add option to enforce atom chirality (819fe9ec) · Commits · 郑智淋 / lammps

src/USER-MISC/fix_bond_react.cpp

+93 −1

Original line number	Diff line number	Diff line
		@@ -36,6 +36,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
		#include "group.h"
		#include "citeme.h"
		#include "math_const.h"
		#include "math_extra.h"
		#include "memory.h"
		#include "error.h"

		@@ -297,6 +298,7 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
		memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges");
		memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
		memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms");

		for (int j = 0; j < nreacts; j++)
		for (int i = 0; i < max_natoms; i++) {
		@@ -304,6 +306,9 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		if (update_edges_flag[j] == 1) custom_edges[i][j] = 1;
		else custom_edges[i][j] = 0;
		delete_atoms[i][j] = 0;
		for (int k = 0; k < 6; k++) {
		chiral_atoms[i][k][j] = 0;
		}
		}

		// read all map files afterward
		@@ -430,6 +435,7 @@ FixBondReact::~FixBondReact()
		memory->destroy(landlocked_atoms);
		memory->destroy(custom_edges);
		memory->destroy(delete_atoms);
		memory->destroy(chiral_atoms);

		memory->destroy(nevery);
		memory->destroy(cutsq);
		@@ -1649,10 +1655,11 @@ evaluate constraints: return 0 if any aren't satisfied
		int FixBondReact::check_constraints()
		{
		tagint atom1,atom2,atom3;
		double delx,dely,delz,rsq;
		double unwrap[3],delx,dely,delz,rsq;
		double delx1,dely1,delz1,delx2,dely2,delz2;
		double rsq1,rsq2,r1,r2,c,t,prrhob;

		imageint *image = atom->image;
		double **x = atom->x;

		for (int i = 0; i < nconstraints; i++) {
		@@ -1701,6 +1708,30 @@ int FixBondReact::check_constraints()
		}
		}
		}

		// let's also check chirality within 'check_constraint'
		for (int i = 0; i < onemol->natoms; i++) {
		if (chiral_atoms[i][0][rxnID] == 1) {
		double my4coords[12];
		// already ensured, by transitive property, that chiral simulation atom has four neighs
		for (int j = 0; j < 4; j++) {
		atom1 = atom->map(glove[i][1]);
		// loop over known types involved in chiral center
		for (int jj = 0; jj < 4; jj++) {
		if (atom->type[atom->map(xspecial[atom1][j])] == chiral_atoms[i][jj+2][rxnID]) {
		atom2 = atom->map(xspecial[atom1][j]);
		domain->unmap(x[atom2],image[atom2],unwrap);
		for (int k = 0; k < 3; k++) {
		my4coords[3*jj+k] = unwrap[k];
		}
		break;
		}
		}
		}
		if (get_chirality(my4coords) != chiral_atoms[i][1][rxnID]) return 0;
		}
		}

		return 1;
		}

		@@ -1741,6 +1772,33 @@ double FixBondReact::get_temperature()
		return t;
		}

		/* ----------------------------------------------------------------------
		return handedness (1 or -1) of a chiral center, given ordered set of coordinates
		------------------------------------------------------------------------- */

		int FixBondReact::get_chirality(double four_coords[12])
		{
		// define oriented plane with first three coordinates
		double vec1[3],vec2[3],vec3[3],vec4[3],mean3[3],dot;

		for (int i = 0; i < 3; i++) {
		vec1[i] = four_coords[i]-four_coords[i+3];
		vec2[i] = four_coords[i+3]-four_coords[i+6];
		}

		MathExtra::cross3(vec1,vec2,vec3);

		for (int i = 0; i < 3; i++) {
		mean3[i] = (four_coords[i] + four_coords[i+3] +
		four_coords[i+6])/3;
		vec4[i] = four_coords[i+9] - mean3[i];
		}

		dot = MathExtra::dot3(vec3,vec4);
		dot = dot/fabs(dot);
		return (int) dot;
		}

		/* ----------------------------------------------------------------------
		Get xspecials for current molecule templates
		------------------------------------------------------------------------- */
		@@ -2869,6 +2927,7 @@ void FixBondReact::read(int myrxn)
		}
		else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
		else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
		else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral);
		else if (strstr(line,"constraints")) {
		sscanf(line,"%d",&nconstr);
		memory->grow(constraints,nconstraints+nconstr,MAXCONARGS,"bond/react:constraints");
		@@ -2900,6 +2959,8 @@ void FixBondReact::read(int myrxn)
		CustomEdges(line, myrxn);
		} else if (strcmp(keyword,"DeleteIDs") == 0) {
		DeleteAtoms(line, myrxn);
		} else if (strcmp(keyword,"ChiralIDs") == 0) {
		ChiralCenters(line, myrxn);
		} else if (strcmp(keyword,"Constraints") == 0) {
		Constraints(line, myrxn);
		} else error->one(FLERR,"Bond/react: Unknown section in map file");
		@@ -2977,6 +3038,37 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn)
		}
		}

		void FixBondReact::ChiralCenters(char *line, int myrxn)
		{
		int tmp;
		for (int i = 0; i < nchiral; i++) {
		readline(line);
		sscanf(line,"%d",&tmp);
		chiral_atoms[tmp-1][0][myrxn] = 1;
		if (onemol->xflag == 0)
		error->one(FLERR,"Bond/react: Molecule template 'Coords' section required for chiralIDs keyword");
		if ((int) onemol_nxspecial[tmp-1][0] != 4)
		error->one(FLERR,"Bond/react: Chiral atoms must have exactly four first neighbors");
		for (int j = 0; j < 4; j++) {
		for (int k = j+1; k < 4; k++) {
		if (onemol->type[onemol_xspecial[tmp-1][j]-1] ==
		onemol->type[onemol_xspecial[tmp-1][k]-1])
		error->one(FLERR,"Bond/react: First neighbors of chiral atoms must be of mutually different types");
		}
		}
		// record order of atom types, and coords
		double my4coords[12];
		for (int j = 0; j < 4; j++) {
		chiral_atoms[tmp-1][j+2][myrxn] = onemol->type[onemol_xspecial[tmp-1][j]-1];
		for (int k = 0; k < 3; k++) {
		my4coords[3*j+k] = onemol->x[onemol_xspecial[tmp-1][j]-1][k];
		}
		}
		// get orientation
		chiral_atoms[tmp-1][1][myrxn] = get_chirality(my4coords);
		}
		}

		void FixBondReact::Constraints(char *line, int myrxn)
		{
		double tmp[MAXCONARGS];

src/USER-MISC/fix_bond_react.h

+16 −1

Original line number	Diff line number	Diff line
		@@ -110,7 +110,7 @@ class FixBondReact : public Fix {

		int ibonding,jbonding;
		int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
		int nedge,nequivalent,ncustom,ndelete,nconstr; // # edge, equivalent, custom atoms in mapping file
		int nedge,nequivalent,ncustom,ndelete,nchiral,nconstr; // # edge, equivalent, custom atoms in mapping file
		int attempted_rxn; // there was an attempt!
		int *local_rxn_count;
		int *ghostly_rxn_count;
		@@ -126,6 +126,7 @@ class FixBondReact : public Fix {
		int **landlocked_atoms; // all atoms at least three bonds away from edge atoms
		int **custom_edges; // atoms in molecule templates with incorrect valences
		int **delete_atoms; // atoms in pre-reacted templates to delete
		int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types

		int nxspecial,onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors
		tagint xspecial,onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list
		@@ -149,6 +150,7 @@ class FixBondReact : public Fix {
		void Equivalences(char *,int);
		void CustomEdges(char *,int);
		void DeleteAtoms(char *,int);
		void ChiralCenters(char *,int);
		void Constraints(char *,int);

		void make_a_guess ();
		@@ -159,6 +161,7 @@ class FixBondReact : public Fix {
		void ring_check();
		int check_constraints();
		double get_temperature();
		int get_chirality(double[12]); // get handedness given an ordered set of coordinates

		void open(char *);
		void readline(char *);
		@@ -249,6 +252,18 @@ E: Bond/react: A deleted atom cannot remain bonded to an atom that is not delete

		Self-explanatory.

		E: Bond/react: First neighbors of chiral atoms must be of mutually different types

		Self-explanatory.

		E: Bond/react: Chiral atoms must have exactly four first neighbors

		Self-explanatory.

		E: Bond/react: Molecule template 'Coords' section required for chiralIDs keyword

		The coordinates of atoms in the pre-reacted template are used to determine chirality.

		E: Bond/react special bond generation overflow

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

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