C++ Force::compute方法代码示例

//.........这里部分代码省略.........
  force.cutforce = in.force_cut;
  thermo.nstat = in.thermo_nstat;


  if(me == 0)
    printf("# Create System:\n");

  if(in.datafile) {
    read_lammps_data(atom, comm, neighbor, integrate, thermo, in.datafile, in.units);
    MMD_float volume = atom.box.xprd * atom.box.yprd * atom.box.zprd;
    in.rho = 1.0 * atom.natoms / volume;
    force.setup();

  } else {
    create_box(atom, in.nx, in.ny, in.nz, in.rho);

    comm.setup(neighbor.cutneigh, atom);

    neighbor.setup(atom);

    integrate.setup();

    force.setup();


    create_atoms(atom, in.nx, in.ny, in.nz, in.rho);
    thermo.setup(in.rho, integrate, atom, in.units);

    create_velocity(in.t_request, atom, thermo);

  }

  if(me == 0)
    printf("# Done .... \n");

  if(me == 0) {
    fprintf(stdout, "# " VARIANT_STRING " output ...\n");
    fprintf(stdout, "# Systemparameters: \n");
    fprintf(stdout, "\t# MPI processes: %i\n", neighbor.threads->mpi_num_threads);
    fprintf(stdout, "\t# OpenMP threads: %i\n", neighbor.threads->omp_num_threads);
    fprintf(stdout, "\t# Inputfile: %s\n", input_file == 0 ? "in.lj.miniMD" : input_file);
    fprintf(stdout, "\t# Datafile: %s\n", in.datafile ? in.datafile : "None");
    fprintf(stdout, "\t# ForceStyle: %s\n", in.forcetype == FORCELJ ? "LJ" : "EAM");
    fprintf(stdout, "\t# Units: %s\n", in.units == 0 ? "LJ" : "METAL");
    fprintf(stdout, "\t# Atoms: %i\n", atom.natoms);
    fprintf(stdout, "\t# System size: %2.2lf %2.2lf %2.2lf (unit cells: %i %i %i)\n", atom.box.xprd, atom.box.yprd, atom.box.zprd, in.nx, in.ny, in.nz);
    fprintf(stdout, "\t# Density: %lf\n", in.rho);
    fprintf(stdout, "\t# Force cutoff: %lf\n", force.cutforce);
    fprintf(stdout, "\t# Neigh cutoff: %lf\n", neighbor.cutneigh);
    fprintf(stdout, "\t# Half neighborlists: %i\n", neighbor.halfneigh);
    fprintf(stdout, "\t# Neighbor bins: %i %i %i\n", neighbor.nbinx, neighbor.nbiny, neighbor.nbinz);
    fprintf(stdout, "\t# Neighbor frequency: %i\n", neighbor.every);
    fprintf(stdout, "\t# Timestep size: %lf\n", integrate.dt);
    fprintf(stdout, "\t# Thermo frequency: %i\n", thermo.nstat);
    fprintf(stdout, "\t# Ghost Newton: %i\n", ghost_newton);
    fprintf(stdout, "\t# Use SSE intrinsics: %i\n", force.use_sse);
    fprintf(stdout, "\t# Do safe exchange: %i\n", comm.do_safeexchange);
    fprintf(stdout, "\t# Size of float: %i\n\n",sizeof(MMD_float));
  }

  comm.exchange(atom);
  comm.borders(atom);

  atom.d_x->upload();
  atom.d_v->upload();
  //atom.d_vold->upload();
  neighbor.build(atom);

  if (me == 0) printf("# Starting dynamics ...\n");
  if (me == 0) printf("# Timestep T U P Time\n");
  thermo.compute(0,atom,neighbor,force,timer,comm);
  force.compute(atom,neighbor,comm.me);
  timer.barrier_start(TIME_TOTAL);
  integrate.run(atom,force,neighbor,comm,thermo,timer);
  timer.barrier_stop(TIME_TOTAL);

  int natoms;
  MPI_Allreduce(&atom.nlocal,&natoms,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD);
  thermo.compute(-1,atom,neighbor,force,timer,comm);

  if(me == 0) {
    double time_other=timer.array[TIME_TOTAL]-timer.array[TIME_FORCE]-timer.array[TIME_NEIGH]-timer.array[TIME_COMM];
    printf("\n\n");
    printf("# Performance Summary:\n");
    printf("# MPI_proc OMP_threads nsteps natoms t_total t_force t_neigh t_comm t_other performance perf/thread grep_string t_extra\n");
    printf("%i %i %i %i %lf %lf %lf %lf %lf %lf %lf PERF_SUMMARY %lf\n\n\n",
       nprocs,num_threads,integrate.ntimes,natoms,
       timer.array[TIME_TOTAL],timer.array[TIME_FORCE],timer.array[TIME_NEIGH],timer.array[TIME_COMM],time_other,
       1.0*natoms*integrate.ntimes/timer.array[TIME_TOTAL],1.0*natoms*integrate.ntimes/timer.array[TIME_TOTAL]/nprocs/num_threads,timer.array[TIME_TEST]);

  }

  if(yaml_output)
  output(in,atom,force,neighbor,comm,thermo,integrate,timer,screen_yaml);

  MPI_Barrier(MPI_COMM_WORLD);
  MPI_Finalize();
  delete opencl;
  return 0;
}

//.........这里部分代码省略.........
      ghost_newton = 0;
    }
  }

  if(in.forcetype == FORCELJ) force = (Force*) new ForceLJ();

  threads.mpi_me = me;
  threads.mpi_num_threads = nprocs;
  threads.omp_me = 0;
  threads.omp_num_threads = num_threads;

  atom.threads = &threads;
  comm.threads = &threads;
  force->threads = &threads;
  integrate.threads = &threads;
  neighbor.threads = &threads;
  thermo.threads = &threads;

  force->epsilon = in.epsilon;
  force->sigma = in.sigma;
  force->sigma6 = in.sigma*in.sigma*in.sigma*in.sigma*in.sigma*in.sigma;

  neighbor.ghost_newton = ghost_newton;

  omp_set_num_threads(num_threads);

  neighbor.timer = &timer;
  force->timer = &timer;
  comm.check_safeexchange = check_safeexchange;
  comm.do_safeexchange = do_safeexchange;
  force->use_sse = use_sse;
  neighbor.halfneigh = halfneigh;

  if(halfneigh < 0) force->use_oldcompute = 1;

  if(use_sse) {
#ifdef VARIANT_REFERENCE

    if(me == 0) printf("ERROR: Trying to run with -sse with miniMD reference version. Use SSE variant instead. Exiting.\n");

    MPI_Finalize();
    exit(0);
#endif
  }

  if(num_steps > 0) in.ntimes = num_steps;

  if(system_size > 0) {
    in.nx = system_size;
    in.ny = system_size;
    in.nz = system_size;
  }

  if(nx > 0) {
    in.nx = nx;
    if(ny > 0)
      in.ny = ny;
    else if(system_size < 0)
      in.ny = nx;

    if(nz > 0)
      in.nz = nz;
    else if(system_size < 0)
      in.nz = nx;
  }