Merge pull request #773 from lammps/couple-simple (9a70f2d1) · Commits · 郑智淋 / lammps

examples/COUPLE/simple/README

+22 −19

Original line number	Diff line number	Diff line
		@@ -17,33 +17,36 @@ additional wrapper library that interfaces the C interface of the
		LAMMPS library to Fortran and also translates the MPI communicator
		from Fortran to C.

		Once you have built LAMMPS as a library (see examples/COUPLE/README),
		you can then build any of the driver codes with compile lines like
		these, which include paths to the LAMMPS library interface, MPI (an
		installed MPICH in this case), and FFTW (assuming you built LAMMPS as
		a library with its PPPM solver).
		First build LAMMPS as a library (see examples/COUPLE/README), e.g.

		This builds the C++ driver with the LAMMPS library using a C++ compiler:
		make mode=shlib mpi

		g++ -I/home/sjplimp/lammps/src -c simple.cpp
		g++ -L/home/sjplimp/lammps/src simple.o \
		-llammps -lfftw -lmpich -lmpl -lpthread -o simpleCC
		You can then build any of the driver codes with compile lines like
		these, which include paths to the LAMMPS library interface, and
		linking with FFTW (only needed if you built LAMMPS as a library with
		its PPPM solver).

		This builds the C driver with the LAMMPS library using a C compiler:
		This builds the C++ driver with the LAMMPS library using the mpiCC
		(C++) compiler:

		gcc -I/home/sjplimp/lammps/src -c simple.c
		gcc -L/home/sjplimp/lammps/src simple.o \
		-llammps -lfftw -lmpich -lmpl -lpthread -lstdc++ -o simpleC
		mpiCC -I/home/sjplimp/lammps/src -c simple.cpp
		mpiCC -L/home/sjplimp/lammps/src simple.o -llammps -lfftw -o simpleCC

		This builds the C driver with the LAMMPS library using the mpicc (C)
		compiler:

		mpicc -I/home/sjplimp/lammps/src -c simple.c
		mpicc -L/home/sjplimp/lammps/src simple.o -llammps -lfftw -o simpleC

		This builds the Fortran wrapper and driver with the LAMMPS library
		using a Fortran and C compiler, using the wrapper in the fortran
		directory:
		using the mpicc (C) and mpifort (Fortran) compilers, using the wrapper
		in the fortran directory:

		cp ../fortran/libfwrapper.c .
		gcc -I/home/sjplimp/lammps/src -c libfwrapper.c
		gfortran -I/home/sjplimp/lammps/src -c simple.f90
		gfortran -L/home/sjplimp/lammps/src simple.o libfwrapper.o \
		-llammps -lfftw -lfmpich -lmpich -lpthread -lstdc++ -o simpleF
		mpicc -I/home/sjplimp/lammps/src -c libfwrapper.c
		mpifort -c simple.f90
		mpifort -L/home/sjplimp/lammps/src simple.o libfwrapper.o \
		-llammps -lfftw -o simpleF

		You then run simpleCC, simpleC, or simpleF on a parallel machine
		on some number of processors Q with 2 arguments:

examples/COUPLE/simple/simple.c

+1 −1

Original line number	Diff line number	Diff line
		@@ -145,7 +145,7 @@ int main(int narg, char **arg)
		for (i = 0; i < natoms; i++) type[i] = 1;

		lammps_command(lmp,"delete_atoms group all");
		lammps_create_atoms(lmp,natoms,NULL,type,x,v);
		lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);
		lammps_command(lmp,"run 10");
		}

examples/COUPLE/simple/simple.cpp

+9 −8

Original line number	Diff line number	Diff line
		@@ -109,11 +109,11 @@ int main(int narg, char **arg)
		int natoms = static_cast<int> (lmp->atom->natoms);
		x = new double[3*natoms];
		v = new double[3*natoms];
		lammps_gather_atoms(lmp,"x",1,3,x);
		lammps_gather_atoms(lmp,"v",1,3,v);
		lammps_gather_atoms(lmp,(char *) "x",1,3,x);
		lammps_gather_atoms(lmp,(char *) "v",1,3,v);
		double epsilon = 0.1;
		x[0] += epsilon;
		lammps_scatter_atoms(lmp,"x",1,3,x);
		lammps_scatter_atoms(lmp,(char *) "x",1,3,x);

		// these 2 lines are the same

		@@ -124,21 +124,22 @@ int main(int narg, char **arg)
		// extract force on single atom two different ways

		if (lammps == 1) {
		double f = (double ) lammps_extract_atom(lmp,"f");
		double f = (double ) lammps_extract_atom(lmp,(char *) "f");
		printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);

		double fx = (double ) lammps_extract_variable(lmp,"fx","all");
		double fx = (double )
		lammps_extract_variable(lmp,(char ) "fx",(char ) "all");
		printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
		}

		// use commands_string() and commands_list() to invoke more commands

		char *strtwo = "run 10\nrun 20";
		char strtwo = (char ) "run 10\nrun 20";
		if (lammps == 1) lammps_commands_string(lmp,strtwo);

		char *cmds[2];
		cmds[0] = "run 10";
		cmds[1] = "run 20";
		cmds[0] = (char *) "run 10";
		cmds[1] = (char *) "run 20";
		if (lammps == 1) lammps_commands_list(lmp,2,cmds);

		// delete all atoms

examples/COUPLE/simple/simple.f90

+6 −3

Original line number	Diff line number	Diff line
		@@ -115,9 +115,12 @@ PROGRAM f_driver
		CALL lammps_get_natoms(ptr,natoms)
		ALLOCATE(x(3*natoms))

		CALL lammps_gather_atoms(ptr,'x',1,3,x);
		x(1) = x(1) + epsilon
		CALL lammps_scatter_atoms(ptr,'x',1,3,x);
		! these calls are commented out, b/c libfwrapper.c
		! needs to be updated to use gather_atoms and scatter_atoms

		!CALL lammps_gather_atoms(ptr,'x',1,3,x);
		!x(1) = x(1) + epsilon
		!CALL lammps_scatter_atoms(ptr,'x',1,3,x);

		DEALLOCATE(x)

src/create_bonds.cpp

+3 −7

Original line number	Diff line number	Diff line
		@@ -306,10 +306,6 @@ void CreateBonds::many()
		nadd_bonds,atom->nbonds);
		}
		}
		// trigger clearing the list of available neighbor list requests
		// and a full rebuild of them during the next run setup.
		// otherwise the request from this command may linger around.
		neighbor->init();
		}

		/* ---------------------------------------------------------------------- */
		@@ -342,7 +338,7 @@ void CreateBonds::single_bond()
		bond_atom[m][num_bond[m]] = batom2;
		num_bond[m]++;
		}
		++atom->nbonds;
		atom->nbonds++;

		if (force->newton_bond) return;

		@@ -390,7 +386,7 @@ void CreateBonds::single_angle()
		angle_atom3[m][num_angle[m]] = aatom3;
		num_angle[m]++;
		}
		++atom->nangles;
		atom->nangles++;

		if (force->newton_bond) return;

		@@ -454,7 +450,7 @@ void CreateBonds::single_dihedral()
		dihedral_atom4[m][num_dihedral[m]] = datom4;
		num_dihedral[m]++;
		}
		++atom->ndihedrals;
		atom->ndihedrals++;

		if (force->newton_bond) return;

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