Merge pull request #1 from boutproject/v1.1

STORM v1.1

.gitignore

@@ -59,7 +59,8 @@ BOUT.settings
 *.bmp
 *.pdf
 
-*filaments
+storm3d/storm
+*/make.config
 data_*
 *.txt
 storm2d/storm2d

README.md

@@ -61,3 +61,7 @@ https://doi.org/10.1088/0741-3335/58/11/115010
 
 [4] F. Militello, B. Dudson, L. Easy, A. Kirk and P. Naylor, Plasma Physics and
 Controlled Fusion 59, 125013 (2017), https://doi.org/10.1088/1361-6587/aa9252
+
+[5] D. Hoare, F. Militello, J.T. Omotani, F. Riva, S. Newton, T. Nicholas, D.
+Ryan and N.R. Walkden, Plasma Physics and Controlled Fusion 61, 105013 (2019),
+https://doi.org/10.1088/1361-6587/ab34f8

shared/fast_output.cxx

@@ -0,0 +1,121 @@
+/*
+  Copyright L. Easy, F. Militello, T. Nicholas, J. Omotani, F. Riva, N.
+  Walkden, UKAEA, 2017, 2018
+  email: [email protected]
+
+  This file is part of the STORM module of BOUT++.
+
+  STORM 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.
+
+  STORM 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 STORM.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
+#include <boutcomm.hxx>
+#include "fast_output.hxx"
+#include <../src/fileio/formatfactory.hxx>
+#include <bout/solver.hxx>
+#include <string>
+
+FastOutput::FastOutput() {
+  // Get options
+  Options* global_options = Options::getRoot();
+  Options* options = global_options->getSection("fast_output");
+  std::string type;
+  OPTION(options, type, "none");
+  if (type=="monitor") {
+    enable_monitor = true;
+    // Calculate output frequency
+    BoutReal output_timestep;
+    global_options->get("timestep", output_timestep, 1.);
+    int frequency_multiplier;
+    OPTION(options, frequency_multiplier, 100); // multiple of the output frequency to call fast_output at
+    setTimestep(output_timestep / double(frequency_multiplier));
+  } else if (type == "timestep") {
+    enable_timestep = true;
+    // Check that solver:monitor_timestep is true, otherwise type=timestep does nothing
+    bool monitor_timestep;
+    OPTION(global_options, monitor_timestep, false);
+    if (!monitor_timestep) {
+      throw BoutException("fast_output:type=timestep but solver:monitor_timestep=false, so FastOutput would do nothing. You probably want to set solver:monitor_timestep=true.");
+    }
+  } else if (type == "none") {
+    // don't enable anything
+  } else {
+    throw BoutException("Unrecognized option for FastOutput: type=%s", type.c_str());
+  }
+  if (enable_monitor || enable_timestep) {
+    enabled = true;
+    // Read more options
+    std::string prefix;
+    OPTION(options, prefix, "BOUT.fast");
+    std::string dump_ext;
+    OPTION(options, dump_ext, "nc");
+    std::string datadir;
+    OPTION(global_options, datadir, "data");
+    bool append;
+    OPTION(global_options, append, false);
+
+    std::string filename = "%s/" + prefix + ".%s";
+
+    // Initialize output_file
+    output_file = Datafile(options);
+    if (append) {
+      output_file.opena(filename.c_str(), datadir.c_str(), dump_ext.c_str());
+    } else {
+      output_file.openw(filename.c_str(), datadir.c_str(), dump_ext.c_str());
+    }
+
+    // Add the time to the output
+    int MYPE;
+    MPI_Comm_rank(BoutComm::get(), &MYPE);
+    if (MYPE == 0)
+      output_file.add(current_time, "time", true);
+  }
+}
+
+void FastOutput::add(const std::string name, Field3D &f, const int ix_global, const int iy_global, const int iz_global) {
+  int ix = ix_global - mesh->OffsetX;
+  int iy = iy_global - mesh->OffsetY;
+  int iz = iz_global - mesh->OffsetZ;
+
+  if (ix>=mesh->xstart && ix<=mesh->xend && iy>=mesh->ystart && iy<=mesh->yend && iz>=0 && iz<mesh->LocalNz) {
+    // Store a reference to the field
+    field3d_list.push_back(&f);
+
+    // Store the indices of the element to output
+    field3d_inds.push_back({ix, iy, iz});
+
+    // Extend output_vals
+    output_vals.push_back(0.);
+
+    // Add to the output_file
+    output_file.add(output_vals.back(), name.c_str(), true);
+    // Store the indices as attributes of the variable
+    output_file.setAttribute(name, "ix", ix_global);
+    output_file.setAttribute(name, "iy", iy_global);
+    output_file.setAttribute(name, "iz", iz_global);
+  }
+}
+
+int FastOutput::monitor_method(BoutReal simtime) {
+  // Set time
+  current_time = simtime;
+
+  // Set values to output
+  for (size_t i=0; i<output_vals.size(); i++) {
+    output_vals[i] = field3d_list[i]->operator[](field3d_inds[i]);
+  }
+
+  output_file.write();
+
+  return 0;
+}

shared/fast_output.hxx

@@ -0,0 +1,61 @@
+/*
+  Copyright L. Easy, F. Militello, T. Nicholas, J. Omotani, F. Riva, N.
+  Walkden, UKAEA, 2017, 2018
+  email: [email protected]
+
+  This file is part of the STORM module of BOUT++.
+
+  STORM 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.
+
+  STORM 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 STORM.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
+#ifndef __FAST_OUTPUT_H__
+#define __FAST_OUTPUT_H__
+
+#include <bout/monitor.hxx>
+#include <bout/physicsmodel.hxx>
+#include <bout/region.hxx>
+#include <datafile.hxx>
+#include <globals.hxx>
+#include <deque>
+class Solver;
+
+// Subclass of BOUT++ Monitor class so we can pass to Solver::
+class FastOutput : public Monitor {
+  public:
+    FastOutput();
+    FastOutput(FastOutput &f) = delete;
+    FastOutput &operator=(FastOutput &f) = delete;
+
+    /// Add a point to the output: the element of f with global indices
+    /// {ix,iy,iz} will be written when monitor_method() is called
+    void add(const std::string name, Field3D &f, const int ix, const int iy, const int iz);
+
+    /// Writes added points to output_file
+    int monitor_method(BoutReal simtime);
+
+    bool enabled=false, enable_monitor=false, enable_timestep=false;
+
+    /// provide Monitor::call method which is called by the Solver
+    int call(Solver* UNUSED(solver), BoutReal time, int UNUSED(iter), int UNUSED(nout)) {
+      return monitor_method(time);
+    }
+  private:
+    Datafile output_file;
+    std::deque<Field3D*> field3d_list;
+    std::deque<Ind3D> field3d_inds;
+    BoutReal current_time;
+    std::deque<BoutReal> output_vals;
+};
+
+#endif //__FAST_OUTPUT_H__