apps/benchmarks/CNT/CMakeLists.txt

+waLBerla_link_files_to_builddir( *.dat )
+
+waLBerla_add_executable( NAME 01_cnt_film
+   FILES 01_cnt_film.cpp
+        Config.cpp
+        FilmSpecimen.cpp
+        InitializeCNTs.cpp
+        SQLProperties.cpp
+        Statistics.cpp
+      DEPENDS walberla::blockforest walberla::core walberla::mesa_pd walberla::sqlite walberla::vtk )

apps/benchmarks/CNT/Config.cpp

+//======================================================================================================================
+//
+//  This file is part of waLBerla. waLBerla 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.
+//
+//  waLBerla 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 waLBerla (see COPYING.txt). If not, see <http://www.gnu.org/licenses/>.
+//
+//! \file
+//! \author Igor Ostanin <i.ostanin@skoltech.ru>
+//! \author Grigorii Drozdov <drozd013@umn.edu>
+//! \author Sebastian Eibl <sebastian.eibl@fau.de>
+//
+//======================================================================================================================
+
+#include "Config.h"
+#include "TerminalColors.h"
+
+#include "core/mpi/Gatherv.h"
+#include "core/mpi/MPIIO.h"
+#include "core/mpi/RecvBuffer.h"
+#include "core/mpi/SendBuffer.h"
+
+namespace walberla {
+namespace mesa_pd {
+
+void saveConfig(const shared_ptr<data::ParticleStorage>& ps,
+                const std::string& filename,
+                const IO_MODE io_mode)
+{
+   mpi::SendBuffer sb;
+
+   for (const auto& p : *ps)
+   {
+      using namespace walberla::mesa_pd::data::particle_flags;
+      if (isSet(p.getFlags(), GHOST)) continue; //skip ghosts
+
+      sb << static_cast<int64_t> (p.getSegmentID());
+      sb << static_cast<int64_t> (p.getClusterID());
+//      sb << static_cast<int64_t> (p.getGroupID());
+
+      sb << static_cast<double> (p.getPosition()[0]);
+      sb << static_cast<double> (p.getPosition()[1]);
+      sb << static_cast<double> (p.getPosition()[2]);
+
+      Vec3 orient = p.getRotation().getMatrix() * Vec3(1,0,0);
+      // Now orient has the shape (sin(th)cos(ph), sin(th)sin(ph), cos(th))
+      sb << static_cast<double> (std::acos(orient[2]));
+      sb << static_cast<double> (std::atan2(orient[1], orient[0]));
+
+      sb << static_cast<double> (p.getLinearVelocity()[0]);
+      sb << static_cast<double> (p.getLinearVelocity()[1]);
+      sb << static_cast<double> (p.getLinearVelocity()[2]);
+
+      sb << static_cast<double> (p.getAngularVelocity()[0]);
+      sb << static_cast<double> (p.getAngularVelocity()[1]);
+      sb << static_cast<double> (p.getAngularVelocity()[2]);
+   }
+
+   switch (io_mode)
+   {
+      case IO_MODE::REDUCE_TO_ROOT:
+      {
+         WALBERLA_LOG_INFO_ON_ROOT(CYAN << "Saving configuration (reduce to root): " << filename << RESET);
+         walberla::mpi::RecvBuffer rb;
+         walberla::mpi::gathervBuffer(sb, rb);
+         WALBERLA_ROOT_SECTION()
+         {
+            uint_t dataSize = sizeof(mpi::RecvBuffer::ElementType) * rb.size();
+            std::ofstream binfile;
+            binfile.open(filename + ".sav",
+                         std::ios::out | std::ios::binary);
+            binfile.write(reinterpret_cast< const char * >(rb.ptr()), numeric_cast<std::streamsize>(dataSize));
+            binfile.close();
+         }
+         break;
+      }
+      case IO_MODE::USE_MPI_IO:
+      {
+         WALBERLA_LOG_INFO_ON_ROOT(CYAN << "Saving configuration (MPIIO): " << filename << RESET);
+         walberla::mpi::writeMPIIO(filename + ".mpiio", sb);
+         break;
+      }
+      case IO_MODE::ONE_FILE_PER_RANK:
+      {
+         WALBERLA_LOG_INFO_ON_ROOT(CYAN << "Saving configuration (one file per process): " << filename << RESET);
+         uint_t dataSize = sizeof(mpi::SendBuffer::ElementType) * sb.size();
+         std::ofstream binfile;
+         binfile.open(filename + "_" + std::to_string(mpi::MPIManager::instance()->rank()) + ".sav",
+                      std::ios::out | std::ios::binary);
+         binfile.write(reinterpret_cast< const char * >(sb.ptr()), numeric_cast<std::streamsize>(dataSize));
+         binfile.close();
+      }
+         break;
+      default:
+      WALBERLA_ABORT("Unknown IO_MODE");
+   }
+}
+
+} //namespace mesa_pd
+} //namespace walberla

src/mesa_pd/data/shape/ShapeTypes.cpp → apps/benchmarks/CNT/Config.h

@@ -13,27 +13,25 @@
 //  You should have received a copy of the GNU General Public License along
 //  with waLBerla (see COPYING.txt). If not, see <http://www.gnu.org/licenses/>.
 //
-//! \file ShapeTypes.cpp
+//! \file
+//! \author Igor Ostanin <i.ostanin@skoltech.ru>
+//! \author Grigorii Drozdov <drozd013@umn.edu>
 //! \author Sebastian Eibl <sebastian.eibl@fau.de>
 //
 //======================================================================================================================
 
-#include <mesa_pd/data/shape/Box.h>
-#include <mesa_pd/data/shape/CylindricalBoundary.h>
-#include <mesa_pd/data/shape/HalfSpace.h>
-#include <mesa_pd/data/shape/Ellipsoid.h>
-#include <mesa_pd/data/shape/Sphere.h>
+#pragma once
+
+#include "mesa_pd/data/ParticleStorage.h"
 
 namespace walberla {
 namespace mesa_pd {
-namespace data {
 
-const int Box::SHAPE_TYPE                ;
-const int CylindricalBoundary::SHAPE_TYPE;
-const int HalfSpace::SHAPE_TYPE          ;
-const int Ellipsoid::SHAPE_TYPE          ;
-const int Sphere::SHAPE_TYPE             ;
+enum class IO_MODE {REDUCE_TO_ROOT, USE_MPI_IO, ONE_FILE_PER_RANK};
+
+void saveConfig(const shared_ptr<data::ParticleStorage>& ps,
+                const std::string& filename,
+                const IO_MODE io_mode);
 
-} //namespace data
 } //namespace mesa_pd
-} //namespace walberla
+} //namespace walberla
\ No newline at end of file

apps/benchmarks/CNT/FilmSpecimen.h

+//======================================================================================================================
+//
+//  This file is part of waLBerla. waLBerla 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.
+//
+//  waLBerla 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 waLBerla (see COPYING.txt). If not, see <http://www.gnu.org/licenses/>.
+//
+//! \file
+//! \author Igor Ostanin <i.ostanin@skoltech.ru>
+//! \author Grigorii Drozdov <drozd013@umn.edu>
+//! \author Sebastian Eibl <sebastian.eibl@fau.de>
+//
+//======================================================================================================================
+
+//======================================================================================================================
+//
+//  THIS FILE IS GENERATED - PLEASE CHANGE THE TEMPLATE !!!
+//
+//======================================================================================================================
+
+#pragma once
+
+#include "core/config/Config.h"
+
+#include <string>
+
+namespace walberla {
+namespace mesa_pd {
+
+struct FilmSpecimen
+{
+   real_t sizeX = 0; //Specimen length (x direction)
+   real_t sizeY = 0; //Specimen length (y direction)
+   real_t sizeZ = 0; //Specimen length (z direction)
+   bool oopp = false; //Specimen out-of-plane periodicity (0 - film, 1 - cnt material)
+   uint_t numBlocksX = 1; //Number of blocks in x direction
+   uint_t numBlocksY = 1; //Number of blocks in y direction
+   uint_t numBlocksZ = 1; //Number of blocks in z direction
+   real_t min_OOP = 0; //Out-of-plane angle minimum
+   real_t max_OOP = 0; //Out-of-plane angle maximum
+   int numCNTs = 0; //Number of CNTs
+   int numSegs = 0; //Number of segments in a CNT
+   real_t spacing = 0; //Segment half-spacing
+   real_t localDamping = 0; //Local damping coefficient
+   real_t viscousDamping = 0; //Viscous damping coefficient
+   uint_t seed = 0; //random generator seed
+   int vdW = 0; //type of vdW interaction model
+   int simulationSteps = 0; //Relaxation duration
+   int saveVTKEveryNthStep = 0; //timesteps between saving VTK outputs
+   int saveEnergyEveryNthStep = 0; //timesteps between saving energies
+   int saveConfEveryNthStep = 0; //timesteps between saving confs
+   std::string vtkFolder = "."; //Folder for VTK files
+   std::string energyFolder = "."; //Folder for energy files
+   std::string confFolder = "."; //Folder for conf files
+   bool useMPIIO = false; //Write a single file instead of one file per process
+   std::string sqlFile = "cnt.sqlite"; //database file
+   std::string initialConfigurationFile = ""; //restart from checkpoint
+};
+
+void loadFromConfig(FilmSpecimen& params,
+                    const Config::BlockHandle& cfg);
+
+} //namespace mesa_pd
+} //namespace walberla
\ No newline at end of file

apps/benchmarks/CNT/GenerateFilmSpecimen.py

+#! /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from FilmSpecimenGenerator import Config
+
+cfg = Config()
+cfg.add_parameter("sizeX",                    "real_t",     "0",     "Specimen length (x direction)")
+cfg.add_parameter("sizeY",                    "real_t",     "0",     "Specimen length (y direction)")
+cfg.add_parameter("sizeZ",                    "real_t",     "0",     "Specimen length (z direction)")
+cfg.add_parameter("oopp",                     "bool",       "false", "Specimen out-of-plane periodicity (0 - film, 1 - cnt material)")
+cfg.add_parameter("numBlocksX",               "uint_t",     "1",     "Number of blocks in x direction")
+cfg.add_parameter("numBlocksY",               "uint_t",     "1",     "Number of blocks in y direction")
+cfg.add_parameter("numBlocksZ",               "uint_t",     "1",     "Number of blocks in z direction")
+cfg.add_parameter("min_OOP",                  "real_t",     "0",     "Out-of-plane angle minimum")
+cfg.add_parameter("max_OOP",                  "real_t",     "0",     "Out-of-plane angle maximum")
+cfg.add_parameter("numCNTs",                  "int",        "0",     "Number of CNTs")
+cfg.add_parameter("numSegs",                  "int",        "0",     "Number of segments in a CNT")
+cfg.add_parameter("spacing",                  "real_t",     "0",     "Segment half-spacing")
+cfg.add_parameter("localDamping",             "real_t",     "0",     "Local damping coefficient")
+cfg.add_parameter("viscousDamping",           "real_t",     "0",     "Viscous damping coefficient")
+cfg.add_parameter("seed",                     "uint_t",     "0",     "random generator seed")
+cfg.add_parameter("vdW",                      "int",        "0",     "type of vdW interaction model")
+cfg.add_parameter("simulationSteps",          "int",        "0",     "Relaxation duration")
+cfg.add_parameter("saveVTKEveryNthStep",      "int",        "0",     "timesteps between saving VTK outputs")
+cfg.add_parameter("saveEnergyEveryNthStep",   "int",        "0",     "timesteps between saving energies")
+cfg.add_parameter("saveConfEveryNthStep",     "int",        "0",     "timesteps between saving confs")
+cfg.add_parameter("vtkFolder",                "std::string", '"."',   "Folder for VTK files")
+cfg.add_parameter("energyFolder",             "std::string", '"."',   "Folder for energy files")
+cfg.add_parameter("confFolder",               "std::string", '"."',   "Folder for conf files")
+cfg.add_parameter("useMPIIO",                 "bool",       "false", "Write a single file instead of one file per process")
+cfg.add_parameter("sqlFile",                  "std::string", '"cnt.sqlite"',   "database file")
+cfg.add_parameter("initialConfigurationFile", "std::string", '""',   "restart from checkpoint")
+
+cfg.generate()
+
+