(be4f7404) · Commits · 郑智淋 / lammps

src/fix_evaporate.cpp

+58 −6

Original line number	Diff line number	Diff line
		@@ -21,6 +21,7 @@
		#include "domain.h"
		#include "region.h"
		#include "comm.h"
		#include "force.h"
		#include "group.h"
		#include "random_park.h"
		#include "random_mars.h"
		@@ -162,7 +163,8 @@ void FixEvaporate::init()

		void FixEvaporate::pre_exchange()
		{
		int i,iwhichglobal,iwhichlocal;
		int i,j,m,iwhichglobal,iwhichlocal;
		int ndel,ndeltopo[4];

		if (update->ntimestep != next_reneighbor) return;

		@@ -197,9 +199,10 @@ void FixEvaporate::pre_exchange()
		nbefore -= ncount;

		// ndel = total # of atom deletions, in or out of region
		// ndeltopo[1,2,3,4] = ditto for bonds, angles, dihedrals, impropers
		// mark[] = 1 if deleted

		int ndel = 0;
		ndel = 0;
		for (i = 0; i < nlocal; i++) mark[i] = 0;

		// atomic deletions
		@@ -226,12 +229,14 @@ void FixEvaporate::pre_exchange()
		// bcast mol ID and delete all atoms in that molecule on any proc
		// update deletion count by total # of atoms in molecule
		// shrink list of eligible candidates as any of my atoms get marked
		// keep ndel,ncount,nall,nbefore current after each molecule deletion
		// keep ndel,ndeltopo,ncount,nall,nbefore current after each mol deletion

		} else {
		int me,proc,iatom,imolecule,ndelone,ndelall;
		int *molecule = atom->molecule;

		ndeltopo[0] = ndeltopo[1] = ndeltopo[2] = ndeltopo[3] = 0;

		while (nall && ndel < nflux) {

		// pick an iatom,imolecule on proc me to delete
		@@ -245,7 +250,8 @@ void FixEvaporate::pre_exchange()
		} else me = -1;

		// bcast mol ID to delete all atoms from
		// delete single iatom if mol ID = 0
		// if mol ID > 0, delete any atom in molecule and decrement counters
		// if mol ID == 0, delete single iatom

		MPI_Allreduce(&me,&proc,1,MPI_INT,MPI_MAX,world);
		MPI_Bcast(&imolecule,1,MPI_INT,proc,world);
		@@ -254,6 +260,44 @@ void FixEvaporate::pre_exchange()
		if (imolecule && molecule[i] == imolecule) {
		mark[i] = 1;
		ndelone++;

		if (atom->avec->bonds_allow) {
		if (force->newton_bond) ndeltopo[0] += atom->num_bond[i];
		else {
		for (j = 0; j < atom->num_bond[i]; j++) {
		m = atom->map(atom->bond_atom[i][j]);
		if (m >= 0 && m < nlocal) ndeltopo[0]++;
		}
		}
		}
		if (atom->avec->angles_allow) {
		if (force->newton_bond) ndeltopo[1] += atom->num_angle[i];
		else {
		for (j = 0; j < atom->num_angle[i]; j++) {
		m = atom->map(atom->angle_atom2[i][j]);
		if (m >= 0 && m < nlocal) ndeltopo[1]++;
		}
		}
		}
		if (atom->avec->dihedrals_allow) {
		if (force->newton_bond) ndeltopo[2] += atom->num_dihedral[i];
		else {
		for (j = 0; j < atom->num_dihedral[i]; j++) {
		m = atom->map(atom->dihedral_atom2[i][j]);
		if (m >= 0 && m < nlocal) ndeltopo[2]++;
		}
		}
		}
		if (atom->avec->impropers_allow) {
		if (force->newton_bond) ndeltopo[3] += atom->num_improper[i];
		else {
		for (j = 0; j < atom->num_improper[i]; j++) {
		m = atom->map(atom->improper_atom2[i][j]);
		if (m >= 0 && m < nlocal) ndeltopo[3]++;
		}
		}
		}

		} else if (me == proc && i == iatom) {
		mark[i] = 1;
		ndelone++;
		@@ -273,7 +317,6 @@ void FixEvaporate::pre_exchange()
		// update ndel,ncount,nall,nbefore

		MPI_Allreduce(&ndelone,&ndelall,1,MPI_INT,MPI_SUM,world);
		ndel += ndelall;
		MPI_Allreduce(&ncount,&nall,1,MPI_INT,MPI_SUM,world);
		MPI_Scan(&ncount,&nbefore,1,MPI_INT,MPI_SUM,world);
		nbefore -= ncount;
		@@ -292,11 +335,20 @@ void FixEvaporate::pre_exchange()
		}
		}

		// reset global natoms
		// reset global natoms and bonds, angles, etc
		// if global map exists, reset it now instead of waiting for comm
		// since deleting atoms messes up ghosts

		atom->natoms -= ndel;
		if (molflag) {
		int all[4];
		MPI_Allreduce(ndeltopo,all,4,MPI_INT,MPI_SUM,world);
		atom->nbonds -= all[0];
		atom->nangles -= all[1];
		atom->ndihedrals -= all[2];
		atom->nimpropers -= all[3];
		}

		if (ndel && atom->map_style) {
		atom->nghost = 0;
		atom->map_init();

src/fix_rigid.cpp

+5 −5

Original line number	Diff line number	Diff line
		@@ -1910,14 +1910,14 @@ int FixRigid::unpack_exchange(int nlocal, double *buf)
		eflags[nlocal] = static_cast<int> (buf[m++]);
		if (dorientflag) {
		dorient[nlocal][0] = buf[m++];
		dorient[nlocal][0] = buf[m++];
		dorient[nlocal][0] = buf[m++];
		dorient[nlocal][1] = buf[m++];
		dorient[nlocal][2] = buf[m++];
		}
		if (qorientflag) {
		qorient[nlocal][0] = buf[m++];
		qorient[nlocal][0] = buf[m++];
		qorient[nlocal][0] = buf[m++];
		qorient[nlocal][0] = buf[m++];
		qorient[nlocal][1] = buf[m++];
		qorient[nlocal][2] = buf[m++];
		qorient[nlocal][3] = buf[m++];
		}
		return m;
		}

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