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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11700 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-04-04 16:36:51 +00:00
parent 3e9c22df24
commit 1646c124b1
19 changed files with 75 additions and 116 deletions
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65
src/FLD/pair_lubricateU.cpp
View File

@ -107,14 +107,11 @@ PairLubricateU::~PairLubricateU()
void PairLubricateU::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int i,j;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int nall = nlocal + nghost;
@ -184,7 +181,7 @@ void PairLubricateU::compute(int eflag, int vflag)
void PairLubricateU::stage_one()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int i,j,ii,inum,itype;
double **x = atom->x;
double **v = atom->v;
@ -192,17 +189,12 @@ void PairLubricateU::stage_one()
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
double vxmu2f = force->vxmu2f;
double inv_inertia,mo_inertia;
int *ilist;
double radi;
int nprocs = comm->nprocs;
inum = list->inum;
ilist = list->ilist;
@ -398,23 +390,18 @@ void PairLubricateU::intermediates(int nall, double **xl)
void PairLubricateU::stage_two(double **x)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int i,j,ii,inum,itype;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
double vxmu2f = force->vxmu2f;
double inv_inertia,mo_inertia;
int *ilist;
double radi;
int nprocs = comm->nprocs;
inum = list->inum;
ilist = list->ilist;
@ -582,11 +569,10 @@ void PairLubricateU::stage_two(double **x)
void PairLubricateU::compute_Fh(double **x)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
double rsq,r,h_sep,radi;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
double inv_inertia;
double vt1,vt2,vt3;
int *ilist,*jlist,*numneigh,**firstneigh;
double **v = atom->v;
@ -601,7 +587,7 @@ void PairLubricateU::compute_Fh(double **x)
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh;
inum = list->inum;
ilist = list->ilist;
@ -819,11 +805,10 @@ void PairLubricateU::compute_Fh(double **x)
void PairLubricateU::compute_RU()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
@ -832,7 +817,6 @@ void PairLubricateU::compute_RU()
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
@ -840,7 +824,7 @@ void PairLubricateU::compute_RU()
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu;
inum = list->inum;
ilist = list->ilist;
@ -1098,11 +1082,10 @@ void PairLubricateU::compute_RU()
void PairLubricateU::compute_RU(double **x)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
double **v = atom->v;
@ -1117,7 +1100,7 @@ void PairLubricateU::compute_RU(double **x)
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu;
inum = list->inum;
ilist = list->ilist;
@ -1378,27 +1361,23 @@ void PairLubricateU::compute_RU(double **x)
void PairLubricateU::compute_RE()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int newton_pair = force->newton_pair;
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
double xl[3],a_sq,a_sh,a_pu;
inum = list->inum;
ilist = list->ilist;
@ -1560,26 +1539,22 @@ void PairLubricateU::compute_RE()
void PairLubricateU::compute_RE(double **x)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3;
double inv_inertia;
int *ilist,*jlist,*numneigh,**firstneigh;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int newton_pair = force->newton_pair;
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
double xl[3],a_sq,a_sh,a_pu;
if (!flagHI) return;
@ -1849,7 +1824,7 @@ void PairLubricateU::init_style()
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair lubricateU requires ghost atoms store velocity");
int irequest = neighbor->request(this);
neighbor->request(this);
// require that atom radii are identical within each type
// require monodisperse system with same radii for all types

8
src/REPLICA/neb.cpp
View File

@ -505,8 +505,14 @@ void NEB::open(char *file)
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
sprintf(gunzip,"gunzip -c %s",file);
sprintf(gunzip,"gzip -c -d %s",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
#else
fp = popen(gunzip,"r");
#endif
#else
error->one(FLERR,"Cannot open gzipped file");
#endif

22
src/RIGID/fix_rigid_small.cpp
View File

@ -66,7 +66,7 @@ enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};
FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
int i,ibody;
int i;
scalar_flag = 1;
extscalar = 0;
@ -327,7 +327,7 @@ int FixRigidSmall::setmask()
void FixRigidSmall::init()
{
int i,ibody;
int i;
triclinic = domain->triclinic;
@ -597,7 +597,7 @@ void FixRigidSmall::post_force(int vflag)
void FixRigidSmall::final_integrate()
{
int i,ibody;
double dtfm,xy,xz,yz;
double dtfm;
//check(3);
@ -787,7 +787,6 @@ void FixRigidSmall::pre_neighbor()
imageint *image = atom->image;
int nlocal = atom->nlocal;
int ibody;
imageint idim,otherdims;
for (int i = 0; i < nlocal; i++) {
@ -944,7 +943,6 @@ void FixRigidSmall::deform(int flag)
void FixRigidSmall::set_xv()
{
int ibody,itype;
int xbox,ybox,zbox;
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double ione[3],exone[3],eyone[3],ezone[3],vr[6],p[3][3];
@ -1112,9 +1110,7 @@ void FixRigidSmall::set_xv()
void FixRigidSmall::set_v()
{
int ibody,itype;
int xbox,ybox,zbox;
double dx,dy,dz;
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
double ione[3],exone[3],eyone[3],ezone[3],delta[3],vr[6];
@ -1539,7 +1535,7 @@ void FixRigidSmall::ring_farthest(int n, char *cbuf)
void FixRigidSmall::setup_bodies_static()
{
int i,itype,ibody;
int i,ibody;
// extended = 1 if any particle in a rigid body is finite size
// or has a dipole moment
@ -1703,7 +1699,7 @@ void FixRigidSmall::setup_bodies_static()
for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++)
for (i = 0; i < 6; i++) itensor[ibody][i] = 0.0;
double dx,dy,dz,rad;
double dx,dy,dz;
double *inertia;
for (i = 0; i < nlocal; i++) {
@ -1988,8 +1984,6 @@ void FixRigidSmall::setup_bodies_static()
// error check that re-computed momemts of inertia match diagonalized ones
// do not do test for bodies with params read from infile
double *inew;
double norm;
for (ibody = 0; ibody < nlocal_body; ibody++) {
if (infile && inbody[ibody]) continue;
@ -2616,8 +2610,6 @@ int FixRigidSmall::pack_comm(int n, int *list, double *buf,
int i,j;
double *xcm,*vcm,*quat,*omega,*ex_space,*ey_space,*ez_space;
int nlocal = atom->nlocal;
int m = 0;
if (commflag == INITIAL) {
@ -2692,7 +2684,7 @@ int FixRigidSmall::pack_comm(int n, int *list, double *buf,
void FixRigidSmall::unpack_comm(int n, int first, double *buf)
{
int i,j,last,flag;
int i,j,last;
double *xcm,*vcm,*quat,*omega,*ex_space,*ey_space,*ez_space;
int m = 0;
@ -2845,8 +2837,6 @@ void FixRigidSmall::unpack_reverse_comm(int n, int *list, double *buf)
int i,j,k;
double *fcm,*torque,*vcm,*angmom,*xcm;
int nlocal = atom->nlocal;
int m = 0;
if (commflag == FORCE_TORQUE) {

14
src/SRD/fix_srd.cpp
View File

@ -465,7 +465,6 @@ void FixSRD::pre_neighbor()
{
int i,j,m,ix,iy,iz,jx,jy,jz,ibin,jbin,lo,hi;
double rsq,cutbinsq;
double xlamda[3];
// grow SRD per-atom bin arrays if necessary
@ -700,7 +699,6 @@ void FixSRD::pre_neighbor()
void FixSRD::post_force(int vflag)
{
int i,m,ix,iy,iz;
double xlamda[3];
// zero per-timestep stats
@ -831,8 +829,8 @@ void FixSRD::reset_velocities()
{
int i,j,n,ix,iy,iz,ibin,axis,sign,irandom;
double u[3],vsum[3];
double vx,vy,vz,vsq,tbin,scale;
double *vave,*vnew,*xlamda;
double vsq,tbin,scale;
double *vave,*xlamda;
double vstream[3];
// if requested, perform a dynamic shift of bin positions
@ -1260,7 +1258,7 @@ void FixSRD::xbin_unpack(double *buf, BinAve *vbin, int n, int *list, int nval)
void FixSRD::collisions_single()
{
int i,j,k,m,type,nbig,ibin,ibounce,inside,collide_flag,lineside;
int i,j,k,m,type,nbig,ibin,ibounce,inside,collide_flag;
double dt,t_remain;
double norm[3],xscoll[3],xbcoll[3],vsnew[3];
Big *big;
@ -1639,7 +1637,6 @@ int FixSRD::inside_line(double *xs, double *xb, double *vs, double *vb,
Big *big, double dt_step)
{
double pmc0[2],pmc1[2],n0[2],n1[2];
double n1_n0[2],pmc1_pmc0[2];
// 1 and 2 = start and end of timestep
// pmc = P - C, where P = position of S, C = position of B
@ -2013,7 +2010,7 @@ double FixSRD::collision_ellipsoid_exact(double *xs, double *xb,
double vs_vb[3],xs_xb[3],omega_ex[3],omega_ey[3],omega_ez[3];
double excoll[3],eycoll[3],ezcoll[3],delta[3],xbody[3],nbody[3];
double ax,bx,cx,ay,by,cy,az,bz,cz;
double a,b,c,scale;
double a,b,c;
double *omega = big->omega;
double *ex = big->ex;
@ -2902,7 +2899,6 @@ void FixSRD::big_static()
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *type = atom->type;
double skinhalf = 0.5 * neighbor->skin;
@ -3880,7 +3876,7 @@ void FixSRD::velocity_stats(int groupnum)
double FixSRD::newton_raphson(double t1, double t2)
{
double f1,f2,df,tlo,thi;
double f1,df,tlo,thi;
lineside(t1,f1,df);
if (f1 < 0.0) {
tlo = t1;

3
src/USER-OMP/pppm_cg_omp.h
View File

@ -42,15 +42,12 @@ class PPPMCGOMP : public PPPMCG, public ThrOMP {
virtual void fieldforce_ik();
virtual void fieldforce_ad();
virtual void fieldforce_peratom();
// virtual void make_rho();
private:
void compute_rho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
const FFT_SCALAR &, const FFT_SCALAR &);
void compute_drho1d_thr(FFT_SCALAR * const * const, const FFT_SCALAR &,
const FFT_SCALAR &, const FFT_SCALAR &);
// void slabcorr(int);
};
}

2
src/USER-REAXC/fix_qeq_reax.cpp
View File

@ -515,7 +515,7 @@ void FixQEqReax::init_matvec()
void FixQEqReax::compute_H()
{
int inum, jnum, *ilist, *jlist, *numneigh, **firstneigh;
int i, j, ii, jj, temp, newnbr, flag;
int i, j, ii, jj, flag;
double **x, SMALL = 0.0001;
double dx, dy, dz, r_sqr;

12
src/USER-REAXC/fix_reaxc_bonds.cpp
View File

@ -118,8 +118,6 @@ void FixReaxCBonds::init()
void FixReaxCBonds::end_of_step()
{
bigint ntimestep = update->ntimestep;
Output_ReaxC_Bonds(update->ntimestep,fp);
if (me == 0) fflush(fp);
}
@ -129,8 +127,8 @@ void FixReaxCBonds::end_of_step()
void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
{
int i, j, k, itype, jtype, iatom;
int b, nbuf, nbuf_local, inode;
int i, j;
int nbuf, nbuf_local;
int nlocal_max, numbonds, numbonds_max;
double *buf;
@ -177,7 +175,7 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
void FixReaxCBonds::FindBond(struct _reax_list *lists, int &numbonds)
{
int *ilist, i, ii, inum;
int j, pj, nj, jtype;
int j, pj, nj;
tagint jtag;
double bo_tmp,bo_cut;
@ -249,8 +247,8 @@ void FixReaxCBonds::PassBuffer(double *buf, int &nbuf_local)
void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local,
int natoms, int maxnum)
{
int i, j, k, l, itype, jtype;
int inode, nlocal_tmp, numbonds, molid;
int i, j, k, itype;
int inode, nlocal_tmp, numbonds;
tagint itag,jtag;
int nlocal = atom->nlocal;
bigint ntimestep = update->ntimestep;

2
src/USER-REAXC/pair_reax_c.cpp
View File

@ -816,7 +816,7 @@ void PairReaxC::FindBond()
tmpid[i][nj] = j;
tmpbo[i][nj] = bo_tmp;
nj ++;
if (nj > MAXSPECBOND) error->all(FLERR,"Increase MAXSPECBOND in fix_reaxc_species.h");
if (nj > MAXSPECBOND) error->all(FLERR,"Increase MAXSPECBOND in reaxc_defs.h");
}
}
}

8
src/USER-REAXC/reaxc_allocate.cpp
View File

@ -47,8 +47,6 @@
int PreAllocate_Space( reax_system *system, control_params *control,
storage *workspace, MPI_Comm comm )
{
int i;
int mincap = system->mincap;
double safezone = system->safezone;
@ -759,15 +757,11 @@ void ReAllocate( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data )
{
int i, j, k, p;
int num_bonds, est_3body, nflag, Nflag, Hflag, mpi_flag, ret, total_send;
int num_bonds, est_3body, nflag, Nflag, Hflag, ret;
int renbr, newsize;
reallocate_data *realloc;
reax_list *far_nbrs;
sparse_matrix *H;
grid *g;
neighbor_proc *nbr_pr;
mpi_out_data *nbr_data;
MPI_Comm comm;
char msg[200];

1
src/USER-REAXC/reaxc_bond_orders.cpp
View File

@ -554,7 +554,6 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
int pk, k, j;
/* Virial Tallying variables */
real f_scaler;
rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp;
/* Initializations */

2
src/USER-REAXC/reaxc_defs.h
View File

@ -117,7 +117,7 @@
#define MAX_BOND 20
#define MAXREAXBOND 24 /* used in fix_reaxc_bonds.cpp and pair_reax_c.cpp */
#define MAXSPECBOND 12 /* used in fix_species.cpp and pair_reax_c.cpp */
#define MAXSPECBOND 24 /* used in fix_species.cpp and pair_reax_c.cpp */
/******************* ENUMERATIONS *************************/
enum geo_formats { CUSTOM, PDB, ASCII_RESTART, BINARY_RESTART, GF_N };

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

@ -160,7 +160,7 @@ void Torsion_Angles( reax_system *system, control_params *control,
{
int i, j, k, l, pi, pj, pk, pl, pij, plk, natoms;
int type_i, type_j, type_k, type_l;
int start_j, end_j, start_k, end_k;
int start_j, end_j;
int start_pj, end_pj, start_pk, end_pk;
int num_frb_intrs = 0;
@ -203,7 +203,7 @@ void Torsion_Angles( reax_system *system, control_params *control,
// Virial tallying variables
real delil[3], deljl[3], delkl[3];
real eng_tmp, f_scaler, fi_tmp[3], fj_tmp[3], fk_tmp[3];
real eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3];
// sprintf( fname, "tor%d.out", system->my_rank );
// ftor = fopen( fname, "w" );
@ -227,8 +227,6 @@ void Torsion_Angles( reax_system *system, control_params *control,
trying to form a 4-body interaction out of this neighborhood */
if( system->my_atoms[j].orig_id < system->my_atoms[k].orig_id &&
bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs) ) {
start_k = Start_Index(k, bonds);
end_k = End_Index(k, bonds);
pj = pbond_jk->sym_index; // pj points to j on k's list
/* do the same check as above:

3
src/USER-SPH/fix_meso_stationary.cpp
View File

@ -75,7 +75,6 @@ void FixMesoStationary::initial_integrate(int vflag) {
double *e = atom->e;
double *de = atom->de;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int i;
@ -99,9 +98,7 @@ void FixMesoStationary::final_integrate() {
double *de = atom->de;
double *rho = atom->rho;
double *drho = atom->drho;
int *type = atom->type;
int *mask = atom->mask;
double *mass = atom->mass;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;

19
src/compute_rdf.h
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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -34,20 +34,19 @@ class ComputeRDF : public Compute {
void compute_array();
private:
int first;
int nbin; // # of rdf bins
int npairs; // # of rdf pairs
double delr,delrinv; // bin width and its inverse
int ***rdfpair; // map 2 type pair to rdf pair for each histo
int **nrdfpair; // # of histograms for each type pair
int nbin; // # of rdf bins
int npairs; // # of rdf pairs
double delr,delrinv; // bin width and its inverse
int ***rdfpair; // map 2 type pair to rdf pair for each histo
int **nrdfpair; // # of histograms for each type pair
int *ilo,*ihi,*jlo,*jhi;
double **hist; // histogram bins
double **histall; // summed histogram bins across all procs
double **hist; // histogram bins
double **histall; // summed histogram bins across all procs
int *typecount;
int *icount,*jcount;
class NeighList *list; // half neighbor list
class NeighList *list; // half neighbor list
};
}

4
src/fix_setforce.h
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@ -1,4 +1,4 @@
/* ----------------------------------------------------------------------
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -45,7 +45,7 @@ class FixSetForce : public Fix {
char *idregion;
int xvar,yvar,zvar,xstyle,ystyle,zstyle;
double foriginal[3],foriginal_all[3];
int varany,force_flag;
int force_flag;
int nlevels_respa;
int maxatom;

1
src/fix_spring.h
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@ -48,7 +48,6 @@ class FixSpring : public Fix {
double masstotal,masstotal2;
int nlevels_respa;
double espring,ftotal[4];
int force_flag;
void spring_tether();
void spring_couple();

12
src/group.cpp
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@ -502,9 +502,15 @@ void Group::assign(int narg, char **arg)
MPI_Allreduce(&rlocal,&all,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen,"%.15g atoms in group %s\n",all,names[igroup]);
if (logfile)
fprintf(logfile,"%.15g atoms in group %s\n",all,names[igroup]);
if (dynamic[igroup]) {
if (screen) fprintf(screen,"dynamic group %s\n",names[igroup]);
if (logfile) fprintf(logfile,"dynamic group %s\n",names[igroup]);
} else {
if (screen)
fprintf(screen,"%.15g atoms in group %s\n",all,names[igroup]);
if (logfile)
fprintf(logfile,"%.15g atoms in group %s\n",all,names[igroup]);
}
}
}

6
src/read_data.cpp
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@ -1352,6 +1352,7 @@ void ReadData::paircoeffs()
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,1);
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
force->pair->coeff(narg,arg);
buf = next + 1;
}
@ -1377,6 +1378,7 @@ void ReadData::pairIJcoeffs()
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,0);
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
force->pair->coeff(narg,arg);
buf = next + 1;
}
@ -1398,6 +1400,7 @@ void ReadData::bondcoeffs()
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,0);
if (narg == 0) error->all(FLERR,"Unexpected end of BondCoeffs section");
force->bond->coeff(narg,arg);
buf = next + 1;
}
@ -1421,6 +1424,7 @@ void ReadData::anglecoeffs(int which)
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"bb",0);
else if (which == 2) parse_coeffs(buf,"ba",0);
if (narg == 0) error->all(FLERR,"Unexpected end of AngleCoeffs section");
force->angle->coeff(narg,arg);
buf = next + 1;
}
@ -1447,6 +1451,7 @@ void ReadData::dihedralcoeffs(int which)
else if (which == 3) parse_coeffs(buf,"at",0);
else if (which == 4) parse_coeffs(buf,"aat",0);
else if (which == 5) parse_coeffs(buf,"bb13",0);
if (narg == 0) error->all(FLERR,"Unexpected end of DihedralCoeffs section");
force->dihedral->coeff(narg,arg);
buf = next + 1;
}
@ -1469,6 +1474,7 @@ void ReadData::impropercoeffs(int which)
*next = '\0';
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"aa",0);
if (narg == 0) error->all(FLERR,"Unexpected end of ImproperCoeffs section");
force->improper->coeff(narg,arg);
buf = next + 1;
}

1
src/special.h
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@ -27,7 +27,6 @@ class Special : protected Pointers {
private:
int me,nprocs;
tagint **onetwo,**onethree,**onefour;
int dihedral_flag;
// data used by ring callback methods