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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11617 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-03-10 15:56:49 +00:00
parent 3d6ac732ad
commit 5e1d34a23d
32 changed files with 66 additions and 101 deletions
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15
src/atom_vec_body.cpp
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@ -562,7 +562,7 @@ int AtomVecBody::pack_border(int n, int *list, double *buf,
{
int i,j,m;
double dx,dy,dz;
double *quat,*c1,*c2,*c3,*inertia;
double *quat,*inertia;
m = 0;
if (pbc_flag == 0) {
@ -642,7 +642,7 @@ int AtomVecBody::pack_border_vel(int n, int *list, double *buf,
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
double *quat,*c1,*c2,*c3,*inertia;
double *quat,*inertia;
m = 0;
if (pbc_flag == 0) {
@ -775,7 +775,7 @@ int AtomVecBody::pack_border_vel(int n, int *list, double *buf,
int AtomVecBody::pack_border_hybrid(int n, int *list, double *buf)
{
int i,j,m;
double *quat,*c1,*c2,*c3,*inertia;
double *quat,*inertia;
m = 0;
for (i = 0; i < n; i++) {
@ -805,7 +805,7 @@ int AtomVecBody::pack_border_hybrid(int n, int *list, double *buf)
void AtomVecBody::unpack_border(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*c1,*c2,*c3,*inertia;
double *quat,*inertia;
m = 0;
last = first + n;
@ -853,7 +853,7 @@ void AtomVecBody::unpack_border(int n, int first, double *buf)
void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*c1,*c2,*c3,*inertia;
double *quat,*inertia;
m = 0;
last = first + n;
@ -907,7 +907,7 @@ void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
int AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
{
int i,j,m,last;
double *quat,*c1,*c2,*c3,*inertia;
double *quat,*inertia;
m = 0;
last = first + n;
@ -1346,9 +1346,6 @@ int AtomVecBody::data_vel_hybrid(int m, char **values)
void AtomVecBody::pack_data(double **buf)
{
double c2mc1[2],c3mc1[3],norm[3];
double area;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;

2
src/balance.cpp
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@ -781,7 +781,7 @@ void Balance::dumpout(bigint tstep, FILE *bfp)
int nx = comm->procgrid[0] + 1;
int ny = comm->procgrid[1] + 1;
int nz = comm->procgrid[2] + 1;
//int nz = comm->procgrid[2] + 1;
if (dimension == 2) {
int m = 0;

1
src/change_box.cpp
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@ -70,7 +70,6 @@ void ChangeBox::command(int narg, char **arg)
memset(ops,0,(narg-1)*sizeof(Operation));
nops = 0;
int index;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 ||

2
src/compute_angle_local.cpp
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@ -48,9 +48,7 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
tflag = eflag = -1;
nvalues = 0;
int i;
for (int iarg = 3; iarg < narg; iarg++) {
i = iarg-3;
if (strcmp(arg[iarg],"theta") == 0) tflag = nvalues++;
else if (strcmp(arg[iarg],"eng") == 0) eflag = nvalues++;
else error->all(FLERR,"Invalid keyword in compute angle/local command");

1
src/compute_bond_local.cpp
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@ -119,7 +119,6 @@ int ComputeBondLocal::compute_bonds(int flag)
int i,m,n,nb,atom1,atom2,imol,iatom,btype;
tagint tagprev;
double delx,dely,delz,rsq;
double *dbuf,*ebuf,*fbuf;
double *ptr;
double **x = atom->x;

3
src/compute_cluster_atom.cpp
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@ -94,7 +94,7 @@ void ComputeClusterAtom::init_list(int id, NeighList *ptr)
void ComputeClusterAtom::compute_peratom()
{
int i,j,ii,jj,inum,jnum,n;
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
@ -156,7 +156,6 @@ void ComputeClusterAtom::compute_peratom()
jlist = firstneigh[i];
jnum = numneigh[i];
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;

9
src/compute_dihedral_local.cpp
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@ -50,9 +50,7 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
pflag = -1;
nvalues = 0;
int i;
for (int iarg = 3; iarg < narg; iarg++) {
i = iarg-3;
if (strcmp(arg[iarg],"phi") == 0) pflag = nvalues++;
else error->all(FLERR,"Invalid keyword in compute dihedral/local command");
}
@ -111,7 +109,7 @@ int ComputeDihedralLocal::compute_dihedrals(int flag)
int i,m,n,nd,atom1,atom2,atom3,atom4,imol,iatom;
tagint tagprev;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv;
double s,c;
double *pbuf;
@ -207,8 +205,11 @@ int ComputeDihedralLocal::compute_dihedrals(int flag)
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
rginv = ra2inv = rb2inv = 0.0;
ra2inv = rb2inv = 0.0;
/* DEAD CODE
rginv = 0.0;
if (rg > 0) rginv = 1.0/rg;
*/
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);

2
src/compute_gyration_molecule.cpp
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@ -223,7 +223,7 @@ void ComputeGyrationMolecule::compute_array()
void ComputeGyrationMolecule::molcom()
{
tagint imol;
double dx,dy,dz,massone;
double massone;
double unwrap[3];
for (int i = 0; i < nmolecules; i++)

2
src/compute_improper_local.cpp
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@ -51,9 +51,7 @@ ComputeImproperLocal::ComputeImproperLocal(LAMMPS *lmp, int narg, char **arg) :
cflag = -1;
nvalues = 0;
int i;
for (int iarg = 3; iarg < narg; iarg++) {
i = iarg-3;
if (strcmp(arg[iarg],"chi") == 0) cflag = nvalues++;
else error->all(FLERR,"Invalid keyword in compute improper/local command");
}

2
src/compute_property_local.cpp
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@ -342,8 +342,6 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// invoke half neighbor list (will copy or build if necessary)

1
src/compute_temp_profile.cpp
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@ -55,7 +55,6 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
ncount += 2;
nbinx = nbiny = nbinz = 1;
int lastarg;
int iarg = 6;
if (strcmp(arg[iarg],"x") == 0) {

2
src/domain.cpp
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@ -693,7 +693,7 @@ void Domain::box_too_small_check()
Molecule **onemols = atom->avec->onemols;
int nlocal = atom->nlocal;
double delx,dely,delz,rsq,r;
double delx,dely,delz,rsq;
double maxbondme = 0.0;
int lostbond = output->thermo->lostbond;

6
src/fix_box_relax.cpp
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@ -812,7 +812,7 @@ int FixBoxRelax::modify_param(int narg, char **arg)
void FixBoxRelax::compute_sigma()
{
double pdeviatoric[3][3],htmp[3][3];
double pdeviatoric[3][3];//,htmp[3][3];
double tmp1[3][3],sigma_tensor[3][3],h_invtmp[3][3];
// reset reference box dimensions
@ -829,7 +829,7 @@ void FixBoxRelax::compute_sigma()
h0_inv[3] = domain->h_inv[3];
h0_inv[4] = domain->h_inv[4];
h0_inv[5] = domain->h_inv[5];
/* DEAD CODE
htmp[0][0] = h0[0];
htmp[1][1] = h0[1];
htmp[2][2] = h0[2];
@ -839,7 +839,7 @@ void FixBoxRelax::compute_sigma()
htmp[2][1] = 0.0;
htmp[2][0] = 0.0;
htmp[1][0] = 0.0;
*/
h_invtmp[0][0] = h0_inv[0];
h_invtmp[1][1] = h0_inv[1];
h_invtmp[2][2] = h0_inv[2];

2
src/fix_nh.cpp
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@ -1172,7 +1172,7 @@ void FixNH::write_restart(FILE *fp)
double *list;
memory->create(list,nsize,"nh:list");
int n = pack_restart_data(list);
pack_restart_data(list);
if (comm->me == 0) {
int size = nsize * sizeof(double);

4
src/fix_press_berendsen.cpp
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@ -347,8 +347,8 @@ void FixPressBerendsen::end_of_step()
// compute new T,P
if (pstyle == ISO) {
double tmp = temperature->compute_scalar();
tmp = pressure->compute_scalar();
temperature->compute_scalar();
pressure->compute_scalar();
} else {
temperature->compute_vector();
pressure->compute_vector();

13
src/image.cpp
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@ -692,7 +692,7 @@ void Image::draw_triangle(double *x, double *y, double *z, double *surfaceColor)
{
double d1[3], d1len, d2[3], d2len, normal[3], invndotd;
double xlocal[3], ylocal[3], zlocal[3];
double center[3], bounds[6];
//double center[3];
double surface[3];
double depth;
@ -722,10 +722,11 @@ void Image::draw_triangle(double *x, double *y, double *z, double *surfaceColor)
if (invndotd == 0) return;
double r[3],u[3];
/* DEAD CODE
center[0] = (xlocal[0] + ylocal[0] + zlocal[0]) / 3;
center[1] = (xlocal[1] + ylocal[1] + zlocal[1]) / 3;
center[2] = (xlocal[2] + ylocal[2] + zlocal[2]) / 3;
*/
r[0] = MathExtra::dot3(camRight,xlocal);
r[1] = MathExtra::dot3(camRight,ylocal);
@ -1088,7 +1089,7 @@ void Image::write_PPM(FILE *fp)
{
fprintf (fp,"P6\n%d %d\n255\n",width,height);
int x,y;
int y;
for (y = height-1; y >= 0; y --)
fwrite(&writeBuffer[y*width*3],3,width,fp);
}
@ -1878,7 +1879,7 @@ int ColorMap::minmax(double mindynamic, double maxdynamic)
double *ColorMap::value2color(double value)
{
double lo,hi;
double lo;//,hi;
value = MAX(value,locurrent);
value = MIN(value,hicurrent);
@ -1887,10 +1888,10 @@ double *ColorMap::value2color(double value)
if (locurrent == hicurrent) value = 0.0;
else value = (value-locurrent) / (hicurrent-locurrent);
lo = 0.0;
hi = 1.0;
//hi = 1.0;
} else {
lo = locurrent;
hi = hicurrent;
//hi = hicurrent;
}
if (mstyle == CONTINUOUS) {

5
src/irregular.cpp
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@ -193,21 +193,20 @@ int Irregular::migrate_check()
// this check needs to observe PBC
// cannot check via comm->procneigh since it ignores PBC
AtomVec *avec = atom->avec;
double **x = atom->x;
int nlocal = atom->nlocal;
int *periodicity = domain->periodicity;
int *myloc = comm->myloc;
int *procgrid = comm->procgrid;
int newproc,igx,igy,igz,glo,ghi;
int igx,igy,igz,glo,ghi;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (x[i][0] < sublo[0] || x[i][0] >= subhi[0] ||
x[i][1] < sublo[1] || x[i][1] >= subhi[1] ||
x[i][2] < sublo[2] || x[i][2] >= subhi[2]) {
newproc = coord2proc(x[i],igx,igy,igz);
coord2proc(x[i],igx,igy,igz);
glo = myloc[0] - 1;
ghi = myloc[0] + 1;

4
src/min.cpp
View File

@ -547,10 +547,6 @@ void Min::force_clear()
{
if (external_force_clear) return;
int i;
if (external_force_clear) return;
// clear global force array
// nall includes ghosts only if either newton flag is set

4
src/min_linesearch.cpp
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@ -586,7 +586,7 @@ int MinLineSearch::linemin_forcezero(double eoriginal, double &alpha)
{
int i,m,n;
double fdothall,fdothme,hme,hmax,hmaxall;
double de_ideal,de;
double de;
double *xatom,*x0atom,*fatom,*hatom;
double alpha_max, alpha_init, alpha_del;
@ -884,7 +884,7 @@ double MinLineSearch::alpha_step(double alpha, int resetflag)
double MinLineSearch::compute_dir_deriv(double &ff)
{
int i,m,n;
double *xatom,*hatom, *fatom;
double *hatom, *fatom;
double dot[2],dotall[2];
double fh;

1
src/molecule.cpp
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@ -231,7 +231,6 @@ void Molecule::compute_inertia()
// inertia = 3 eigenvalues = principal moments of inertia
// evectors and exzy = 3 evectors = principal axes of rigid body
int ierror;
double cross[3];
double tensor[3][3],evectors[3][3];

5
src/neigh_stencil.cpp
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@ -63,13 +63,12 @@ void Neighbor::stencil_half_bin_2d_no_newton(NeighList *list,
void Neighbor::stencil_half_ghost_bin_2d_no_newton(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int nstencil = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
for (int j = -sy; j <= sy; j++)
for (int i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq) {
stencilxyz[nstencil][0] = i;
stencilxyz[nstencil][1] = j;

19
src/pair.cpp
View File

@ -233,14 +233,11 @@ void Pair::init()
void Pair::reinit()
{
int i,j;
double tmp;
etail = ptail = 0.0;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
tmp = init_one(i,j);
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++) {
init_one(i,j);
if (tail_flag) {
etail += etail_ij;
ptail += ptail_ij;
@ -494,7 +491,7 @@ void Pair::init_tables(double cut_coul, double *cut_respa)
void Pair::init_tables_disp(double cut_lj_global)
{
int masklo,maskhi;
double r, rsq, r2inv, force_coul, force_lj;
double rsq;
double g_ewald_6 = force->kspace->g_ewald_6;
double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2;
@ -531,7 +528,7 @@ void Pair::init_tables_disp(double cut_lj_global)
rsq_lookup.i = i << ndispshiftbits;
rsq_lookup.i |= maskhi;
}
r = sqrtf(rsq_lookup.f);
// r = sqrtf(rsq_lookup.f); DEAD CODE
rsq = rsq_lookup.f;
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2);
@ -567,7 +564,7 @@ void Pair::init_tables_disp(double cut_lj_global)
// deltas at itablemax only needed if corresponding rsq < cut*cut
// if so, compute deltas between rsq and cut*cut
double f_tmp,c_tmp,e_tmp,p_tmp = 0.0,v_tmp = 0.0;
double f_tmp,e_tmp;
double cut_lj_globalsq;
itablemin = minrsq_lookup.i & ndispmask;
itablemin >>= ndispshiftbits;
@ -578,7 +575,7 @@ void Pair::init_tables_disp(double cut_lj_global)
if (rsq_lookup.f < (cut_lj_globalsq = cut_lj_global * cut_lj_global)) {
rsq_lookup.f = cut_lj_globalsq;
r = sqrtf(rsq_lookup.f);
// r = sqrtf(rsq_lookup.f); DEAD CODE
register double x2 = g2*rsq, a2 = 1.0/x2;
x2 = a2*exp(-x2);
@ -1152,7 +1149,7 @@ void Pair::ev_tally4(int i, int j, int k, int m, double evdwl,
void Pair::ev_tally_tip4p(int key, int *list, double *v,
double ecoul, double alpha)
{
int i,j;
int i;
if (eflag_either) {
if (eflag_global) eng_coul += ecoul;

3
src/pair_born_coul_wolf.cpp
View File

@ -84,7 +84,6 @@ void PairBornCoulWolf::compute(int eflag, int vflag)
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -285,7 +284,7 @@ void PairBornCoulWolf::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style born/coul/wolf requires atom attribute q");
int irequest = neighbor->request(this);
neighbor->request(this);
cut_coulsq = cut_coul * cut_coul;
}

14
src/pair_coul_wolf.cpp
View File

@ -53,11 +53,11 @@ PairCoulWolf::~PairCoulWolf()
void PairCoulWolf::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int i,j,ii,jj,inum,jnum;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
double rsq,forcecoul,factor_coul;
double prefactor;
double r,rexp;
double r;
int *ilist,*jlist,*numneigh,**firstneigh;
double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq;
@ -68,9 +68,7 @@ void PairCoulWolf::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
@ -95,7 +93,6 @@ void PairCoulWolf::compute(int eflag, int vflag)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -112,7 +109,6 @@ void PairCoulWolf::compute(int eflag, int vflag)
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cut_coulsq) {
r = sqrt(rsq);
@ -214,7 +210,7 @@ void PairCoulWolf::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair coul/wolf requires atom attribute q");
int irequest = neighbor->request(this);
neighbor->request(this);
cut_coulsq = cut_coul*cut_coul;
}
@ -298,8 +294,8 @@ double PairCoulWolf::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r6inv,r,prefactor,rexp;
double forcecoul,forceborn,phicoul;
double r,prefactor;
double forcecoul,phicoul;
double e_shift,f_shift,dvdrr,erfcc,erfcd;
e_shift = erfc(alf*cut_coul) / cut_coul;

2
src/pair_gauss.cpp
View File

@ -63,7 +63,7 @@ void PairGauss::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double r,rsq;
double rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;

6
src/pair_hybrid.cpp
View File

@ -189,16 +189,14 @@ void PairHybrid::allocate()
void PairHybrid::settings(int narg, char **arg)
{
int i,m,istyle;
if (narg < 1) error->all(FLERR,"Illegal pair_style command");
// delete old lists, since cannot just change settings
if (nstyles) {
for (m = 0; m < nstyles; m++) delete styles[m];
for (int m = 0; m < nstyles; m++) delete styles[m];
delete [] styles;
for (m = 0; m < nstyles; m++) delete [] keywords[m];
for (int m = 0; m < nstyles; m++) delete [] keywords[m];
delete [] keywords;
}

1
src/pair_lj_smooth_linear.cpp
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@ -69,7 +69,6 @@ void PairLJSmoothLinear::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;

9
src/read_data.cpp
View File

@ -757,7 +757,7 @@ void ReadData::header()
void ReadData::atoms()
{
int i,m,nchunk,eof;
int nchunk,eof;
if (me == 0) {
if (screen) fprintf(screen," reading atoms ...\n");
@ -807,7 +807,7 @@ void ReadData::atoms()
void ReadData::velocities()
{
int i,m,nchunk,eof;
int nchunk,eof;
if (me == 0) {
if (screen) fprintf(screen," reading velocities ...\n");
@ -1146,7 +1146,7 @@ void ReadData::impropers(int firstpass)
void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
{
int i,m,nchunk,eof;
int nchunk,eof;
int mapflag = 0;
if (atom->map_style == 0) {
@ -1261,7 +1261,6 @@ void ReadData::bodies(int firstpass)
void ReadData::mass()
{
int i,m;
char *next;
char *buf = new char[atom->ntypes*MAXLINE];
@ -1269,7 +1268,7 @@ void ReadData::mass()
if (eof) error->all(FLERR,"Unexpected end of data file");
char *original = buf;
for (i = 0; i < atom->ntypes; i++) {
for (int i = 0; i < atom->ntypes; i++) {
next = strchr(buf,'\n');
*next = '\0';
atom->set_mass(buf);

3
src/read_restart.cpp
View File

@ -611,9 +611,7 @@ void ReadRestart::file_search(char *infile, char *outfile)
void ReadRestart::header(int incompatible)
{
int px,py,pz;
int xperiodic,yperiodic,zperiodic;
int boundary[3][2];
// read flags and fields until flag = -1
@ -859,7 +857,6 @@ void ReadRestart::type_arrays()
void ReadRestart::force_fields()
{
int n;
char *style;
int flag = read_int();

4
src/set.cpp
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@ -723,7 +723,7 @@ void Set::setrandom(int keyword)
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
atom->style_match("line"); // DEAD CODE?
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
RanPark *random = new RanPark(lmp,1);
@ -787,8 +787,6 @@ void Set::setrandom(int keyword)
// set quaternions to random orientations in 3d or 2d
} else if (keyword == QUAT_RANDOM) {
int *ellipsoid = atom->ellipsoid;
int *tri = atom->tri;
int nlocal = atom->nlocal;
double *quat;

18
src/variable.cpp
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@ -680,8 +680,8 @@ void Variable::compute_atom(int ivar, int igroup,
double *vstore;
if (style[ivar] == ATOM) {
double tmp = evaluate(data[ivar][0],&tree);
tmp = collapse_tree(tree);
evaluate(data[ivar][0],&tree);
collapse_tree(tree);
} else vstore = reader[ivar]->fix->vstore;
int groupbit = group->bitmask[igroup];
@ -2543,27 +2543,27 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
// evaluate args
Tree *newtree;
double tmp,value1,value2,value3;
double value1,value2,value3;
if (tree) {
newtree = new Tree();
Tree *argtree;
if (narg == 1) {
tmp = evaluate(arg1,&argtree);
evaluate(arg1,&argtree);
newtree->left = argtree;
newtree->middle = newtree->right = NULL;
} else if (narg == 2) {
tmp = evaluate(arg1,&argtree);
evaluate(arg1,&argtree);
newtree->left = argtree;
newtree->middle = NULL;
tmp = evaluate(arg2,&argtree);
evaluate(arg2,&argtree);
newtree->right = argtree;
} else if (narg == 3) {
tmp = evaluate(arg1,&argtree);
evaluate(arg1,&argtree);
newtree->left = argtree;
tmp = evaluate(arg2,&argtree);
evaluate(arg2,&argtree);
newtree->middle = argtree;
tmp = evaluate(arg3,&argtree);
evaluate(arg3,&argtree);
newtree->right = argtree;
}
treestack[ntreestack++] = newtree;

2
src/write_data.cpp
View File

@ -422,7 +422,7 @@ void WriteData::bonds()
// pack my bond data into buf
int foo = atom->avec->pack_bond(buf);
atom->avec->pack_bond(buf);
// write one chunk of info per proc to file
// proc 0 pings each proc, receives its chunk, writes to file