;
int iparam_ij,*ilist,*jlist,*numneigh,**firstneigh;
int nj,*neighptrj;
int *ilist,*jlist,*numneigh,**firstneigh;
int jnum,i,j,ii,jj;
double xtmp,ytmp,ztmp,rsq,delrj[3];
double **x = atom->x;
int *type = atom->type;
const int inum = list->inum;
ilist = list->ilist;

2
src/USER-OMP/pair_eam_alloy_omp.cpp
View File

@ -152,7 +152,7 @@ void PairEAMAlloyOMP::read_file(char *filename)
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
file->elements = new char*[file->nelements];
for (int i = 0; i < file->nelements; i++) {

2
src/USER-OMP/pair_eam_fs_omp.cpp
View File

@ -152,7 +152,7 @@ void PairEAMFSOMP::read_file(char *filename)
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
file->elements = new char*[file->nelements];
for (int i = 0; i < file->nelements; i++) {

9
src/USER-OMP/pair_edip_omp.cpp
View File

@ -78,8 +78,8 @@ void PairEDIPOMP::compute(int eflag, int vflag)
template <int EVFLAG, int EFLAG, int VFLAG_ATOM>
void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,k,ii,inum,jnum;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
int i,j,k,ii,jnum;
int itype,jtype,ktype,ijparam,ikparam;
double xtmp,ytmp,ztmp,evdwl;
int *ilist,*jlist,*numneigh,**firstneigh;
register int preForceCoord_counter;
@ -115,7 +115,6 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
double exp3B_ik;
double exp3BDerived_ik;
double qFunction;
double qFunctionDerived;
double tauFunction;
double tauFunctionDerived;
double expMinusBetaZeta_iZeta_i;
@ -152,7 +151,6 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -283,8 +281,6 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
(interpolTMP-interpolIDX);
qFunctionDerived = -mu * qFunction;
forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i;
forceModCoord = 0.0;
@ -358,7 +354,6 @@ void PairEDIPOMP::eval(int iifrom, int iito, ThrData * const thr)
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
dr_ik[0] = x[k].x - xtmp;
dr_ik[1] = x[k].y - ytmp;

6
src/USER-OMP/pair_gran_hertz_history_omp.cpp
View File

@ -132,6 +132,7 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
@ -145,6 +146,7 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -201,8 +203,8 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
mi = rmass[i];
mj = rmass[j];
} else {
mi = mass[type[i]];
mj = mass[type[j]];
mi = mass[itype];
mj = mass[jtype];
}
if (fix_rigid) {
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];

131
src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
View File

@ -715,22 +715,21 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
const double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int i,j,ii,jj,jnum,itype,jtype,itable;
int n,vlist[6];
int key;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double r,r2inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double factor_coul;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];
dbl3_t x1,x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
@ -738,13 +737,13 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl = ecoul = 0.0;
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
@ -783,7 +782,6 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
@ -792,7 +790,7 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype]) { // lj
r2inv = 1.0/rsq;
if (ORDER6) { // long-range lj
@ -810,7 +808,7 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
register double f = special_lj[ni], t = rn*(1.0-f);
forcelj = f*(rn *= rn)*lj1i[jtype]-
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype];
if (EFLAG)
if (EFLAG)
evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype];
}
}
@ -857,12 +855,12 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
evdwl,0.0,forcelj,delx,dely,delz,thr);
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus) {
if (itype == typeO || jtype == typeO) {
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh_thr[j].a < 0) {
hneigh_thr[j].a = jH1 = atom->map(atom->tag[j] + 1);
@ -890,7 +888,7 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
}
// test current rsq against cutoff and compute Coulombic force
if (rsq < cut_coulsq && ORDER1) {
r2inv = 1.0 / rsq;
if (!CTABLE || rsq <= tabinnersq) {
@ -902,7 +900,7 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
forcecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
@ -1020,7 +1018,7 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
@ -1059,7 +1057,7 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (EVFLAG) ev_tally_list_thr(this,key,vlist,v,ecoul,alpha,thr);
}
}
@ -1071,17 +1069,15 @@ void PairLJLongTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const thr)
{
double r, rsq, r2inv, forcecoul = 0.0, forcelj, cforce, fpair;
double rsq, r2inv, forcecoul = 0.0, forcelj, cforce;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
const int newton_pair = force->newton_pair;
const double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
const double cut_out_on = cut_respa[0];
@ -1091,26 +1087,23 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
const double cut_out_on_sq = cut_out_on*cut_out_on;
const double cut_out_off_sq = cut_out_off*cut_out_off;
int *jneigh, *jneighn, typei, typej, ni;
int ni;
const int order1 = (ewald_order|(ewald_off^-1))&(1<<1);
double qri;
vector xi, d;
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int i,j,ii,jj,jnum,itype,jtype;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double fO[3],fH[3],fd[3];
dbl3_t x1,x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double *lj1i, *lj2i;
ilist = listinner->ilist;
numneigh = listinner->numneigh;
firstneigh = listinner->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
@ -1143,14 +1136,11 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
jlist = firstneigh[i];
jnum = numneigh[i];
offseti = offset[itype];
lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype];
lj1i = lj1[itype]; lj2i = lj2[itype];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j].x;
@ -1158,7 +1148,7 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype] && rsq < cut_out_off_sq ) { // lj
r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
@ -1182,12 +1172,12 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
f[j][2] -= delz*forcelj;
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus && order1) {
if (itype == typeO || jtype == typeO) {
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh_thr[j].a < 0) {
hneigh_thr[j].a = jH1 = atom->map(atom->tag[j] + 1);
@ -1215,7 +1205,7 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
}
// test current rsq against cutoff and compute Coulombic force
if (rsq < cut_coulsq && rsq < cut_out_off_sq) {
r2inv = 1.0 / rsq;
qri = qqrd2e*qtmp;
@ -1289,7 +1279,7 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
@ -1313,19 +1303,17 @@ void PairLJLongTIP4PLongOMP::eval_inner(int iifrom, int iito, ThrData * const th
void PairLJLongTIP4PLongOMP::eval_middle(int iifrom, int iito, ThrData * const thr)
{
double r, rsq, r2inv, forcecoul,forcelj, cforce, fpair;
double rsq, r2inv, forcecoul,forcelj, cforce;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
double * const * const f = thr->get_f();
const double * const q = atom->q;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
const double * const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
const double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
const int newton_pair = force->newton_pair;
const int order1 = (ewald_order|(ewald_off^-1))&(1<<1);
const double cut_in_off = cut_respa[0];
@ -1340,24 +1328,21 @@ void PairLJLongTIP4PLongOMP::eval_middle(int iifrom, int iito, ThrData * const t
const double cut_out_on_sq = cut_out_on*cut_out_on;
const double cut_out_off_sq = cut_out_off*cut_out_off;
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int i,j,ii,jj,jnum,itype,jtype;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double fO[3],fH[3],fd[3];
dbl3_t x1,x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double qri;
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
double *lj1i, *lj2i;
ilist = listmiddle->ilist;
numneigh = listmiddle->numneigh;
firstneigh = listmiddle->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
@ -1390,14 +1375,11 @@ void PairLJLongTIP4PLongOMP::eval_middle(int iifrom, int iito, ThrData * const t
jlist = firstneigh[i];
jnum = numneigh[i];
offseti = offset[itype];
lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype];
lj1i = lj1[itype]; lj2i = lj2[itype];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j].x;
@ -1405,7 +1387,7 @@ void PairLJLongTIP4PLongOMP::eval_middle(int iifrom, int iito, ThrData * const t
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype] && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq ) { // lj
r2inv = 1.0/rsq;
register double rn = r2inv*r2inv*r2inv;
@ -1433,12 +1415,12 @@ void PairLJLongTIP4PLongOMP::eval_middle(int iifrom, int iito, ThrData * const t
f[j][2] -= delz*forcelj;
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus && order1) {
if (itype == typeO || jtype == typeO) {
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh_thr[j].a < 0) {
hneigh_thr[j].a = jH1 = atom->map(atom->tag[j] + 1);
@ -1466,7 +1448,7 @@ void PairLJLongTIP4PLongOMP::eval_middle(int iifrom, int iito, ThrData * const t
}
// test current rsq against cutoff and compute Coulombic force
if (rsq < cut_coulsq && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq) {
r2inv = 1.0 / rsq;
qri = qqrd2e*qtmp;
@ -1544,7 +1526,7 @@ void PairLJLongTIP4PLongOMP::eval_middle(int iifrom, int iito, ThrData * const t
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
@ -1570,7 +1552,7 @@ template < const int EVFLAG, const int EFLAG,
const int NEWTON_PAIR, const int CTABLE, const int LJTABLE, const int ORDER1, const int ORDER6 >
void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const thr)
{
double evdwl,ecoul,fvirial,fpair;
double evdwl,ecoul,fvirial;
evdwl = ecoul = 0.0;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
@ -1583,28 +1565,25 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
const double qqrd2e = force->qqrd2e;
const double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist);
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
int i,j,ii,jj,jnum,itype,jtype;
int n,vlist[6];
int key;
int iH1,iH2,jH1,jH2;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double fraction,table;
double r,r2inv,forcecoul,forcelj,cforce, respa_coul, respa_lj, frespa;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double xiM[3],xjM[3],fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];// f1[3];
double r2inv,forcecoul,forcelj,cforce, respa_coul, respa_lj, frespa;
double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];
dbl3_t x1,x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq,qri;
int respa_flag;
int ni;
double *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
const double cut_in_off = cut_respa[2];
const double cut_in_on = cut_respa[3];
const double cut_in_diff = cut_in_on - cut_in_off;
const double cut_in_off_sq = cut_in_off*cut_in_off;
const double cut_in_on_sq = cut_in_on*cut_in_on;
@ -1612,7 +1591,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
ilist = listouter->ilist;
numneigh = listouter->numneigh;
firstneigh = listouter->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
@ -1652,8 +1631,6 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
ni = sbmask(j);
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j].x;
@ -1661,7 +1638,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
respa_coul = 0;
respa_lj = 0;
if (rsq < cut_ljsq[itype][jtype]) { // lj
@ -1730,7 +1707,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
f[j][0] -= delx*forcelj;
f[j][1] -= dely*forcelj;
f[j][2] -= delz*forcelj;
if (EVFLAG) {
fvirial = forcelj + respa_lj*r2inv;
ev_tally_thr(this,i,j,nlocal,/*newton_pair = */ 1,
@ -1738,12 +1715,12 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
}
}
// adjust rsq and delxyz for off-site O charge(s)
// ADDITIONAL REQEUST REQUIRED HERE!!!!!
if (rsq < cut_coulsqplus) {
if (itype == typeO || jtype == typeO) {
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh_thr[j].a < 0) {
hneigh_thr[j].a = jH1 = atom->map(atom->tag[j] + 1);
@ -1818,7 +1795,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
}
}
}
}
cforce = forcecoul * r2inv;
fvirial = (forcecoul + respa_coul) * r2inv;
@ -1932,7 +1909,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
fH[2] = 0.5 * alpha * fd[2];
f[j][0] += fO[0];
f[j][1] += fO[1];
@ -1958,7 +1935,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
fH[2] = 0.5 * alpha * fd[2];
domain->closest_image(&x[j].x,&x[jH1].x,xH1);
domain->closest_image(&x[j].x,&x[jH2].x,xH2);
@ -1974,7 +1951,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
vlist[n++] = jH1;
vlist[n++] = jH2;
}
if (EVFLAG) ev_tally_list_thr(this,key,vlist,v,ecoul,alpha,thr);
}
}

1
src/USER-OMP/pppm_cg_omp.cpp
View File

@ -22,6 +22,7 @@
#include "error.h"
#include "fix_omp.h"
#include "force.h"
#include "neighbor.h"
#include "memory.h"
#include "math_const.h"
#include "math_special.h"

39
src/USER-OMP/pppm_disp_tip4p_omp.cpp
View File

@ -60,8 +60,6 @@ void PPPMDispTIP4POMP::allocate()
{
PPPMDispTIP4P::allocate();
const int nthreads = comm->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(none)
#endif
@ -78,7 +76,7 @@ void PPPMDispTIP4POMP::allocate()
}
if (function[1] + function[2]) {
ThrData * thr = fix->get_thr(tid);
thr->init_pppm_disp(order_6,memory);
thr->init_pppm_disp(order_6,memory);
}
}
}
@ -136,12 +134,11 @@ void PPPMDispTIP4POMP::compute_gf()
double unitky = (2.0*MY_PI/yprd);
double unitkz = (2.0*MY_PI/zprd_slab);
int tid,nn,nnfrom,nnto,nx,ny,nz,k,l,m;
int tid,nn,nnfrom,nnto,k,l,m;
int kper,lper,mper;
double snx,sny,snz,snx2,sny2,snz2;
double sqk;
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double sum1,dot1,dot2;
double numerator,denominator;
const int nnx = nxhi_fft-nxlo_fft+1;
@ -191,7 +188,7 @@ void PPPMDispTIP4POMP::compute_gf()
if (sqk != 0.0) {
numerator = 4.0*MY_PI/sqk;
denominator = gf_denom(snx2,sny2,snz2, gf_b, order);
denominator = gf_denom(snx2,sny2,snz2, gf_b, order);
greensfn[nn] = numerator*sx*sy*sz*wx*wy*wz/denominator;
} else greensfn[nn] = 0.0;
}
@ -258,7 +255,7 @@ void PPPMDispTIP4POMP::compute_gf_6()
argz = 0.5*qz*zprd_slab/nz_pppm_6;
if (argz != 0.0) wz = pow(sin(argz)/argz,order_6);
wz *= wz;
for (l = nylo_fft_6; l <= nyhi_fft_6; l++) {
lper = l - ny_pppm_6*(2*l/ny_pppm_6);
qy = unitky*lper;
@ -285,10 +282,10 @@ void PPPMDispTIP4POMP::compute_gf_6()
argx = 0.5*qx*xprd/nx_pppm_6;
if (argx != 0.0) wx = pow(sin(argx)/argx,order_6);
wx *= wx;
sqk = pow(qx,2.0) + pow(qy,2.0) + pow(qz,2.0);
denominator = gf_denom(snx2,sny2,snz2, gf_b_6, order_6);
denominator = gf_denom(snx2,sny2,snz2, gf_b_6, order_6);
rtsqk = sqrt(sqk);
term = (1-2*sqk*inv2ew*inv2ew)*sx*sy*sz +
2*sqk*rtsqk*inv2ew*inv2ew*inv2ew*rtpi*erfc(rtsqk*inv2ew);
@ -418,7 +415,6 @@ void PPPMDispTIP4POMP::particle_map(double dxinv, double dyinv,
// no local atoms => nothing to do
if (atom->nlocal == 0) return;
const int * _noalias const type = atom->type;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
int3_t * _noalias const p2g = (int3_t *) part2grid[0];
const double boxlox = boxlo[0];
@ -526,7 +522,7 @@ void PPPMDispTIP4POMP::make_rho_c()
const int ny = p2g[i].b;
const int nz = p2g[i].t;
// pre-screen whether this atom will ever come within
// pre-screen whether this atom will ever come within
// reach of the data segement this thread is updating.
if ( ((nz+nlower-nzlo_out)*ix*iy >= jto)
|| ((nz+nupper-nzlo_out+1)*ix*iy < jfrom) ) continue;
@ -618,7 +614,7 @@ void PPPMDispTIP4POMP::make_rho_g()
const int ny = p2g[i].b;
const int nz = p2g[i].t;
// pre-screen whether this atom will ever come within
// pre-screen whether this atom will ever come within
// reach of the data segement this thread is updating.
if ( ((nz+nlower_6-nzlo_out_6)*ix*iy >= jto)
|| ((nz+nupper_6-nzlo_out_6+1)*ix*iy < jfrom) ) continue;
@ -720,7 +716,7 @@ void PPPMDispTIP4POMP::make_rho_a()
const int ny = p2g[i].b;
const int nz = p2g[i].t;
// pre-screen whether this atom will ever come within
// pre-screen whether this atom will ever come within
// reach of the data segement this thread is updating.
if ( ((nz+nlower_6-nzlo_out_6)*ix*iy >= jto)
|| ((nz+nupper_6-nzlo_out_6+1)*ix*iy < jfrom) ) continue;
@ -1026,7 +1022,6 @@ void PPPMDispTIP4POMP::fieldforce_g_ik()
// ek = 3 components of E-field on particle
const double * const * const x = atom->x;
const double qqrd2e = force->qqrd2e;
#if defined(_OPENMP)
#pragma omp parallel default(none)
@ -1681,7 +1676,7 @@ void PPPMDispTIP4POMP::fieldforce_a_peratom()
// this if protects against having more threads than local atoms
if (ifrom < nlocal) {
for (int i = ifrom; i < ito; i++) {
for (i = ifrom; i < ito; i++) {
nx = part2grid_6[i][0];
ny = part2grid_6[i][1];
@ -1776,20 +1771,20 @@ void PPPMDispTIP4POMP::fieldforce_a_peratom()
lj6 = B[7*type]*0.5;
if (eflag_atom)
eatom[i] += u0*lj0 + u1*lj1 + u2*lj2 +
eatom[i] += u0*lj0 + u1*lj1 + u2*lj2 +
u3*lj3 + u4*lj4 + u5*lj5 + u6*lj6;
if (vflag_atom) {
vatom[i][0] += v00*lj0 + v01*lj1 + v02*lj2 + v03*lj3 +
vatom[i][0] += v00*lj0 + v01*lj1 + v02*lj2 + v03*lj3 +
v04*lj4 + v05*lj5 + v06*lj6;
vatom[i][1] += v10*lj0 + v11*lj1 + v12*lj2 + v13*lj3 +
vatom[i][1] += v10*lj0 + v11*lj1 + v12*lj2 + v13*lj3 +
v14*lj4 + v15*lj5 + v16*lj6;
vatom[i][2] += v20*lj0 + v21*lj1 + v22*lj2 + v23*lj3 +
vatom[i][2] += v20*lj0 + v21*lj1 + v22*lj2 + v23*lj3 +
v24*lj4 + v25*lj5 + v26*lj6;
vatom[i][3] += v30*lj0 + v31*lj1 + v32*lj2 + v33*lj3 +
vatom[i][3] += v30*lj0 + v31*lj1 + v32*lj2 + v33*lj3 +
v34*lj4 + v35*lj5 + v36*lj6;
vatom[i][4] += v40*lj0 + v41*lj1 + v42*lj2 + v43*lj3 +
vatom[i][4] += v40*lj0 + v41*lj1 + v42*lj2 + v43*lj3 +
v44*lj4 + v45*lj5 + v46*lj6;
vatom[i][5] += v50*lj0 + v51*lj1 + v52*lj2 + v53*lj3 +
vatom[i][5] += v50*lj0 + v51*lj1 + v52*lj2 + v53*lj3 +
v54*lj4 + v55*lj5 + v56*lj6;
}
}

3
src/USER-REAXC/fix_qeq_reax.cpp
View File

@ -608,7 +608,7 @@ int FixQEqReax::CG( double *b, double *x )
{
int i, j, imax;
double tmp, alpha, beta, b_norm;
double sig_old, sig_new, sig0;
double sig_old, sig_new;
imax = 200;
@ -622,7 +622,6 @@ int FixQEqReax::CG( double *b, double *x )
b_norm = parallel_norm( b, n );
sig_new = parallel_dot( r, d, n );
sig0 = sig_new;
for( i = 1; i < imax && sqrt(sig_new) / b_norm > tolerance; ++i ) {
comm->forward_comm_fix(this); //Dist_vector( d );

11
src/USER-REAXC/fix_reaxc_species.cpp
View File

@ -486,17 +486,15 @@ AtomCoord chAnchor(AtomCoord in1, AtomCoord in2)
void FixReaxCSpecies::FindMolecule ()
{
int i,j,ii,jj,inum,jnum,n,itype,jtype,itag,jtag,loop,looptot;
int i,j,ii,jj,inum,itype,jtype,loop,looptot;
int change,done,anychange;
int *mask = atom->mask;
int *ilist, *jlist, *numneigh, **firstneigh;
int *ilist;
double bo_tmp,bo_cut;
double **spec_atom = f_SPECBOND->array_atom;
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
numneigh = reaxc->list->numneigh;
firstneigh = reaxc->list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@ -568,7 +566,7 @@ void FixReaxCSpecies::SortMolecule(int &Nmole)
memory->destroy(molmap);
molmap = NULL;
int m, n, idlo, idhi;
int n, idlo, idhi;
int *mask =atom->mask;
int lo = ntotal;
int hi = -ntotal;
@ -636,8 +634,7 @@ void FixReaxCSpecies::SortMolecule(int &Nmole)
void FixReaxCSpecies::FindSpecies(int Nmole, int &Nspec)
{
int inum, *ilist;
int i, j, k, l, m, n, itype, cid;
int k, l, m, n, itype, cid;
int flag_identity, flag_mol, flag_spec;
int flag_tmp;
int *mask =atom->mask;

14
src/USER-REAXC/reaxc_bond_orders.cpp
View File

@ -804,7 +804,7 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
storage *workspace, reax_list **lists, output_controls *out_control )
{
int i, j, pj, type_i, type_j;
int start_i, end_i, sym_index, num_bonds;
int start_i, end_i, sym_index;
real val_i, Deltap_i, Deltap_boc_i;
real val_j, Deltap_j, Deltap_boc_j;
real f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5;
@ -833,7 +833,6 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
// Num_Entries(i, bonds), sizeof(bond_data), compare_bonds );
#endif
num_bonds = 0;
p_boc1 = system->reax_param.gp.l[0];
p_boc2 = system->reax_param.gp.l[1];
@ -1172,20 +1171,9 @@ void BO( reax_system *system, control_params *control, simulation_data *data,
workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
workspace->dDelta_lp_temp[j] = workspace->Clp[j];
}
//fprintf( stderr, "%d\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
//j, workspace->Delta[j], workspace->Delta_e[j], workspace->Delta_boc[j],
//workspace->nlp[j], system->reaxprm.sbp[type_j].nlp_opt,
//workspace->Delta_lp[j], workspace->Clp[j], workspace->dDelta_lp[j] );
//fprintf( stdout, "%d(%d) %24.15f\n",
// j, workspace->bond_mark[j], workspace->total_bond_order[j] );
}
//Print_Bonds( system, bonds, "pbonds.out" );
#if defined(TEST_ENERGIES) || defined(TEST_FORCES)
fprintf( stderr, "Number of bonds: %d\n", num_bonds );
Print_Bond_List( system, control, data, lists, out_control);
#endif
}

13
src/USER-REAXC/reaxc_lookup.cpp
View File

@ -237,10 +237,10 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
/* fill in the lookup table entries for existing atom types.
only lower half should be enough. */
for( i = 0; i < num_atom_types; ++i )
if( aggregated[i] )
for( i = 0; i < num_atom_types; ++i ) {
if( aggregated[i] ) {
//for( j = 0; j < num_atom_types; ++j )
for( j = i; j < num_atom_types; ++j )
for( j = i; j < num_atom_types; ++j ) {
if( aggregated[j] ) {
LR[i][j].xmin = 0;
LR[i][j].xmax = control->nonb_cut;
@ -305,11 +305,12 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
Natural_Cubic_Spline( &h[1], &fCEclmb[1],
&(LR[i][j].CEclmb[1]), control->tabulate+1,
comm );
}
else{
} else{
LR[i][j].n = 0;
}
}
}
}
free(h);
free(fh);
free(fvdw);

9
src/USER-REAXC/reaxc_multi_body.cpp
View File

@ -51,18 +51,17 @@ void Atom_Energy( reax_system *system, control_params *control,
real exp_ovun2n, exp_ovun6, exp_ovun8;
real inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
real e_un, CEunder1, CEunder2, CEunder3, CEunder4;
real p_lp1, p_lp2, p_lp3;
real p_lp2, p_lp3;
real p_ovun2, p_ovun3, p_ovun4, p_ovun5, p_ovun6, p_ovun7, p_ovun8;
real eng_tmp, f_tmp;
real eng_tmp;
single_body_parameters *sbp_i, *sbp_j;
single_body_parameters *sbp_i;
two_body_parameters *twbp;
bond_data *pbond;
bond_order_data *bo_ij;
reax_list *bonds = (*lists) + BONDS;
/* Initialize parameters */
p_lp1 = system->reax_param.gp.l[15];
p_lp3 = system->reax_param.gp.l[5];
p_ovun3 = system->reax_param.gp.l[32];
p_ovun4 = system->reax_param.gp.l[31];
@ -161,7 +160,6 @@ void Atom_Energy( reax_system *system, control_params *control,
j = bonds->select.bond_list[pj].nbr;
type_j = system->my_atoms[j].type;
bo_ij = &(bonds->select.bond_list[pj].bo_data);
sbp_j = &(system->reax_param.sbp[ type_j ]);
twbp = &(system->reax_param.tbp[ type_i ][ type_j ]);
sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
@ -221,7 +219,6 @@ void Atom_Energy( reax_system *system, control_params *control,
/* tally into per-atom energy */
if( system->pair_ptr->evflag) {
eng_tmp = e_ov + e_un;
f_tmp = CEover3 + CEunder3;
system->pair_ptr->ev_tally(i,i,system->n,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
}

6
src/USER-REAXC/reaxc_traj.cpp
View File

@ -131,7 +131,6 @@ int Write_Header( reax_system *system, control_params *control,
output_controls *out_control, mpi_datatypes *mpi_data )
{
int num_hdr_lines, my_hdr_lines, buffer_req;
MPI_Status status;
char ensembles[ens_N][25] = { "NVE", "NVT", "fully flexible NPT",
"semi isotropic NPT", "isotropic NPT" };
char reposition[3][25] = { "fit to periodic box", "CoM to center of box",
@ -339,7 +338,7 @@ int Write_Header( reax_system *system, control_params *control,
mpi_data->world, system->my_rank,
my_hdr_lines, num_hdr_lines );
MPI_File_write_all( out_control->trj, out_control->buffer,
num_hdr_lines, mpi_data->header_line, &status );
num_hdr_lines, mpi_data->header_line, MPI_STATUS_IGNORE );
out_control->trj_offset = (num_hdr_lines) * HEADER_LINE_LEN;
}
else {
@ -549,7 +548,6 @@ int Write_Frame_Header( reax_system *system, control_params *control,
mpi_datatypes *mpi_data )
{
int me, num_frm_hdr_lines, my_frm_hdr_lines, buffer_req;
MPI_Status status;
me = system->my_rank;
/* frame header lengths */
@ -670,7 +668,7 @@ int Write_Frame_Header( reax_system *system, control_params *control,
me, my_frm_hdr_lines, num_frm_hdr_lines );
MPI_File_write_all(out_control->trj, out_control->buffer, my_frm_hdr_lines,
mpi_data->header_line, &status);
mpi_data->header_line, MPI_STATUS_IGNORE);
out_control->trj_offset += (num_frm_hdr_lines) * HEADER_LINE_LEN;
}
else {

5
src/USER-SPH/atom_vec_meso.cpp
View File

@ -475,7 +475,7 @@ int AtomVecMeso::pack_border_vel(int n, int *list, double *buf, int pbc_flag,
int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
@ -527,9 +527,6 @@ int AtomVecMeso::pack_border_vel(int n, int *list, double *buf, int pbc_flag,
buf[m++] = vest[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;

2
src/USER-SPH/pair_sph_rhosum.cpp
View File

@ -66,7 +66,7 @@ void PairSPHRhoSum::init_style() {
void PairSPHRhoSum::compute(int eflag, int vflag) {
int i, j, ii, jj, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz;
double r, rsq, imass, h, ih, ihsq;
double rsq, imass, h, ih, ihsq;
int *jlist;
double wf;
// neighbor list variables

6
src/VORONOI/compute_voronoi_atom.cpp
View File

@ -227,12 +227,6 @@ void ComputeVoronoi::buildCells()
// setup bounds for voro++ domain for orthogonal and triclinic simulation boxes
if( domain->triclinic ) {
// triclinic box: embed parallelepiped into orthogonal voro++ domain
double mx, my, sxy,sxz,syz;
mx = (boxhi[0]-boxlo[0])/(subhi[0]-sublo[0]);
my = (boxhi[1]-boxlo[1])/(subhi[1]-sublo[1]);
sxy = domain->xy/mx;
sxz = domain->xz/mx;
syz = domain->yz/my;
// cutghost is in lamda coordinates for triclinic boxes, use subxx_lamda
double *h = domain->h, cuttri[3];

4
src/XTC/dump_xtc.cpp
View File

@ -360,7 +360,7 @@ static int *buf = NULL;
static int magicints[] = {
0, 0, 0, 0, 0, 0, 0, 0, 0,
8, 10, 12, 16, 20, 25, 32, 40, 50, 64,
80, 101, 128, 161, 203, 256, 322, 406, IMGMAX, 645,
80, 101, 128, 161, 203, 256, 322, 406, 512, 645,
812, 1024, 1290, 1625, 2048, 2580, 3250, 4096, 5060, 6501,
8192, 10321, 13003, 16384, 20642, 26007, 32768, 41285, 52015, 65536,
82570, 104031, 131072, 165140, 208063, 262144, 330280, 416127,
@ -371,7 +371,7 @@ static int magicints[] = {
#define FIRSTIDX 9
/* note that magicints[FIRSTIDX-1] == 0 */
#define LASTIDX (sizeof(magicints) / sizeof(*magicints))
#define LASTIDX (sizeof(magicints) / sizeof(int) - 1 )
/*__________________________________________________________________________
|

2
src/delete_bonds.cpp
View File

@ -63,7 +63,7 @@ void DeleteBonds::command(int narg, char **arg)
// set style and which = type value
int style;
int style = -1;
if (strcmp(arg[1],"multi") == 0) style = MULTI;
else if (strcmp(arg[1],"atom") == 0) style = ATOM;
else if (strcmp(arg[1],"bond") == 0) style = BOND;

4
src/dump_cfg.cpp
View File

@ -44,6 +44,8 @@ enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom
DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
DumpCustom(lmp, narg, arg)
{
multifile_override = 0;
if (narg < 10 ||
strcmp(arg[5],"mass") != 0 || strcmp(arg[6],"type") != 0 ||
(strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) ||
@ -115,7 +117,7 @@ DumpCFG::~DumpCFG()
void DumpCFG::init_style()
{
if (multifile == 0)
if (multifile == 0 && !multifile_override)
error->all(FLERR,"Dump cfg requires one snapshot per file");
DumpCustom::init_style();

2
src/dump_cfg.h
View File

@ -26,6 +26,8 @@ namespace LAMMPS_NS {
class DumpCFG : public DumpCustom {
public:
int multifile_override; // used by write_dump command
DumpCFG(class LAMMPS *, int, char **);
virtual ~DumpCFG();