C++ AtomVec::pack_restart方法代码示例

void WriteRestart::write(char *file)
{
  // special case where reneighboring is not done in integrator
  //   on timestep restart file is written (due to build_once being set)
  // if box is changing, must be reset, else restart file will have
  //   wrong box size and atoms will be lost when restart file is read
  // other calls to pbc and domain and comm are not made,
  //   b/c they only make sense if reneighboring is actually performed

  if (neighbor->build_once) domain->reset_box();

  // natoms = sum of nlocal = value to write into restart file
  // if unequal and thermo lostflag is "error", don't write restart file

  bigint nblocal = atom->nlocal;

  if(region)
  {
      nblocal = 0.;
      for (int i = 0; i < atom->nlocal; i++)
          if(region->match(atom->x[i][0],atom->x[i][1],atom->x[i][2]))
             nblocal += 1;
  }
  
  MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
  if (natoms != atom->natoms && output->thermo->lostflag == ERROR && !region) 
    error->all(FLERR,"Atom count is inconsistent, cannot write restart file");

  // check if filename contains "%"

  int multiproc;
  if (strchr(file,'%')) multiproc = 1;
  else multiproc = 0;

  // open single restart file or base file for multiproc case

  if (me == 0) {
    char *hfile;
    if (multiproc) {
      hfile = new char[strlen(file) + 16];
      char *ptr = strchr(file,'%');
      *ptr = '\0';
      sprintf(hfile,"%s%s%s",file,"base",ptr+1);
      *ptr = '%';
    } else hfile = file;
    fp = fopen(hfile,"wb");
    if (fp == NULL) {
      char str[512];
      sprintf(str,"Cannot open restart file %s",hfile);
      error->one(FLERR,str);
    }
    if (multiproc) delete [] hfile;
  }

  // proc 0 writes header, groups, ntype-length arrays, force field
  // all procs write fix info

  if (me == 0) {
    header();
    group->write_restart(fp);
    type_arrays();
    force_fields();
  }

  modify->write_restart(fp);

  // communication buffer for all my atom's info
  // max_size = largest buffer needed by any proc

  int max_size;
  int send_size = atom->avec->size_restart();
  MPI_Allreduce(&send_size,&max_size,1,MPI_INT,MPI_MAX,world);

  double *buf;
  if (me == 0) memory->create(buf,max_size,"write_restart:buf");
  else memory->create(buf,send_size,"write_restart:buf");

  // pack my atom data into buf

  AtomVec *avec = atom->avec;
  int n = 0;

  if(!region) 
  {
      for (int i = 0; i < atom->nlocal; i++) n += avec->pack_restart(i,&buf[n]);
  }
  else
  {
      for (int i = 0; i < atom->nlocal; i++)
          if(region->match(atom->x[i][0],atom->x[i][1],atom->x[i][2]))
             n += avec->pack_restart(i,&buf[n]);

      send_size = n;
  }

  // if any fix requires it, remap each atom's coords via PBC
  // is because fix changes atom coords (excepting an integrate fix)
  // just remap in buffer, not actual atoms

  if (modify->restart_pbc_any) {
//.........这里部分代码省略.........

//.........这里部分代码省略.........
  file_layout(send_size);

  // header info is complete
  // if multiproc output:
  //   close header file, open multiname file on each writing proc,
  //   write PROCSPERFILE into new file

  if (multiproc) {
    if (me == 0) fclose(fp);

    char *multiname = new char[strlen(file) + 16];
    char *ptr = strchr(file,'%');
    *ptr = '\0';
    sprintf(multiname,"%s%d%s",file,icluster,ptr+1);
    *ptr = '%';

    if (filewriter) {
      fp = fopen(multiname,"wb");
      if (fp == NULL) {
        char str[128];
        sprintf(str,"Cannot open restart file %s",multiname);
        error->one(FLERR,str);
      }
      write_int(PROCSPERFILE,nclusterprocs);
    }

    delete [] multiname;
  }

  // pack my atom data into buf

  AtomVec *avec = atom->avec;
  int n = 0;
  for (int i = 0; i < atom->nlocal; i++) n += avec->pack_restart(i,&buf[n]);

  // if any fix requires it, remap each atom's coords via PBC
  // is because fix changes atom coords (excepting an integrate fix)
  // just remap in buffer, not actual atoms

  if (modify->restart_pbc_any) {
    int triclinic = domain->triclinic;
    double *lo,*hi,*period;

    if (triclinic == 0) {
      lo = domain->boxlo;
      hi = domain->boxhi;
      period = domain->prd;
    } else {
      lo = domain->boxlo_lamda;
      hi = domain->boxhi_lamda;
      period = domain->prd_lamda;
    }

    int xperiodic = domain->xperiodic;
    int yperiodic = domain->yperiodic;
    int zperiodic = domain->zperiodic;

    double *x;
    int m = 0;
    for (int i = 0; i < atom->nlocal; i++) {
      x = &buf[m+1];
      if (triclinic) domain->x2lamda(x,x);

      if (xperiodic) {
        if (x[0] < lo[0]) x[0] += period[0];
        if (x[0] >= hi[0]) x[0] -= period[0];