additional topology overflow check for reactions (97be57be) · Commits · 郑智淋 / lammps

doc/src/fix_bond_react.txt

+7 −0

Original line number	Diff line number	Diff line
		@@ -203,6 +203,13 @@ new types must also be defined during the setup of a given simulation.
		A discussion of correctly handling this is also provided on the
		"molecule"_molecule.html command page.

		NOTE: When a reaction includes edge atoms, it is possible that the
		resulting topology/atom (e.g. special bonds, dihedrals, etc.) exceeds
		both that of the reaction templates and the existing system. As when
		inserting molecules, this topology overflow must be accounted for by
		using the relevant "extra" keywords to the "read_data"_read_data.html
		or "create_box"_create_box.html commands.

		The map file is a text document with the following format:

		A map file has a header and a body. The header of map file the

src/USER-MISC/fix_bond_react.cpp

+10 −0

Original line number	Diff line number	Diff line
		@@ -2322,6 +2322,8 @@ void FixBondReact::update_everything()
		nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
		nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
		}
		if (nspecial[atom->map(update_mega_glove[jj+1][i])][2] > atom->maxspecial)
		error->one(FLERR,"Bond/react special bond generation overflow");
		for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
		special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
		}
		@@ -2383,6 +2385,8 @@ void FixBondReact::update_everything()
		bond_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->bond_type[j][p];
		bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
		num_bond[atom->map(update_mega_glove[jj+1][i])]++;
		if (num_bond[atom->map(update_mega_glove[jj+1][i])] > atom->bond_per_atom)
		error->one(FLERR,"Bond/react bonds/atom exceed system bonds/atom");
		delta_bonds++;
		}
		}
		@@ -2457,6 +2461,8 @@ void FixBondReact::update_everything()
		angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
		angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
		num_angle[atom->map(update_mega_glove[jj+1][i])]++;
		if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom)
		error->one(FLERR,"Bond/react angles/atom exceed system angles/atom");
		delta_angle++;
		}
		}
		@@ -2538,6 +2544,8 @@ void FixBondReact::update_everything()
		dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
		dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
		num_dihedral[atom->map(update_mega_glove[jj+1][i])]++;
		if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom)
		error->one(FLERR,"Bond/react dihedrals/atom exceed system dihedrals/atom");
		delta_dihed++;
		}
		}
		@@ -2619,6 +2627,8 @@ void FixBondReact::update_everything()
		improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
		improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
		num_improper[atom->map(update_mega_glove[jj+1][i])]++;
		if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom)
		error->one(FLERR,"Bond/react impropers/atom exceed system impropers/atom");
		delta_imprp++;
		}
		}

Admin message