replace STL map with atom->map in special, better code comments (2e0d69b0) · Commits · 郑智淋 / lammps

src/RIGID/fix_rigid_small.cpp

+5 −3

Original line number	Diff line number	Diff line
		@@ -1571,9 +1571,9 @@ void FixRigidSmall::create_bodies(tagint *bodyID)
		}

		// perform rendezvous operation
		// each proc owns random subset of bodies, receives all atoms in the bodies
		// func = compute bbox of each body, flag atom closest to geometric center
		// when done: each atom has atom ID of owning atom of its body
		// each proc owns random subset of bodies
		// receives all atoms in those bodies
		// func = compute bbox of each body, find atom closest to geometric center

		char *buf;
		int nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
		@@ -1627,6 +1627,8 @@ int FixRigidSmall::rendezvous_body(int n, char *inbuf,
		MPI_Comm world = frsptr->world;

		// setup hash
		// use STL map instead of atom->map
		// b/c know nothing about body ID values specified by user
		// ncount = number of bodies assigned to me
		// key = body ID
		// value = index into Ncount-length data structure

src/comm.cpp

+17 −3

Original line number	Diff line number	Diff line
		@@ -728,13 +728,27 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag,

		/* ----------------------------------------------------------------------
		rendezvous communication operation
		three stages:
		first Irregular converts inbuf from caller decomp to rvous decomp
		callback operates on data in rendevous decomp
		last Irregular converts outbuf from rvous decomp back to caller decomp
		inputs:
		n = # of input datums
		proclist = proc that owns each input datum in rendezvous decomposition
		inbuf = list of input datums
		insize = size in bytes of each input datum
		callback = caller function to invoke in rendezvous decomposition
		outputs:
		nout = # of output datums (function return)
		outbuf = list of output datums
		outsize = size in bytes of each output datum
		------------------------------------------------------------------------- */

		int Comm::rendezvous(int n, int proclist, char inbuf, int insize,
		int (callback)(int, char , int &, char &, void *),
		char &outbuf, int outsize, void ptr)
		{
		// comm data from caller decomposition to rendezvous decomposition
		// comm inbuf from caller decomposition to rendezvous decomposition

		Irregular *irregular = new Irregular(lmp);

		@@ -747,7 +761,7 @@ int Comm::rendezvous(int n, int proclist, char inbuf, int insize,
		delete irregular;

		// peform rendezvous computation via callback()
		// callback() allocates proclist_rvous and outbuf_rvous
		// callback() allocates/populates proclist_rvous and outbuf_rvous

		int *proclist_rvous;
		char *outbuf_rvous;
		@@ -757,7 +771,7 @@ int Comm::rendezvous(int n, int proclist, char inbuf, int insize,

		memory->sfree(inbuf_rvous);

		// comm data from rendezvous decomposition back to caller
		// comm outbuf from rendezvous decomposition back to caller
		// caller will free outbuf

		irregular = new Irregular(lmp);

src/read_data.cpp

+4 −4

Original line number	Diff line number	Diff line
		@@ -121,7 +121,7 @@ void ReadData::command(int narg, char **arg)
		if (narg < 1) error->all(FLERR,"Illegal read_data command");

		MPI_Barrier(world);
		double time1 = MPI_Wtime;
		double time1 = MPI_Wtime();

		// optional args

		@@ -912,13 +912,13 @@ void ReadData::command(int narg, char **arg)
		// total time

		MPI_Barrier(world);
		double time2 = MPI_Wtime;
		double time2 = MPI_Wtime();

		if (comm->me == 0) {
		if (screen)
		fprintf(screen," read_atoms CPU = %g secs\n",time2-time1);
		fprintf(screen," read_data CPU = %g secs\n",time2-time1);
		if (logfile)
		fprintf(logfile," read_atoms CPU = %g secs\n",time2-time1);
		fprintf(logfile," read_data CPU = %g secs\n",time2-time1);
		}
		}

src/read_restart.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -82,7 +82,7 @@ void ReadRestart::command(int narg, char **arg)
		error->all(FLERR,"Cannot read_restart after simulation box is defined");

		MPI_Barrier(world);
		double time1 = MPI_Wtime;
		double time1 = MPI_Wtime();

		MPI_Comm_rank(world,&me);
		MPI_Comm_size(world,&nprocs);
		@@ -569,7 +569,7 @@ void ReadRestart::command(int narg, char **arg)
		// total time

		MPI_Barrier(world);
		double time2 = MPI_Wtime;
		double time2 = MPI_Wtime();

		if (comm->me == 0) {
		if (screen)

src/special.cpp

+64 −25

Original line number	Diff line number	Diff line
		@@ -108,9 +108,11 @@ void Special::build()
		memory->smalloc((bigint) ncount*sizeof(InRvous),"special:inbuf");

		// setup input buf to rendezvous comm
		// one datum for each owned atom: datum = proc, atomID
		// one datum for each bond partner: datum = atomID, bond partner ID
		// input datums = pairs of bonded atoms
		// owning proc for each datum = random hash of atomID
		// one datum for each owned atom: datum = owning proc, atomID
		// one datum for each bond partner: datum = atomID, bond partner ID
		// add inverted datum when netwon_bond on

		m = 0;
		for (i = 0; i < nlocal; i++) {
		@@ -140,7 +142,8 @@ void Special::build()
		}

		// perform rendezvous operation
		// each proc owns random subset of atoms, receives all their bond partners
		// each proc owns random subset of atoms
		// receives all info to form and return their onetwo lists

		int nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
		rendezvous_1234,
		@@ -151,6 +154,7 @@ void Special::build()
		memory->sfree(inbuf);

		// set nspecial[0] and onetwo for all owned atoms based on output info
		// output datums = pairs of atoms that are 1-2 neighbors

		MPI_Allreduce(&max_rvous,&maxall,1,MPI_INT,MPI_MAX,world);
		memory->create(onetwo,nlocal,maxall,"special:onetwo");
		@@ -200,9 +204,10 @@ void Special::build()
		memory->smalloc((bigint) ncount*sizeof(InRvous),"special:inbuf");

		// setup input buf to rendezvous comm
		// one datum for each owned atom: datum = proc, atomID
		// one datum for each bond partner: datum = atomID, bond partner ID
		// input datums = all pairs of onetwo atoms (they are 1-3 neighbors)
		// owning proc for each datum = random hash of atomID
		// one datum for each owned atom: datum = owning proc, atomID
		// one datum for each onetwo pair: datum = atomID1, atomID2

		m = 0;
		for (i = 0; i < nlocal; i++) {
		@@ -226,7 +231,8 @@ void Special::build()
		}

		// perform rendezvous operation
		// each proc owns random subset of atoms, receives all their bond partners
		// each proc owns random subset of atoms
		// receives all info to form and return their onethree lists

		nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
		rendezvous_1234,
		@@ -237,6 +243,7 @@ void Special::build()
		memory->sfree(inbuf);

		// set nspecial[1] and onethree for all owned atoms based on output info
		// output datums = pairs of atoms that are 1-3 neighbors

		MPI_Allreduce(&max_rvous,&maxall,1,MPI_INT,MPI_MAX,world);
		memory->create(onethree,nlocal,maxall,"special:onethree");
		@@ -284,9 +291,10 @@ void Special::build()
		memory->smalloc((bigint) ncount*sizeof(InRvous),"special:inbuf");

		// setup input buf to rendezvous comm
		// one datum for each owned atom: datum = proc, atomID
		// one datum for each partner: datum = atomID, bond partner ID
		// input datums = all pairs of onethree and onetwo atoms (they're 1-4 neighbors)
		// owning proc for each datum = random hash of atomID
		// one datum for each owned atom: datum = owning proc, atomID
		// one datum for each onethree/onetwo pair: datum = atomID1, atomID2

		m = 0;
		for (i = 0; i < nlocal; i++) {
		@@ -309,9 +317,8 @@ void Special::build()
		}

		// perform rendezvous operation
		// each proc owns random subset of bodies, receives all atoms in the bodies
		// func = compute bbox of each body, flag atom closest to geometric center
		// when done: each atom has atom ID of owning atom of its body
		// each proc owns random subset of atoms
		// receives all info to form and return their onefour lists

		nreturn = comm->rendezvous(ncount,proclist,(char *) inbuf,sizeof(InRvous),
		rendezvous_1234,
		@@ -322,6 +329,7 @@ void Special::build()
		memory->sfree(inbuf);

		// set nspecial[2] and onefour for all owned atoms based on output info
		// output datums = pairs of atoms that are 1-4 neighbors

		MPI_Allreduce(&max_rvous,&maxall,1,MPI_INT,MPI_MAX,world);
		memory->create(onefour,nlocal,maxall,"special:onefour");
		@@ -934,21 +942,28 @@ int Special::rendezvous_1234(int n, char *inbuf,
		int i,j,m;

		Special sptr = (Special ) ptr;
		Atom *atom = sptr->atom;
		Memory *memory = sptr->memory;

		// setup hash
		// clear atom map so it can be here as a hash table
		// faster than an STL map for large atom counts

		atom->map_clear();

		// initialize hash
		// ncount = number of atoms assigned to me
		// key = atom ID
		// value = index into Ncount-length data structure

		InRvous in = (InRvous ) inbuf;
		std::map<tagint,int> hash;
		//std::map<tagint,int> hash;
		tagint id;

		int ncount = 0;
		for (i = 0; i < n; i++)
		if (in[i].me >= 0)
		hash[in[i].atomID] = ncount++;
		//hash[in[i].atomID] = ncount++;
		atom->map_one(in[i].atomID,ncount++);

		// procowner = caller proc that owns each atom
		// atomID = ID of each rendezvous atom I own
		@@ -961,7 +976,8 @@ int Special::rendezvous_1234(int n, char *inbuf,
		for (m = 0; m < ncount; m++) npartner[m] = 0;

		for (i = 0; i < n; i++) {
		m = hash.find(in[i].atomID)->second;
		//m = hash.find(in[i].atomID)->second;
		m = atom->map(in[i].atomID);
		if (in[i].me >= 0) {
		procowner[m] = in[i].me;
		atomID[m] = in[i].atomID;
		@@ -979,7 +995,8 @@ int Special::rendezvous_1234(int n, char *inbuf,

		for (i = 0; i < n; i++) {
		if (in[i].me >= 0) continue;
		m = hash.find(in[i].atomID)->second;
		//m = hash.find(in[i].atomID)->second;
		m = atom->map(in[i].atomID);
		partner[m][npartner[m]++] = in[i].partnerID;
		}

		@@ -1011,6 +1028,12 @@ int Special::rendezvous_1234(int n, char *inbuf,
		memory->destroy(npartner);
		memory->destroy(partner);

		// re-create atom map

		atom->map_init(0);
		atom->nghost = 0;
		atom->map_set();

		return nout;
		}

		@@ -1027,21 +1050,28 @@ int Special::rendezvous_trim(int n, char *inbuf,
		int i,j,m;

		Special sptr = (Special ) ptr;
		Atom *atom = sptr->atom;
		Memory *memory = sptr->memory;

		// setup hash
		// clear atom map so it can be here as a hash table
		// faster than an STL map for large atom counts

		atom->map_clear();

		// initialize hash
		// ncount = number of atoms assigned to me
		// key = atom ID
		// value = index into Ncount-length data structure

		InRvous in = (InRvous ) inbuf;
		std::map<tagint,int> hash;
		//std::map<tagint,int> hash;
		tagint id;

		int ncount = 0;
		for (i = 0; i < n; i++)
		if (in[i].me >= 0)
		hash[in[i].atomID] = ncount++;
		//hash[in[i].atomID] = ncount++;
		atom->map_one(in[i].atomID,ncount++);

		// procowner = caller proc that owns each atom
		// atomID = ID of each rendezvous atom I own
		@@ -1055,7 +1085,8 @@ int Special::rendezvous_trim(int n, char *inbuf,
		for (m = 0; m < ncount; m++) npartner[m] = 0;

		for (i = 0; i < n; i++) {
		m = hash.find(in[i].atomID)->second;
		//m = hash.find(in[i].atomID)->second;
		m = atom->map(in[i].atomID);
		if (in[i].me >= 0) {
		procowner[m] = in[i].me;
		atomID[m] = in[i].atomID;
		@@ -1073,7 +1104,8 @@ int Special::rendezvous_trim(int n, char *inbuf,

		for (i = 0; i < n; i++) {
		if (in[i].me >= 0 \|\| in[i].me == -2) continue;
		m = hash.find(in[i].atomID)->second;
		//m = hash.find(in[i].atomID)->second;
		m = atom->map(in[i].atomID);
		partner[m][npartner[m]++] = in[i].partnerID;
		}

		@@ -1090,7 +1122,8 @@ int Special::rendezvous_trim(int n, char *inbuf,
		for (i = 0; i < n; i++) {
		if (in[i].me != -2) continue;
		actual = in[i].partnerID;
		m = hash.find(in[i].atomID)->second;
		//m = hash.find(in[i].atomID)->second;
		m = atom->map(in[i].atomID);
		for (j = 0; j < npartner[m]; j++)
		if (partner[m][j] == actual) {
		flag[m][j] = 1;
		@@ -1128,6 +1161,12 @@ int Special::rendezvous_trim(int n, char *inbuf,
		memory->destroy(partner);
		memory->destroy(flag);

		// re-create atom map

		atom->map_init(0);
		atom->nghost = 0;
		atom->map_set();

		return nout;
		}

		@@ -1150,9 +1189,9 @@ void Special::fix_alteration()

		void Special::timer_output(double time1)
		{
		double t2 = MPI_Wtime();
		double time2 = MPI_Wtime();
		if (comm->me == 0) {
		if (screen) fprintf(screen," special bonds CPU = %g secs\n",t2-t1);
		if (logfile) fprintf(logfile," special bonds CPU = %g secs\n",t2-t1);
		if (screen) fprintf(screen," special bonds CPU = %g secs\n",time2-time1);
		if (logfile) fprintf(logfile," special bonds CPU = %g secs\n",time2-time1);
		}
		}

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