Implementation of Triply Periodic Minimal Surfaces (TPMS) in OpenMC

.gitignore

@@ -106,3 +106,6 @@ CMakeSettings.json
 
 # Python pickle files
 *.pkl
+
+# Validation
+validation

CMakeLists.txt

@@ -243,6 +243,12 @@ if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/vendor/pugixml/CMakeLists.txt")
     turned off or failed. Please update submodules and try again.")
 endif()
 
+#===============================================================================
+# boost library
+#===============================================================================
+
+find_package(Boost 1.85.0 REQUIRED)
+
 #===============================================================================
 # pugixml library
 #===============================================================================
@@ -430,6 +436,8 @@ list(APPEND libopenmc_SOURCES
   src/tallies/trigger.cpp
   src/thermal.cpp
   src/timer.cpp
+  src/tpms.cpp
+  src/tpms_functions.cpp
   src/track_output.cpp
   src/universe.cpp
   src/urr.cpp

README.md

@@ -1,3 +1,67 @@
+# TPMS branch specific (INL developers)
+
+<img src="https://media1.tenor.com/m/98dCgWDs4rsAAAAC/epic-sax-guy-sax.gif" width="100px" align="center">
+
+## Installation
+
+##### create a new conda env:
+```
+conda create -n openmc-TPMS moose-dev=2024.10.01=mpich
+conda deactivate
+conda activate openmc-TPMS
+# conda install boost=1.85.0 # not needed anymore
+```
+##### clone the project to your local repo:
+```
+git clone [email protected]:paul-ferney/openmc.git
+cd openmc
+git checkout TPMS
+```
+##### install openmc python API in dev mode:
+```
+python -m pip install -e .[test]
+```
+##### check that your compilers are from your conda env:
+```
+which $CC && which $CXX
+>>> /opt/anaconda3/envs/openmc-TPMS/bin/mpicc
+>>> /opt/anaconda3/envs/openmc-TPMS/bin/mpicxx
+```
+##### create a build directory and make your project:
+```
+mkdir ./build && cd ./build
+cmake .. && make -j 12
+cd ..
+```
+##### test openmc:
+```
+cd tests/regression_tests/TPMS/base_no_tpms
+python base_no_tpms.py
+../../../build/bin/openmc
+```
+
+## Trouble shooting
+### Shared libraries conflict
+When running cmake, you might get: 
+Warning Cannot generate a safe runtime search path for target libopenmc because files in some directories may conflict with libraries in implicit directories:
+```
+CMake Warning at CMakeLists.txt:463 (add_library):
+  Cannot generate a safe runtime search path for target libopenmc because
+  files in some directories may conflict with libraries in implicit
+  directories:
+
+    runtime library [libpng.dylib] in /opt/anaconda3/envs/openmc-TPMS/lib may be hidden by files in:
+      /opt/homebrew/lib
+    runtime library [libpugixml.1.dylib] in /opt/anaconda3/envs/openmc-TPMS/lib may be hidden by files in:
+      /opt/homebrew/lib
+
+  Some of these libraries may not be found correctly.
+```
+There is a conflict between your conda env shared libraries and shared libraries installed somewhere else. You want cmake to strictly use your conda libs. Run instead:
+```
+cmake .. -DCMAKE_PREFIX_PATH=/opt/anaconda3/envs/openmc-TPMS/ -DOPENMC_USE_MPI=ON -DCMAKE_FIND_USE_CMAKE_SYSTEM_PATH=FALSE -DCMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH=FALSE 
+```
+
 # OpenMC Monte Carlo Particle Transport Code
 
 [![License](https://img.shields.io/badge/license-MIT-green)](https://docs.openmc.org/en/latest/license.html)

include/openmc/bisect.h

@@ -0,0 +1,91 @@
+// taken fom boost1.85 - boost::math::tools::bisect
+//
+// Boost Software License - Version 1.0 - August 17th, 2003
+
+// Permission is hereby granted, free of charge, to any person or organization
+// obtaining a copy of the software and accompanying documentation covered by
+// this license (the "Software") to use, reproduce, display, distribute,
+// execute, and transmit the Software, and to prepare derivative works of the
+// Software, and to permit third-parties to whom the Software is furnished to
+// do so, all subject to the following:
+//
+// The copyright notices in the Software and this entire statement, including
+// the above license grant, this restriction and the following disclaimer,
+// must be included in all copies of the Software, in whole or in part, and
+// all derivative works of the Software, unless such copies or derivative
+// works are solely in the form of machine-executable object code generated by
+// a source language processor.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+// SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+// FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+// ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+// DEALINGS IN THE SOFTWARE.
+
+#ifndef OPENMC_BISECT_H
+#define OPENMC_BISECT_H
+
+#include <iostream>
+
+template<class F, class Tol>
+std::pair<double, double> bisect(
+  F f, double min, double max, Tol tol, std::uintmax_t& max_iter)
+{
+  double fmin = f(min);
+  double fmax = f(max);
+  if (fmin == 0) {
+    max_iter = 2;
+    return std::make_pair(min, min);
+  }
+  if (fmax == 0) {
+    max_iter = 2;
+    return std::make_pair(max, max);
+  }
+
+  //
+  // Error checking:
+  //
+  if (min >= max) {
+    throw std::invalid_argument("Arguments min and max in wrong order");
+  }
+  if (fmin * fmax >= 0) {
+    throw std::invalid_argument(
+      "No change of sign, either there is no root to find, or there are "
+      "multiple roots in the interval");
+  }
+
+  //
+  // Three function invocations so far:
+  //
+  std::uintmax_t count = max_iter;
+  if (count < 3) {
+    count = 0;
+  } else {
+    count -= 3;
+  }
+
+  while (count && (0 == tol(min, max))) {
+    double mid = (min + max) / 2;
+    double fmid = f(mid);
+    if ((mid == max) || (mid == min))
+      break;
+    if (fmid == 0) {
+      min = max = mid;
+      break;
+    } else if (std::signbit(fmid) != std::signbit(fmin)) {
+      max = mid;
+    } else {
+      min = mid;
+      fmin = fmid;
+    }
+    --count;
+  }
+
+  max_iter -= count;
+
+  return std::make_pair(min, max);
+}
+
+#endif

include/openmc/cell.h

@@ -99,6 +99,7 @@ class Region {
 
   //! Get Boolean of if the cell is simple or not
   bool is_simple() const { return simple_; }
+  int32_t cell_id() const { return cell_id_; }
 
 private:
   //----------------------------------------------------------------------------
@@ -144,6 +145,7 @@ class Region {
   // TODO: Should this be a vector of some other type
   vector<int32_t> expression_;
   bool simple_; //!< Does the region contain only intersections?
+  int32_t cell_id_;
 };
 
 //==============================================================================

include/openmc/surface.h

@@ -2,6 +2,7 @@
 #define OPENMC_SURFACE_H
 
 #include <limits> // For numeric_limits
+#include <list>
 #include <string>
 #include <unordered_map>
 
@@ -16,6 +17,9 @@
 #include "openmc/position.h"
 #include "openmc/vector.h"
 
+#include "tpms.h"
+#include "tpms_functions.h"
+
 namespace openmc {
 
 //==============================================================================
@@ -52,6 +56,7 @@ class Surface {
   //! \return true if the point is on the "positive" side of the surface and
   //!   false otherwise.
   bool sense(Position r, Direction u) const;
+  virtual bool is_tpms() const { return false; };
 
   //! Determine the direction of a ray reflected from the surface.
   //! \param[in] r The point at which the ray is incident.
@@ -76,7 +81,15 @@ class Surface {
   //! \param u The direction of the ray.
   //! \param coincident A hint to the code that the given point should lie
   //!   exactly on the surface.
-  virtual double distance(Position r, Direction u, bool coincident) const = 0;
+  virtual double distance(Position r, Direction u, bool coincident) const
+  {
+    return 0.;
+  };
+  virtual double distance(
+    Position r, Direction u, bool coincident, double max_range) const
+  {
+    return 0.;
+  };
 
   //! Compute the local outward normal direction of the surface.
   //! \param r A 3D Cartesian coordinate.
@@ -327,6 +340,55 @@ class SurfaceQuadric : public CSGSurface {
   double A_, B_, C_, D_, E_, F_, G_, H_, J_, K_;
 };
 
+//==============================================================================
+// TPMS surfaces
+//==============================================================================
+
+class SurfaceTPMS : public CSGSurface {
+public:
+  explicit SurfaceTPMS(pugi::xml_node surf_node);
+  bool is_tpms() const { return true; };
+  double evaluate(Position r) const;
+  double distance(
+    Position r, Direction u, bool coincident, double max_range) const;
+  Direction normal(Position r) const;
+  void to_hdf5_inner(hid_t group_id) const;
+
+  double isovalue, pitch;
+  double x0, y0, z0;
+  double a, b, c, d, e, f, g, h, i;
+  std::string surface_type;
+
+private:
+  std::list<std::string> tpms_types = {"Schwarz_P", "Gyroid", "Diamond"};
+};
+
+//==============================================================================
+// Interpolated TPMS surfaces
+//==============================================================================
+
+class SurfaceFunctionTPMS : public CSGSurface {
+public:
+  explicit SurfaceFunctionTPMS(pugi::xml_node surf_node);
+  ~SurfaceFunctionTPMS();
+  bool is_tpms() const { return true; };
+  double evaluate(Position r) const;
+  double distance(
+    Position r, Direction u, bool coincident, double max_range) const;
+  Direction normal(Position r) const;
+  void to_hdf5_inner(hid_t group_id) const;
+
+  FunctionForTPMS* fPitch;
+  FunctionForTPMS* fIsovalue;
+  double x0, y0, z0;
+  double a, b, c, d, e, f, g, h, i;
+  std::string surface_type;
+  std::string function_type;
+
+private:
+  std::list<std::string> tpms_types = {"Schwarz_P", "Gyroid", "Diamond"};
+};
+
 //==============================================================================
 //! A toroidal surface described by the quartic torus lies in the x direction
 //