(7e36fc9b) · Commits · 郑智淋 / lammps

src/MOLECULE/fix_bond_create.cpp

+63 −34

Original line number	Diff line number	Diff line
		@@ -111,8 +111,9 @@ FixBondCreate::FixBondCreate(LAMMPS lmp, int narg, char *arg) :

		if (atom->molecular == 0)
		error->all("Cannot use fix bond/create with non-molecular systems");
		if (iatomtype == jatomtype && inewtype != jnewtype)
		error->all("Inconsistent new atom types in fix bond/create command");
		if (iatomtype == jatomtype &&
		((imaxbond != jmaxbond) \|\| (inewtype != jnewtype)))
		error->all("Inconsistent iparam/jparam values in fix bond/create command");

		// initialize Marsaglia RNG with processor-unique seed

		@@ -254,12 +255,10 @@ void FixBondCreate::setup(int vflag)
		}
		}

		// if newton_bond is set, need to communicate ghost counts
		// use reverseflag to toggle operations inside pack/unpack methods
		// if newton_bond is set, need to sum bondcount

		reverseflag = 0;
		commflag = 0;
		if (newton_bond) comm->reverse_comm_fix(this);
		reverseflag = 1;
		}

		/* ---------------------------------------------------------------------- */
		@@ -276,6 +275,11 @@ void FixBondCreate::post_integrate()

		comm->communicate();

		// forward comm of bondcount, so ghosts have it

		commflag = 0;
		comm->comm_fix(this);

		// resize bond partner list and initialize it
		// probability array overlays distsq array
		// needs to be atom->nmax in length
		@@ -300,7 +304,7 @@ void FixBondCreate::post_integrate()
		}

		// loop over neighbors of my atoms
		// setup possible partner list of bonds to create
		// each atom sets one closest eligible partner atom ID to bond with

		double **x = atom->x;
		int *tag = atom->tag;
		@@ -329,9 +333,13 @@ void FixBondCreate::post_integrate()

		possible = 0;
		if (itype == iatomtype && jtype == jatomtype) {
		if (imaxbond == 0 \|\| bondcount[i] < imaxbond) possible = 1;
		if ((imaxbond == 0 \|\| bondcount[i] < imaxbond) &&
		(jmaxbond == 0 \|\| bondcount[j] < jmaxbond))
		possible = 1;
		} else if (itype == jatomtype && jtype == iatomtype) {
		if (jmaxbond == 0 \|\| bondcount[i] < jmaxbond) possible = 1;
		if ((jmaxbond == 0 \|\| bondcount[i] < jmaxbond) &&
		(imaxbond == 0 \|\| bondcount[j] < imaxbond))
		possible = 1;
		}
		if (!possible) continue;

		@@ -352,8 +360,10 @@ void FixBondCreate::post_integrate()
		}
		}

		// reverse comm of partner info
		// reverse comm of distsq and partner
		// not needed if newton_pair off since I,J pair was seen by both procs

		commflag = 1;
		if (force->newton_pair) comm->reverse_comm_fix(this);

		// each atom now knows its winning partner
		@@ -365,9 +375,11 @@ void FixBondCreate::post_integrate()
		if (partner[i]) probability[i] = random->uniform();
		}

		commflag = 1;
		comm->comm_fix(this);

		// create bonds
		// create bonds for atoms I own
		// if other atom is owned by another proc, it should create same bond
		// if both atoms list each other as winning bond partner
		// and probability constraint is satisfied

		@@ -393,8 +405,8 @@ void FixBondCreate::post_integrate()
		if (0.5*(min+max) >= fraction) continue;
		}

		// store bond with atom I
		// if newton_bond is set, only store with I or J
		// if not newton_bond, store bond with both I and J

		if (!newton_bond \|\| tag[i] < tag[j]) {
		if (num_bond[i] == atom->bond_per_atom)
		@@ -458,6 +470,15 @@ int FixBondCreate::pack_comm(int n, int list, double buf,
		int i,j,m;

		m = 0;

		if (commflag == 0) {
		for (i = 0; i < n; i++) {
		j = list[i];
		buf[m++] = bondcount[j];
		}
		return 1;

		} else {
		for (i = 0; i < n; i++) {
		j = list[i];
		buf[m++] = partner[j];
		@@ -465,6 +486,7 @@ int FixBondCreate::pack_comm(int n, int list, double buf,
		}
		return 2;
		}
		}

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

		@@ -474,11 +496,18 @@ void FixBondCreate::unpack_comm(int n, int first, double *buf)

		m = 0;
		last = first + n;

		if (commflag == 0) {
		for (i = first; i < last; i++)
		bondcount[i] = static_cast<int> (buf[m++]);

		} else {
		for (i = first; i < last; i++) {
		partner[i] = static_cast<int> (buf[m++]);
		probability[i] = buf[m++];
		}
		}
		}

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

		@@ -489,17 +518,17 @@ int FixBondCreate::pack_reverse_comm(int n, int first, double *buf)
		m = 0;
		last = first + n;

		if (reverseflag) {
		if (commflag == 0) {
		for (i = first; i < last; i++)
		buf[m++] = bondcount[i];
		return 1;

		} else {
		for (i = first; i < last; i++) {
		buf[m++] = partner[i];
		buf[m++] = distsq[i];
		buf[m++] = partner[i];
		}
		return 2;

		} else {
		for (i = first; i < last; i++)
		buf[m++] = bondcount[i];
		return 1;
		}
		}

		@@ -511,19 +540,19 @@ void FixBondCreate::unpack_reverse_comm(int n, int list, double buf)

		m = 0;

		if (reverseflag) {
		if (commflag == 0) {
		for (i = 0; i < n; i++) {
		j = list[i];
		if (buf[m+1] < distsq[j]) {
		partner[j] = static_cast<int> (buf[m++]);
		distsq[j] = buf[m++];
		} else m += 2;
		bondcount[j] += static_cast<int> (buf[m++]);
		}

		} else {
		for (i = 0; i < n; i++) {
		j = list[i];
		bondcount[j] += static_cast<int> (buf[m++]);
		if (buf[m] < distsq[j]) {
		distsq[j] = buf[m++];
		partner[j] = static_cast<int> (buf[m++]);
		} else m += 2;
		}
		}
		}

src/MOLECULE/fix_bond_create.h

+7 −4

Original line number	Diff line number	Diff line
		@@ -48,14 +48,17 @@ class FixBondCreate : public Fix {
		int inewtype,jnewtype;
		double cutsq,fraction;

		int createcount,createcounttotal;
		int createcount,createcounttotal; // bond formation stats

		int nmax;
		int partner,bondcount;
		double distsq,probability;
		int *bondcount; // count of created bonds this atom is part of
		int *partner; // ID of preferred atom for this atom to bond to
		double *distsq; // distance to preferred bond partner
		double *probability; // random # to use in decision to form bond

		class RanMars *random;
		class NeighList *list;
		int countflag,reverseflag;
		int countflag,commflag;
		int nlevels_respa;
		};

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