faster, simpler, 'more completely random' way to do this (d413eb9e) · Commits · 郑智淋 / lammps

src/create_atoms.cpp

+91 −86

Original line number	Diff line number	Diff line
		@@ -110,11 +110,11 @@ void CreateAtoms::command(int narg, char **arg)
		remapflag = 0;
		mode = ATOM;
		int molseed;
		int nboxseed;
		int insertseed;
		varflag = 0;
		vstr = xstr = ystr = zstr = NULL;
		quatone[0] = quatone[1] = quatone[2] = 0.0;
		nlattpts = created_Nmask = nbox = nboxflag = 0;
		nlattpts = ninsert = insertflag = 0;
		Nmask = NULL;

		nbasis = domain->lattice->nbasis;
		@@ -200,9 +200,9 @@ void CreateAtoms::command(int narg, char **arg)
		iarg += 5;
		} else if (strcmp(arg[iarg],"insert") == 0) {
		if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
		nbox = force->inumeric(FLERR,arg[iarg+1]);
		nboxseed = force->inumeric(FLERR,arg[iarg+2]);
		nboxflag = 1;
		ninsert = force->inumeric(FLERR,arg[iarg+1]);
		insertseed = force->inumeric(FLERR,arg[iarg+2]);
		insertflag = 1;
		iarg += 3;
		} else error->all(FLERR,"Illegal create_atoms command");
		}
		@@ -241,8 +241,8 @@ void CreateAtoms::command(int narg, char **arg)
		ranmol = new RanMars(lmp,molseed+comm->me);
		}

		if (nboxflag) {
		ranbox = new RanMars(lmp,nboxseed+comm->me);
		if (insertflag) {
		ranbox = new RanMars(lmp,insertseed+comm->me);
		}

		// error check and further setup for variable test
		@@ -821,71 +821,78 @@ void CreateAtoms::add_lattice()
		void CreateAtoms::lattice_mask()
		{

		// Nmask will be used to choose which lattice points to insert
		Nmask = new int[nlattpts];
		for (int i = 0; i < nlattpts; i++)
		Nmask[i] = 1;

		if (nbox == 0 && nboxflag && me == 0) error->warning(FLERR,"Specifying an 'insert' value of '0' is equivalent to no 'insert' keyword");
		if (ninsert == 0 && insertflag && me == 0)
		error->warning(FLERR,"Specifying an 'insert' value of '0' is equivalent to no 'insert' keyword");

		int nboxme = 0;
		if (nbox > 0) {
		if (ninsert > 0) {
		int nboxme;
		if (nprocs > 1) {
		int *allnlattpts = new int[nprocs]();
		int allnboxmes[nprocs];
		int cumsum_lattpts[nprocs];
		for (size_t i = 0; i < nprocs; i++)
		allnboxmes[i] = 0;

		MPI_Allgather(&nlattpts, 1, MPI_INT, allnlattpts, 1, MPI_INT, world);

		if (me == 0) {
		int total_lattpts = 0;
		for (int i = 0; i < nprocs; i++)
		for (int i = 0; i < nprocs; i++) {
		total_lattpts += allnlattpts[i];
		cumsum_lattpts[i] = total_lattpts;
		}

		if (nbox > total_lattpts) error->all(FLERR,"Attempting to insert more particles than available lattice points");
		if (nbox < 0) error->all(FLERR,"Cannot insert a negative number of particles (in this universe)");

		// adjust nboxme based on personal number of eligible lattice points

		nboxme = round(nbox*nlattpts/total_lattpts);

		// limit nboxme to available lattice points on this processor

		if (nboxme > nlattpts) nboxme = nlattpts;

		// readjust so that all nboxme's add to exactly nbox

		int sum_nboxme;
		MPI_Allreduce(&nboxme,&sum_nboxme,1,MPI_INT,MPI_SUM,world);

		if (nbox != sum_nboxme) {
		if (ninsert > total_lattpts)
		error->all(FLERR,"Attempting to insert more particles than available lattice points");
		if (ninsert < 0)
		error->all(FLERR,"Cannot insert a negative number of particles (in this universe)");

		int diff = nbox - sum_nboxme;
		int diff_sign = 1;
		if (diff < 0) {
		diff_sign = -1;
		diff = -diff;
		// using proc 0, let's insert N particles onto available lattice points by instead
		// poking [nlattpts - N] holes into the lattice, randomly
		int allNmask[total_lattpts];
		for (int i = 0; i < total_lattpts; i++)
		allNmask[i] = 1;
		int nholes = total_lattpts - ninsert;
		int noptions = total_lattpts;
		for (int i = 0; i < nholes; i++) {
		int hindex = ceil(ranbox->uniform()*noptions);
		int optcount = 0;
		for (int j = 0; j < total_lattpts; j++) {
		if (allNmask[j] == 1) {
		optcount++;
		if (optcount == hindex) {
		allNmask[j] = 0;
		noptions--;
		break;
		}
		}
		}
		}

		// go around adding or subtracting one from all processors (if there's space) until equal
		int which_proc = 0;
		int success_me = 0, success_all = 0;
		int failed_me = 0, failed_all = 0;
		while (success_all < diff && failed_all < nprocs) {
		if (me == which_proc++ && !failed_me)
		if (nboxme < nlattpts) {
		nboxme += diff_sign;
		success_me++;
		} else {
		failed_me == 1;
		// tell individual procs their nboxme (personal # to insert)
		int iproc = 0;
		while (allnlattpts[iproc] == 0 && iproc < nprocs)
		iproc++;
		for (int i = 0; i < total_lattpts; i++) {
		if (i == cumsum_lattpts[iproc]) {
		iproc++;
		while (allnlattpts[iproc] == 0 && iproc < nprocs)
		iproc++;
		}
		MPI_Allreduce(&success_me,&success_all,1,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(&failed_me,&failed_all,1,MPI_INT,MPI_SUM,world);
		if (which_proc > nprocs)
		which_proc = 0;
		allnboxmes[iproc] += allNmask[i];
		}
		// should have guaranteed success at this point
		if (failed_all == nprocs) error->warning(FLERR,"This is an uncaught error. Ask developer");
		}
		MPI_Scatter(&allnboxmes, 1, MPI_INT, &nboxme, 1, MPI_INT, 0, world);
		delete [] allnlattpts;
		} else nboxme = nbox;
		} else nboxme = ninsert;

		// probably faster to have individual processors 're-choose' their random points
		// Nmask will be used to indicate which lattice points to insert
		if (nlattpts < nboxme) printf("WHOAA\n"); //debug
		Nmask = new int[nlattpts];
		for (int i = 0; i < nlattpts; i++)
		Nmask[i] = 1;

		// let's insert N particles onto available lattice points by instead
		// poking [nlattpts - N] holes into the lattice, randomly
		@@ -907,8 +914,6 @@ void CreateAtoms::lattice_mask()
		}
		}

		created_Nmask = 1;

		}

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

src/create_atoms.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -54,7 +54,7 @@ class CreateAtoms : protected Pointers {
		void add_molecule(double , double = NULL);
		int nlattpts; // number of eligible lattice points
		int *Nmask; // used to insert N number of particles on lattice
		int created_Nmask,nbox,nboxflag;
		int ninsert,insertflag;
		int vartest(double *); // evaluate a variable with new atom position
		};

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