C++ Fix::compute_array方法代码示例

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;
      }
    }
  }
}

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 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.........

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 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 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.........