Array3D.cc

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// Copyright (C) 2008--2018, 2020, 2021, 2022, 2023 Ed Bueler and Constantine Khroulev
//
// This file is part of PISM.
//
// PISM is free software; you can redistribute it and/or modify it under the
// terms of the GNU General Public License as published by the Free Software
// Foundation; either version 3 of the License, or (at your option) any later
// version.
//
// PISM is distributed in the hope that it will be useful, but WITHOUT ANY
// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
// details.
//
// You should have received a copy of the GNU General Public License
// along with PISM; if not, write to the Free Software
// Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 
#include <cstring>
#include <cstdlib>
#include <cassert>
#include <memory>
#include <petscvec.h>
 
#include "pism/util/array/Array3D.hh"
 
#include "pism/util/ConfigInterface.hh"
#include "pism/util/Context.hh"
#include "pism/util/Grid.hh"
#include "pism/util/VariableMetadata.hh"
#include "pism/util/array/Array_impl.hh"
#include "pism/util/array/Scalar.hh"
#include "pism/util/error_handling.hh"
#include "pism/util/io/IO_Flags.hh"
#include "pism/util/io/io_helpers.hh"
 
namespace pism {
namespace array {
 
// this file contains method for derived class array::Array3D
 
Array3D::Array3D(std::shared_ptr<const Grid> grid, const std::string &name, Kind ghostedp,
                 const std::vector<double> &levels, unsigned int stencil_width)
    : Array(grid, name, ghostedp, 1, stencil_width, levels) {
  set_begin_access_use_dof(true);
}
 
//! Set all values of scalar quantity to given a single value in a particular column.
void Array3D::set_column(int i, int j, double c) {
  PetscErrorCode ierr;
#if (Pism_DEBUG == 1)
  assert(m_array != NULL);
  check_array_indices(i, j, 0);
#endif
 
  double ***arr = (double ***)m_array;
 
  if (c == 0.0) {
    ierr = PetscMemzero(arr[j][i], levels().size() * sizeof(double));
    PISM_CHK(ierr, "PetscMemzero");
  } else {
    unsigned int nlevels = levels().size();
    for (unsigned int k = 0; k < nlevels; k++) {
      arr[j][i][k] = c;
    }
  }
}
 
void Array3D::set_column(int i, int j, const double *input) {
#if (Pism_DEBUG == 1)
  check_array_indices(i, j, 0);
#endif
  double ***arr       = (double ***)m_array;
  PetscErrorCode ierr = PetscMemcpy(arr[j][i], input, m_impl->zlevels.size() * sizeof(double));
  PISM_CHK(ierr, "PetscMemcpy");
}
 
#if (Pism_DEBUG == 1)
static bool legal_level(const std::vector<double> &levels, double z) {
  double z_min     = levels.front();
  double z_max     = levels.back();
  const double eps = 1.0e-6;
  return not(z < z_min - eps || z > z_max + eps);
}
#endif
 
//! Return value of scalar quantity at level z (m) above base of ice (by linear interpolation).
double Array3D::interpolate(int i, int j, double z) const {
  const auto &zs = levels();
  auto N         = zs.size();
 
#if (Pism_DEBUG == 1)
  assert(m_array != NULL);
  check_array_indices(i, j, 0);
 
  if (not legal_level(zs, z)) {
    throw RuntimeError::formatted(PISM_ERROR_LOCATION,
                                  "Array3D interpolate(): level %f is not legal; name = %s", z,
                                  m_impl->name.c_str());
  }
#endif
 
  const auto *column = get_column(i, j);
 
  if (z >= zs[N - 1]) {
    return column[N - 1];
  }
 
  if (z <= zs[0]) {
    return column[0];
  }
 
  auto mcurr = gsl_interp_accel_find(m_impl->bsearch_accel, zs.data(), N, z);
 
  const double incr = (z - zs[mcurr]) / (zs[mcurr + 1] - zs[mcurr]);
  const double valm = column[mcurr];
  return valm + incr * (column[mcurr + 1] - valm);
}
 
double *Array3D::get_column(int i, int j) {
#if (Pism_DEBUG == 1)
  check_array_indices(i, j, 0);
#endif
  return ((double ***)m_array)[j][i];
}
 
const double *Array3D::get_column(int i, int j) const {
#if (Pism_DEBUG == 1)
  check_array_indices(i, j, 0);
#endif
  return ((double ***)m_array)[j][i];
}
 
//! Copies a horizontal slice at level z of an Array3D into `output`.
void extract_surface(const Array3D &data, double z, Scalar &output) {
  array::AccessScope list{ &data, &output };
 
  ParallelSection loop(output.grid()->com);
  try {
    for (auto p = output.grid()->points(); p; p.next()) {
      const int i = p.i(), j = p.j();
      output(i, j) = data.interpolate(i, j, z);
    }
  } catch (...) {
    loop.failed();
  }
  loop.check();
}
 
 
//! Copies the values of an Array3D at the ice surface (specified by the level `z`) into
//! `output`.
void extract_surface(const Array3D &data, const Scalar &z, Scalar &output) {
  array::AccessScope list{ &data, &output, &z };
 
  ParallelSection loop(output.grid()->com);
  try {
    for (auto p = output.grid()->points(); p; p.next()) {
      const int i = p.i(), j = p.j();
      output(i, j) = data.interpolate(i, j, z(i, j));
    }
  } catch (...) {
    loop.failed();
  }
  loop.check();
}
 
/** Sum a 3-D vector in the Z direction to create a 2-D vector.
 
Note that this sums up all the values in a column, including ones
above the ice. This may or may not be what you need. Also, take a look
at IceModel::compute_ice_enthalpy(PetscScalar &result) in iMreport.cc.
 
As for the difference between array::Array2D and array::Scalar, the
former can store fields with more than 1 "degree of freedom" per grid
point (such as 2D fields on the "staggered" grid, with the first
degree of freedom corresponding to the i-offset and second to
j-offset).
 
array::Scalar is just array::Array2D with "dof == 1", and
array::Vector is array::Array2D with "dof == 2". (Plus some extra
methods, of course.)
 
Either one of array::Array2D and array::Scalar would work in this
case.
 
Computes output = A*output + B*sum_columns(input) + C
 
@see https://github.com/pism/pism/issues/229 */
void sum_columns(const Array3D &data, double A, double B, Scalar &output) {
  const unsigned int Mz = data.grid()->Mz();
 
  AccessScope access{ &data, &output };
 
  for (auto p = data.grid()->points(); p; p.next()) {
    const int i = p.i(), j = p.j();
 
    const double *column = data.get_column(i, j);
 
    double scalar_sum = 0.0;
    for (unsigned int k = 0; k < Mz; ++k) {
      scalar_sum += column[k];
    }
    output(i, j) = A * output(i, j) + B * scalar_sum;
  }
}
 
void Array3D::copy_from(const Array3D &input) {
  array::AccessScope list{ this, &input };
 
  assert(levels().size() == input.levels().size());
  assert(ndof() == input.ndof());
 
  // 3D arrays have more than one level and ndof() of 1, collections of fields have one
  // level and ndof() > 1
  auto N = std::max((size_t)ndof(), levels().size());
 
  ParallelSection loop(m_impl->grid->com);
  try {
    for (auto p = m_impl->grid->points(); p; p.next()) {
      const int i = p.i(), j = p.j();
 
#if PETSC_VERSION_LT(3, 12, 0)
      PetscMemmove(this->get_column(i, j), const_cast<double *>(input.get_column(i, j)),
                   N * sizeof(double));
#else
      PetscArraymove(this->get_column(i, j), input.get_column(i, j), N);
#endif
    }
  } catch (...) {
    loop.failed();
  }
  loop.check();
 
  update_ghosts();
 
  inc_state_counter();
}
 
std::shared_ptr<Array3D> Array3D::duplicate(Kind ghostedp) const {
 
  auto result =
      std::make_shared<Array3D>(this->grid(), this->get_name(), ghostedp, this->levels());
 
  result->metadata() = this->metadata();
 
  return result;
}
 
void Array3D::regrid_impl(const File &file, io::Default default_value) {
 
  auto log = grid()->ctx()->log();
 
  auto variable = metadata(0);
 
  auto V = file.find_variable(variable.get_name(), variable["standard_name"]);
 
  petsc::TemporaryGlobalVec tmp(dm());
 
  if (not V.exists) {
    set_default_value_or_stop(file.filename(), variable, default_value, *log, tmp);
  } else {
    grid::InputGridInfo input_grid(file, V.name, variable.unit_system(), grid()->registration());
 
    input_grid.report(*log, 4, variable.unit_system());
 
    io::check_input_grid(input_grid, *grid(), levels());
 
    LocalInterpCtx lic(input_grid, *grid(), levels(), m_impl->interpolation_type);
 
    // Note: this call will read the last time record (the index is set in `lic` based on
    // info in `input_grid`).
    petsc::VecArray tmp_array(tmp);
    io::regrid_spatial_variable(variable, *grid(), lic, file, tmp_array.get());
  }
 
  if (m_impl->ghosted) {
    global_to_local(*dm(), tmp, vec());
  } else {
    PetscErrorCode ierr = VecCopy(tmp, vec());
    PISM_CHK(ierr, "VecCopy");
  }
}
 
} // end of namespace array
} // end of namespace pism