From 1646c124b1c32ae6e053786a8fb3ead27642a8ec Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 4 Apr 2014 16:36:51 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11700 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/FLD/pair_lubricateU.cpp | 65 ++++++++----------------- src/REPLICA/neb.cpp | 8 ++- src/RIGID/fix_rigid_small.cpp | 22 +++------ src/SRD/fix_srd.cpp | 14 ++---- src/USER-OMP/pppm_cg_omp.h | 3 -- src/USER-REAXC/fix_qeq_reax.cpp | 2 +- src/USER-REAXC/fix_reaxc_bonds.cpp | 12 ++--- src/USER-REAXC/pair_reax_c.cpp | 2 +- src/USER-REAXC/reaxc_allocate.cpp | 8 +-- src/USER-REAXC/reaxc_bond_orders.cpp | 1 - src/USER-REAXC/reaxc_defs.h | 2 +- src/USER-REAXC/reaxc_torsion_angles.cpp | 6 +-- src/USER-SPH/fix_meso_stationary.cpp | 3 -- src/compute_rdf.h | 19 ++++---- src/fix_setforce.h | 4 +- src/fix_spring.h | 1 - src/group.cpp | 12 +++-- src/read_data.cpp | 6 +++ src/special.h | 1 - 19 files changed, 75 insertions(+), 116 deletions(-) diff --git a/src/FLD/pair_lubricateU.cpp b/src/FLD/pair_lubricateU.cpp index 4a48800697..146b033aa8 100644 --- a/src/FLD/pair_lubricateU.cpp +++ b/src/FLD/pair_lubricateU.cpp @@ -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 diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 7754bd7a10..5fd168a943 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -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 diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 40c9a9a708..39bfc82c29 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -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) { diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 4a1d067bd1..3db73bab51 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -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; diff --git a/src/USER-OMP/pppm_cg_omp.h b/src/USER-OMP/pppm_cg_omp.h index e1184138f3..91f09ebbfa 100644 --- a/src/USER-OMP/pppm_cg_omp.h +++ b/src/USER-OMP/pppm_cg_omp.h @@ -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); - }; } diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 94c6295878..ba96d7b211 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -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; diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 4d67378153..e62bcc13a6 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -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; diff --git a/src/USER-REAXC/pair_reax_c.cpp b/src/USER-REAXC/pair_reax_c.cpp index 706d0ebd1d..b7b2a8238d 100644 --- a/src/USER-REAXC/pair_reax_c.cpp +++ b/src/USER-REAXC/pair_reax_c.cpp @@ -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"); } } } diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp index 1fdf444c51..9352fd2c1d 100644 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ b/src/USER-REAXC/reaxc_allocate.cpp @@ -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]; diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp index 297fb8fbfc..cffbb45723 100644 --- a/src/USER-REAXC/reaxc_bond_orders.cpp +++ b/src/USER-REAXC/reaxc_bond_orders.cpp @@ -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 */ diff --git a/src/USER-REAXC/reaxc_defs.h b/src/USER-REAXC/reaxc_defs.h index 1b28336f0a..6a1406387c 100644 --- a/src/USER-REAXC/reaxc_defs.h +++ b/src/USER-REAXC/reaxc_defs.h @@ -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 }; diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp index 1cbcc5892a..b19598d97c 100644 --- a/src/USER-REAXC/reaxc_torsion_angles.cpp +++ b/src/USER-REAXC/reaxc_torsion_angles.cpp @@ -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: diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp index 101b2639f1..d61edcfc20 100644 --- a/src/USER-SPH/fix_meso_stationary.cpp +++ b/src/USER-SPH/fix_meso_stationary.cpp @@ -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; diff --git a/src/compute_rdf.h b/src/compute_rdf.h index 8436593c9d..794fcc9ee6 100644 --- a/src/compute_rdf.h +++ b/src/compute_rdf.h @@ -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 }; } diff --git a/src/fix_setforce.h b/src/fix_setforce.h index 5ced70a473..e18a34ea4a 100644 --- a/src/fix_setforce.h +++ b/src/fix_setforce.h @@ -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; diff --git a/src/fix_spring.h b/src/fix_spring.h index c1fe8ec499..c6e806cbf7 100644 --- a/src/fix_spring.h +++ b/src/fix_spring.h @@ -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(); diff --git a/src/group.cpp b/src/group.cpp index 04afbf462a..2e93562b1a 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -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]); + } } } diff --git a/src/read_data.cpp b/src/read_data.cpp index 085603be54..2b925b8a5b 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -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; } diff --git a/src/special.h b/src/special.h index 90a23a3408..71988724a2 100644 --- a/src/special.h +++ b/src/special.h @@ -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