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Merged
97gamjak merged 13 commits into from
Aug 31, 2026
Merged

Strong types #527

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2e05479
enhancement: add strong types for vdw internal and external type
97gamjak Aug 15, 2026
6d8b82b
chore: update changelog
97gamjak Aug 15, 2026
01f5c38
cleanup: add morse params
97gamjak Aug 17, 2026
fa62f2c
clenaup: add strong type for lj params
97gamjak Aug 17, 2026
d931a77
cleanup: lj and morse param type handling
97gamjak Aug 19, 2026
15364bb
Merge remote-tracking branch 'origin/dev' into strong_types
97gamjak Aug 22, 2026
5ee0ede
enhancement: add BuckinghamParams strong type
97gamjak Aug 22, 2026
83331e2
cleanup: make guff pair use array instead of vector
97gamjak Aug 24, 2026
4e701a2
Merge remote-tracking branch 'origin/dev' into strong_types
97gamjak Aug 25, 2026
e688c7a
chore: add license headers
97gamjak Aug 25, 2026
4853364
chore: update to mstd 0.2.3
97gamjak Aug 26, 2026
3f4ca3d
chore: fix mpi build issues
97gamjak Aug 26, 2026
f6c15ba
Merge remote-tracking branch 'origin/dev' into strong_types
97gamjak Aug 30, 2026
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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Expand Up @@ -171,7 +171,7 @@ if(Git_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
# Update submodules as needed
option(GIT_SUBMODULE "Check submodules during build" ON)

if(GIT_SUBMODULE)
if(GIT_SUBMODULE AND NOT EXISTS "${PROJECT_SOURCE_DIR}/external/mstd/include/")
message(STATUS "Submodule update")
execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
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10 changes: 8 additions & 2 deletions benchmarks/perf/perfBenchSetup.hpp
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Expand Up @@ -38,6 +38,7 @@
#include "matrix.hpp"
#include "molecule.hpp"
#include "simulationBox.hpp"
#include "strongTypes.hpp"

namespace potential
{
Expand Down Expand Up @@ -109,7 +110,7 @@ namespace benchSetup
atom->setShiftForce({0.0, 0.0, 0.0});
atom->setMass(12.0);
atom->setAtomType(i % 2);
atom->setInternalGlobalVDWType(i % 2);
atom->setInternalGlobalVDWType(VdwType{i % 2});
atom->setPartialCharge((i % 2 == 0) ? 0.4 : -0.4);

molecule.addAtom(atom);
Expand All @@ -131,7 +132,12 @@ namespace benchSetup
)
);

auto pair = potential::LennardJonesPair(0UL, 1UL, 12.0, 2.0, 3.0);
auto pair = potential::LennardJonesPair(
ExtVdwType(0),
ExtVdwType(1),
12.0,
LJParams{.c6 = 2.0, .c12 = 3.0}
);
potential.setNonCoulombPairsMatrix(0, 1, pair);
potential.setNonCoulombPairsMatrix(1, 0, pair);

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26 changes: 17 additions & 9 deletions benchmarks/perf/perfInterWater.cpp
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Expand Up @@ -29,6 +29,8 @@
#include <iostream>
#include <memory>

#include "strongTypes.hpp"

#ifdef PQ_WITH_CALLGRIND
#include <valgrind/callgrind.h>
#else
Expand Down Expand Up @@ -90,7 +92,7 @@ int main()
atom->setAtomicNumber(atomicNumber);
atom->setPosition(pos);
atom->setAtomType(0);
atom->setInternalGlobalVDWType(0);
atom->setInternalGlobalVDWType(VdwType{0});
atom->setPartialCharge(charge);
atom->setForceToZero();
return atom;
Expand Down Expand Up @@ -130,14 +132,20 @@ int main()
}

InterWaterState state;
state._oxygenCharge = -0.82;
state._hydrogenCharge = 0.41;
state._nonCoulombPairOO =
std::make_unique<LennardJonesPair>(CUTOFF, -2.0, 4.0);
state._nonCoulombPairOH =
std::make_unique<LennardJonesPair>(CUTOFF, -0.5, 1.5);
state._nonCoulombPairHH =
std::make_unique<LennardJonesPair>(CUTOFF, -0.2, 0.8);
state._oxygenCharge = -0.82;
state._hydrogenCharge = 0.41;
state._nonCoulombPairOO = std::make_unique<LennardJonesPair>(
CUTOFF,
LJParams{.c6 = 2.0, .c12 = 4.0}
);
state._nonCoulombPairOH = std::make_unique<LennardJonesPair>(
CUTOFF,
LJParams{.c6 = 0.5, .c12 = 1.5}
);
state._nonCoulombPairHH = std::make_unique<LennardJonesPair>(
CUTOFF,
LJParams{.c6 = 0.2, .c12 = 0.8}
);

InterWater interWater(
std::move(state),
Expand Down
16 changes: 13 additions & 3 deletions benchmarks/perf/perfNonCoulombPairs.cpp
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Expand Up @@ -42,9 +42,19 @@ static constexpr std::uint64_t ITERATIONS = 20000;

int main()
{
auto lj = potential::LennardJonesPair(9.0, 2.0, 3.0);
auto buck = potential::BuckinghamPair(9.0, 1.0, 0.3, 2.0);
auto morse = potential::MorsePair(9.0, 1.0, 2.0, 1.5);
auto lj = potential::LennardJonesPair(9.0, LJParams{.c6 = 2.0, .c12 = 3.0});
auto buck = potential::BuckinghamPair(
9.0,
BuckinghamParams{.scaling = 1.0, .dRho = 0.3, .c6 = 2.0}
);
auto morse = potential::MorsePair(
9.0,
MorseParams{
.dissociationEnergy = 1.0,
.wellWidth = 2.0,
.equilibriumDistance = 1.5
}
);

CALLGRIND_ZERO_STATS;

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3 changes: 2 additions & 1 deletion benchmarks/src/benchmarkSetup.hpp
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Expand Up @@ -28,6 +28,7 @@
#include "atom.hpp"
#include "molecule.hpp"
#include "simulationBox.hpp"
#include "strongTypes.hpp"
#include "vector3d.hpp"

namespace benchmarkSetup
Expand Down Expand Up @@ -68,7 +69,7 @@ namespace benchmarkSetup
atom->setForce({0.1, -0.2, 0.05});
atom->setMass(12.0);
atom->setAtomType(0);
atom->setInternalGlobalVDWType(0);
atom->setInternalGlobalVDWType(VdwType{0});
atom->setPartialCharge(atomIndex++ % 2 == 0 ? 0.4 : -0.4);
atom->setShiftForce({0.0, 0.0, 0.0});

Expand Down
3 changes: 1 addition & 2 deletions benchmarks/src/potential/benchmarkForceCalculation.cpp
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Expand Up @@ -50,8 +50,7 @@ namespace

const auto pair = std::make_shared<potential::LennardJonesPair>(
benchmarkSetup::cutOff,
1.0,
1.0
LJParams{.c6 = 1.0, .c12 = 1.0}
);
nonCoulomb->setGuffNonCoulPair({1, 1, 0, 0}, pair);

Expand Down
19 changes: 16 additions & 3 deletions benchmarks/src/potential/benchmarkPairPotentials.cpp
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Expand Up @@ -67,19 +67,32 @@ namespace

void BM_LennardJones(benchmark::State& state)
{
potential::LennardJonesPair potential(9.0, 2.0, 3.0);
potential::LennardJonesPair potential(
9.0,
LJParams{.c6 = 2.0, .c12 = 3.0}
);
runNonCoulombBenchmark(state, potential);
}

void BM_Buckingham(benchmark::State& state)
{
potential::BuckinghamPair potential(9.0, 1.0, 0.3, 2.0);
potential::BuckinghamPair potential(
9.0,
BuckinghamParams{.scaling = 1.0, .dRho = 0.3, .c6 = 2.0}
);
runNonCoulombBenchmark(state, potential);
}

void BM_Morse(benchmark::State& state)
{
potential::MorsePair potential(9.0, 1.0, 2.0, 1.5);
potential::MorsePair potential(
9.0,
MorseParams{
.dissociationEnergy = 1.0,
.wellWidth = 2.0,
.equilibriumDistance = 1.5
}
);
runNonCoulombBenchmark(state, potential);
}

Expand Down
5 changes: 5 additions & 0 deletions changes/developer/enhancement.strong-types.md
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Expand Up @@ -2,3 +2,8 @@
- add strong type for `BondId`
- add strong type for `AngleId`
- add strong type for `DihedralId`
- add strong types for `ExtVdwType` and `VdwType`
- add strong type for morse params aka `MorseParams`
- add strong type for lennard jones params aka `LJParams`
- add strong type for bukcingham params aka `BuckinghamParams`
- make guff pari used `std::array` instead of `std::vector`
2 changes: 1 addition & 1 deletion external/mstd
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Submodule mstd updated 4 files
+14 −0 CHANGELOG.md
+10 −10 include/mstd/enum.hpp
+42 −20 include/mstd/types/strong_type.hpp
+13 −13 include/mstd/types/strong_type.tpp
2 changes: 2 additions & 0 deletions include/config/defaults.hpp
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Expand Up @@ -131,6 +131,8 @@ namespace defaults
static constexpr double ABS_ENERGY_CONV_DEFAULT = 1.0e-6;
static constexpr double MAX_FORCE_CONV_DEFAULT = 1.0e-6;
static constexpr double RMS_FORCE_CONV_DEFAULT = 1.0e-6;

static constexpr auto NUM_GUFF_COEFFICIENTS = 22;
// clang-format on

} // namespace defaults
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12 changes: 12 additions & 0 deletions include/config/guffCoefficients.hpp
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Expand Up @@ -24,39 +24,51 @@

#define _GUFF_COEFFICIENTS_HPP_

#include "strongTypes.hpp"

namespace constants
{
// clang-format off
// values calculated from the original SPC publication
static constexpr double SPC_LJ_C6_OO = -625.455653639347; // A^6 kcal mol^-1
static constexpr double SPC_LJ_C12_OO = 629358.472583307; // A^12 kcal mol^-1
static constexpr LJParams SPC_LJ_PARAMS_OO{.c6 = SPC_LJ_C6_OO, .c12 = SPC_LJ_C12_OO};

static constexpr double SPC_E_LJ_C6_OO = SPC_LJ_C6_OO; // A^6 kcal mol^-1
static constexpr double SPC_E_LJ_C12_OO = SPC_LJ_C12_OO; // A^12 kcal mol^-1
static constexpr LJParams SPC_E_LJ_PARAMS_OO{.c6 = SPC_E_LJ_C6_OO, .c12 = SPC_E_LJ_C12_OO};

static constexpr double SPC_FW_LJ_C6_OO = -625.5024676571352; // A^6 kcal mol^-1
static constexpr double SPC_FW_LJ_C12_OO = 629326.9774051674; // A^12 kcal mol^-1
static constexpr LJParams SPC_FW_LJ_PARAMS_OO{.c6 = SPC_FW_LJ_C6_OO, .c12 = SPC_FW_LJ_C12_OO};

static constexpr double QSPC_FW_LJ_C6_OO = -625.5020652114152; // A^6 kcal mol^-1
static constexpr double QSPC_FW_LJ_C12_OO = 629326.5724987736; // A^12 kcal mol^-1
static constexpr LJParams QSPC_FW_LJ_PARAMS_OO{.c6 = QSPC_FW_LJ_C6_OO, .c12 = QSPC_FW_LJ_C12_OO};

static constexpr double SPC_DC_LJ_C6_OO = -779.8414665600154; // A^6 kcal mol^-1
static constexpr double SPC_DC_LJ_C12_OO = 773048.5510230307; // A^12 kcal mol^-1
static constexpr LJParams SPC_DC_LJ_PARAMS_OO{.c6 = SPC_DC_LJ_C6_OO, .c12 = SPC_DC_LJ_C12_OO};

static constexpr double H2O_DC_LJ_C6_OO = -590.6923729027751; // A^6 kcal mol^-1
static constexpr double H2O_DC_LJ_C12_OO = 615459.8371975797; // A^12 kcal mol^-1
static constexpr LJParams H2O_DC_LJ_PARAMS_OO{.c6 = H2O_DC_LJ_C6_OO, .c12 = H2O_DC_LJ_C12_OO};

static constexpr double TIP3P_LJ_C6_OO = -595.067688427684; // A^6 kcal mol^-1
static constexpr double TIP3P_LJ_C12_OO = 582015.099443679; // A^12 kcal mol^-1
static constexpr LJParams TIP3P_LJ_PARAMS_OO{.c6 = TIP3P_LJ_C6_OO, .c12 = TIP3P_LJ_C12_OO};

static constexpr double OPC3_LJ_C6_OO = -668.637501352773; // A^6 kcal mol^-1
static constexpr double OPC3_LJ_C12_OO = 683996.561589584; // A^12 kcal mol^-1
static constexpr LJParams OPC3_LJ_PARAMS_OO{.c6 = OPC3_LJ_C6_OO, .c12 = OPC3_LJ_C12_OO};

static constexpr double SPC_MTR_LJ_C6_OO = -613.527724665392; // A^6 kcal mol^-1
static constexpr double SPC_MTR_LJ_C12_OO = 629302.103250478; // A^12 kcal mol^-1
static constexpr LJParams SPC_MTR_LJ_PARAMS_OO{.c6 = SPC_MTR_LJ_C6_OO, .c12 = SPC_MTR_LJ_C12_OO};

static constexpr double TIP3P_MTR_LJ_C6_OO = -454.1108986615679; // A^6 kcal mol^-1
static constexpr double TIP3P_MTR_LJ_C12_OO = 513862.3326959847; // A^12 kcal mol^-1
static constexpr LJParams TIP3P_MTR_LJ_PARAMS_OO{.c6 = TIP3P_MTR_LJ_C6_OO, .c12 = TIP3P_MTR_LJ_C12_OO};
// clang-format on

} // namespace constants
Expand Down
6 changes: 3 additions & 3 deletions include/forceField/forcefield.tpp.hpp
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Expand Up @@ -88,10 +88,10 @@ namespace forceField
const auto vdwType1 = molecule1->getInternalGlobalVDWType(atomIndex1);
const auto vdwType2 = molecule2->getInternalGlobalVDWType(atomIndex2);

const auto indices =
{molType1, molType2, atomType1, atomType2, vdwType1, vdwType2};
const auto indices = {molType1, molType2, atomType1, atomType2};

const auto nonCoulombPair = nonCoulPot.getNonCoulPair(indices);
const auto nonCoulombPair =
nonCoulPot.getNonCoulPair(indices, {vdwType1, vdwType2});

if (distance < nonCoulombPair->getRadialCutOff())
{
Expand Down
13 changes: 7 additions & 6 deletions include/input/guffDatReader.hpp
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Expand Up @@ -106,12 +106,13 @@ namespace input::guffdat
const double rncCutOff
);
void addGuffPair(
const size_t molType1,
const size_t molType2,
const size_t atomType1,
const size_t atomType2,
const std::vector<double> &coefficients,
const double rncCutOff
const size_t molType1,
const size_t molType2,
const size_t atomType1,
const size_t atomType2,
const std::array<double, defaults::NUM_GUFF_COEFFICIENTS>
&coefficients,
const double rncCutOff
);

/********************
Expand Down
12 changes: 6 additions & 6 deletions include/molsys/atom.hpp
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Expand Up @@ -49,8 +49,8 @@ namespace molsys
std::string _name;
std::string _atomTypeName;

size_t _externalGlobalVDWType;
size_t _internalGlobalVDWType;
ExtVdwType _externalGlobalVDWType;
VdwType _internalGlobalVDWType;

size_t _externalAtomType;
size_t _atomType;
Expand Down Expand Up @@ -125,8 +125,8 @@ namespace molsys
[[nodiscard]] size_t getExternalAtomType() const;
[[nodiscard]] size_t getAtomType() const;

[[nodiscard]] size_t getExternalGlobalVDWType() const;
[[nodiscard]] size_t getInternalGlobalVDWType() const;
[[nodiscard]] ExtVdwType getExternalGlobalVDWType() const;
[[nodiscard]] VdwType getInternalGlobalVDWType() const;

[[nodiscard]]
AtomNumber getAtomicNumber() const
Expand Down Expand Up @@ -166,8 +166,8 @@ namespace molsys

void setAtomType(const size_t atomType);
void setExternalAtomType(const size_t externalAtomType);
void setExternalGlobalVDWType(const size_t externalGlobalVDWType);
void setInternalGlobalVDWType(const size_t internalGlobalVDWType);
void setExternalGlobalVDWType(const ExtVdwType externalGlobalVDWType);
void setInternalGlobalVDWType(const VdwType internalGlobalVDWType);

void setPosition(const linearAlgebra::Vec3D &position);
void setVelocity(const linearAlgebra::Vec3D &velocity);
Expand Down
16 changes: 9 additions & 7 deletions include/molsys/molecule.hpp
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Expand Up @@ -32,6 +32,7 @@
#include <vector> // for vector

#include "atom.hpp" // for Atom
#include "strongTypes.hpp"

namespace molsys
{
Expand Down Expand Up @@ -109,8 +110,8 @@ namespace molsys
void scale(const linearAlgebra::tensor3D &, const Box &);
void scaleVelocity(const linearAlgebra::tensor3D &, const Box &);

[[nodiscard]] size_t getNumberOfAtomTypes();
[[nodiscard]] std::vector<size_t> getExternalGlobalVDWTypes() const;
[[nodiscard]] size_t getNumberOfAtomTypes();
[[nodiscard]] std::vector<ExtVdwType> getExternalGlobalVDWTypes() const;

[[nodiscard]] std::vector<double> getAtomMasses() const;
[[nodiscard]] std::vector<double> getPartialCharges() const;
Expand Down Expand Up @@ -184,12 +185,13 @@ namespace molsys
const size_t index
) const;

[[nodiscard]] AtomNumber getAtomicNumber(const size_t index) const;
[[nodiscard]] double getAtomMass(const size_t index) const;
[[nodiscard]] double getPartialCharge(const size_t index) const;
[[nodiscard]] size_t getAtomType(const size_t index) const;
[[nodiscard]] size_t getInternalGlobalVDWType(const size_t index) const;
[[nodiscard]] AtomNumber getAtomicNumber(const size_t index) const;
[[nodiscard]] double getAtomMass(const size_t index) const;
[[nodiscard]] double getPartialCharge(const size_t index) const;
[[nodiscard]] size_t getAtomType(const size_t index) const;
[[nodiscard]] std::string getAtomName(const size_t index) const;
[[nodiscard]]
VdwType getInternalGlobalVDWType(const size_t index) const;

/***************************
* standard getter methods *
Expand Down
8 changes: 5 additions & 3 deletions include/molsys/moleculeType.hpp
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Expand Up @@ -29,6 +29,8 @@
#include <string_view> // for string_view
#include <vector> // for vector

#include "strongTypes.hpp"

namespace molsys
{
/**
Expand All @@ -49,7 +51,7 @@ namespace molsys
std::vector<std::string> _atomNames;
std::vector<size_t> _atomTypes;
std::vector<size_t> _externalAtomTypes;
std::vector<size_t> _externalGlobalVDWTypes;
std::vector<ExtVdwType> _externalGlobalVDWTypes;
std::vector<double> _partialCharges;

std::map<size_t, size_t> _externalToInternalAtomTypes;
Expand All @@ -68,7 +70,7 @@ namespace molsys
void addAtomName(const std::string &atomName);
void addExternalAtomType(const size_t externalAtomType);
void addPartialCharge(const double partialCharge);
void addExternalGlobalVDWType(const size_t externalGlobalVDWType);
void addExternalGlobalVDWType(const ExtVdwType externalGlobalVDWType);

void addExternalToInternalAtomTypeElement(const size_t, const size_t);
void addAtomType(const size_t atomType);
Expand Down Expand Up @@ -104,7 +106,7 @@ namespace molsys

[[nodiscard]] std::vector<std::string> getAtomNames() const;
[[nodiscard]] std::vector<size_t> &getExternalAtomTypes();
[[nodiscard]] std::vector<size_t> &getExternalGlobalVDWTypes();
[[nodiscard]] std::vector<ExtVdwType> &getExternalGlobalVDWTypes();
[[nodiscard]] std::vector<double> &getPartialCharges();

[[nodiscard]] std::map<size_t, size_t> getExternalToInternalAtomTypes(
Expand Down
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