Merge pull request #1517 from jrgissing/bond/react-clarify-template-check-messages (a39a35af) · Commits · 郑智淋 / lammps

doc/src/Errors_messages.txt

+6 −6

Original line number	Diff line number	Diff line
		@@ -636,12 +636,12 @@ Please ensure reaction map files are properly formatted. :dd

		{Bond/react: Atom affected by reaction too close to template edge} :dt

		This means an atom which changes type during the reaction is too close
		to an 'edge' atom defined in the superimpose file. This could cause
		incorrect assignment of bonds, angle, etc. Generally, this means you
		must include more atoms in your templates, such that there are at
		least two atoms between each atom involved in the reaction and an edge
		atom. :dd
		This means an atom which changes type or connectivity during the
		reaction is too close to an 'edge' atom defined in the superimpose
		file. This could cause incorrect assignment of bonds, angle, etc.
		Generally, this means you must include more atoms in your templates,
		such that there are at least two atoms between each atom involved in
		the reaction and an edge atom. :dd

		{Bond/react: Fix bond/react needs ghost atoms from farther away} :dt

doc/src/Errors_warnings.txt

+8 −4

Original line number	Diff line number	Diff line
		@@ -82,10 +82,14 @@ bond/angle/dihedral. LAMMPS computes this by taking the maximum bond
		length, multiplying by the number of bonds in the interaction (e.g. 3
		for a dihedral) and adding a small amount of stretch. :dd

		{Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type} :dt

		You may want to double-check that all atom types are properly assigned
		in the post-reaction template. :dd
		{Bond/react: Atom affected by reaction too close to template edge} :dt

		This means an atom which changes type or connectivity during the
		reaction is too close to an 'edge' atom defined in the superimpose
		file. This could cause incorrect assignment of bonds, angle, etc.
		Generally, this means you must include more atoms in your templates,
		such that there are at least two atoms between each atom involved in
		the reaction and an edge atom. :dd

		{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt

src/USER-MISC/fix_bond_react.cpp

+15 −8

Original line number	Diff line number	Diff line
		@@ -157,6 +157,7 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :

		// this looks excessive
		// the price of vectorization (all reactions in one command)?
		memory->create(rxn_name,nreacts,MAXLINE,"bond/react:rxn_name");
		memory->create(nevery,nreacts,"bond/react:nevery");
		memory->create(cutsq,nreacts,2,"bond/react:cutsq");
		memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol");
		@@ -207,8 +208,7 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :

		iarg++;

		iarg++; // read in reaction name here
		//for example, rxn_name[rxn] = ...
		rxn_name[rxn] = arg[iarg++];

		int igroup = group->find(arg[iarg++]);
		if (igroup == -1) error->all(FLERR,"Could not find fix group ID");
		@@ -1720,8 +1720,11 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
		// bad molecule templates check
		// if atoms change types, but aren't landlocked, that's bad
		for (int i = 0; i < twomol->natoms; i++) {
		if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0)
		error->one(FLERR,"Bond/react: Atom affected by reaction too close to template edge");
		if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) {
		char str[128];
		snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]);
		error->all(FLERR,str);
		}
		}

		// additionally, if a bond changes type, but neither involved atom is landlocked, bad
		@@ -1737,7 +1740,9 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
		onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
		if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
		if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
		error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
		char str[128];
		snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]);
		error->all(FLERR,str);
		}
		}
		}
		@@ -1747,7 +1752,9 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
		onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
		if (onemol_batom == equivalences[i][1][myrxn]) {
		if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
		error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
		char str[128];
		snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]);
		error->all(FLERR,str);
		}
		}
		}
		@@ -1763,7 +1770,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
		int ii = reverse_equiv[i][1][myrxn] - 1;
		for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
		if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
		error->one(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted");
		error->all(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted");
		}
		}
		}
		@@ -1774,7 +1781,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
		for (int i = 0; i < twomol->natoms; i++) {
		if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
		char str[128];
		sprintf(str,"Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
		snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]);
		error->warning(FLERR,str);
		break;
		}

src/USER-MISC/fix_bond_react.h

+8 −12

Original line number	Diff line number	Diff line
		@@ -67,6 +67,7 @@ class FixBondReact : public Fix {
		int *groupbits;

		int rxnID; // integer ID for identifying current bond/react
		char **rxn_name; // name of reaction
		int *reaction_count;
		int *reaction_count_total;
		int nmax; // max num local atoms
		@@ -213,14 +214,14 @@ E: Bond/react: Unknown section in map file

		Please ensure reaction map files are properly formatted.

		E: Bond/react: Atom affected by reaction too close to template edge
		E or W: Bond/react: Atom affected by reaction %s too close to template edge

		This means an atom which changes type during the reaction is too close
		to an 'edge' atom defined in the superimpose file. This could cause
		incorrect assignment of bonds, angle, etc. Generally, this means you
		must include more atoms in your templates, such that there are at
		least two atoms between each atom involved in the reaction and an edge
		atom.
		This means an atom which changes type or connectivity during the
		reaction is too close to an 'edge' atom defined in the superimpose
		file. This could cause incorrect assignment of bonds, angle, etc.
		Generally, this means you must include more atoms in your templates,
		such that there are at least two atoms between each atom involved in
		the reaction and an edge atom.

		E: Bond/react: Fix bond/react needs ghost atoms from farther away

		@@ -233,11 +234,6 @@ E: Bond/react: A deleted atom cannot remain bonded to an atom that is not delete

		Self-explanatory.

		W: Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type

		You may want to double-check that all atom types are properly assigned
		in the post-reaction template.

		E: Bond/react special bond generation overflow

		The number of special bonds per-atom created by a reaction exceeds the

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