diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index e47bbda556..90083b0666 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -127,7 +127,7 @@ void ComputeTI::init() for (int m = 0; m < nterms; m++) { ivar1[m] = input->variable->find(var1[m]); ivar2[m] = input->variable->find(var2[m]); - if (ivar1[m] < 0 || ivar2 < 0) + if (ivar1[m] < 0 || ivar2[m] < 0) error->all(FLERR,"Variable name for compute ti does not exist"); if (!input->variable->equalstyle(ivar1[m]) || !input->variable->equalstyle(ivar2[m])) @@ -185,7 +185,7 @@ double ComputeTI::compute_scalar() double *eatom = pptr[m]->eatom; - if (force->newton) npair += atom->nghost; + if (force->newton_pair) npair += atom->nghost; for (int i = 0; i < npair; i++) if ((ilo[m]<=type[i])&(ihi[m]>=type[i])) eng += eatom[i]; MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world); diff --git a/src/Make.py b/src/Make.py index d02620aa35..c704cb7037 100755 --- a/src/Make.py +++ b/src/Make.py @@ -73,7 +73,7 @@ support = ["Makefile","Make.sh","Makefile.package.empty", extlibs = {"USER-ATC": "atc", "USER-AWPMD": "awpmd", "USER-COLVARS": "colvars", "USER-CUDA": "cuda","GPU": "gpu","MEAM": "meam", "POEMS": "poems", - "REAX": "reax"} + "USER-QMMM": "qmmm", "REAX": "reax"} # help messages diff --git a/src/Makefile b/src/Makefile index 555b87e8bc..019bb4bed9 100755 --- a/src/Makefile +++ b/src/Makefile @@ -22,7 +22,7 @@ PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars \ user-omp user-phonon user-qmmm user-reaxc user-sph PACKLIB = gpu kim meam poems reax voronoi \ - user-atc user-awpmd user-colvars user-cuda user-molfile + user-atc user-awpmd user-colvars user-qmmm user-cuda user-molfile PACKALL = $(PACKAGE) $(PACKUSER) @@ -50,7 +50,7 @@ help: @echo 'make install-python install LAMMPS wrapper in Python' @echo '' @echo 'make package list available packages' - @echo 'make package-status status of all packages' + @echo 'make package-status (ps) status of all packages' @echo 'make yes-package install a single package in src dir' @echo 'make no-package remove a single package from src dir' @echo 'make yes-all install all packages in src dir' @@ -61,9 +61,9 @@ help: @echo 'make no-user remove all user packages' @echo 'make no-lib remove all packages with external libs' @echo '' - @echo 'make package-update replace src files with package files' + @echo 'make package-update (pu) replace src files with updated package files' @echo 'make package-overwrite replace package files with src files' - @echo 'make package-diff diff src files against package files' + @echo 'make package-diff (pd) diff src files against package files' @echo '' @echo 'make machine build LAMMPS where machine is one of:' @echo '' @@ -108,18 +108,18 @@ purge: Purge.list # Create a tarball of src dir and packages tar: - @cd STUBS; make clean + @cd STUBS; $(MAKE) clean @cd ..; tar cvzf src/$(ROOT)_src.tar.gz \ src/Make* src/Package.sh src/MAKE src/*.cpp src/*.h src/STUBS \ $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \ --exclude=*/.svn - @cd STUBS; make + @cd STUBS; $(MAKE) @echo "Created $(ROOT)_src.tar.gz" # Make MPI STUBS library stubs: - @cd STUBS; make clean; make + @cd STUBS; $(MAKE) clean; $(MAKE) # Create Makefile.lib, Makefile.shlib, and Makefile.list diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index f29ba5fb3d..e5de887cd3 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -54,7 +54,7 @@ void FixQEQCombOMP::init() if (!atom->q_flag) error->all(FLERR,"Fix qeq/comb/omp requires atom attribute q"); - if (NULL == force->pair_match("comb3",0)) + if (NULL != force->pair_match("comb3",0)) error->all(FLERR,"No support for comb3 currently available in USER-OMP"); comb = (PairComb *) force->pair_match("comb/omp",1); @@ -79,10 +79,6 @@ void FixQEQCombOMP::init() } int irequest = neighbor->request(this); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->fix = 1; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; neighbor->requests[irequest]->omp = use_omp; } diff --git a/src/USER-OMP/neigh_full_omp.cpp b/src/USER-OMP/neigh_full_omp.cpp index f8036727dd..ee36e5610e 100644 --- a/src/USER-OMP/neigh_full_omp.cpp +++ b/src/USER-OMP/neigh_full_omp.cpp @@ -255,7 +255,7 @@ void Neighbor::full_bin_omp(NeighList *list) { // bin owned & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -367,7 +367,7 @@ void Neighbor::full_bin_ghost_omp(NeighList *list) { // bin owned & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; @@ -510,7 +510,7 @@ void Neighbor::full_multi_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/neigh_gran_omp.cpp b/src/USER-OMP/neigh_gran_omp.cpp index 36f07fa095..55ab604b02 100644 --- a/src/USER-OMP/neigh_gran_omp.cpp +++ b/src/USER-OMP/neigh_gran_omp.cpp @@ -96,7 +96,7 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list) touchptr = ipage_touch->vget(); shearptr = dpage_shear->vget(); } - + xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; @@ -271,7 +271,7 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; @@ -424,7 +424,7 @@ void Neighbor::granular_bin_newton_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; @@ -533,7 +533,7 @@ void Neighbor::granular_bin_newton_tri_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; diff --git a/src/USER-OMP/neigh_half_bin_omp.cpp b/src/USER-OMP/neigh_half_bin_omp.cpp index 3974d9f6ab..65fa07a48a 100644 --- a/src/USER-OMP/neigh_half_bin_omp.cpp +++ b/src/USER-OMP/neigh_half_bin_omp.cpp @@ -35,7 +35,7 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -152,7 +152,7 @@ void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; @@ -299,7 +299,7 @@ void Neighbor::half_bin_newton_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -447,7 +447,7 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/neigh_half_multi_omp.cpp b/src/USER-OMP/neigh_half_multi_omp.cpp index ee5c3cf6f4..cc93bf6367 100644 --- a/src/USER-OMP/neigh_half_multi_omp.cpp +++ b/src/USER-OMP/neigh_half_multi_omp.cpp @@ -36,7 +36,7 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -158,7 +158,7 @@ void Neighbor::half_multi_newton_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -314,7 +314,7 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; diff --git a/src/USER-OMP/neigh_respa_omp.cpp b/src/USER-OMP/neigh_respa_omp.cpp index 6ac70cf9d7..409090c9ea 100644 --- a/src/USER-OMP/neigh_respa_omp.cpp +++ b/src/USER-OMP/neigh_respa_omp.cpp @@ -143,7 +143,7 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list) tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; - else if (minchange = domain->minimum_image_check(delx,dely,delz)) + else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; @@ -328,7 +328,7 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list) tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; - else if (minchange = domain->minimum_image_check(delx,dely,delz)) + else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; @@ -390,7 +390,7 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -506,7 +506,7 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list) tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; - else if (minchange = domain->minimum_image_check(delx,dely,delz)) + else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; @@ -569,7 +569,7 @@ void Neighbor::respa_bin_newton_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -688,7 +688,7 @@ void Neighbor::respa_bin_newton_omp(NeighList *list) tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; - else if (minchange = domain->minimum_image_check(delx,dely,delz)) + else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; @@ -732,7 +732,7 @@ void Neighbor::respa_bin_newton_omp(NeighList *list) tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; - else if (minchange = domain->minimum_image_check(delx,dely,delz)) + else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; @@ -795,7 +795,7 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list) { // bin local & ghost atoms - bin_atoms(); + if (binatomflag) bin_atoms(); const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; @@ -919,7 +919,7 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list) tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; - else if (minchange = domain->minimum_image_check(delx,dely,delz)) + else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index c9e6b126e2..23d8fb8226 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -337,6 +337,11 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : "atom property that isn't allocated"); pack_choice[i] = &ComputePropertyAtom::pack_corner3z; + } else if (strcmp(arg[iarg],"nbonds") == 0) { + if (!atom->molecule_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_nbonds; } else if (strstr(arg[iarg],"i_") == arg[iarg]) { int flag; index[i] = atom->find_custom(&arg[iarg][2],flag); @@ -1687,6 +1692,21 @@ void ComputePropertyAtom::pack_corner3z(int n) /* ---------------------------------------------------------------------- */ +void ComputePropertyAtom::pack_nbonds(int n) +{ + int *num_bond = atom->num_bond; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = num_bond[i]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + void ComputePropertyAtom::pack_iname(int n) { int *ivector = atom->ivector[index[n]]; diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h index a5d2c5832d..01e623011d 100644 --- a/src/compute_property_atom.h +++ b/src/compute_property_atom.h @@ -121,6 +121,8 @@ class ComputePropertyAtom : public Compute { void pack_corner3y(int); void pack_corner3z(int); + void pack_nbonds(int); + void pack_iname(int); void pack_dname(int); };