diff --git a/src/ML-SNAP/compute_sna_atom.cpp b/src/ML-SNAP/compute_sna_atom.cpp index daec59e3f0..9dce3d6e6d 100644 --- a/src/ML-SNAP/compute_sna_atom.cpp +++ b/src/ML-SNAP/compute_sna_atom.cpp @@ -35,7 +35,7 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { - // code common to all SNAP computes + // begin code common to all SNAP computes double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; @@ -160,12 +160,15 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) : if (switchinnerflag && !(sinnerflag && dinnerflag)) error->all( FLERR, - "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword"); + "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) error->all( FLERR, - "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword"); + "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword", + style); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, nelements, switchinnerflag); diff --git a/src/ML-SNAP/compute_sna_grid.cpp b/src/ML-SNAP/compute_sna_grid.cpp index f8da915051..dc92ee2b15 100644 --- a/src/ML-SNAP/compute_sna_grid.cpp +++ b/src/ML-SNAP/compute_sna_grid.cpp @@ -37,7 +37,7 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) : arg += nargbase; narg -= nargbase; - // code common to all SNAP computes + // begin code common to all SNAP computes double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; @@ -61,22 +61,25 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem, ntypes + 1, "sna/grid:radelem"); // offset by 1 to match up with types - memory->create(wjelem, ntypes + 1, "sna/grid:wjelem"); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); rcutfac = utils::numeric(FLERR, arg[3], false, lmp); rfac0 = utils::numeric(FLERR, arg[4], false, lmp); twojmax = utils::inumeric(FLERR, arg[5], false, lmp); - for (int i = 0; i < ntypes; i++) radelem[i + 1] = utils::numeric(FLERR, arg[6 + i], false, lmp); for (int i = 0; i < ntypes; i++) - wjelem[i + 1] = utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); + radelem[i + 1] = + utils::numeric(FLERR, arg[6 + i], false, lmp); + for (int i = 0; i < ntypes; i++) + wjelem[i + 1] = + utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); // construct cutsq double cut; cutmax = 0.0; - memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/grid:cutsq"); + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { cut = 2.0 * radelem[i] * rcutfac; if (cut > cutmax) cutmax = cut; @@ -157,14 +160,17 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) : } if (switchinnerflag && !(sinnerflag && dinnerflag)) - error->all(FLERR, - "Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword", - style); + error->all( + FLERR, + "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) - error->all(FLERR, - "Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword", - style); + error->all( + FLERR, + "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword", + style); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, nelements, switchinnerflag); diff --git a/src/ML-SNAP/compute_sna_grid_local.cpp b/src/ML-SNAP/compute_sna_grid_local.cpp index 079ecac319..8b0121b9ce 100644 --- a/src/ML-SNAP/compute_sna_grid_local.cpp +++ b/src/ML-SNAP/compute_sna_grid_local.cpp @@ -37,7 +37,7 @@ ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) : arg += nargbase; narg -= nargbase; - // code common to all SNAP computes + // begin code common to all SNAP computes double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; @@ -61,23 +61,25 @@ ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem, ntypes + 1, - "sna/grid/local:radelem"); // offset by 1 to match up with types - memory->create(wjelem, ntypes + 1, "sna/grid/local:wjelem"); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); rcutfac = utils::numeric(FLERR, arg[3], false, lmp); rfac0 = utils::numeric(FLERR, arg[4], false, lmp); twojmax = utils::inumeric(FLERR, arg[5], false, lmp); - for (int i = 0; i < ntypes; i++) radelem[i + 1] = utils::numeric(FLERR, arg[6 + i], false, lmp); for (int i = 0; i < ntypes; i++) - wjelem[i + 1] = utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); + radelem[i + 1] = + utils::numeric(FLERR, arg[6 + i], false, lmp); + for (int i = 0; i < ntypes; i++) + wjelem[i + 1] = + utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp); // construct cutsq double cut; cutmax = 0.0; - memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/grid/local:cutsq"); + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { cut = 2.0 * radelem[i] * rcutfac; if (cut > cutmax) cutmax = cut; @@ -158,14 +160,17 @@ ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) : } if (switchinnerflag && !(sinnerflag && dinnerflag)) - error->all(FLERR, - "Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword", - style); + error->all( + FLERR, + "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) - error->all(FLERR, - "Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword", - style); + error->all( + FLERR, + "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword", + style); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, nelements, switchinnerflag); diff --git a/src/ML-SNAP/compute_snad_atom.cpp b/src/ML-SNAP/compute_snad_atom.cpp index 623eb16268..1cd2278b00 100644 --- a/src/ML-SNAP/compute_snad_atom.cpp +++ b/src/ML-SNAP/compute_snad_atom.cpp @@ -34,7 +34,8 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snad(nullptr), radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { - // code common to all SNAP computes + + // begin code common to all SNAP computes double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; @@ -58,8 +59,8 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem, ntypes + 1, "snad/atom:radelem"); // offset by 1 to match up with types - memory->create(wjelem, ntypes + 1, "snad/atom:wjelem"); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); rcutfac = utils::numeric(FLERR, arg[3], false, lmp); rfac0 = utils::numeric(FLERR, arg[4], false, lmp); @@ -76,7 +77,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : double cut; cutmax = 0.0; - memory->create(cutsq, ntypes + 1, ntypes + 1, "snad/atom:cutsq"); + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { cut = 2.0 * radelem[i] * rcutfac; if (cut > cutmax) cutmax = cut; @@ -159,12 +160,15 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : if (switchinnerflag && !(sinnerflag && dinnerflag)) error->all( FLERR, - "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword"); + "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) error->all( FLERR, - "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword"); + "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword", + style); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, nelements, switchinnerflag); @@ -174,7 +178,7 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) : if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2; // end code common to all SNAP computes - + yoffset = nvalues; zoffset = 2*nvalues; size_peratom_cols = 3*nvalues*atom->ntypes; diff --git a/src/ML-SNAP/compute_snap.cpp b/src/ML-SNAP/compute_snap.cpp index 2aa503021c..fb10fa0fbe 100644 --- a/src/ML-SNAP/compute_snap.cpp +++ b/src/ML-SNAP/compute_snap.cpp @@ -41,7 +41,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : array_flag = 1; extarray = 0; - // code common to all SNAP computes + // begin code common to all SNAP computes double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; @@ -65,8 +65,8 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem, ntypes + 1, "snap:radelem"); // offset by 1 to match up with types - memory->create(wjelem, ntypes + 1, "snap:wjelem"); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); rcutfac = utils::numeric(FLERR, arg[3], false, lmp); rfac0 = utils::numeric(FLERR, arg[4], false, lmp); @@ -83,7 +83,7 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : double cut; cutmax = 0.0; - memory->create(cutsq, ntypes + 1, ntypes + 1, "snap:cutsq"); + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { cut = 2.0 * radelem[i] * rcutfac; if (cut > cutmax) cutmax = cut; @@ -166,12 +166,15 @@ ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) : if (switchinnerflag && !(sinnerflag && dinnerflag)) error->all( FLERR, - "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword"); + "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) error->all( FLERR, - "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword"); + "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword", + style); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, nelements, switchinnerflag); diff --git a/src/ML-SNAP/compute_snav_atom.cpp b/src/ML-SNAP/compute_snav_atom.cpp index 74d52e231a..4b7b0caa64 100644 --- a/src/ML-SNAP/compute_snav_atom.cpp +++ b/src/ML-SNAP/compute_snav_atom.cpp @@ -34,7 +34,8 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snav(nullptr), radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr) { - // code common to all SNAP computes + + // begin code common to all SNAP computes double rfac0, rmin0; int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag; @@ -58,8 +59,8 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : // process required arguments - memory->create(radelem, ntypes + 1, "snav/atom:radelem"); // offset by 1 to match up with types - memory->create(wjelem, ntypes + 1, "snav/atom:wjelem"); + memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types + memory->create(wjelem, ntypes + 1, "sna/atom:wjelem"); rcutfac = utils::numeric(FLERR, arg[3], false, lmp); rfac0 = utils::numeric(FLERR, arg[4], false, lmp); @@ -76,7 +77,7 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : double cut; cutmax = 0.0; - memory->create(cutsq, ntypes + 1, ntypes + 1, "snav/atom:cutsq"); + memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq"); for (int i = 1; i <= ntypes; i++) { cut = 2.0 * radelem[i] * rcutfac; if (cut > cutmax) cutmax = cut; @@ -159,12 +160,15 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : if (switchinnerflag && !(sinnerflag && dinnerflag)) error->all( FLERR, - "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword"); + "Illegal compute {} command:, style switchinnerflag = 1, missing sinner/dinner keyword", + style); if (!switchinnerflag && (sinnerflag || dinnerflag)) error->all( FLERR, - "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword"); + "Illegal compute {} command:, style switchinnerflag = 0, unexpected sinner/dinner keyword", + style); + snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag, wselfallflag, nelements, switchinnerflag); @@ -174,8 +178,8 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) : if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2; // end code common to all SNAP computes - - size_peratom_cols = 6*nvalues*atom->ntypes; + + size_peratom_cols = 6*nvalues*atom->ntypes; comm_reverse = size_peratom_cols; peratom_flag = 1;