C++ Fix类代码示例

CFix operator*(const Fix &x, const CFix &y)
{
  return CFix(x.get_re() * y.get_re(),
              x.get_re() * y.get_im(),
              x.get_shift() + y.get_shift(),
              0, 0);
}

void ComputeSlice::extract_one(int m, double *vec, int stride)
{
  int i,j;

  // invoke the appropriate compute if needed

  if (which[m] == COMPUTE) {
    Compute *compute = modify->compute[value2index[m]];

    if (argindex[m] == 0) {
      if (!(compute->invoked_flag & INVOKED_VECTOR)) {
	compute->compute_vector();
	compute->invoked_flag |= INVOKED_VECTOR;
      }
      double *cvector = compute->vector;
      j = 0;
      for (i = nstart; i < nstop; i += nskip) {
	vec[j] = cvector[i-1];
	j += stride;
      }
      
    } else {
      if (!(compute->invoked_flag & INVOKED_ARRAY)) {
	compute->compute_array();
	compute->invoked_flag |= INVOKED_ARRAY;
      }
      double **carray = compute->array;
      int icol = argindex[m]-1;
      j = 0;
      for (i = nstart; i < nstop; i += nskip) {
	vec[j] = carray[i-1][icol];
	j += stride;
      }
    }

  // access fix fields, check if fix frequency is a match
    
  } else if (which[m] == FIX) {
    if (update->ntimestep % modify->fix[value2index[m]]->global_freq)
      error->all(FLERR,"Fix used in compute slice not computed at compatible time");
    Fix *fix = modify->fix[value2index[m]];

    if (argindex[m] == 0) {
      j = 0;
      for (i = nstart; i < nstop; i += nskip) {
	vec[j] = fix->compute_vector(i-1);
	j += stride;
      }
    } else {
      int icol = argindex[m]-1;
      j = 0;
      for (i = nstart; i < nstop; i += nskip) {
	vec[j] = fix->compute_array(i-1,icol);
	j += stride;
      }
    }
  }
}

Constraint::Constraint(ConstraintKind kind, Fix fix,
                       Type first, Type second, ConstraintLocator *locator,
                       ArrayRef<TypeVariableType *> typeVars)
  : Kind(kind), TheFix(fix.getKind()), FixData(fix.getData()), 
    HasRestriction(false), HasFix(true),
    IsActive(false), RememberChoice(false), IsFavored(false),
    NumTypeVariables(typeVars.size()),
    Types{ first, second, Identifier() }, Locator(locator)
{
  assert(!first.isNull());
  assert(!second.isNull());
  std::copy(typeVars.begin(), typeVars.end(), getTypeVariablesBuffer().begin());
}

double Properties::max_radius()
{
  const double maxtype = max_type();
  double maxRadius = -1.0;

  // check local particles
  for (int i=0;i<atom->nlocal;i++)
  {
    const double irad = atom->radius[i];
    // maximum
    if (irad > maxRadius)
      maxRadius = irad;
  }

  // check all fixes
  // such as fix insert, fix change/type, fix wall, fix pour
  for(int i=0;i<modify->nfix;i++)
  {
      // checks
      Fix *fix = modify->fix[i];

      if(!fix->use_rad_for_cut_neigh_and_ghost())
          continue;

      // loop over all types since min_rad(int) and max_rad(int) need a type
      for (int j=1;j<maxtype+1;j++)
      {
        const double f_maxrad = fix->max_rad(j);
        if(f_maxrad > SMALL &&  f_maxrad > maxRadius)
          maxRadius = f_maxrad;
      }
  }

  //Get min/max from other procs
  double maxRadius_all;
  MPI_Allreduce(&maxRadius,&maxRadius_all, 1, MPI_DOUBLE, MPI_MAX, world);
  maxRadius = maxRadius_all;

  //error check
  if(maxRadius <= SMALL)
    error->all(FLERR,"Atom radius must be bigger than zero for granular simulations");

  return  maxRadius;
}

void *lammps_extract_fix(void *ptr, char *id, int style, int type,
			 int i, int j)
{
  LAMMPS *lmp = (LAMMPS *) ptr;

  int ifix = lmp->modify->find_fix(id);
  if (ifix < 0) return NULL;
  Fix *fix = lmp->modify->fix[ifix];

  if (style == 0) {
    double *dptr = (double *) malloc(sizeof(double));
    if (type == 0) {
      if (!fix->scalar_flag) return NULL;
      *dptr = fix->compute_scalar();
      return (void *) dptr;
    }
    if (type == 1) {
      if (!fix->vector_flag) return NULL;
      *dptr = fix->compute_vector(i);
      return (void *) dptr;
    }
    if (type == 2) {
      if (!fix->array_flag) return NULL;
      *dptr = fix->compute_array(i,j);
      return (void *) dptr;
    }
  }

  if (style == 1) {
    if (!fix->peratom_flag) return NULL;
    if (type == 1) return (void *) fix->vector_atom;
    if (type == 2) return (void *) fix->array_atom;
  }

  if (style == 2) {
    if (!fix->local_flag) return NULL;
    if (type == 1) return (void *) fix->vector_local;
    if (type == 2) return (void *) fix->array_local;
  }

  return NULL;
}

void FixGrem::init()
{

  if (domain->triclinic)
    error->all(FLERR,"Triclinic cells are not supported");

  // set temperature and pressure ptrs

  int icompute = modify->find_compute(id_temp);
  if (icompute < 0)
    error->all(FLERR,"Temperature compute ID for fix grem does not exist");
  temperature = modify->compute[icompute];

  icompute = modify->find_compute(id_ke);
  if (icompute < 0)
    error->all(FLERR,"KE compute ID for fix grem does not exist");
  ke = modify->compute[icompute];

  icompute = modify->find_compute(id_pe);
  if (icompute < 0)
    error->all(FLERR,"PE compute ID for fix grem does not exist");
  pe = modify->compute[icompute];

  int ifix = modify->find_fix(id_nh);
  if (ifix < 0)
    error->all(FLERR,"Fix id for nvt or npt fix does not exist");
  Fix *nh = modify->fix[ifix];

  double *t_start = (double *)nh->extract("t_start",ifix);
  double *t_stop = (double *)nh->extract("t_stop",ifix);
  if ((t_start != NULL) && (t_stop != NULL) && (ifix == 0)) {
    tbath = *t_start;
    if (*t_start != *t_stop)
      error->all(FLERR,"Thermostat temperature ramp not allowed");
  } else
    error->all(FLERR,"Problem extracting target temperature from fix nvt or npt");

  pressref = 0.0;
  if (pressflag) {
    int *p_flag = (int *)nh->extract("p_flag",ifix);
    double *p_start = (double *) nh->extract("p_start",ifix);
    double *p_stop = (double *) nh->extract("p_stop",ifix);
    if ((p_flag != NULL) && (p_start != NULL) && (p_stop != NULL)
        && (ifix == 1)) {
      ifix = 0;
      pressref = p_start[0];
      if ((p_start[0] != p_stop[0]) || (p_flag[0] != 1)) ++ ifix;
      if ((p_start[1] != p_stop[1]) || (p_flag[0] != 1)) ++ ifix;
      if ((p_start[2] != p_stop[2]) || (p_flag[0] != 1)) ++ ifix;
      if ((p_start[0] != p_start[1]) || (p_start[1] != p_start[2])) ++ifix;
      if ((p_flag[3] != 0) || (p_flag[4] != 0) || (p_flag[5] != 0)) ++ifix;
      if (ifix > 0)
        error->all(FLERR,"Unsupported pressure settings in fix npt");
    } else
      error->all(FLERR,"Problem extracting target pressure from fix npt");
  }
}

int FixAppendAtoms::get_spatial()
{
  if (update->ntimestep % freq == 0) {
    int ifix = modify->find_fix(spatialid);
    if (ifix < 0)
      error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
    Fix *fix = modify->fix[ifix];

    int failed = 0;
    int count = 0;
    while (failed < 2) {
      double tmp = fix->compute_vector(2*count);
      if (tmp == 0.0) failed++;
      else failed = 0;
      count++;
    }
    double *pos = new double[count-2];
    double *val = new double[count-2];
    for (int loop=0; loop < count-2; loop++) {
      pos[loop] = fix->compute_vector(2*loop);
      val[loop] = fix->compute_vector(2*loop+1);
    }

    // always ignore the first and last

    double binsize = 2.0;
    double min_energy=0.0;
    double max_energy=0.0;
    int header = static_cast<int> (size / binsize);
    advance = 0;

    for (int loop=1; loop <= header; loop++) {
        max_energy += val[loop];
    }
    for (int loop=count-2-2*header; loop <=count-3-header; loop++) {
      min_energy += val[loop];
    }
    max_energy /= header;
    min_energy /= header;

    double shockfront_min = 0.0;
    double shockfront_max = 0.0;
    double shockfront_loc = 0.0;
    int front_found1 = 0;
    for (int loop=count-3-header; loop > header; loop--) {
      if (front_found1 == 1) continue;
      if (val[loop] > min_energy + 0.1*(max_energy - min_energy)) {
        shockfront_max = pos[loop];
        front_found1=1;
      }
    }
    int front_found2 = 0;
    for (int loop=header+1; loop <=count-3-header; loop++) {
      if (val[loop] > min_energy + 0.6*(max_energy - min_energy)) {
        shockfront_min = pos[loop];
        front_found2=1;
      }
    }
    if      (front_found1 + front_found2 == 0) shockfront_loc = 0.0;
    else if (front_found1 + front_found2 == 1)
      shockfront_loc = shockfront_max + shockfront_min;
    else if (front_found1 == 1 && front_found2 == 1 &&
             shockfront_max-shockfront_min > spatlead/2.0)
      shockfront_loc = shockfront_max;
    else shockfront_loc = (shockfront_max + shockfront_min) / 2.0;
    if (comm->me == 0)
      printf("SHOCK: %g %g %g %g %g\n", shockfront_loc, shockfront_min,
             shockfront_max, domain->boxlo[2], domain->boxhi[2]);

    if (domain->boxhi[2] - shockfront_loc < spatlead) advance = 1;

    delete [] pos;
    delete [] val;
  }

  advance_sum = 0;
  MPI_Allreduce(&advance,&advance_sum,1,MPI_INT,MPI_SUM,world);

  if (advance_sum > 0) return 1;
  else return 0;
}

//.........这里部分代码省略.........
  } else {
    sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
    sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
    sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
  }

  if (style == BOX || style == REGION) {
    if (domain->xperiodic) {
      if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
      if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
    }
    if (domain->yperiodic) {
      if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
      if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
    }
    if (domain->zperiodic) {
      if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
      if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
    }
  }

  // add atoms in one of 3 ways

  bigint natoms_previous = atom->natoms;
  int nlocal_previous = atom->nlocal;

  if (style == SINGLE) add_single();
  else if (style == RANDOM) add_random();
  else add_lattice();

  // invoke set_arrays() for fixes that need initialization of new atoms

  int nlocal = atom->nlocal;
  for (int m = 0; m < modify->nfix; m++) {
    Fix *fix = modify->fix[m];
    if (fix->create_attribute)
    {
      fix->pre_set_arrays();
      for (int i = nlocal_previous; i < nlocal; i++)
        fix->set_arrays(i);
    }
  }

  // clean up

  if (domain->lattice) delete [] basistype;

  // new total # of atoms

  bigint nblocal = atom->nlocal;
  MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
  if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
    error->all(FLERR,"Too many total atoms");

  // print status

  if (comm->me == 0) {
    if (screen)
      fprintf(screen,"Created " BIGINT_FORMAT " atoms\n",
              atom->natoms-natoms_previous);
    if (logfile)
      fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
              atom->natoms-natoms_previous);
  }

  // reset simulation now that more atoms are defined
  // add tags for newly created atoms if possible
  // if global map exists, reset it
  // change these to MAXTAGINT when allow tagint = bigint

  if (atom->natoms > MAXSMALLINT) {
    if (comm->me == 0)
      error->warning(FLERR,"Total atom count exceeds ID limit, "
                     "atoms will not have individual IDs");
    atom->tag_enable = 0;
  }
  if (atom->natoms <= MAXSMALLINT) atom->tag_extend();

  if (atom->map_style) {
    atom->nghost = 0;
    atom->map_init();
    atom->map_set();
  }

  // if a molecular system, set nspecial to 0 for new atoms
  // NOTE: 31May12, don't think this is needed, avec->create_atom() does it

  //if (atom->molecular) {
  //  int **nspecial = atom->nspecial;
  //  for (int i = nlocal_previous; i < atom->nlocal; i++) {
  //    nspecial[i][0] = 0;
  //    nspecial[i][1] = 0;
  //    nspecial[i][2] = 0;
  //  }
  //}

  // error checks on coarsegraining
  if(force->cg_active())
    error->cg(FLERR,"create_atoms");
}

FixGrem::FixGrem(LAMMPS *lmp, int narg, char **arg) :
  Fix(lmp, narg, arg)
{
  if (narg < 7) error->all(FLERR,"Illegal fix grem command");

  scalar_flag = 1;
  vector_flag = 1;
  size_vector = 3;
  global_freq = 1;
  extscalar = 1;
  extvector = 1;

  scale_grem = 1.0;

  // tbath - temp of bath, the same as defined in thermostat

  lambda = force->numeric(FLERR,arg[3]);
  eta = force->numeric(FLERR,arg[4]);
  h0 = force->numeric(FLERR,arg[5]);

  int n = strlen(arg[6])+1;
  id_nh = new char[n];
  strcpy(id_nh,arg[6]);

  // create a new compute temp style
  // id = fix-ID + temp
  // compute group = all since pressure is always global (group all)
  //   and thus its KE/temperature contribution should use group all

  n = strlen(id) + 6;
  id_temp = new char[n];
  strcpy(id_temp,id);
  strcat(id_temp,"_temp");

  char **newarg = new char*[3];
  newarg[0] = id_temp;
  newarg[1] = (char *) "all";
  newarg[2] = (char *) "temp";
  modify->add_compute(3,newarg);
  delete [] newarg;

  // create a new compute pressure style
  // id = fix-ID + press, compute group = all
  // pass id_temp as 4th arg to pressure constructor

  n = strlen(id) + 7;
  id_press = new char[n];
  strcpy(id_press,id);
  strcat(id_press,"_press");

  newarg = new char*[5];
  newarg[0] = id_press;
  newarg[1] = (char *) "all";
  newarg[2] = (char *) "PRESSURE/GREM";
  newarg[3] = id_temp;
  newarg[4] = id;
  modify->add_compute(5,newarg);
  delete [] newarg;

  // create a new compute ke style
  // id = fix-ID + ke

  n = strlen(id) + 8;
  id_ke = new char[n];
  strcpy(id_ke,id);
  strcat(id_ke,"_ke");

  newarg = new char*[3];
  newarg[0] = id_ke;
  newarg[1] = (char *) "all";
  newarg[2] = (char *) "ke";
  modify->add_compute(3,newarg);
  delete [] newarg;

  // create a new compute pe style
  // id = fix-ID + pe

  n = strlen(id) + 9;
  id_pe = new char[n];
  strcpy(id_pe,id);
  strcat(id_pe,"_pe");

  newarg = new char*[3];
  newarg[0] = id_pe;
  newarg[1] = (char *) "all";
  newarg[2] = (char *) "pe";
  modify->add_compute(3,newarg);
  delete [] newarg;

  int ifix = modify->find_fix(id_nh);
  if (ifix < 0)
    error->all(FLERR,"Fix id for nvt or npt fix does not exist");
  Fix *nh = modify->fix[ifix];

  pressflag = 0;
  int *p_flag = (int *)nh->extract("p_flag",ifix);
  if ((p_flag == NULL) || (ifix != 1) || (p_flag[0] == 0)
      || (p_flag[1] == 0) || (p_flag[2] == 0)) {
    pressflag = 0;
  } else if ((p_flag[0] == 1) && (p_flag[1] == 1)
//.........这里部分代码省略.........

void FixAveTime::invoke_vector(bigint ntimestep)
{
  int i,j,m;
  
  // zero if first step

  if (irepeat == 0)
    for (i = 0; i < nrows; i++)
      for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
  
  // accumulate results of computes,fixes,variables to local copy
  // compute/fix/variable may invoke computes so wrap with clear/add
  
  modify->clearstep_compute();
  
  for (j = 0; j < nvalues; j++) {
    m = value2index[j];
    
    // invoke compute if not previously invoked
    
    if (which[j] == COMPUTE) {
      Compute *compute = modify->compute[m];
      
      if (argindex[j] == 0) {
	if (!(compute->invoked_flag & INVOKED_VECTOR)) {
	  compute->compute_vector();
	  compute->invoked_flag |= INVOKED_VECTOR;
	}
	double *cvector = compute->vector;
	for (i = 0; i < nrows; i++)
	  column[i] = cvector[i];
	
      } else {
	if (!(compute->invoked_flag & INVOKED_ARRAY)) {
	  compute->compute_array();
	  compute->invoked_flag |= INVOKED_ARRAY;
	}
	double **carray = compute->array;
	int icol = argindex[j]-1;
	for (i = 0; i < nrows; i++)
	  column[i] = carray[i][icol];
      }
      
    // access fix fields, guaranteed to be ready
      
    } else if (which[j] == FIX) {
      Fix *fix = modify->fix[m];
      if (argindex[j] == 0)
	for (i = 0; i < nrows; i++)
	  column[i] = fix->compute_vector(i);
      else {
	int icol = argindex[j]-1;
	for (i = 0; i < nrows; i++)
	  column[i] = fix->compute_array(i,icol);
      }
    }
    
    // add columns of values to array or just set directly if offcol is set
    
    if (offcol[j]) {
      for (i = 0; i < nrows; i++)
	array[i][j] = column[i];
    } else {
      for (i = 0; i < nrows; i++)
	array[i][j] += column[i];
    }
  }
  
  // done if irepeat < nrepeat
  // else reset irepeat and nvalid
  
  irepeat++;
  if (irepeat < nrepeat) {
    nvalid += nevery;
    modify->addstep_compute(nvalid);
    return;
  }
  
  irepeat = 0;
  nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
  modify->addstep_compute(nvalid);
  
  // average the final result for the Nfreq timestep
  
  double repeat = nrepeat;
  for (i = 0; i < nrows; i++)
    for (j = 0; j < nvalues; j++)
      if (offcol[j] == 0) array[i][j] /= repeat;
  
  // if ave = ONE, only single Nfreq timestep value is needed
  // if ave = RUNNING, combine with all previous Nfreq timestep values
  // if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
  
  if (ntimestep >= startstep) {
    if (ave == ONE) {
      for (i = 0; i < nrows; i++)
	for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
      norm = 1;
      
    } else if (ave == RUNNING) {
//.........这里部分代码省略.........

void ComputeChunkSpreadAtom::compute_peratom()
{
  invoked_peratom = update->ntimestep;

  // grow local vector_atom or array_atom if necessary

  if (atom->nmax > nmax) {
    if (nvalues == 1) {
      memory->destroy(vector_atom);
      nmax = atom->nmax;
      memory->create(vector_atom,nmax,"chunk/spread/atom:vector_atom");
    } else {
      memory->destroy(array_atom);
      nmax = atom->nmax;
      memory->create(array_atom,nmax,nvalues,"chunk/spread/atom:array_atom");
    }
  }

  // compute chunk/atom assigns atoms to chunk IDs
  // extract ichunk index vector from compute
  // ichunk = 1 to Nchunk for included atoms, 0 for excluded atoms

  int nchunk = cchunk->setup_chunks();
  cchunk->compute_ichunk();
  int *ichunk = cchunk->ichunk;

  // loop over values, access compute or fix
  // loop over atoms, use chunk ID of each atom to store value from compute/fix

  int *mask = atom->mask;
  int nlocal = atom->nlocal;

  int i,m,n,index,nstride;
  double *ptr;

  for (m = 0; m < nvalues; m++) {
    n = value2index[m];

    // copy compute/fix values into vector_atom or array_atom
    // nstride between values for each atom

    if (nvalues == 1) {
      ptr = vector_atom;
      nstride = 1;
    } else {
      ptr = &array_atom[0][m];
      nstride = nvalues;
    }

    // invoke compute if not previously invoked

    if (which[m] == COMPUTE) {
      Compute *compute = modify->compute[n];

      if (argindex[m] == 0) {
        if (!(compute->invoked_flag & INVOKED_VECTOR)) {
          compute->compute_vector();
          compute->invoked_flag |= INVOKED_VECTOR;
        }
	double *cvector = compute->vector;
	for (i = 0; i < nlocal; i++, ptr += nstride) {
	  *ptr = 0.0;
	  if (!(mask[i] & groupbit)) continue;
	  index = ichunk[i]-1;
	  if (index < 0 || index >= nchunk) continue;
	  *ptr = cvector[index];
	}

      } else {
        if (!(compute->invoked_flag & INVOKED_ARRAY)) {
          compute->compute_array();
          compute->invoked_flag |= INVOKED_ARRAY;
        }
        int icol = argindex[m]-1;
        double **carray = compute->array;
	for (i = 0; i < nlocal; i++, ptr += nstride) {
	  *ptr = 0.0;
	  if (!(mask[i] & groupbit)) continue;
	  index = ichunk[i]-1;
	  if (index < 0 || index >= nchunk) continue;
	  *ptr = carray[index][icol];
	}
      }

    // access fix data, check if fix frequency is a match
    // are assuming the fix global vector/array is per-chunk data
    // check if index exceeds fix output length/rows

    } else if (which[m] == FIX) {
      Fix *fix = modify->fix[n];
      if (update->ntimestep % fix->global_freq)
        error->all(FLERR,"Fix used in compute chunk/spread/atom not "
                   "computed at compatible time");

      if (argindex[m] == 0) {
        int nfix = fix->size_vector;
        for (i = 0; i < nlocal; i++, ptr += nstride) {
          *ptr = 0.0;
          if (!(mask[i] & groupbit)) continue;
          index = ichunk[i]-1;
//.........这里部分代码省略.........

Fix operator*(const int x, const Fix &y)
{
  return Fix(x * y.get_re(),
             y.get_shift(),
             0, 0);
}

void FixAveTime::invoke_vector(bigint ntimestep)
{
  int i,j,m;

  // first sample within single Nfreq epoch
  // zero out arrays that accumulate over many samples, but not across epochs
  // invoke setup_chunks() to determine current nchunk
  //   re-allocate per-chunk arrays if needed
  // invoke lock() in two cases:
  //   if nrepeat > 1: so nchunk cannot change until Nfreq epoch is over,
  //     will be unlocked on last repeat of this Nfreq
  //   if ave = RUNNING/WINDOW and not yet locked:
  //     set forever, will be unlocked in fix destructor
  // wrap setup_chunks in clearstep/addstep b/c it may invoke computes
  //   both nevery and nfreq are future steps,
  //   since call below to cchunk->ichunk()
  //     does not re-invoke internal cchunk compute on this same step

  if (irepeat == 0) {
    if (any_variable_length) {
      modify->clearstep_compute();
      int nrows_new = column_length(1);
      modify->addstep_compute(ntimestep+nevery);
      modify->addstep_compute(ntimestep+nfreq);

      if (all_variable_length && nrows_new != nrows) {
        nrows = nrows_new;
        memory->destroy(column);
        memory->create(column,nrows,"ave/time:column");
        allocate_arrays();
      }

      bigint ntimestep = update->ntimestep;
      int lockforever_flag = 0;
      for (i = 0; i < nvalues; i++) {
        if (!varlen[i]) continue;
        if (nrepeat > 1 && ave == ONE) {
          Compute *compute = modify->compute[value2index[i]];
          compute->lock(this,ntimestep,ntimestep+(nrepeat-1)*nevery);
        } else if ((ave == RUNNING || ave == WINDOW) && !lockforever) {
          Compute *compute = modify->compute[value2index[i]];
          compute->lock(this,update->ntimestep,-1);
          lockforever_flag = 1;
        }
      }
      if (lockforever_flag) lockforever = 1;
    }

    for (i = 0; i < nrows; i++)
      for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
  }

  // accumulate results of computes,fixes,variables to local copy
  // compute/fix/variable may invoke computes so wrap with clear/add

  modify->clearstep_compute();

  for (j = 0; j < nvalues; j++) {
    m = value2index[j];

    // invoke compute if not previously invoked

    if (which[j] == COMPUTE) {
      Compute *compute = modify->compute[m];

      if (argindex[j] == 0) {
        if (!(compute->invoked_flag & INVOKED_VECTOR)) {
          compute->compute_vector();
          compute->invoked_flag |= INVOKED_VECTOR;
        }
        double *cvector = compute->vector;
        for (i = 0; i < nrows; i++)
          column[i] = cvector[i];

      } else {
        if (!(compute->invoked_flag & INVOKED_ARRAY)) {
          compute->compute_array();
          compute->invoked_flag |= INVOKED_ARRAY;
        }
        double **carray = compute->array;
        int icol = argindex[j]-1;
        for (i = 0; i < nrows; i++)
          column[i] = carray[i][icol];
      }

    // access fix fields, guaranteed to be ready

    } else if (which[j] == FIX) {
      Fix *fix = modify->fix[m];
      if (argindex[j] == 0)
        for (i = 0; i < nrows; i++)
          column[i] = fix->compute_vector(i);
      else {
        int icol = argindex[j]-1;
        for (i = 0; i < nrows; i++)
          column[i] = fix->compute_array(i,icol);
      }
    }

    // add columns of values to array or just set directly if offcol is set
//.........这里部分代码省略.........

void FixAveHisto::end_of_step()
{
  int i,j,m;

  // skip if not step which requires doing something
  // error check if timestep was reset in an invalid manner

  bigint ntimestep = update->ntimestep;
  if (ntimestep < nvalid_last || ntimestep > nvalid) 
    error->all(FLERR,"Invalid timestep reset for fix ave/histo");
  if (ntimestep != nvalid) return;
  nvalid_last = nvalid;

  // zero if first step

  if (irepeat == 0) {
    stats[0] = stats[1] = 0.0;
    stats[2] = BIG;
    stats[3] = -BIG;
    for (i = 0; i < nbins; i++) bin[i] = 0.0;
  }

  // accumulate results of computes,fixes,variables to local copy
  // compute/fix/variable may invoke computes so wrap with clear/add

  modify->clearstep_compute();

  for (i = 0; i < nvalues; i++) {
    m = value2index[i];
    j = argindex[i];

    // atom attributes

    if (which[i] == X)
      bin_atoms(&atom->x[0][j],3);
    else if (which[i] == V)
      bin_atoms(&atom->v[0][j],3);
    else if (which[i] == F)
      bin_atoms(&atom->f[0][j],3);

    // invoke compute if not previously invoked

    if (which[i] == COMPUTE) {
      Compute *compute = modify->compute[m];

      if (kind == GLOBAL && mode == SCALAR) {
        if (j == 0) {
          if (!(compute->invoked_flag & INVOKED_SCALAR)) {
            compute->compute_scalar();
            compute->invoked_flag |= INVOKED_SCALAR;
          }
          bin_one(compute->scalar);
        } else {
          if (!(compute->invoked_flag & INVOKED_VECTOR)) {
            compute->compute_vector();
            compute->invoked_flag |= INVOKED_VECTOR;
          }
          bin_one(compute->vector[j-1]);
        }
      } else if (kind == GLOBAL && mode == VECTOR) {
        if (j == 0) {
          if (!(compute->invoked_flag & INVOKED_VECTOR)) {
            compute->compute_vector();
            compute->invoked_flag |= INVOKED_VECTOR;
          }
          bin_vector(compute->size_vector,compute->vector,1);
        } else {
          if (!(compute->invoked_flag & INVOKED_ARRAY)) {
            compute->compute_array();
            compute->invoked_flag |= INVOKED_ARRAY;
          }
          if (compute->array)
            bin_vector(compute->size_array_rows,&compute->array[0][j-1],
                       compute->size_array_cols);
        }

      } else if (kind == PERATOM) {
        if (!(compute->invoked_flag & INVOKED_PERATOM)) {
          compute->compute_peratom();
          compute->invoked_flag |= INVOKED_PERATOM;
        }
        if (j == 0)
          bin_atoms(compute->vector_atom,1);
        else if (compute->array_atom)
          bin_atoms(&compute->array_atom[0][j-1],compute->size_peratom_cols);

      } else if (kind == LOCAL) {
        if (!(compute->invoked_flag & INVOKED_LOCAL)) {
          compute->compute_local();
          compute->invoked_flag |= INVOKED_LOCAL;
        }
        if (j == 0)
          bin_vector(compute->size_local_rows,compute->vector_local,1);
        else if (compute->array_local)
          bin_vector(compute->size_local_rows,&compute->array_local[0][j-1],
                     compute->size_local_cols);
      }

      // access fix fields, guaranteed to be ready

//.........这里部分代码省略.........

int NeighborKokkos::init_lists_kokkos()
{
  int i;

  for (i = 0; i < nlist_host; i++) delete lists_host[i];
  delete [] lists_host;
  delete [] pair_build_host;
  delete [] stencil_create_host;
  nlist_host = 0;

  for (i = 0; i < nlist_device; i++) delete lists_device[i];
  delete [] lists_device;
  delete [] pair_build_device;
  delete [] stencil_create_device;
  nlist_device = 0;

  nlist = 0;
  for (i = 0; i < nrequest; i++) {
    if (requests[i]->kokkos_device) nlist_device++;
    else if (requests[i]->kokkos_host) nlist_host++;
    else nlist++;
  }

  lists_host = new NeighListKokkos<LMPHostType>*[nrequest];
  pair_build_host = new PairPtrHost[nrequest];
  stencil_create_host = new StencilPtrHost[nrequest];
  for (i = 0; i < nrequest; i++) {
    lists_host[i] = NULL;
    pair_build_host[i] = NULL;
    stencil_create_host[i] = NULL;
  }

  for (i = 0; i < nrequest; i++) {
    if (!requests[i]->kokkos_host) continue;
    lists_host[i] = new NeighListKokkos<LMPHostType>(lmp);
    lists_host[i]->index = i;
    lists_host[i]->dnum = requests[i]->dnum;
    if (requests[i]->pair) {
      Pair *pair = (Pair *) requests[i]->requestor;
      pair->init_list(requests[i]->id,lists_host[i]);
    }
    if (requests[i]->fix) {
      Fix *fix = (Fix *) requests[i]->requestor;
      fix->init_list(requests[i]->id,lists_host[i]);
    }
  }

  lists_device = new NeighListKokkos<LMPDeviceType>*[nrequest];
  pair_build_device = new PairPtrDevice[nrequest];
  stencil_create_device = new StencilPtrDevice[nrequest];
  for (i = 0; i < nrequest; i++) {
    lists_device[i] = NULL;
    pair_build_device[i] = NULL;
    stencil_create_device[i] = NULL;
  }

  for (i = 0; i < nrequest; i++) {
    if (!requests[i]->kokkos_device) continue;
    lists_device[i] = new NeighListKokkos<LMPDeviceType>(lmp);
    lists_device[i]->index = i;
    lists_device[i]->dnum = requests[i]->dnum;
    if (requests[i]->pair) {
      Pair *pair = (Pair *) requests[i]->requestor;
      pair->init_list(requests[i]->id,lists_device[i]);
    }
    if (requests[i]->fix) {
      Fix *fix = (Fix *) requests[i]->requestor;
      fix->init_list(requests[i]->id,lists_device[i]);
    }
  }

  // 1st time allocation of xhold

  if (dist_check)
      xhold = DAT::tdual_x_array("neigh:xhold",maxhold);

  // return # of non-Kokkos lists

  return nlist;
}