diff --git a/src/BPM/fix_update_special_bonds.cpp b/src/BPM/fix_update_special_bonds.cpp index b5b0f56194..b6bf8b433f 100644 --- a/src/BPM/fix_update_special_bonds.cpp +++ b/src/BPM/fix_update_special_bonds.cpp @@ -154,7 +154,7 @@ void FixUpdateSpecialBonds::pre_exchange() void FixUpdateSpecialBonds::pre_force(int /*vflag*/) { - int ilist, nlist, i1, i2, j, jj, jnum; + int i1, i2, j, jj, jnum; int *jlist, *numneigh, **firstneigh; tagint tag1, tag2; NeighList *list; diff --git a/src/EXTRA-COMPUTE/compute_rattlers_atom.h b/src/EXTRA-COMPUTE/compute_rattlers_atom.h index 257bae8374..79a0a0a982 100644 --- a/src/EXTRA-COMPUTE/compute_rattlers_atom.h +++ b/src/EXTRA-COMPUTE/compute_rattlers_atom.h @@ -38,8 +38,7 @@ class ComputeRattlersAtom : public Compute { void unpack_reverse_comm(int, int *, double *) override; private: - int pstyle, cutstyle; - int ncontacts_rattler, max_tries, nmax, invoked_peratom; + int cutstyle, ncontacts_rattler, max_tries, nmax, invoked_peratom; int *ncontacts; double *rattler; class NeighList *list; diff --git a/src/EXTRA-COMPUTE/compute_slcsa_atom.cpp b/src/EXTRA-COMPUTE/compute_slcsa_atom.cpp index 509362a73b..6c272938b6 100644 --- a/src/EXTRA-COMPUTE/compute_slcsa_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_slcsa_atom.cpp @@ -33,21 +33,20 @@ #include #include -#include using namespace LAMMPS_NS; static const char cite_compute_slcsa_atom_c[] = - "compute slcsa/atom command: doi:10.1088/0965-0393/21/5/055020\n\n" + "compute slcsa/atom command: doi:10.1016/j.commatsci.2023.112534\n\n" "@Article{Lafourcade2023,\n" " author = {P. Lafourcade and J.-B. Maillet and C. Denoual and E. Duval and A. Allera and A. " "M. Goryaeva and M.-C. Marinica},\n" " title = {Robust crystal structure identification at extreme conditions using a " "density-independent spectral descriptor and supervised learning},\n" " journal = {Computational Materials Science},\n" - " year = 2023,\n" - " volume = XX,\n" - " pages = {XXXXXX}\n" + " year = 2023,\n" + " volume = 230,\n" + " pages = 112534\n" "}\n\n"; /* ---------------------------------------------------------------------- */ @@ -79,6 +78,8 @@ ComputeSLCSAAtom::ComputeSLCSAAtom(LAMMPS *lmp, int narg, char **arg) : // # LR bias vector // vector with 1 row x nclasses cols + if (lmp->citeme) lmp->citeme->add(cite_compute_slcsa_atom_c); + if (narg != 11) utils::missing_cmd_args(FLERR, "compute slcsa/atom", error); int twojmax = utils::inumeric(FLERR, arg[3], false, lmp); diff --git a/src/EXTRA-COMPUTE/compute_slcsa_atom.h b/src/EXTRA-COMPUTE/compute_slcsa_atom.h index 6d7cd90c31..ba373a53a8 100644 --- a/src/EXTRA-COMPUTE/compute_slcsa_atom.h +++ b/src/EXTRA-COMPUTE/compute_slcsa_atom.h @@ -53,14 +53,12 @@ class ComputeSLCSAAtom : public Compute { value_t descriptorval; int nmax; int ncols; - int nevery; int ncomps; int nclasses; const char *database_mean_descriptor_file; const char *lda_scalings_file; const char *lr_decision_file; const char *lr_bias_file; - const char *covmat_file; const char *maha_file; class NeighList *list; diff --git a/src/EXTRA-FIX/fix_nonaffine_displacement.cpp b/src/EXTRA-FIX/fix_nonaffine_displacement.cpp index c1de50c41d..a426a8fb55 100644 --- a/src/EXTRA-FIX/fix_nonaffine_displacement.cpp +++ b/src/EXTRA-FIX/fix_nonaffine_displacement.cpp @@ -202,7 +202,7 @@ void FixNonaffineDisplacement::init() // need an occasional half neighbor list if (cut_style == RADIUS) { - auto req = neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_OCCASIONAL); + neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_OCCASIONAL); } else { auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); if (cut_style == CUSTOM) { @@ -233,7 +233,7 @@ void FixNonaffineDisplacement::init_list(int /*id*/, NeighList *ptr) /* ---------------------------------------------------------------------- */ -void FixNonaffineDisplacement::setup(int vflag) +void FixNonaffineDisplacement::setup(int /*vflag*/) { post_force(0); // Save state if needed before starting the 1st timestep } @@ -285,7 +285,6 @@ void FixNonaffineDisplacement::restart(char *buf) void FixNonaffineDisplacement::integrate_velocity() { - int i,n; dtv = update->dt; double **v = atom->v; @@ -306,7 +305,6 @@ void FixNonaffineDisplacement::integrate_velocity() void FixNonaffineDisplacement::save_reference_state() { - int i, n; double **x = atom->x; int *mask = atom->mask; @@ -354,15 +352,14 @@ void FixNonaffineDisplacement::calculate_D2Min() int i, j, k, l, ii, jj, inum, jnum, itype, jtype; double evol, j2, edev; - double r[3], r0[3], rsq, rsq0, radsum, temp[3]; + double r[3], r0[3], rsq, radsum, temp[3]; double X_tmp[3][3], Y_tmp[3][3], F_tmp[3][3], E[3][3]; - double Y_inv[3][3] = {0.0}; // Zero for 2d since not all entries used + double Y_inv[3][3] = {{0.0,0.0,0.0},{0.0,0.0,0.0},{0.0,0.0,0.0}}; // Zero for 2d since not all entries used int *ilist, *jlist, *numneigh, **firstneigh; double **x = atom->x; double **x0 = array_atom; double *radius = atom->radius; - tagint *tag = atom->tag; int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; diff --git a/src/EXTRA-MOLECULE/dihedral_quadratic.cpp b/src/EXTRA-MOLECULE/dihedral_quadratic.cpp index f576e6efdd..a7c0dc3eb1 100644 --- a/src/EXTRA-MOLECULE/dihedral_quadratic.cpp +++ b/src/EXTRA-MOLECULE/dihedral_quadratic.cpp @@ -338,7 +338,7 @@ void DihedralQuadratic::born_matrix(int nd, int i1, int i2, int i3, int i4, double sb1,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2; double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2; double c2mag,sc1,sc2,s12,c; - double s1,s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2; + double cx,cy,cz,cmag,dx,phi,si,siinv,sin2; int **dihedrallist = neighbor->dihedrallist; double **x = atom->x; @@ -405,8 +405,6 @@ void DihedralQuadratic::born_matrix(int nd, int i1, int i2, int i3, int i4, if (sc2 < SMALL) sc2 = SMALL; sc2 = 1.0/sc2; - s1 = sc1 * sc1; - s2 = sc2 * sc2; s12 = sc1 * sc2; c = (c0 + c1mag*c2mag) * s12;