Release 3.0.0

qcscine · Aug 26, 2024 · 24d8b83 · 24d8b83
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diff --git a/.conan_test_package/conanfile.py b/.conan_test_package/conanfile.py
@@ -1,6 +1,6 @@
 __copyright__ = """This file is part of SCINE Kinetx.
 This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,12 @@
 Changelog
 =========
 
+Release 3.0.0
+-------------
+
+- Update address in license
+- Interface Sundials and add CVODE-BDF integrator
+
 Release 2.0.0
 -------------
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.9)
 # tree must then provide a properly namespaced target with the same name as
 # your project.
 project(Kinetx
-  VERSION 2.0.0
+  VERSION 3.0.0
   DESCRIPTION "Kinetic models for reaction networks."
 )
 

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:

diff --git a/README.rst b/README.rst
@@ -42,7 +42,14 @@ release as archived on Zenodo (please use the DOI of the respective release).
 In addition, we kindly request you to cite the following articles when using KiNetX:
 
 - \J. Proppe, M. Reiher, "Mechanism Deduction from Noisy Chemical Reaction Networks", *J. Chem. Theory Comput.*, **2019**, *15*, 357.
-- \M. Bensberg, M. Reiher, "Concentration-Flux-Steered Mechanism Exploration with an Organocatalysis Application", *arXiv:2212.14135 [physics.chem-ph]*, **2022**.
+- \M. Bensberg, M. Reiher, "Concentration-Flux-Steered Mechanism Exploration with an Organocatalysis Application", *Isr. J. Chem.*, **2022**, *63*, e202200123.
+
+Furthermore, when publishing results obtained with any SCINE module, please cite the following paper:
+
+T. Weymuth, J. P. Unsleber, P. L. Türtscher, M. Steiner, J.-G. Sobez, C. H. Müller, M. Mörchen,
+V. Klasovita, S. A. Grimmel, M. Eckhoff, K.-S. Csizi, F. Bosia, M. Bensberg, M. Reiher,
+"SCINE—Software for chemical interaction networks", *J. Chem. Phys.*, **2024**, *160*, 222501
+(DOI `10.1063/5.0206974 <https://doi.org/10.1063/5.0206974>`_).
 
 Support and Contact
 -------------------

diff --git a/conanfile.py b/conanfile.py
@@ -1,6 +1,6 @@
 __copyright__ = """This file is part of SCINE Kinetx.
 This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 
@@ -9,7 +9,7 @@
 
 class ScineKinetxConan(ScineConan):
     name = "scine_kinetx"
-    version = "2.0.0"
+    version = "3.0.0"
     url = "https://github.com/qcscine/kinetx"
     description = """ """
     options = {
@@ -29,7 +29,7 @@ class ScineKinetxConan(ScineConan):
     requires = ["eigen/[~=3.3.7]"]
     cmake_name = "Kinetx"
     cmake_definitions = {
-        "CMAKE_UNITY_BUILD": "ON",
+        "CMAKE_UNITY_BUILD": "OFF",
         "CMAKE_UNITY_BUILD_BATCH_SIZE": 16
     }
 

diff --git a/dev b/dev
diff --git a/src/Kinetx/App/main.cpp b/src/Kinetx/App/main.cpp
@@ -1,16 +1,17 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 
+#include "Kinetx/Integrator/CashKarp5.h"
+#include "Kinetx/Integrator/Cvode.h"
+#include "Kinetx/Integrator/ExplicitEuler.h"
+#include "Kinetx/Integrator/ImplicitEuler.h"
 #include "Kinetx/Network.h"
 #include "Kinetx/RandomNetworkFactory.h"
 #include "Kinetx/ReferenceNetworks.h"
-#include "Kinetx/RungeKutta/CashKarp5.h"
-#include "Kinetx/RungeKutta/ExplicitEuler.h"
-#include "Kinetx/RungeKutta/ImplicitEuler.h"
 #include <cmath>
 #include <iomanip>
 #include <iostream>
@@ -22,107 +23,26 @@ int main() {
   auto net = ret.first;
   auto concentrations = ret.second;
 
-  // Minimal Bromate Oscillator
-  // https://pubs.acs.org/doi/pdf/10.1021/j100259a030
-  //  Eigen::VectorXd masses(10);
-  //  masses << 127.90, 79.90, 1.01, 112.91, 96.91, 159.81, 18.02, 111.90, 140.12, 140.12;
-  //  Eigen::SparseMatrix<double> rf(7, 1);
-  //  rf.insert(0, 0) = 2.1;
-  //  rf.insert(1, 0) = 2.0e9;
-  //  rf.insert(2, 0) = 8.0e9;
-  //  rf.insert(3, 0) = 1.0e4;
-  //  rf.insert(4, 0) = 6.5e5;
-  //  rf.insert(5, 0) = 9.6;
-  //  rf.insert(6, 0) = 4.0e7;
-  //  Eigen::SparseMatrix<double> rb(7, 1);
-  //  rb.insert(0, 0) = 1.0e4;
-  //  rb.insert(1, 0) = 5.0e-5;
-  //  rb.insert(2, 0) = 110.0;
-  //  rb.insert(3, 0) = 2.0e7;
-  //  rb.insert(4, 0) = 2.4e7;
-  //  rb.insert(5, 0) = 1.3e-4;
-  //  rb.insert(6, 0) = 2.1e-10;
-  //  Eigen::SparseMatrix<int> sf(7, 10);
-  //  sf.insert(0, 0) = 1;
-  //  sf.insert(0, 1) = 1;
-  //  sf.insert(0, 2) = 2;
-  //  sf.insert(1, 1) = 1;
-  //  sf.insert(1, 2) = 1;
-  //  sf.insert(1, 3) = 1;
-  //  sf.insert(2, 1) = 1;
-  //  sf.insert(2, 2) = 1;
-  //  sf.insert(2, 4) = 1;
-  //  sf.insert(3, 0) = 1;
-  //  sf.insert(3, 2) = 1;
-  //  sf.insert(3, 3) = 1;
-  //  sf.insert(4, 2) = 1;
-  //  sf.insert(4, 7) = 1;
-  //  sf.insert(4, 8) = 1;
-  //  sf.insert(5, 6) = 1;
-  //  sf.insert(5, 7) = 1;
-  //  sf.insert(5, 9) = 1;
-  //  sf.insert(6, 3) = 2;
-  //  Eigen::SparseMatrix<int> sb(7, 10);
-  //  sb.insert(0, 3) = 1;
-  //  sb.insert(0, 4) = 1;
-  //  sb.insert(1, 4) = 2;
-  //  sb.insert(2, 5) = 1;
-  //  sb.insert(2, 6) = 1;
-  //  sb.insert(3, 6) = 1;
-  //  sb.insert(3, 7) = 2;
-  //  sb.insert(4, 3) = 1;
-  //  sb.insert(4, 9) = 1;
-  //  sb.insert(5, 8) = 1;
-  //  sb.insert(5, 0) = 1;
-  //  sb.insert(5, 2) = 2;
-  //  sb.insert(6, 0) = 1;
-  //  sb.insert(6, 2) = 1;
-  //  sb.insert(6, 4) = 1;
-  //  Network net(masses, {rf, rb}, {sf, sb, sb - sf});
-  //  Eigen::VectorXd concentrations = Eigen::VectorXd::Zero(net.nCompounds);
-  //  concentrations[0] = 6.0e-2;
-  //  concentrations[1] = 3.0e-4;
-  //  concentrations[2] = 1.5;
-  //  concentrations[6] = 22.0;
-  //  concentrations[8] = 1.5e-4;
-  // concentrations[0] = 0.1999e-1;
-  // concentrations[1] = 0.3347e-6;
-  // concentrations[2] = 0.1500e+1;
-  // concentrations[3] = 0.4606e-10;
-  // concentrations[4] = 0.8271e-6;
-  // concentrations[5] = 0.3020e-4;
-  // concentrations[6] = 0.0;
-  // concentrations[7] = 0.2627e-9;
-  // concentrations[8] = 0.1427e-3;
-  // concentrations[9] = 0.7321e-5;
-
-  // Random Network
-  // auto net = NetworkFactory::random();
-  // Eigen::VectorXd concentrations(net.nCompounds);
-  // concentrations.setZero();
-  // concentrations[0] = 0.3;
-
   // Explicit Euler
   // ExplicitEuler solver(net);
-  // Cash-Karp
-  CashKarp5 solver(net);
   // Implicit Euler
   // ImplicitEuler solver(net);
+  // Cash-Karp
+  // CashKarp5 solver(net);
+  // Cvode
+  Cvode solver(net);
   double t = 0.0;
-  double dt = 1e-8;
-  // for (unsigned int i=0;i<1e5;i++){
-  std::cout << std::scientific << std::setprecision(6) << t << "  " << dt << "  " << concentrations.transpose() << "  "
-            << concentrations.dot(net.masses) << std::endl;
-  Eigen::VectorXd concentrationFlux = Eigen::VectorXd::Zero(concentrations.size());
+  double dt = 1e-1;
   Eigen::VectorXd edgeFlux = Eigen::VectorXd::Zero(net.nReactions);
   Eigen::VectorXd forwardEdgeFlux = Eigen::VectorXd::Zero(net.nReactions);
   Eigen::VectorXd backwardEdgeFlux = Eigen::VectorXd::Zero(net.nReactions);
-  for (unsigned int i = 0; i < 2e8; i++) {
+  for (unsigned int i = 0; i < 2e6; i++) {
     double told = t;
+    Eigen::VectorXd concentrationFlux = Eigen::VectorXd::Zero(concentrations.size());
     solver.propagate(concentrations, concentrationFlux, edgeFlux, forwardEdgeFlux, backwardEdgeFlux, t, dt);
     if (t != told && i % 1000 == 0)
-      std::cout << std::scientific << std::setprecision(6) << t << "  " << dt << "  " << concentrations.transpose()
-                << "  " << concentrations.dot(net.masses) << std::endl;
+      std::cout << std::scientific << std::setprecision(6) << t << "  " << dt << " | " << concentrations.transpose()
+                << " | " << concentrations.dot(net.masses) << " | " << (concentrationFlux / dt).transpose() << std::endl;
   }
 
   return 1;

diff --git a/src/Kinetx/CMakeLists.txt b/src/Kinetx/CMakeLists.txt
@@ -26,10 +26,35 @@ target_compile_definitions(Kinetx
 )
 include(AddEigen)
 add_eigen(Kinetx PUBLIC)
-target_link_libraries(Kinetx
-  PRIVATE
-    $<$<BOOL:${OpenMP_CXX_FOUND}>:OpenMP::OpenMP_CXX>
+include(ImportSundials)
+import_sundials()
+
+target_link_libraries(Kinetx PRIVATE
+  $<$<BOOL:${OpenMP_CXX_FOUND}>:OpenMP::OpenMP_CXX>
+  sundials_cvode
+  sundials_sunmatrixdense
+  sundials_sunmatrixsparse
+  sundials_sunnonlinsolnewton
+  sundials_sunnonlinsolfixedpoint
+)
+target_include_directories(Kinetx PRIVATE
+  ${sundials_SOURCE_DIR}/include
 )
+if(SCINE_PARALLELIZE)
+  target_link_libraries(Kinetx PRIVATE    
+    sundials_nvecopenmp
+  )
+  target_include_directories(Kinetx PRIVATE
+    sundials_nvecopenmp
+  )
+else()
+  target_link_libraries(Kinetx PRIVATE
+    sundials_nvecserial
+  )
+  target_include_directories(Kinetx PRIVATE
+    sundials_nvecserial
+  )
+endif()
 
 # Add namespaced aliases
 add_library(Scine::Kinetx ALIAS Kinetx)
@@ -68,19 +93,6 @@ if(SCINE_BUILD_TESTS)
     ${CMAKE_DL_LIBS}
   )
   add_test(NAME Kinetx COMMAND Kinetx_tests)
-
-  # # App tests
-  # find_package(PythonInterp REQUIRED)
-  # add_test(
-  #   NAME Sparrow_App
-  #   COMMAND ${PYTHON_EXECUTABLE} -B -m pytest test_sparrow.py${TEST_SELECTION} --junitxml=${CMAKE_CURRENT_BINARY_DIR}/app_report.xml
-  #   WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/Tests/AppTests
-  # )
-  # set_tests_properties(Sparrow_App PROPERTIES
-  #   ENVIRONMENT SCINE_MODULE_PATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{SCINE_MODULE_PATH}
-  #   ENVIRONMENT PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}
-  #   ENVIRONMENT PATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PATH}
-  # )
 endif()
 
 # Set the RPATH to be used when installing.
@@ -166,7 +178,7 @@ if(SCINE_BUILD_PYTHON_BINDINGS)
   if(SCINE_BUILD_TESTS)
     add_test(
       NAME Kinetx_Python_Bindings
-      COMMAND ${PYTHON_EXECUTABLE} -B -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/Python/Tests --junitxml=${CMAKE_CURRENT_BINARY_DIR}/pytest_report.xml
+      COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -s ${CMAKE_CURRENT_SOURCE_DIR}/Python/Tests --junitxml=${CMAKE_CURRENT_BINARY_DIR}/pytest_report.xml
       WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     )
     set_tests_properties(Kinetx_Python_Bindings PROPERTIES

diff --git a/src/Kinetx/Files.cmake b/src/Kinetx/Files.cmake
@@ -11,14 +11,18 @@ set(KINETX_LIB_FILES
 	${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RandomNetworkFactory.h
 	${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/ReferenceNetworks.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/ReferenceNetworks.h
-  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RungeKutta/CashKarp5.h
-  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RungeKutta/CashKarp5.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RungeKutta/ExplicitEuler.h
-  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RungeKutta/ExplicitEuler.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RungeKutta/ImplicitEuler.h
-  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RungeKutta/ImplicitEuler.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RungeKutta/RungeKutta.h
-  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/RungeKutta/RungeKutta.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/CashKarp5.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/CashKarp5.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/Cvode.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/Cvode.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/ExplicitEuler.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/ExplicitEuler.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/Integrator.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/Integrator.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/ImplicitEuler.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/ImplicitEuler.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/RungeKutta.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/Kinetx/Integrator/RungeKutta.cpp
 )
 
 set(KINETX_TEST_FILES
@@ -32,5 +36,5 @@ set(KINETX_PYTHON_CPPS
   ${CMAKE_CURRENT_SOURCE_DIR}/Python/NetworkBuilderPython.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/Python/ReferenceNetworksPython.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/Python/RandomNetworkFactoryPython.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/Python/RungeKuttaPython.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/Python/IntegratorsPython.cpp
 )
diff --git a/src/Kinetx/Kinetx/RungeKutta/CashKarp5.cpp → src/Kinetx/Kinetx/Integrator/CashKarp5.cpp b/src/Kinetx/Kinetx/RungeKutta/CashKarp5.cpp → src/Kinetx/Kinetx/Integrator/CashKarp5.cpp
@@ -1,11 +1,11 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 
-#include "Kinetx/RungeKutta/CashKarp5.h"
+#include "Kinetx/Integrator/CashKarp5.h"
 #include <Eigen/Dense>
 
 namespace Scine {

diff --git a/src/Kinetx/Kinetx/RungeKutta/CashKarp5.h → src/Kinetx/Kinetx/Integrator/CashKarp5.h b/src/Kinetx/Kinetx/RungeKutta/CashKarp5.h → src/Kinetx/Kinetx/Integrator/CashKarp5.h
@@ -1,13 +1,13 @@
 /**
  * @file
  * @copyright This code is licensed under the 3-clause BSD license.\n
- *            Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.\n
+ *            Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.\n
  *            See LICENSE.txt for details.
  */
 #ifndef KINETX_CASHKARP5_H_
 #define KINETX_CASHKARP5_H_
 
-#include "Kinetx/RungeKutta/RungeKutta.h"
+#include "Kinetx/Integrator/RungeKutta.h"
 
 namespace Scine {
 namespace Kinetx {