Merge pull request #1706 from TOFarmer/create_bonds_improper (4f57332a) · Commits · 郑智淋 / lammps

doc/src/create_bonds.txt

+43 −30

src/create_bonds.cpp

+106 −2

Original line number	Original line	Diff line number	Diff line
	@@ -12,7 +12,9 @@
	------------------------------------------------------------------------- */		------------------------------------------------------------------------- */

	/* ----------------------------------------------------------------------		/* ----------------------------------------------------------------------
	Contributing authors: Mike Salerno (NRL) added single methods		Contributing authors:
			Mike Salerno (NRL) added single methods
			Thomas Farmer (ISIS) added single/improper
	------------------------------------------------------------------------- */		------------------------------------------------------------------------- */

	#include "create_bonds.h"		#include "create_bonds.h"
	@@ -31,7 +33,7 @@

	using namespace LAMMPS_NS;		using namespace LAMMPS_NS;

	enum{MANY,SBOND,SANGLE,SDIHEDRAL};		enum{MANY,SBOND,SANGLE,SDIHEDRAL,SIMPROPER};

	/* ---------------------------------------------------------------------- */		/* ---------------------------------------------------------------------- */

	@@ -100,6 +102,18 @@ void CreateBonds::command(int narg, char **arg)
	(datom2 == datom3) \|\| (datom2 == datom4) \|\| (datom3 == datom4))		(datom2 == datom3) \|\| (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) {
			style = SIMPROPER;
			if (narg < 6) error->all(FLERR,"Illegal create_bonds command");
			dtype = force->inumeric(FLERR,arg[1]);
			datom1 = force->tnumeric(FLERR,arg[2]);
			datom2 = force->tnumeric(FLERR,arg[3]);
			datom3 = force->tnumeric(FLERR,arg[4]);
			datom4 = force->tnumeric(FLERR,arg[5]);
			if ((datom1 == datom2) \|\| (datom1 == datom3) \|\| (datom1 == datom4) \|\|
			(datom2 == datom3) \|\| (datom2 == datom4) \|\| (datom3 == datom4))
			error->all(FLERR,"Illegal create_bonds command");
			iarg = 6;
	} else error->all(FLERR,"Illegal create_bonds command");		} else error->all(FLERR,"Illegal create_bonds command");

	// optional args		// optional args
	@@ -132,6 +146,9 @@ void CreateBonds::command(int narg, char **arg)
	} else if (style == SDIHEDRAL) {		} else if (style == SDIHEDRAL) {
	if (dtype <= 0 \|\| dtype > atom->ndihedraltypes)		if (dtype <= 0 \|\| dtype > atom->ndihedraltypes)
	error->all(FLERR,"Invalid dihedral type in create_bonds command");		error->all(FLERR,"Invalid dihedral type in create_bonds command");
			} else if (style == SIMPROPER) {
			if (dtype <= 0 \|\| dtype > atom->nimpropertypes)
			error->all(FLERR,"Invalid improper type in create_bonds command");
	}		}

	// invoke creation method		// invoke creation method
	@@ -140,6 +157,7 @@ void CreateBonds::command(int narg, char **arg)
	else if (style == SBOND) single_bond();		else if (style == SBOND) single_bond();
	else if (style == SANGLE) single_angle();		else if (style == SANGLE) single_angle();
	else if (style == SDIHEDRAL) single_dihedral();		else if (style == SDIHEDRAL) single_dihedral();
			else if (style == SIMPROPER) single_improper();

	// trigger special list build		// trigger special list build

	@@ -512,3 +530,89 @@ void CreateBonds::single_dihedral()
	num_dihedral[m]++;		num_dihedral[m]++;
	}		}
	}		}

			/* ---------------------------------------------------------------------- */

			void CreateBonds::single_improper()
			{
			int m;

			// check that 4 atoms exist

			const int nlocal = atom->nlocal;
			const int idx1 = atom->map(datom1);
			const int idx2 = atom->map(datom2);
			const int idx3 = atom->map(datom3);
			const int idx4 = atom->map(datom4);

			int count = 0;
			if ((idx1 >= 0) && (idx1 < nlocal)) count++;
			if ((idx2 >= 0) && (idx2 < nlocal)) count++;
			if ((idx3 >= 0) && (idx3 < nlocal)) count++;
			if ((idx4 >= 0) && (idx4 < nlocal)) count++;

			int allcount;
			MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
			if (allcount != 4)
			error->all(FLERR,"Create_bonds single/improper atoms do not exist");

			// create bond once or 4x if newton_bond set

			int *num_improper = atom->num_improper;
			int **improper_type = atom->improper_type;
			tagint **improper_atom1 = atom->improper_atom1;
			tagint **improper_atom2 = atom->improper_atom2;
			tagint **improper_atom3 = atom->improper_atom3;
			tagint **improper_atom4 = atom->improper_atom4;

			if ((m = idx2) >= 0) {
			if (num_improper[m] == atom->improper_per_atom)
			error->one(FLERR,
			"New improper exceeded impropers per atom in create_bonds");
			improper_type[m][num_improper[m]] = dtype;
			improper_atom1[m][num_improper[m]] = datom1;
			improper_atom2[m][num_improper[m]] = datom2;
			improper_atom3[m][num_improper[m]] = datom3;
			improper_atom4[m][num_improper[m]] = datom4;
			num_improper[m]++;
			}
			atom->nimpropers++;

			if (force->newton_bond) return;

			if ((m = idx1) >= 0) {
			if (num_improper[m] == atom->improper_per_atom)
			error->one(FLERR,
			"New improper exceeded impropers per atom in create_bonds");
			improper_type[m][num_improper[m]] = dtype;
			improper_atom1[m][num_improper[m]] = datom1;
			improper_atom2[m][num_improper[m]] = datom2;
			improper_atom3[m][num_improper[m]] = datom3;
			improper_atom4[m][num_improper[m]] = datom4;
			num_improper[m]++;
			}

			if ((m = idx3) >= 0) {
			if (num_improper[m] == atom->improper_per_atom)
			error->one(FLERR,
			"New improper exceeded impropers per atom in create_bonds");
			improper_type[m][num_improper[m]] = dtype;
			improper_atom1[m][num_improper[m]] = datom1;
			improper_atom2[m][num_improper[m]] = datom2;
			improper_atom3[m][num_improper[m]] = datom3;
			improper_atom4[m][num_improper[m]] = datom4;
			num_improper[m]++;
			}

			if ((m = idx4) >= 0) {
			if (num_improper[m] == atom->improper_per_atom)
			error->one(FLERR,
			"New improper exceeded impropers per atom in create_bonds");
			improper_type[m][num_improper[m]] = dtype;
			improper_atom1[m][num_improper[m]] = datom1;
			improper_atom2[m][num_improper[m]] = datom2;
			improper_atom3[m][num_improper[m]] = datom3;
			improper_atom4[m][num_improper[m]] = datom4;
			num_improper[m]++;
			}
			}

src/create_bonds.h

+13 −0

Original line number	Original line	Diff line number	Diff line
	@@ -39,6 +39,7 @@ class CreateBonds : protected Pointers {
	void single_bond();		void single_bond();
	void single_angle();		void single_angle();
	void single_dihedral();		void single_dihedral();
			void single_improper();
	};		};

	}		}
	@@ -87,6 +88,10 @@ E: Invalid dihedral type in create_bonds command

	UNDOCUMENTED		UNDOCUMENTED

			E: Invalid improper type in create_bonds command

			UNDOCUMENTED

	E: Create_bonds requires a pair style be defined		E: Create_bonds requires a pair style be defined

	Self-explanatory.		Self-explanatory.
	@@ -135,4 +140,12 @@ E: New dihedral exceeded dihedrals per atom in create_bonds

	UNDOCUMENTED		UNDOCUMENTED

			E: Create_bonds single/improper atoms do not exist

			UNDOCUMENTED

			E: New improper exceeded impropers per atom in create_bonds

			UNDOCUMENTED

	*/		*/

Original line number	Original line	Diff line number	Diff line
	@@ -23,11 +23,14 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
	btype = bond type of new bond		btype = bond type of new bond
	batom1,batom2 = atom IDs for two atoms in bond		batom1,batom2 = atom IDs for two atoms in bond
	{single/angle} args = atype aatom1 aatom2 aatom3		{single/angle} args = atype aatom1 aatom2 aatom3
	atype = bond type of new angle		atype = angle type of new angle
	aatom1,aatom2,aatom3 = atom IDs for three atoms in angle		aatom1,aatom2,aatom3 = atom IDs for three atoms in angle
	{single/dihedral} args = dtype datom1 datom2 datom3 datom4		{single/dihedral} args = dtype datom1 datom2 datom3 datom4
	dtype = bond type of new dihedral		dtype = dihedral type of new dihedral
	datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral :pre		datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral
			{single/improper} args = itype iatom1 iatom2 iatom3 iatom4
			itype = improper type of new improper
			iatom1,iatom2,iatom3,iatom4 = atom IDs for four atoms in improper :pre
	zero or more keyword/value pairs may be appended :l		zero or more keyword/value pairs may be appended :l
	keyword = {special} :l		keyword = {special} :l
	{special} value = {yes} or {no} :pre		{special} value = {yes} or {no} :pre
	@@ -38,51 +41,54 @@ keyword = {special} :l
	create_bonds many all all 1 1.0 1.2		create_bonds many all all 1 1.0 1.2
	create_bonds many surf solvent 3 2.0 2.4		create_bonds many surf solvent 3 2.0 2.4
	create_bonds single/bond 1 1 2		create_bonds single/bond 1 1 2
	create_bonds single/angle 5 52 98 107 special no :pre		create_bonds single/angle 5 52 98 107 special no
			create_bonds single/dihedral 2 4 19 27 101
			create_bonds single/improper 3 23 26 31 57 :pre

	[Description:]		[Description:]

	Create bonds between pairs of atoms that meet a specified distance		Create bonds between pairs of atoms that meet a specified distance
	criteria. Or create a single bond, angle, or dihedral between 2, 3,		criteria. Or create a single bond, angle, dihedral or improper between 2, 3,
	or 4 specified atoms.		or 4 specified atoms.

	The new bond (angle, dihedral) interactions will then be computed		The new bond (angle, dihedral, improper) interactions will then be computed
	during a simulation by the bond (angle, dihedral) potential defined by		during a simulation by the bond (angle, dihedral, improper) potential defined by
	the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html,		the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html,
	"angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html,		"angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html,
	"dihedral_style"_dihedral_style.html,		"dihedral_style"_dihedral_style.html,
	"dihedral_coeff"_dihedral_coeff.html commands.		"dihedral_coeff"_dihedral_coeff.html, "improper_style"_improper_style.html,
			"improper_coeff"_improper_coeff.html commands.

	The {many} style is useful for adding bonds to a system, e.g. between		The {many} style is useful for adding bonds to a system, e.g. between
	nearest neighbors in a lattice of atoms, without having to enumerate		nearest neighbors in a lattice of atoms, without having to enumerate
	all the bonds in the data file read by the "read_data"_read_data.html		all the bonds in the data file read by the "read_data"_read_data.html

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