enrich the AIMD interface (8930a88e) · Commits · 郑智淋 / lammps

src/MESSAGE/fix_client_md.cpp

+60 −37

Original line number	Diff line number	Diff line
		@@ -28,8 +28,9 @@ using namespace LAMMPS_NS;
		using namespace CSLIB_NS;
		using namespace FixConst;

		enum{REAL,METAL}
		enum{SETUP=1,STEP};
		enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
		enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,CHARGE};
		enum{FORCES=1,ENERGY,VIRIAL};

		/* ---------------------------------------------------------------------- */
		@@ -44,14 +45,32 @@ FixClientMD::FixClientMD(LAMMPS lmp, int narg, char *arg) :
		if (sizeof(tagint) != 4)
		error->all(FLERR,"Fix client/md requires 4-byte atom IDs");

		if (strcmp(update->unit_style,"real") == 0) units = REAL;
		else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
		else error->all(FLERR,"Units must be real or metal for fix client/md");

		scalar_flag = 1;
		global_freq = 1;
		extscalar = 1;
		virial_flag = 1;
		thermo_virial = 1;

		if (domain->dimension == 2)
		box[0][2] = box[1][2] = box[2][0] = box[2][1] = box[2][2] = 0.0;

		maxatom = 0;
		xpbc = NULL;

		// unit conversion factors

		double inv_nprocs = 1.0 / comm->nprocs;

		fconvert = econvert = vconvert = 1.0;
		if (units == REAL) {
		fconvert = 1.0;
		econvert = 1.0;
		vconvert = 1.0;
		}
		}

		/* ---------------------------------------------------------------------- */
		@@ -101,34 +120,28 @@ void FixClientMD::setup(int vflag)
		{
		CSlib cs = (CSlib ) lmp->cslib;

		// required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
		// required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
		// optional fields: others in enum above

		int nfields = 6;
		if (domain->dimension == 2) nfields++;
		if (domain->triclinic) nfields++;
		int nfields = 8;
		if (atom->q_flag) nfields++;

		cs->send(SETUP,nfields);

		cs->pack_int(DIM,domain->dimension);
		cs->pack(PERIODICITY,1,3,domain->periodicity);

		pack_box();
		cs->pack(ORIGIN,4,3,domain->boxlo);
		cs->pack(BOX,4,9,&box[0][0]);

		cs->pack_int(NATOMS,atom->natoms);
		cs->pack_int(NTYPES,atom->ntypes);
		cs->pack(BOXLO,4,3,domain->boxlo);
		cs->pack(BOXHI,4,3,domain->boxhi);

		cs->pack_parallel(TYPES,1,atom->nlocal,atom->tag,1,atom->type);
		pack_coords();
		cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);

		if (domain->dimension == 2) cs->pack_int(DIM,domain->dimension);
		if (domain->triclinic) {
		double boxtilt[3];
		boxtilt[0] = domain->xy;
		if (domain->dimension == 3) {
		boxtilt[1] = domain->xz;
		boxtilt[2] = domain->yz;
		} else boxtilt[1] = boxtilt[2] = 0.0;
		cs->pack(BOXTILT,4,3,boxtilt);
		}
		if (atom->q_flag)
		cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q);

		@@ -156,7 +169,7 @@ void FixClientMD::post_force(int vflag)
		else evflag = 0;

		// required fields: COORDS
		// optional fields: BOXLO, BOXHI, BOXTILT
		// optional fields: ORIGIN, BOX

		// send coords

		@@ -164,7 +177,6 @@ void FixClientMD::post_force(int vflag)

		int nfields = 1;
		if (domain->box_change) nfields += 2;
		if (domain->box_change && domain->triclinic) nfields++;;

		cs->send(STEP,nfields);

		@@ -172,17 +184,9 @@ void FixClientMD::post_force(int vflag)
		cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);

		if (domain->box_change) {
		cs->pack(BOXLO,4,3,domain->boxlo);
		cs->pack(BOXHI,4,3,domain->boxhi);
		if (domain->triclinic) {
		double boxtilt[3];
		boxtilt[0] = domain->xy;
		if (domain->dimension == 3) {
		boxtilt[1] = domain->xz;
		boxtilt[2] = domain->yz;
		} else boxtilt[1] = boxtilt[2] = 0.0;
		cs->pack(BOXTILT,4,3,boxtilt);
		}
		pack_box();
		cs->pack(ORIGIN,4,3,domain->boxlo);
		cs->pack(BOX,4,9,&box[0][0]);
		}

		// recv forces, energy, virial
		@@ -230,6 +234,26 @@ void FixClientMD::pack_coords()
		}
		}

		/* ----------------------------------------------------------------------
		pack box info into box = 3 edge vectors of simulation box
		------------------------------------------------------------------------- */

		void FixClientMD::pack_box()
		{
		double *boxlo = domain->boxlo;
		double *boxhi = domain->boxhi;

		box[0][0] = boxhi[0] - boxlo[0];
		box[0][1] = 0.0;
		box[0][2] = 0.0;
		box[1][0] = domain->xy;
		box[1][1] = boxhi[1] - boxlo[1];
		box[1][2] = 0.0;
		box[2][0] = domain->xz;
		box[2][1] = domain->yz;
		box[2][2] = boxhi[2] - boxlo[2];
		}

		/* ----------------------------------------------------------------------
		receive message from server with forces, energy, virial
		------------------------------------------------------------------------- */
		@@ -254,18 +278,17 @@ void FixClientMD::receive_fev(int vflag)
		m = atom->map(id);
		if (m < 0 \|\| m >= nlocal) j += 3;
		else {
		f[m][0] += forces[j++];
		f[m][1] += forces[j++];
		f[m][2] += forces[j++];
		f[m][0] += fconvert * forces[j++];
		f[m][1] += fconvert * forces[j++];
		f[m][2] += fconvert * forces[j++];
		}
		}

		eng = cs->unpack_double(ENERGY);
		eng = econvert * cs->unpack_double(ENERGY);

		if (vflag) {
		double v = (double ) cs->unpack(VIRIAL);
		double invnprocs = 1.0 / comm->nprocs;
		for (int i = 0; i < 6; i++)
		virial[i] = invnprocs*v[i];
		virial[i] = inv_nprocs * vconvert * v[i];
		}
		}

src/MESSAGE/fix_client_md.h

+5 −1

Original line number	Diff line number	Diff line
		@@ -38,10 +38,14 @@ class FixClientMD : public Fix {

		private:
		void *cslib;
		int maxatom;
		int maxatom,units;
		double box[3][3];
		double eng;
		double *xpbc;

		double inv_nprocs;
		double fconvert,econvert,vconvert;

		void pack_coords();
		void receive_fev(int );
		};

src/MESSAGE/server_md.cpp

+69 −56

Original line number	Diff line number	Diff line
		@@ -33,8 +33,9 @@
		using namespace LAMMPS_NS;
		using namespace CSLIB_NS;

		enum{REAL,METAL}
		enum{SETUP=1,STEP};
		enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
		enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,CHARGE};
		enum{FORCES=1,ENERGY,VIRIAL};

		// NOTE: features that could be added to this interface
		@@ -54,9 +55,13 @@ ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
		if (domain->box_exist == 0)
		error->all(FLERR,"Server command before simulation box is defined");

		if (!atom->map_style) error->all(FLERR,"Server md mode requires atom map");
		if (atom->tag_enable == 0) error->all(FLERR,"Server md mode requires atom IDs");
		if (!atom->map_style) error->all(FLERR,"Server md requires atom map");
		if (atom->tag_enable == 0) error->all(FLERR,"Server md requires atom IDs");
		if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs");

		if (strcmp(update->unit_style,"real") == 0) units = REAL;
		else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
		else error->all(FLERR,"Units must be real or metal for server md");
		}

		/* ---------------------------------------------------------------------- */
		@@ -90,24 +95,31 @@ void ServerMD::loop()

		if (msgID == SETUP) {

		int dim = 0;
		int *periodicity = NULL;
		int natoms = -1;
		int ntypes = -1;
		double *boxlo = NULL;
		double *boxhi = NULL;
		double *boxtilt = NULL;
		double *origin = NULL;
		double *box = NULL;
		int *types = NULL;
		double *coords = NULL;
		double *charge = NULL;

		for (int ifield = 0; ifield < nfield; ifield++) {
		if (fieldID[ifield] == UNITS) {
		char *units = cs->unpack_string(UNITS);
		if (strcmp(units,update->unit_style) != 0)
		error->all(FLERR,"Server md units mis-match with client");
		} else if (fieldID[ifield] == DIM) {
		int dim = cs->unpack_int(DIM);
		if (fieldID[ifield] == DIM) {
		dim = cs->unpack_int(DIM);
		if (dim != domain->dimension)
		error->all(FLERR,"Server md dimension mis-match with client");
		} else if (fieldID[ifield] == PERIODICITY) {
		periodicity = (int *) cs->unpack(PERIODICITY);
		if (periodicity[0] != domain->periodicity[0] \|\|
		periodicity[1] != domain->periodicity[1]
		periodicity[2] != domain->periodicity[2])
		error->all(FLERR,"Server md periodicity mis-match with client");
		} else if (fieldID[ifield] == ORIGIN) {
		origin = (double *) cs->unpack(ORIGIN);
		} else if (fieldID[ifield] == BOX) {
		box = (double *) cs->unpack(BOX);
		} else if (fieldID[ifield] == NATOMS) {
		natoms = cs->unpack_int(NATOMS);
		if (3*natoms > INT_MAX)
		@@ -116,12 +128,6 @@ void ServerMD::loop()
		ntypes = cs->unpack_int(NTYPES);
		if (ntypes != atom->ntypes)
		error->all(FLERR,"Server md ntypes mis-match with client");
		} else if (fieldID[ifield] == BOXLO) {
		boxlo = (double *) cs->unpack(BOXLO);
		} else if (fieldID[ifield] == BOXHI) {
		boxhi = (double *) cs->unpack(BOXHI);
		} else if (fieldID[ifield] == BOXTILT) {
		boxtilt = (double *) cs->unpack(BOXTILT);
		} else if (fieldID[ifield] == TYPES) {
		types = (int *) cs->unpack(TYPES);
		} else if (fieldID[ifield] == COORDS) {
		@@ -131,7 +137,8 @@ void ServerMD::loop()
		} else error->all(FLERR,"Server md setup field unknown");
		}

		if (natoms < 0 \|\| ntypes < 0 \|\| !boxlo \|\| !boxhi \|\| !types \|\| !coords)
		if (dim == 0 \|\| !periodicity \|\| !origin \|\| !box \|\|
		natoms < 0 \|\| ntypes < 0 \|\| !types \|\| !coords)
		error->all(FLERR,"Required server md setup field not received");

		if (charge && atom->q_flag == 0)
		@@ -140,7 +147,11 @@ void ServerMD::loop()
		// reset box, global and local
		// reset proc decomposition

		box_change(boxlo,boxhi,boxtilt);
		if ((box[3] != 0.0 \|\| box[6] != 0.0 \|\| box[7] != 0.0) &&
		domain->triclinic == 0)
		error->all(FLERR,"Server md is not initialized for a triclinic box");

		box_change(origin,box);

		domain->set_initial_box();
		domain->set_global_box();
		@@ -166,7 +177,7 @@ void ServerMD::loop()
		int ntotal;
		MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world);
		if (ntotal != natoms)
		error->all(FLERR,"Server md atom cound does not match client");
		error->all(FLERR,"Server md atom count does not match client");

		atom->map_init();
		atom->map_set();
		@@ -190,29 +201,34 @@ void ServerMD::loop()

		} else if (msgID == STEP) {

		double *boxlo = NULL;
		double *boxhi = NULL;
		double *boxtilt = NULL;
		double *coords = NULL;
		double *origin = NULL;
		double *box = NULL;

		for (int ifield = 0; ifield < nfield; ifield++) {
		if (fieldID[ifield] == BOXLO) {
		boxlo = (double *) cs->unpack(BOXLO);
		} else if (fieldID[ifield] == BOXHI) {
		boxhi = (double *) cs->unpack(BOXHI);
		} else if (fieldID[ifield] == BOXTILT) {
		boxtilt = (double *) cs->unpack(BOXTILT);
		} else if (fieldID[ifield] == COORDS) {
		if (fieldID[ifield] == COORDS) {
		coords = (double *) cs->unpack(COORDS);
		} else if (fieldID[ifield] == ORIGIN) {
		origin = (double *) cs->unpack(ORIGIN);
		} else if (fieldID[ifield] == BOX) {
		box = (double *) cs->unpack(BOX);
		} else error->all(FLERR,"Server md step field unknown");
		}

		if (!coords)
		error->all(FLERR,"Required server md step field not received");

		// change box size/shape, only if both box lo/hi received
		// change box size/shape, only if origin and box received
		// reset global/local box like FixDeform at end_of_step()

		if (boxlo && boxhi) box_change(boxlo,boxhi,boxtilt);
		if (origin && box) {
		if ((box[3] != 0.0 \|\| box[6] != 0.0 \|\| box[7] != 0.0) &&
		domain->triclinic == 0)
		error->all(FLERR,"Server md is not initialized for a triclinic box");
		box_change(origin,box);
		domain->set_global_box();
		domain->set_local_box();
		}

		// assign received coords to owned atoms
		// closest_image() insures xyz matches current server PBC
		@@ -231,9 +247,11 @@ void ServerMD::loop()
		}
		}

		// if no need to reneighbor, just ghost comm
		// else setup_minimal(1) which includes reneigh
		// setup_minimal computes forces for 0 or 1
		// if no need to reneighbor:
		// ghost comm
		// setup_minimal(0) which just computes forces
		// else:
		// setup_minimal(1) for pbc, reset_box, reneigh, forces

		int nflag = neighbor->decide();
		if (nflag == 0) {
		@@ -278,26 +296,21 @@ void ServerMD::loop()
		box change due to received message
		------------------------------------------------------------------------- */

		void ServerMD::box_change(double boxlo, double boxhi, double *boxtilt)
		void ServerMD::box_change(double origin, double box)
		{
		domain->boxlo[0] = boxlo[0];
		domain->boxhi[0] = boxhi[0];
		domain->boxlo[1] = boxlo[1];
		domain->boxhi[1] = boxhi[1];
		if (domain->dimension == 3) {
		domain->boxlo[2] = boxlo[2];
		domain->boxhi[2] = boxhi[2];
		}
		domain->boxlo[0] = origin[0];
		domain->boxlo[1] = origin[1];
		domain->boxlo[2] = origin[2];

		domain->boxhi[0] = origin[0] + box[0];
		domain->boxhi[1] = origin[1] + box[4];
		domain->boxhi[2] = origin[2] + box[8];

		domain->xy = box[3];
		domain->xz = box[6];
		domain->yz = box[7];


		if (boxtilt) {
		if (!domain->triclinic)
		error->all(FLERR,"Server md not setup for triclinic box");
		domain->xy = boxtilt[0];
		if (domain->dimension == 3) {
		domain->xz = boxtilt[1];
		domain->yz = boxtilt[2];
		}
		}
		}

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

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