Added function for creating an improper using single/improper (b8b07061) · Commits · 郑智淋 / lammps

src/create_bonds.cpp

+106 −2

Original line number	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"
		@@ -31,7 +33,7 @@

		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))
		error->all(FLERR,"Illegal create_bonds command");
		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");

		// optional args
		@@ -132,6 +146,9 @@ void CreateBonds::command(int narg, char **arg)
		} else if (style == SDIHEDRAL) {
		if (dtype <= 0 \|\| dtype > atom->ndihedraltypes)
		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
		@@ -140,6 +157,7 @@ void CreateBonds::command(int narg, char **arg)
		else if (style == SBOND) single_bond();
		else if (style == SANGLE) single_angle();
		else if (style == SDIHEDRAL) single_dihedral();
		else if (style == SIMPROPER) single_improper();

		// trigger special list build

		@@ -512,3 +530,89 @@ void CreateBonds::single_dihedral()
		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	Diff line number	Diff line
		@@ -39,6 +39,7 @@ class CreateBonds : protected Pointers {
		void single_bond();
		void single_angle();
		void single_dihedral();
		void single_improper();
		};

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

		UNDOCUMENTED

		E: Invalid improper type in create_bonds command

		UNDOCUMENTED

		E: Create_bonds requires a pair style be defined

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

		UNDOCUMENTED

		E: Create_bonds single/improper atoms do not exist

		UNDOCUMENTED

		E: New improper exceeded impropers per atom in create_bonds

		UNDOCUMENTED

		*/

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