Release 2.1.0

CHANGELOG.rst

@@ -1,6 +1,10 @@
 Changelog
 =========
 
+Release 2.1.0
+-------------
+- rework non-bonded interaction calculation to increase memory efficiency.
+
 Release 2.0.0
 -------------
 - enable electrostatic embedding QM/MM with Turbomole and xtb as QM calculators

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(Swoose
-  VERSION 2.0.0
+  VERSION 2.1.0
   DESCRIPTION "This is the SCINE module Swoose."
 )
 

README.rst

@@ -55,8 +55,15 @@ K.-S. Csizi, M. Reiher, "Automated preparation of nanoscopic structures: Graph-b
 sequence analysis, mismatch detection, and pH-consistent protonation with uncertainty estimates"
 *J. Comput. Chem*, **2024**, *45*, 761-776.
 
-K.-S. Csizi, M. Steiner, M. Reiher, "Quantum Magnifying Glass for Chemistry at the Nanoscale",
-*chemRxiv", **2023**, DOI 10.26434/chemrxiv-2023-t10sc.
+K.-S. Csizi, M. Steiner, M. Reiher, "Nanoscale chemical reaction exploration with a quantum magnifying glass",
+*Nat. Commun.*, **2024**, 15, 5320.
+
+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
 -------------------

conanfile.py

@@ -3,7 +3,7 @@
 
 class ScineSwooseConan(ScineConan):
     name = "scine_swoose"
-    version = "2.0.0"
+    version = "2.1.0"
     url = "https://github.com/qcscine/swoose"
     description = """
 Treat large molecular systems with self-parametrizing system-focused atomistic
@@ -22,8 +22,8 @@ class ScineSwooseConan(ScineConan):
     exports_sources = ["dev/cmake/*", "src/*", "CMakeLists.txt", "README.rst",
                        "LICENSE.txt", "dev/conan/hook.cmake", "dev/conan/glue/*"]
     requires = ["yaml-cpp/0.6.3",
-                "scine_utilities/[==9.0.0]",
-                "scine_molassembler/[==2.0.1]"]
+                "scine_utilities/10.0.0",
+                "scine_molassembler/3.0.0"]
     cmake_name = "Swoose"
 
     def requirements(self):
@@ -32,7 +32,7 @@ def requirements(self):
         }
 
         if self.options.get_safe("database"):
-            self.requires("scine_database/[==1.3.0]")
+            self.requires("scine_database/1.4.0")
 
         if hasattr(super(), "requirements"):
             super().requirements()

manual/swoose_manual.tex

@@ -18,8 +18,8 @@
 
 %%
 % Book metadata
-\title[SCINE Swoose manual]{User Manual \vskip 0.5em {\setlength{\parindent}{0pt} \Huge SCINE Swoose 2.0.0}}
-\author[The SCINE Swoose Developers]{\noindent Christoph Brunken, Katja-Sophia Csizi, Miguel Steiner, Thomas Weymuth, and Markus Reiher}
+\title[SCINE Swoose manual]{User Manual \vskip 0.5em {\setlength{\parindent}{0pt} \Huge SCINE Swoose 2.1.0}}
+\author[The SCINE Swoose Developers]{\noindent Moritz Bensberg, Christoph Brunken, Katja-Sophia Csizi, Miguel Steiner, Thomas Weymuth, and Markus Reiher}
 \publisher{ETH Z\"urich}
 
 %%
@@ -276,7 +276,7 @@ \section{Conan package}
 
 \begin{mdframed}[backgroundcolor=LightSteelBlue!25, linewidth=0pt]
 \begin{verbatim}
-conan install scine_swoose/2.0.0@
+conan install scine_swoose/2.1.0@
 \end{verbatim}
 \end{mdframed}
 
@@ -286,7 +286,7 @@ \section{Conan package}
 
 \begin{mdframed}[backgroundcolor=LightSteelBlue!25, userdefinedwidth=12cm, linewidth=0pt]
 \begin{verbatim}
-conan install -o scine_swoose:python=True scine_swoose/2.0.0@
+conan install -o scine_swoose:python=True scine_swoose/2.1.0@
 \end{verbatim}
 \end{mdframed}
 
@@ -302,7 +302,7 @@ \section{Conan package}
 
 \begin{mdframed}[backgroundcolor=LightSteelBlue!25, linewidth=0pt]
 \begin{verbatim}
-conan install scine_swoose/2.0.0@ -g virtualrunenv
+conan install scine_swoose/2.1.0@ -g virtualrunenv
 \end{verbatim}
 \end{mdframed}
 
@@ -321,7 +321,7 @@ \section{Conan package}
 \begin{mdframed}[backgroundcolor=LightSteelBlue!25, linewidth=0pt]
 \begin{verbatim}
 [requires]
-scine_swoose/[>=2.0.0]@
+scine_swoose/[>=2.1.0]@
 scine_sparrow/[>=5.0.0]@
 scine_xtb_wrapper/[>=3.0.0]@
 

src/Swoose/CMakeLists.txt

@@ -162,6 +162,57 @@ if(SCINE_BUILD_PYTHON_BINDINGS)
   import_pybind11()
   set(PYBIND11_PYTHON_VERSION ${PYTHONVERSION})
 
+  # Figure out which targets the python bindings are going to need copied
+  include(TargetLibName)
+  set(_py_targets_to_copy Swoose)
+  target_lib_type(Scine::UtilsOS _utils_libtype)
+  if(_utils_libtype STREQUAL "SHARED_LIBRARY")
+    list(APPEND _py_targets_to_copy Scine::UtilsOS)
+  endif()
+  unset(_utils_libtype)
+
+  # Generate generator expressions for each targets and figure out filenames
+  # for the python setup file
+  set(swoose_PY_DEPS "")
+  foreach(target ${_py_targets_to_copy})
+    list(APPEND _py_target_gen_exprs "\$<TARGET_FILE:${target}>")
+    target_lib_filename(${target} _target_filename)
+    string(APPEND swoose_PY_DEPS ", \"${_target_filename}\"")
+  endforeach()
+  message(STATUS "Targets to copy for Python bindings: ${_py_targets_to_copy}")
+  unset(_py_targets_to_copy)
+
+  add_custom_command(TARGET Swoose POST_BUILD
+    COMMAND ${CMAKE_COMMAND} -E copy ${_py_target_gen_exprs} ${CMAKE_CURRENT_BINARY_DIR}/scine_swoose
+    COMMENT "Copying required shared libraries into Python package directory"
+  )
+  unset(_py_target_gen_exprs)
+
+  # Utils python dependency
+  include(FindPythonModule)
+  if(scine-utils-os_BINARY_DIR)
+    set(UTILS_PYTHONPATH ${scine-utils-os_BINARY_DIR}/src/Utils)
+  else()
+    find_python_module(scine_utilities)
+    if(PY_SCINE_UTILITIES)
+      set(UTILS_PYTHONPATH ${PY_SCINE_UTILITIES})
+    else()
+      message(WARNING "Utilities Python module not found. Cannot test Python module or generate stubs")
+    endif()
+  endif()
+
+  # Molassembler python dependency
+  if(molassembler_BINARY_DIR)
+    set(MASM_PYTHONPATH ${scine-utils-os_BINARY_DIR}/src/Utils)
+  else()
+    find_python_module(scine_molassembler)
+    if(PY_SCINE_MOLASSEMBLER)
+      set(MASM_PYTHONPATH ${PY_SCINE_MOLASSEMBLER})
+    else()
+      message(WARNING "Molassembler Python module not found. Cannot test Python module or generate stubs")
+    endif()
+  endif()
+
   # Python module
   pybind11_add_module(scine_swoose
     ${SWOOSE_PYTHON_FILES}
@@ -238,15 +289,19 @@ if(SCINE_BUILD_PYTHON_BINDINGS)
   endif()
 
   # Typing stubs
-  include(FindPythonModule)
   find_python_module(pybind11_stubgen)
-  if(PY_PYBIND11_STUBGEN)
+  if(PY_PYBIND11_STUBGEN AND UTILS_PYTHONPATH AND MASM_PYTHONPATH)
     add_custom_command(TARGET scine_swoose POST_BUILD
-      COMMAND ${PYTHON_EXECUTABLE} -m pybind11_stubgen -o . --root-module-suffix \"\" --no-setup-py --bare-numpy-ndarray scine_swoose
+      COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${UTILS_PYTHONPATH}:$ENV{PYTHONPATH} ${PYTHON_EXECUTABLE} -m pybind11_stubgen -o . --root-module-suffix \"\" --no-setup-py --bare-numpy-ndarray scine_swoose
       COMMENT "Generating python package typechecking stubs with pybind11-stubgen"
-    )
-  else()
+      BYPRODUCTS ${CMAKE_CURRENT_BINARY_DIR}/scine_swoose/__init__.pyi
+  )
+  elseif(UTILS_PYTHONPATH AND MASM_PYTHONPATH)
     message(STATUS "Not generating typechecking stubs for python package as pybind11-stubgen was not found")
+  elseif(UTILS_PYTHONPATH)
+    message(STATUS "Not generating typechecking stubs for Python package as SCINE Molassembler dependency was not found")
+  else()
+    message(STATUS "Not generating typechecking stubs for Python package as SCINE Utilities dependency was not found")
   endif()
 
   # Add setuptools file

src/Swoose/Files.cmake

@@ -9,6 +9,10 @@ set(SWOOSE_MODULE_FILES
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/GAFF/GaffCalculatorSettings.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/GAFF/GaffMolecularMechanicsCalculator.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/GAFF/GaffMolecularMechanicsCalculator.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/InteractionExclusion.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/InteractionExclusion.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/ScaledInteractions.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/ScaledInteractions.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/MMExceptions.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/MMParameters.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/MMParameters.h
@@ -24,8 +28,6 @@ set(SWOOSE_MODULE_FILES
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/SFAM/SfamAtomTypeIdentifier.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/Electrostatic.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/Electrostatic.h
-    ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/ElectrostaticTerm.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/ElectrostaticTerm.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/ElectrostaticEvaluator.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/ElectrostaticEvaluator.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/Repulsion.cpp
@@ -75,8 +77,6 @@ set(SWOOSE_MODULE_FILES
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/LennardJones.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/LennardJonesEvaluator.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/LennardJonesEvaluator.h
-    ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/LennardJonesTerm.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/LennardJonesTerm.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/HydrogenBond.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/HydrogenBond.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Swoose/MolecularMechanics/Interactions/HydrogenBondTerm.cpp

src/Swoose/Python/setup.py

@@ -9,7 +9,7 @@
 import os
 
 # Read README.rst for the long description
-with open("README.rst", "r") as fh:
+with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 

src/Swoose/Swoose/MMParametrization/ParametrizationUtils/ReparametrizationHelper.h

@@ -14,7 +14,7 @@
 namespace Scine {
 
 namespace Core {
-class Log;
+struct Log;
 } // namespace Core
 
 namespace MMParametrization {

src/Swoose/Swoose/MMParametrization/ParametrizationUtils/SuperfluousFragmentIdentifier.h

@@ -13,7 +13,7 @@
 namespace Scine {
 
 namespace Core {
-class Log;
+struct Log;
 } // namespace Core
 
 namespace MMParametrization {

src/Swoose/Swoose/MMParametrization/ParametrizationUtils/TitrationHelper.cpp

@@ -92,6 +92,7 @@ double TitrationHelper::getPkaOfTrainingMolecule(std::string dataDirectory) {
 }
 
 double TitrationHelper::getEnergyOfDeprotonationForTrainingMolecule(std::string dataDirectory) {
+  (void)dataDirectory;
   return 0.0;
 }
 

src/Swoose/Swoose/MMParametrization/ReferenceCalculationHelpers/DirectCalculationsHelper.h

@@ -13,7 +13,7 @@
 namespace Scine {
 
 namespace Core {
-class Log;
+struct Log;
 } // namespace Core
 
 namespace Utils {

src/Swoose/Swoose/MachineLearning/MolecularMachineLearningModel.cpp

@@ -191,9 +191,9 @@ Eigen::MatrixXd MolecularMachineLearningModel::getSingleForceFeatures(int atomIn
 }
 
 Eigen::MatrixXd MolecularMachineLearningModel::getSingleForceTargets(int atomIndex) {
-  int nDataPoints = forcesFeatures_.size();
+  const size_t nDataPoints = forcesFeatures_.size();
   Eigen::MatrixXd targets(nDataPoints, 3);
-  for (long unsigned int j = 0; j < nDataPoints; ++j) {
+  for (size_t j = 0; j < nDataPoints; ++j) {
     targets.row(j) = refForces_[j].row(atomIndex);
   }
   return targets;

src/Swoose/Swoose/MolecularMechanics/AtomTypesHolder.h

@@ -28,7 +28,7 @@ class AtomTypesHolder {
   /**
    * @brief Getter for the atom type for an atom with a certain index.
    */
-  std::string getAtomType(int index) const;
+  const std::string& getAtomType(unsigned int index) const;
 
   /**
    * @brief Returns the number of atom types stored in this object.
@@ -42,7 +42,7 @@ class AtomTypesHolder {
 inline AtomTypesHolder::AtomTypesHolder(std::vector<std::string> atomTypes) : atomTypes_(std::move(atomTypes)) {
 }
 
-inline std::string AtomTypesHolder::getAtomType(int index) const {
+inline const std::string& AtomTypesHolder::getAtomType(unsigned int index) const {
   return atomTypes_.at(index);
 }
 

src/Swoose/Swoose/MolecularMechanics/GAFF/GaffMolecularMechanicsCalculator.cpp

@@ -110,7 +110,6 @@ const Utils::Results& GaffMolecularMechanicsCalculator::calculate(std::string de
 const Utils::Results& GaffMolecularMechanicsCalculator::calculateImpl(std::string description) {
   int nAtoms = structure_.size();
   double energy = 0.0;
-
   //  Initialize the atomic derivatives container
   Utils::AtomicSecondDerivativeCollection derivativesForBondedInteractions(nAtoms);
   derivativesForBondedInteractions.setZero();
@@ -119,9 +118,10 @@ const Utils::Results& GaffMolecularMechanicsCalculator::calculateImpl(std::strin
   int nAtomsInitialization = 0;
   if (!onlyCalculateBondedContribution_)
     nAtomsInitialization = nAtoms;
-  Utils::FullSecondDerivativeCollection fullDerivatives(nAtomsInitialization);
-  fullDerivatives.setZero();
+  const unsigned int derivativeOrder = (requiredProperties_.containsSubSet(Utils::Property::Hessian)) ? 2 : 1;
 
+  Utils::DerivativeCollection fullDerivatives(nAtomsInitialization, derivativeOrder);
+  fullDerivatives.setZero();
   double energyBonds = bondsEvaluator_->evaluate(derivativesForBondedInteractions);
   energy += energyBonds;
   double energyAngles = anglesEvaluator_->evaluate(derivativesForBondedInteractions);
@@ -130,7 +130,6 @@ const Utils::Results& GaffMolecularMechanicsCalculator::calculateImpl(std::strin
   energy += energyDihedrals;
   double energyImproperDihedrals = improperDihedralsEvaluator_->evaluate(derivativesForBondedInteractions);
   energy += energyImproperDihedrals;
-
   double energyLennardJones = 0.0;
   double energyElectro = 0.0;
   if (!onlyCalculateBondedContribution_) {
@@ -218,7 +217,6 @@ void GaffMolecularMechanicsCalculator::generatePotentialTerms(const std::string&
   GaffAtomTypeIdentifier atomTypeGenerator(structure_.getElements().size(), structure_.getElements(), listsOfNeighbors_,
                                            atomTypesFile_);
   auto atomTypes = atomTypeGenerator.getAtomTypes();
-
   if (!parametersHaveBeenSetInternally_ || parameterFilePathHasBeenChanged_) {
     if (parameterPath.empty()) {
       GaffParameterDefaultsProvider parameterProvider;
@@ -234,7 +232,8 @@ void GaffMolecularMechanicsCalculator::generatePotentialTerms(const std::string&
     parametersHaveBeenSetInternally_ = true;
     parameterFilePathHasBeenChanged_ = false;
   }
-
+  lennardJonesEvaluator_->setAtomTypesHolder(std::make_shared<AtomTypesHolder>(atomTypes));
+  lennardJonesEvaluator_->setParameters(std::make_shared<GaffParameters>(parameters_));
   generatePotentialTerms(parameters_, topology, atomTypes);
 }
 
@@ -256,15 +255,24 @@ void GaffMolecularMechanicsCalculator::generatePotentialTerms(const GaffParamete
 
   // Generate the potential terms
   GaffPotentialTermsGenerator generator(structure_.size(), atomTypes, topology, parameters, structure_.getPositions(),
-                                        nonCovalentCutoffRadius_, this->getLog());
+                                        this->getLog());
 
   bondsEvaluator_->setBondTerms(generator.getBondedTerms());
   anglesEvaluator_->setAngleTerms(generator.getAngleTerms());
   dihedralsEvaluator_->setDihedralTerms(generator.getDihedralTerms());
   improperDihedralsEvaluator_->setDihedralTerms(generator.getImproperDihedralTerms());
   if (!onlyCalculateBondedContribution_) {
-    lennardJonesEvaluator_->setLennardJonesTerms(generator.getLennardJonesTerms(applyCutoffDuringInitialization_));
-    electrostaticEvaluator_->setElectrostaticTerms(generator.getElectrostaticTerms(applyCutoffDuringInitialization_));
+    lennardJonesEvaluator_->setCutOffRadius(std::make_shared<double>(nonCovalentCutoffRadius_));
+    lennardJonesEvaluator_->resetExclusions(structure_.size());
+    lennardJonesEvaluator_->addExclusions(topology);
+    lennardJonesEvaluator_->resetScaledInteractions(structure_.size());
+    lennardJonesEvaluator_->addScaledInteractionPairs(topology);
+
+    electrostaticEvaluator_->setCutOffRadius(std::make_shared<double>(nonCovalentCutoffRadius_));
+    electrostaticEvaluator_->resetExclusions(structure_.size());
+    electrostaticEvaluator_->addExclusions(topology);
+    electrostaticEvaluator_->resetScaledInteractions(structure_.size());
+    electrostaticEvaluator_->addScaledInteractionPairs(topology);
   }
 }
 
@@ -289,7 +297,6 @@ void GaffMolecularMechanicsCalculator::initialize() {
           SwooseUtilities::TopologyUtils::generateListsOfNeighborsFromBondOrderMatrix(structure_.size(), bondOrders, 0.5);
     }
   }
-
   generatePotentialTerms(parameterFilePath_);
 }