Encapsulate bond parameters

src/core/bonded_interactions/CMakeLists.txt

@@ -17,13 +17,4 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-target_sources(
-  espresso_core
-  PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/angle_cosine.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/angle_cossquare.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/bonded_interaction_data.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/bonded_tab.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/fene.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/rigid_bond.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/thermalized_bond.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/thermalized_bond_utils.cpp)
+target_sources(espresso_core PRIVATE bonded_interaction_data.cpp)

src/core/bonded_interactions/angle_common.hpp

@@ -18,8 +18,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef ANGLE_COMMON_H
-#define ANGLE_COMMON_H
+
+#pragma once
+
 /** \file
  *  Common code for functions calculating angle forces.
  */
@@ -95,5 +96,3 @@ angle_generic_force(Utils::Vector3d const &vec1, Utils::Vector3d const &vec2,
   auto f_mid = -(f_left + f_right);
   return std::make_tuple(f_mid, f_left, f_right);
 }
-
-#endif /* ANGLE_COMMON_H */

src/core/bonded_interactions/angle_cosine.hpp

@@ -18,8 +18,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef ANGLE_COSINE_H
-#define ANGLE_COSINE_H
+
+#pragma once
+
 /** \file
  *  Routines to calculate the angle energy or/and and force
  *  for a particle triple using the potential described in
@@ -50,7 +51,12 @@ struct AngleCosineBond {
 
   static constexpr int num = 2;
 
-  AngleCosineBond(double bend, double phi0);
+  AngleCosineBond(double bend, double phi0) {
+    this->bend = bend;
+    this->phi0 = phi0;
+    this->cos_phi0 = cos(phi0);
+    this->sin_phi0 = sin(phi0);
+  }
 
   std::tuple<Utils::Vector3d, Utils::Vector3d, Utils::Vector3d>
   forces(Utils::Vector3d const &vec1, Utils::Vector3d const &vec2) const;
@@ -98,5 +104,3 @@ inline double AngleCosineBond::energy(Utils::Vector3d const &vec1,
   // trig identity: cos(phi - phi0) = cos(phi)cos(phi0) + sin(phi)sin(phi0)
   return bend * (1 - (cos_phi * cos_phi0 + sin_phi * sin_phi0));
 }
-
-#endif /* ANGLE_COSINE_H */

src/core/bonded_interactions/angle_cossquare.hpp

@@ -18,8 +18,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef ANGLE_COSSQUARE_H
-#define ANGLE_COSSQUARE_H
+
+#pragma once
+
 /** \file
  *  Routines to calculate the angle energy or/and and force
  *  for a particle triple using the potential described in
@@ -31,6 +32,7 @@
 #include <utils/Vector.hpp>
 #include <utils/math/sqr.hpp>
 
+#include <cmath>
 #include <tuple>
 
 /** Parameters for three-body angular potential (cossquare). */
@@ -46,7 +48,11 @@ struct AngleCossquareBond {
 
   static constexpr int num = 2;
 
-  AngleCossquareBond(double bend, double phi0);
+  AngleCossquareBond(double bend, double phi0) {
+    this->bend = bend;
+    this->phi0 = phi0;
+    this->cos_phi0 = cos(phi0);
+  }
 
   std::tuple<Utils::Vector3d, Utils::Vector3d, Utils::Vector3d>
   forces(Utils::Vector3d const &vec1, Utils::Vector3d const &vec2) const;
@@ -87,5 +93,3 @@ inline double AngleCossquareBond::energy(Utils::Vector3d const &vec1,
   auto const cos_phi = calc_cosine(vec1, vec2, true);
   return 0.5 * bend * Utils::sqr(cos_phi - cos_phi0);
 }
-
-#endif /* ANGLE_COSSQUARE_H */

src/core/bonded_interactions/angle_harmonic.hpp

@@ -18,8 +18,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef ANGLE_HARMONIC_H
-#define ANGLE_HARMONIC_H
+
+#pragma once
+
 /** \file
  *  Routines to calculate the angle energy or/and and force
  *  for a particle triple using the potential described in
@@ -91,5 +92,3 @@ inline double AngleHarmonicBond::energy(Utils::Vector3d const &vec1,
   auto const phi = acos(cos_phi);
   return 0.5 * bend * Utils::sqr(phi - phi0);
 }
-
-#endif /* ANGLE_HARMONIC_H */

src/core/bonded_interactions/bonded_coulomb.hpp

@@ -18,8 +18,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef CORE_BN_IA_BONDED_COULOMB_HPP
-#define CORE_BN_IA_BONDED_COULOMB_HPP
+
+#pragma once
+
 /** \file
  *  Routines to calculate the bonded Coulomb potential between
  *  particle pairs.
@@ -85,5 +86,3 @@ BondedCoulomb::energy(double const q1q2, Utils::Vector3d const &dx) const {
   return .0;
 #endif
 }
-
-#endif

src/core/bonded_interactions/bonded_coulomb_sr.hpp

@@ -18,8 +18,9 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef CORE_BN_IA_BONDED_COULOMB_SR_HPP
-#define CORE_BN_IA_BONDED_COULOMB_SR_HPP
+
+#pragma once
+
 /** \file
  *  Routines to calculate the short-range part of the bonded Coulomb potential
  *  between particle pairs. Can be used to subtract certain intramolecular
@@ -98,5 +99,3 @@ inline boost::optional<double> BondedCoulombSR::energy(
   return 0.;
 #endif
 }
-
-#endif

src/core/bonded_interactions/bonded_interaction_data.cpp

@@ -17,7 +17,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 #include "bonded_interaction_data.hpp"
+#include "rigid_bond.hpp"
 #include "system/System.hpp"
+#include "thermalized_bond.hpp"
 
 #include <boost/range/numeric.hpp>
 #include <boost/variant.hpp>
@@ -59,7 +61,23 @@ double maximal_cutoff_bonded() {
 }
 
 void BondedInteractionsMap::on_ia_change() {
+  n_thermalized_bonds = 0;
+#ifdef BOND_CONSTRAINT
+  n_rigid_bonds = 0;
+#endif
+  for (auto &kv : *this) {
+    if (boost::get<ThermalizedBond>(&(*kv.second)) != nullptr) {
+      ++n_thermalized_bonds;
+    }
+#ifdef BOND_CONSTRAINT
+    if (boost::get<RigidBond>(&(*kv.second)) != nullptr) {
+      ++n_rigid_bonds;
+    }
+#endif
+  }
   if (System::is_system_set()) {
-    System::get_system().on_short_range_ia_change();
+    auto &system = System::get_system();
+    system.on_short_range_ia_change();
+    system.on_thermostat_param_change(); // thermalized bonds
   }
 }

src/core/bonded_interactions/bonded_interaction_data.hpp

@@ -143,10 +143,18 @@ class BondedInteractionsMap {
   auto get_zero_based_type(int bond_id) const {
     return contains(bond_id) ? at(bond_id)->which() : 0;
   }
+  auto get_n_thermalized_bonds() const { return n_thermalized_bonds; }
+#ifdef BOND_CONSTRAINT
+  auto get_n_rigid_bonds() const { return n_rigid_bonds; }
+#endif
 
 private:
   container_type m_params = {};
   key_type next_key = static_cast<key_type>(0);
+  int n_thermalized_bonds = 0;
+#ifdef BOND_CONSTRAINT
+  int n_rigid_bonds = 0;
+#endif
   void on_ia_change();
 };
 

src/core/bonded_interactions/bonded_interaction_utils.hpp

@@ -16,8 +16,8 @@
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef CORE_BN_IA_BONDED_INTERACTION_UTILS_HPP
-#define CORE_BN_IA_BONDED_INTERACTION_UTILS_HPP
+
+#pragma once
 
 #include "bonded_interaction_data.hpp"
 
@@ -67,5 +67,3 @@ inline bool pair_bond_enum_exists_between(Particle const &p1,
   return pair_bond_enum_exists_on<BondType>(p1, p2) or
          pair_bond_enum_exists_on<BondType>(p2, p1);
 }
-
-#endif

src/core/bonded_interactions/bonded_interactions.dox

@@ -44,9 +44,9 @@
  *
  *  @subsection bondedIA_new_struct Defining the new interaction
  *
- *  Every interaction resides in its own source .cpp and .hpp files. A simple
- *  example for a bonded interaction is the FENE bond in @ref fene.hpp and
- *  @ref fene.cpp. Use these two files as templates for your interaction.
+ *  Every interaction resides in its own source .hpp file. A simple
+ *  example for a bonded interaction is the FENE bond in @ref fene.hpp.
+ *  Use this file as template for your new interaction.
  *
  *  The first step is to create a new @c struct which represents your new
  *  bond type inside the .hpp file. It needs to have the following members: