A small selection of miscellaneous changes that don't fit in as part
of any larger MR.
molecules.h
kerneloptions.h
nblib.h
molecules.h
kerneloptions.h
nblib.h
particlesequencer.h
particletype.h
simulationstate.h
topology.h
particlesequencer.h
particletype.h
simulationstate.h
topology.h
DESTINATION include/nblib)
endif()
DESTINATION include/nblib)
endif()
*
* The message should give users some hint as to how to remedy the error.
*/
*
* The message should give users some hint as to how to remedy the error.
*/
-class InputException final : NbLibException
+class InputException final : public NbLibException
{
public:
using NbLibException::NbLibException;
{
public:
using NbLibException::NbLibException;
SimdKernels nbnxmSimd = SimdKernels::SimdAuto;
//! The LJ combination rule
CombinationRule ljCombinationRule = CombinationRule::Geometric;
SimdKernels nbnxmSimd = SimdKernels::SimdAuto;
//! The LJ combination rule
CombinationRule ljCombinationRule = CombinationRule::Geometric;
- //! Use i-cluster half-LJ optimization for clusters with <= half LJ
- bool useHalfLJOptimization = false;
//! The pairlist and interaction cut-off
real pairlistCutoff = 1.0;
//! The pairlist and interaction cut-off
real pairlistCutoff = 1.0;
- //! Whether to compute energies (shift forces for virial are always computed on CPU)
- bool computeVirialAndEnergy = false;
//! The Coulomb interaction function
CoulombType coulombType = CoulombType::Pme;
//! Whether to use tabulated PME grid correction instead of analytical, not applicable with simd=no
bool useTabulatedEwaldCorr = false;
//! The number of iterations for each kernel
int numIterations = 100;
//! The Coulomb interaction function
CoulombType coulombType = CoulombType::Pme;
//! Whether to use tabulated PME grid correction instead of analytical, not applicable with simd=no
bool useTabulatedEwaldCorr = false;
//! The number of iterations for each kernel
int numIterations = 100;
- //! Print cycles/pair instead of pairs/cycle
- bool cyclesPerPair = false;
//! The time step
real timestep = 0.001;
};
//! The time step
real timestep = 0.001;
};
#
set(argon "argon-forces-integration")
#
set(argon "argon-forces-integration")
-add_executable(${argon} "")
-
-target_sources(${argon}
- PRIVATE
- argon-forces-integration.cpp
- )
+add_executable(${argon} argon-forces-integration.cpp)
target_link_libraries(${argon} PRIVATE nblib)
set(methane "methane-water-integration")
target_link_libraries(${argon} PRIVATE nblib)
set(methane "methane-water-integration")
-add_executable(${methane} "")
-
-target_sources(${methane}
- PRIVATE
- methane-water-integration.cpp
- )
+add_executable(${methane} methane-water-integration.cpp)
target_link_libraries(${methane} PRIVATE nblib)
target_link_libraries(${methane} PRIVATE nblib)
// can be included via their respective headers.
#include "nblib/nblib.h"
// can be included via their respective headers.
#include "nblib/nblib.h"
-// Main function to write the MD program.
-int main(); // Keep the compiler happy
-
int main()
{
// Create an argon particle with a name and a mass.
int main()
{
// Create an argon particle with a name and a mass.
-// Main function to write the MD program.
-int main(); // Keep the compiler happy
-
int main()
{
// Create the particles
int main()
{
// Create the particles
using ::testing::Eq;
using ::testing::Pointwise;
using ::testing::Eq;
using ::testing::Pointwise;
-//! Compares all element between two lists of lists
-//! Todo: unify this with the identical function in nbkernelsystem test make this a method
-//! of ListOfLists<>
+//! \brief Compares all element between two lists of lists
template<typename T>
void compareLists(const gmx::ListOfLists<T>& list, const std::vector<std::vector<T>>& v)
{
template<typename T>
void compareLists(const gmx::ListOfLists<T>& list, const std::vector<std::vector<T>>& v)
{
TEST(NBlibTest, TopologyListedInteractionsMultipleTypes)
{
TEST(NBlibTest, TopologyListedInteractionsMultipleTypes)
{
- // Todo: add an angle type here
-
Molecule water = WaterMoleculeBuilder{}.waterMolecule();
Molecule methanol = MethanolMoleculeBuilder{}.methanolMolecule();
Molecule water = WaterMoleculeBuilder{}.waterMolecule();
Molecule methanol = MethanolMoleculeBuilder{}.methanolMolecule();
if(GMX_INSTALL_NBLIB_API)
install(FILES
setup.h
if(GMX_INSTALL_NBLIB_API)
install(FILES
setup.h
DESTINATION include/nblib/util)
endif()
DESTINATION include/nblib/util)
endif()
/*! \brief implementation of the Contains trait to look for T in TL
*
/*! \brief implementation of the Contains trait to look for T in TL
*
- * @tparam T type to look for in TL
- * @tparam TL a variadic type, such as std::tuple or TypeList
- * @tparam Ts the template parameters of TL
+ * \tparam T type to look for in TL
+ * \tparam TL a variadic type, such as std::tuple or TypeList
+ * \tparam Ts the template parameters of TL
*
* Note that this clang-format enforced formatting is unfortunate, it should be:
* struct Contains<T, TL<Ts...>> : std::bool_constant<FindIndex<T, TL<Ts...>>{} < sizeof...(Ts)>
*
* Note that this clang-format enforced formatting is unfortunate, it should be:
* struct Contains<T, TL<Ts...>> : std::bool_constant<FindIndex<T, TL<Ts...>>{} < sizeof...(Ts)>