Harmonic potential for external distance interaction

book/content.en/docs/reference/forcefields/external/distance/HarmonicGroovePotential.md

@@ -0,0 +1,36 @@
++++
+title = "HarmonicGroove"
+weight = 100000
++++
+
+# HarmonicGroovePotential
+
+It is a Harmonic potential between particle and a spatial structure.
+
+{{<<katex dispaly>>}}
+U(r) = k(v - v_0)^2
+{{</katex>}}
+
+## Example
+
+```toml
+[[forcefields.external]]
+interaction    = "Distance"
+potential      = "HarmonicGroove"
+shape.name     = "AxisAlignedPlane"
+shape.axis     = "X"
+shape.position = 0.0
+shape.margin   = 1.0
+
+parameters = [
+    {index = 0, k = 1.0, v0 = 1.0},
+    # ...
+]
+```
+
+## Input Reference
+
+- `k`: Floating
+    - It determines the strength of the potential.
+- `v0`: Floating
+    - It determines the native length.

book/content.en/docs/reference/forcefields/external/distance/_index.md

@@ -31,6 +31,7 @@ parameters     = [
   - The following potentials are available.
   - [`"LennardJonesWall"`]({{<relref "LennardJonesWallPotential.md">}})
   - [`"ExcludedVolumeWall"`]({{<relref "ExcludedVolumeWallPotential.md">}})
+  - [`"HarmonicGroove"`]({{<relref "HarmonicGroovePotential.md">}})
   - [`"ImplicitMembrane"`]({{<relref "ImplicitMembranePotential.md">}})
 - `shape`: Table
   - The shape and the position of a structure that interacts with particles.

book/content.en/docs/reference/forcefields/global/_index.md

@@ -12,11 +12,11 @@ bookCollapseSection = true
 
 It depends on the distances between two particles.
 
-## [3SPN2BaseBase](3SPN2BaseBaseInteraction.md)
+## [3SPN2BaseBase]({{<relref "3SPN2BaseBaseInteraction.md">}})
 
 It is specific to 3SPN2 Coarse-Grained DNA model.
 
-## [ProteinDNANonSpecific](ProteinDNANonSpecificInteraction.md)
+## [ProteinDNANonSpecific]({{<relref "ProteinDNANonSpecificInteraction.md">}})
 
 It is a Coarse-Grained hydrogen bond model.
 

book/content.en/docs/reference/forcefields/global/pair/UniformLennardJonesPotential.md

@@ -38,7 +38,7 @@ parameters = [
   - The cutoff distance relative to the maximum {{<katex>}}\sigma_{ij}{{</katex>}}.
 - `index`: Integer
   - The index of the particle.
-- `offset`: Integer (ptional. By default, 0.)
+- `offset`: Integer (optional. By default, 0.)
   - Offset of the index.
 - `sigma`: Floating
   - It determines the effective particle size.

book/content.ja/docs/reference/forcefields/external/distance/HarmonicGroovePotential.md

@@ -0,0 +1,36 @@
++++
+title  = "HarmonicGroove"
+weight = 200000
++++
+
+# HarmonicGroovePotential
+
+シンプルな調和振動子ポテンシャルです。
+
+{{<katex display>}}
+U(r) = k (v - v_0)^2
+{{</katex>}}
+
+## Example
+
+```toml
+[[forcefields.external]]
+interaction    = "Distance"
+potential      = "HarmonicGroove"
+shape.name     = "AxisAlignedPlane"
+shape.axis     = "X"
+shape.position = 0.0
+shape.margin   = 1.0
+
+parameters = [
+    {index = 0, k = 1.0, v0 = 1.0},
+    # ...
+]
+```
+
+## Input Reference
+
+- `k`: 浮動小数点数型
+    - ポテンシャルの強さを指定します。
+- `v0`: 浮動小数点数型
+    - 最安定点を指定します。

book/content.ja/docs/reference/forcefields/external/distance/_index.md

@@ -31,6 +31,7 @@ parameters     = [
   - The following potentials are available.
   - [`"LennardJonesWall"`]({{<relref "LennardJonesWallPotential.md">}})
   - [`"ExcludedVolumeWall"`]({{<relref "ExcludedVolumeWallPotential.md">}})
+  - [`"HarmonicGroove"`]({{<relref "HarmonicGroovePotential.md">}})
   - [`"ImplicitMembrane"`]({{<relref "ImplicitMembranePotential.md">}})
 - `shape`: Table
   - The shape and the position of a structure that interacts with particles.

mjolnir/forcefield/external/CMakeLists.txt

@@ -2,6 +2,7 @@ set(mjolnir_forcefield_external_cpp_files
     "${CMAKE_CURRENT_SOURCE_DIR}/ExcludedVolumeWallPotential.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/ImplicitMembranePotential.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/LennardJonesWallPotential.cpp"
+    "${CMAKE_CURRENT_SOURCE_DIR}/HarmonicGroovePotential.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/RectangularBoxInteraction.cpp"
     )
 set(mjolnir_forcefield_cpp_files

mjolnir/forcefield/external/HarmonicGroovePotential.cpp

@@ -0,0 +1,11 @@
+#include <mjolnir/forcefield/external/HarmonicGroovePotential.hpp>
+
+#ifndef MJOLNIR_SEPARATE_BUILD
+#error "MJOLNIR_SEPARATE_BUILD flag is required"
+#endif
+
+namespace mjolnir
+{
+template class HarmonicGroovePotential<double>;
+template class HarmonicGroovePotential<float>;
+} // mjolnir

mjolnir/forcefield/external/HarmonicGroovePotential.hpp

@@ -0,0 +1,93 @@
+#ifndef MJOLNIR_POTENTIAL_EXTERNAL_HARMONIC_GROOVE_POTENTIAL_HPP
+#define MJOLNIR_POTENTIAL_EXTERNAL_HARMONIC_GROOVE_POTENTIAL_HPP
+#include <mjolnir/core/System.hpp>
+#include <limits>
+
+namespace mjolnir
+{
+
+/*! @brief harmonic potential                                                     *
+ * designed for external force field. Force particle-particle Harmonic potential, *
+ * see mjolnir/forcefield/local/HarmonicPotential.hpp                             */
+template<typename realT>
+class HarmonicGroovePotential
+{
+  public:
+    using real_type      = realT;
+    using parameter_type = std::pair<real_type, real_type>;
+    using container_type = std::vector<parameter_type>;
+
+    static constexpr real_type default_cutoff() noexcept
+    {
+        return std::numeric_limits<real_type>::max();
+    }
+    static constexpr parameter_type default_parameter() noexcept
+    {
+        return std::make_pair(real_type(0), real_type(0));
+    }
+
+  public:
+
+    HarmonicGroovePotential(
+        const std::vector<std::pair<std::size_t, parameter_type>>& params)
+    {
+        this->parameters_.resize(params.size());
+        this->participants_.reserve(params.size());
+        for(const auto& idxp : params)
+        {
+            const auto idx = idxp.first;
+            this->participants_.push_back(idx);
+            if(idx >= this->parameters_.size())
+            {
+                this->parameters_.resize(idx+1, default_parameter());
+            }
+            this->parameters_.at(idx) = idxp.second;
+        }
+    }
+    ~HarmonicGroovePotential(){}
+
+    real_type potential(const std::size_t i, const real_type v) const noexcept
+    {
+        const parameter_type k_v0 = this->parameters_[i];
+        const real_type dv   = v - k_v0.second;
+        return k_v0.first * dv * dv;
+    }
+
+    real_type derivative(const std::size_t i, const real_type v) const noexcept
+    {
+        const parameter_type k_v0 = this->parameters_[i];
+        return 2 * k_v0.first * (v - k_v0.second);
+    }
+
+    real_type max_cutoff_length() const noexcept
+    {
+        return this->default_cutoff();
+    }
+
+    std::vector<std::size_t> const& participants() const noexcept
+    {
+        return participants_;
+    }
+
+    // nothing to do when system parameters change.
+    template<typename T>
+    void update(const System<T>&) const noexcept {return;}
+
+    const char* name() const noexcept {return "HarmonicGroove";}
+
+    container_type&       parameters()       noexcept {return parameters_;}
+    container_type const& parameters() const noexcept {return parameters_;}
+
+  private:
+
+    container_type           parameters_;
+    std::vector<std::size_t> participants_;
+};
+
+#ifndef MJOLNIR_SEPARATE_BUILD
+extern template class HarmonicGroovePotential<double>;
+extern template class HarmonicGroovePotential<float>;
+#endif // MJOLNIR_SEPARATE_BUILD
+
+} // mjolnir
+#endif // MJOLNIR_POTENTIAL_EXTERNAL_HARMONIC_GROOVE_POTENTIAL_HPP

mjolnir/input/read_external_interaction.cpp

@@ -26,10 +26,10 @@ template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<float,  Un
 template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<double, CuboidalPeriodicBoundary>>> read_afm_flexible_fitting_interaction(const toml::value&);
 template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<float,  CuboidalPeriodicBoundary>>> read_afm_flexible_fitting_interaction(const toml::value&);
 
-template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<double, UnlimitedBoundary>       >> read_external_distance_interaction_shape(const toml::value& external);
-template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<float,  UnlimitedBoundary>       >> read_external_distance_interaction_shape(const toml::value& external);
-template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<double, CuboidalPeriodicBoundary>>> read_external_distance_interaction_shape(const toml::value& external);
-template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<float,  CuboidalPeriodicBoundary>>> read_external_distance_interaction_shape(const toml::value& external);
+template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<double, UnlimitedBoundary>       >> read_external_distance_interaction(const toml::value& external);
+template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<float,  UnlimitedBoundary>       >> read_external_distance_interaction(const toml::value& external);
+template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<double, CuboidalPeriodicBoundary>>> read_external_distance_interaction(const toml::value& external);
+template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<float,  CuboidalPeriodicBoundary>>> read_external_distance_interaction(const toml::value& external);
 
 template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<double, UnlimitedBoundary>       >> read_pulling_force_interaction(const toml::value& external);
 template std::unique_ptr<ExternalForceInteractionBase<SimulatorTraits<float,  UnlimitedBoundary>       >> read_pulling_force_interaction(const toml::value& external);