Merge pull request #1913 from jrgissing/molecule_template_moleculeIDs (2b39c996) · Commits · 郑智淋 / lammps

doc/src/Errors_messages.rst

+9 −0

Original line number	Diff line number	Diff line
		@@ -4724,6 +4724,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
		Invalid Masses section in molecule file
		Self-explanatory.

		Invalid molecule ID in molecule file
		Molecule ID must be a non-zero positive integer.

		Invalid Molecules section in molecule file
		Self-explanatory.

		Invalid REAX atom type
		There is a mis-match between LAMMPS atom types and the elements
		listed in the ReaxFF force field file.
		@@ -4790,6 +4796,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
		Atom IDs must be positive integers and within range of defined
		atoms.

		Invalid atom ID in Fragments section of molecule file
		Self-explanatory.

		Invalid atom ID in Impropers section of data file
		Atom IDs must be positive integers and within range of defined
		atoms.

doc/src/molecule.rst

+23 −1

Original line number	Diff line number	Diff line
		@@ -60,6 +60,7 @@ templates include:
		* :doc:`fix rigid/small <fix_rigid>`
		* :doc:`fix shake <fix_shake>`
		* :doc:`fix gcmc <fix_gcmc>`
		* :doc:`fix bond/react <fix_bond_react>`
		* :doc:`create_atoms <create_atoms>`
		* :doc:`atom_style template <atom_style>`

		@@ -144,6 +145,7 @@ appear if the value(s) are different than the default.
		* Na angles = # of angles Na in molecule, default = 0
		* Nd dihedrals = # of dihedrals Nd in molecule, default = 0
		* Ni impropers = # of impropers Ni in molecule, default = 0
		* Nf fragments = # of fragments in molecule, default = 0
		* Mtotal mass = total mass of molecule
		* Xc Yc Zc com = coordinates of center-of-mass of molecule
		* Ixx Iyy Izz Ixy Ixz Iyz inertia = 6 components of inertia tensor of molecule
		@@ -166,7 +168,7 @@ internally.

		These are the allowed section keywords for the body of the file.

		* Coords, Types, Charges, Diameters, Masses = atom-property sections
		* Coords, Types, Molecules, Fragments, Charges, Diameters, Masses = atom-property sections
		* Bonds, Angles, Dihedrals, Impropers = molecular topology sections
		* Special Bond Counts, Special Bonds = special neighbor info
		* Shake Flags, Shake Atoms, Shake Bond Types = SHAKE info
		@@ -223,6 +225,26 @@ listed in order from 1 to Nlines, but LAMMPS does not check for this.

		----------

		Molecules section:

		* one line per atom
		* line syntax: ID molecule-ID
		* molecule-ID = molecule ID of atom

		----------

		Fragments section:

		* one line per fragment
		* line syntax: ID a b c d ...
		* a,b,c,d,... = IDs of atoms in fragment

		The ID of a fragment can only contain alphanumeric characters and
		underscores. The atom IDs should be values from 1 to Natoms, where
		Natoms = # of atoms in the molecule.

		----------

		Charges section:

		* one line per atom

src/GRANULAR/fix_pour.cpp

+14 −2

Original line number	Diff line number	Diff line
		@@ -632,7 +632,13 @@ void FixPour::pre_exchange()
		int n = atom->nlocal - 1;
		atom->tag[n] = maxtag_all + m+1;
		if (mode == MOLECULE) {
		if (atom->molecule_flag) atom->molecule[n] = maxmol_all+1;
		if (atom->molecule_flag) {
		if (onemols[imol]->moleculeflag) {
		atom->molecule[n] = maxmol_all + onemols[imol]->molecule[m];
		} else {
		atom->molecule[n] = maxmol_all+1;
		}
		}
		if (atom->molecular == 2) {
		atom->molindex[n] = 0;
		atom->molatom[n] = m;
		@@ -666,7 +672,13 @@ void FixPour::pre_exchange()
		fixshake->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);

		maxtag_all += natom;
		if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
		if (mode == MOLECULE && atom->molecule_flag) {
		if (onemols[imol]->moleculeflag) {
		maxmol_all += onemols[imol]->nmolecules;
		} else {
		maxmol_all++;
		}
		}
		}

		// warn if not successful with all insertions b/c too many attempts

src/MISC/fix_deposit.cpp

+14 −2

Original line number	Diff line number	Diff line
		@@ -539,7 +539,13 @@ void FixDeposit::pre_exchange()
		n = atom->nlocal - 1;
		atom->tag[n] = maxtag_all + m+1;
		if (mode == MOLECULE) {
		if (atom->molecule_flag) atom->molecule[n] = maxmol_all+1;
		if (atom->molecule_flag) {
		if (onemols[imol]->moleculeflag) {
		atom->molecule[n] = maxmol_all + onemols[imol]->molecule[m];
		} else {
		atom->molecule[n] = maxmol_all+1;
		}
		}
		if (atom->molecular == 2) {
		atom->molindex[n] = 0;
		atom->molatom[n] = m;
		@@ -603,7 +609,13 @@ void FixDeposit::pre_exchange()
		maxtag_all += natom;
		if (maxtag_all >= MAXTAGINT)
		error->all(FLERR,"New atom IDs exceed maximum allowed ID");
		if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
		if (mode == MOLECULE && atom->molecule_flag) {
		if (onemols[imol]->moleculeflag) {
		maxmol_all += onemols[imol]->nmolecules;
		} else {
		maxmol_all++;
		}
		}
		if (atom->map_style) {
		atom->map_init();
		atom->map_set();

src/create_atoms.cpp

+14 −1

Original line number	Diff line number	Diff line
		@@ -490,7 +490,13 @@ void CreateAtoms::command(int narg, char **arg)
		for (int i = 0; i < molcreate; i++) {
		if (tag) offset = tag[ilocal]-1;
		for (int m = 0; m < natoms; m++) {
		if (molecule_flag) molecule[ilocal] = moloffset + i+1;
		if (molecule_flag) {
		if (onemol->moleculeflag) {
		molecule[ilocal] = moloffset + onemol->molecule[m];
		} else {
		molecule[ilocal] = moloffset + 1;
		}
		}
		if (molecular == 2) {
		atom->molindex[ilocal] = 0;
		atom->molatom[ilocal] = m;
		@@ -524,6 +530,13 @@ void CreateAtoms::command(int narg, char **arg)
		}
		ilocal++;
		}
		if (molecule_flag) {
		if (onemol->moleculeflag) {
		moloffset += onemol->nmolecules;
		} else {
		moloffset++;
		}
		}
		}

		// perform irregular comm to migrate atoms to new owning procs

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