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This commit is contained in:
Axel Kohlmeyer
2022-03-06 05:24:29 -05:00
parent 72cbffee7d
commit 005f76a9e6
1 changed files with 109 additions and 122 deletions
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95
src/create_bonds.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
@ -47,8 +46,7 @@ void CreateBonds::command(int narg, char **arg)
{ {
if (domain->box_exist == 0) if (domain->box_exist == 0)
error->all(FLERR, "Create_bonds command before simulation box is defined"); error->all(FLERR, "Create_bonds command before simulation box is defined");
if (atom->tag_enable == 0) if (atom->tag_enable == 0) error->all(FLERR, "Cannot use create_bonds unless atoms have IDs");
error->all(FLERR,"Cannot use create_bonds unless atoms have IDs");
if (atom->molecular != Atom::MOLECULAR) if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR, "Cannot use create_bonds with non-molecular system"); error->all(FLERR, "Cannot use create_bonds with non-molecular system");
@ -79,8 +77,7 @@ void CreateBonds::command(int narg, char **arg)
btype = utils::inumeric(FLERR, arg[1], false, lmp); btype = utils::inumeric(FLERR, arg[1], false, lmp);
batom1 = utils::tnumeric(FLERR, arg[2], false, lmp); batom1 = utils::tnumeric(FLERR, arg[2], false, lmp);
batom2 = utils::tnumeric(FLERR, arg[3], false, lmp); batom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
if (batom1 == batom2) if (batom1 == batom2) error->all(FLERR, "Illegal create_bonds command");
error->all(FLERR,"Illegal create_bonds command");
iarg = 4; iarg = 4;
} else if (strcmp(arg[0], "single/angle") == 0) { } else if (strcmp(arg[0], "single/angle") == 0) {
style = SANGLE; style = SANGLE;
@ -100,8 +97,8 @@ void CreateBonds::command(int narg, char **arg)
datom2 = utils::tnumeric(FLERR, arg[3], false, lmp); datom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
datom3 = utils::tnumeric(FLERR, arg[4], false, lmp); datom3 = utils::tnumeric(FLERR, arg[4], false, lmp);
datom4 = utils::tnumeric(FLERR, arg[5], false, lmp); datom4 = utils::tnumeric(FLERR, arg[5], false, lmp);
if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) || if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) || (datom2 == datom3) ||
(datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4)) (datom2 == datom4) || (datom3 == datom4))
error->all(FLERR, "Illegal create_bonds command"); error->all(FLERR, "Illegal create_bonds command");
iarg = 6; iarg = 6;
} else if (strcmp(arg[0], "single/improper") == 0) { } else if (strcmp(arg[0], "single/improper") == 0) {
@ -112,11 +109,12 @@ void CreateBonds::command(int narg, char **arg)
datom2 = utils::tnumeric(FLERR, arg[3], false, lmp); datom2 = utils::tnumeric(FLERR, arg[3], false, lmp);
datom3 = utils::tnumeric(FLERR, arg[4], false, lmp); datom3 = utils::tnumeric(FLERR, arg[4], false, lmp);
datom4 = utils::tnumeric(FLERR, arg[5], false, lmp); datom4 = utils::tnumeric(FLERR, arg[5], false, lmp);
if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) || if ((datom1 == datom2) || (datom1 == datom3) || (datom1 == datom4) || (datom2 == datom3) ||
(datom2 == datom3) || (datom2 == datom4) || (datom3 == datom4)) (datom2 == datom4) || (datom3 == datom4))
error->all(FLERR, "Illegal create_bonds command"); error->all(FLERR, "Illegal create_bonds command");
iarg = 6; iarg = 6;
} else error->all(FLERR,"Illegal create_bonds command"); } else
error->all(FLERR, "Illegal create_bonds command");
// optional args // optional args
@ -127,7 +125,8 @@ void CreateBonds::command(int narg, char **arg)
if (iarg + 2 > narg) error->all(FLERR, "Illegal create_bonds command"); if (iarg + 2 > narg) error->all(FLERR, "Illegal create_bonds command");
specialflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); specialflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else error->all(FLERR,"Illegal create_bonds command"); } else
error->all(FLERR, "Illegal create_bonds command");
} }
// error checks // error checks
@ -135,8 +134,7 @@ void CreateBonds::command(int narg, char **arg)
if (style == MANY) { if (style == MANY) {
if (btype <= 0 || btype > atom->nbondtypes) if (btype <= 0 || btype > atom->nbondtypes)
error->all(FLERR, "Invalid bond type in create_bonds command"); error->all(FLERR, "Invalid bond type in create_bonds command");
if (specialflag == 0) if (specialflag == 0) error->all(FLERR, "Cannot use special no with create_bonds many");
error->all(FLERR,"Cannot use special no with create_bonds many");
} else if (style == SBOND) { } else if (style == SBOND) {
if (btype <= 0 || btype > atom->nbondtypes) if (btype <= 0 || btype > atom->nbondtypes)
error->all(FLERR, "Invalid bond type in create_bonds command"); error->all(FLERR, "Invalid bond type in create_bonds command");
@ -153,11 +151,16 @@ void CreateBonds::command(int narg, char **arg)
// invoke creation method // invoke creation method
if (style == MANY) many(); if (style == MANY)
else if (style == SBOND) single_bond(); many();
else if (style == SANGLE) single_angle(); else if (style == SBOND)
else if (style == SDIHEDRAL) single_dihedral(); single_bond();
else if (style == SIMPROPER) single_improper(); else if (style == SANGLE)
single_angle();
else if (style == SDIHEDRAL)
single_dihedral();
else if (style == SIMPROPER)
single_improper();
// trigger special list build // trigger special list build
@ -190,8 +193,7 @@ void CreateBonds::many()
// error check on cutoff // error check on cutoff
// if no pair style, neighbor list will be empty // if no pair style, neighbor list will be empty
if (force->pair == nullptr) if (force->pair == nullptr) error->all(FLERR, "Create_bonds requires a pair style be defined");
error->all(FLERR,"Create_bonds requires a pair style be defined");
if (rmax > neighbor->cutneighmax) if (rmax > neighbor->cutneighmax)
error->all(FLERR, "Create_bonds max distance > neighbor cutoff"); error->all(FLERR, "Create_bonds max distance > neighbor cutoff");
if (rmax > neighbor->cutneighmin && comm->me == 0) if (rmax > neighbor->cutneighmin && comm->me == 0)
@ -204,11 +206,8 @@ void CreateBonds::many()
// note that with KSpace, pair with weight = 0 could still be in neigh list // note that with KSpace, pair with weight = 0 could still be in neigh list
if (force->special_lj[1] != 0.0 || force->special_coul[1] != 0.0) if (force->special_lj[1] != 0.0 || force->special_coul[1] != 0.0)
error->all(FLERR,"Create_bonds command requires " error->all(FLERR, "Create_bonds command requires special_bonds 1-2 weights be 0.0");
"special_bonds 1-2 weights be 0.0"); if (force->kspace) error->all(FLERR, "Create_bonds command requires no kspace_style be defined");
if (force->kspace)
error->all(FLERR,"Create_bonds command requires "
"no kspace_style be defined");
// setup domain, communication and neighboring // setup domain, communication and neighboring
// acquire ghosts and build standard neighbor lists // acquire ghosts and build standard neighbor lists
@ -275,7 +274,8 @@ void CreateBonds::many()
delx = x[j][0] - xtmp; delx = x[j][0] - xtmp;
dely = x[j][1] - ytmp; dely = x[j][1] - ytmp;
delz = x[j][2] - ztmp; delz = x[j][2] - ztmp;
} else continue; } else
continue;
rsq = delx * delx + dely * dely + delz * delz; rsq = delx * delx + dely * dely + delz * delz;
if (rsq < rminsq || rsq > rmaxsq) continue; if (rsq < rminsq || rsq > rmaxsq) continue;
@ -291,8 +291,8 @@ void CreateBonds::many()
if (!newton_bond || tag[i] < tag[j]) { if (!newton_bond || tag[i] < tag[j]) {
if (num_bond[i] == atom->bond_per_atom) if (num_bond[i] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom limit " error->one(FLERR, "New bond exceeded bonds per atom limit of {} in create_bonds",
" of {} in create_bonds",atom->bond_per_atom); atom->bond_per_atom);
bond_type[i][num_bond[i]] = btype; bond_type[i][num_bond[i]] = btype;
bond_atom[i][num_bond[i]] = tag[j]; bond_atom[i][num_bond[i]] = tag[j];
num_bond[i]++; num_bond[i]++;
@ -313,8 +313,7 @@ void CreateBonds::many()
bigint nadd_bonds = atom->nbonds - nbonds_previous; bigint nadd_bonds = atom->nbonds - nbonds_previous;
if (comm->me == 0) if (comm->me == 0)
utils::logmesg(lmp,"Added {} bonds, new total = {}\n", utils::logmesg(lmp, "Added {} bonds, new total = {}\n", nadd_bonds, atom->nbonds);
nadd_bonds,atom->nbonds);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -335,8 +334,7 @@ void CreateBonds::single_bond()
int allcount; int allcount;
MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world); MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world);
if (allcount != 2) if (allcount != 2) error->all(FLERR, "Create_bonds single/bond atoms do not exist");
error->all(FLERR,"Create_bonds single/bond atoms do not exist");
// create bond once or 2x if newton_bond set // create bond once or 2x if newton_bond set
@ -384,8 +382,7 @@ void CreateBonds::single_angle()
int allcount; int allcount;
MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world); MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world);
if (allcount != 3) if (allcount != 3) error->all(FLERR, "Create_bonds single/angle atoms do not exist");
error->all(FLERR,"Create_bonds single/angle atoms do not exist");
// create angle once or 3x if newton_bond set // create angle once or 3x if newton_bond set
@ -451,8 +448,7 @@ void CreateBonds::single_dihedral()
int allcount; int allcount;
MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world); MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world);
if (allcount != 4) if (allcount != 4) error->all(FLERR, "Create_bonds single/dihedral atoms do not exist");
error->all(FLERR,"Create_bonds single/dihedral atoms do not exist");
// create bond once or 4x if newton_bond set // create bond once or 4x if newton_bond set
@ -465,8 +461,7 @@ void CreateBonds::single_dihedral()
if ((m = idx2) >= 0) { if ((m = idx2) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom) if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR, error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds");
"New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype; dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1; dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2; dihedral_atom2[m][num_dihedral[m]] = datom2;
@ -480,8 +475,7 @@ void CreateBonds::single_dihedral()
if ((m = idx1) >= 0) { if ((m = idx1) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom) if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR, error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds");
"New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype; dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1; dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2; dihedral_atom2[m][num_dihedral[m]] = datom2;
@ -492,8 +486,7 @@ void CreateBonds::single_dihedral()
if ((m = idx3) >= 0) { if ((m = idx3) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom) if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR, error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds");
"New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype; dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1; dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2; dihedral_atom2[m][num_dihedral[m]] = datom2;
@ -504,8 +497,7 @@ void CreateBonds::single_dihedral()
if ((m = idx4) >= 0) { if ((m = idx4) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom) if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR, error->one(FLERR, "New dihedral exceeded dihedrals per atom in create_bonds");
"New dihedral exceeded dihedrals per atom in create_bonds");
dihedral_type[m][num_dihedral[m]] = dtype; dihedral_type[m][num_dihedral[m]] = dtype;
dihedral_atom1[m][num_dihedral[m]] = datom1; dihedral_atom1[m][num_dihedral[m]] = datom1;
dihedral_atom2[m][num_dihedral[m]] = datom2; dihedral_atom2[m][num_dihedral[m]] = datom2;
@ -537,8 +529,7 @@ void CreateBonds::single_improper()
int allcount; int allcount;
MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world); MPI_Allreduce(&count, &allcount, 1, MPI_INT, MPI_SUM, world);
if (allcount != 4) if (allcount != 4) error->all(FLERR, "Create_bonds single/improper atoms do not exist");
error->all(FLERR,"Create_bonds single/improper atoms do not exist");
// create bond once or 4x if newton_bond set // create bond once or 4x if newton_bond set
@ -551,8 +542,7 @@ void CreateBonds::single_improper()
if ((m = idx2) >= 0) { if ((m = idx2) >= 0) {
if (num_improper[m] == atom->improper_per_atom) if (num_improper[m] == atom->improper_per_atom)
error->one(FLERR, error->one(FLERR, "New improper exceeded impropers per atom in create_bonds");
"New improper exceeded impropers per atom in create_bonds");
improper_type[m][num_improper[m]] = dtype; improper_type[m][num_improper[m]] = dtype;
improper_atom1[m][num_improper[m]] = datom1; improper_atom1[m][num_improper[m]] = datom1;
improper_atom2[m][num_improper[m]] = datom2; improper_atom2[m][num_improper[m]] = datom2;
@ -566,8 +556,7 @@ void CreateBonds::single_improper()
if ((m = idx1) >= 0) { if ((m = idx1) >= 0) {
if (num_improper[m] == atom->improper_per_atom) if (num_improper[m] == atom->improper_per_atom)
error->one(FLERR, error->one(FLERR, "New improper exceeded impropers per atom in create_bonds");
"New improper exceeded impropers per atom in create_bonds");
improper_type[m][num_improper[m]] = dtype; improper_type[m][num_improper[m]] = dtype;
improper_atom1[m][num_improper[m]] = datom1; improper_atom1[m][num_improper[m]] = datom1;
improper_atom2[m][num_improper[m]] = datom2; improper_atom2[m][num_improper[m]] = datom2;
@ -578,8 +567,7 @@ void CreateBonds::single_improper()
if ((m = idx3) >= 0) { if ((m = idx3) >= 0) {
if (num_improper[m] == atom->improper_per_atom) if (num_improper[m] == atom->improper_per_atom)
error->one(FLERR, error->one(FLERR, "New improper exceeded impropers per atom in create_bonds");
"New improper exceeded impropers per atom in create_bonds");
improper_type[m][num_improper[m]] = dtype; improper_type[m][num_improper[m]] = dtype;
improper_atom1[m][num_improper[m]] = datom1; improper_atom1[m][num_improper[m]] = datom1;
improper_atom2[m][num_improper[m]] = datom2; improper_atom2[m][num_improper[m]] = datom2;
@ -590,8 +578,7 @@ void CreateBonds::single_improper()
if ((m = idx4) >= 0) { if ((m = idx4) >= 0) {
if (num_improper[m] == atom->improper_per_atom) if (num_improper[m] == atom->improper_per_atom)
error->one(FLERR, error->one(FLERR, "New improper exceeded impropers per atom in create_bonds");
"New improper exceeded impropers per atom in create_bonds");
improper_type[m][num_improper[m]] = dtype; improper_type[m][num_improper[m]] = dtype;
improper_atom1[m][num_improper[m]] = datom1; improper_atom1[m][num_improper[m]] = datom1;
improper_atom2[m][num_improper[m]] = datom2; improper_atom2[m][num_improper[m]] = datom2;