core: Introduce THERMOSTAT_PER_PARTICLE feature

This replaces BROWNIAN_PER_PARTICLE and LANGEVIN_PER_PARTICLE.

doc/sphinx/advanced_methods.rst

@@ -1486,7 +1486,7 @@ Particle polarizability with thermalized cold Drude oscillators
 
 .. note::
 
-    Requires features ``THOLE``, ``P3M``, ``LANGEVIN_PER_PARTICLE``.
+    Requires features ``THOLE``, ``P3M``, ``THERMOSTAT_PER_PARTICLE``.
 
 .. note::
 
@@ -1515,7 +1515,7 @@ In |es|, the basic ingredients to simulate such a system are split into three bo
 
 The system-wide thermostat has to be applied to the centre of mass and not to
 the core particle directly. Therefore, the particles have to be excluded from
-global thermostatting.  With ``LANGEVIN_PER_PARTICLE`` enabled, we set the
+global thermostatting.  With ``THERMOSTAT_PER_PARTICLE`` enabled, we set the
 friction coefficient of the Drude complex to zero, which allows
 to still use a global Langevin thermostat for non-polarizable particles.
 

doc/sphinx/installation.rst

@@ -315,11 +315,8 @@ General features
       additional degrees of freedom, which for example means that the
       kinetic energy changes at constant temperature is twice as large.
 
--  ``LANGEVIN_PER_PARTICLE`` Allows to choose the Langevin friction coefficient
-   per particle.
-
--  ``BROWNIAN_PER_PARTICLE`` Allows to choose the Brownian friction coefficient
-   per particle.
+-  ``THERMOSTAT_PER_PARTICLE`` Allows setting a per-particle friction
+   coefficient for the Langevin and Brownian thermostats.
 
 -  ``ROTATIONAL_INERTIA``
 

doc/sphinx/inter_non-bonded.rst

@@ -659,7 +659,7 @@ To use the script, compile espresso with the following features:
 
     #define EXTERNAL_FORCES
     #define MASS
-    #define LANGEVIN_PER_PARTICLE
+    #define THERMOSTAT_PER_PARTICLE
     #define ROTATION
     #define ROTATIONAL_INERTIA
     #define ELECTROSTATICS

doc/sphinx/system_setup.rst

@@ -278,7 +278,7 @@ the anisotropic diffusion of anisotropic colloids (rods, etc.).
 
 Using the Langevin thermostat, it is possible to set a
 friction coefficient for every particle individually via the feature
-``LANGEVIN_PER_PARTICLE``.  Consult the reference of the ``part`` command
+``THERMOSTAT_PER_PARTICLE``.  Consult the reference of the ``part`` command
 (chapter :ref:`Setting up particles`) for information on how to achieve this.
 
 .. _LB thermostat:
@@ -426,7 +426,7 @@ Best explained in an example::
 where ``gamma`` (hereinafter :math:`\gamma`) is a viscous friction coefficient.
 In terms of the Python interface and setup, the Brownian thermostat is very
 similar to the :ref:`Langevin thermostat`. The feature
-``BROWNIAN_PER_PARTICLE`` is used to control the per-particle
+``THERMOSTAT_PER_PARTICLE`` is used to control the per-particle
 friction coefficient setup. The major differences are
 its internal integrator implementation and other temporal constraints.
 The integrator is still a symplectic Velocity Verlet-like one.

maintainer/configs/maxset.hpp

@@ -32,8 +32,7 @@
 
 #define BOND_CONSTRAINT
 #define COLLISION_DETECTION
-#define LANGEVIN_PER_PARTICLE
-#define BROWNIAN_PER_PARTICLE
+#define THERMOSTAT_PER_PARTICLE
 
 #define NPT
 

maintainer/configs/no_rotation.hpp

@@ -29,8 +29,7 @@
 // Geometry, equation of motion, thermostat/barostat
 #define MASS
 #define EXTERNAL_FORCES
-#define LANGEVIN_PER_PARTICLE
-#define BROWNIAN_PER_PARTICLE
+#define THERMOSTAT_PER_PARTICLE
 #define BOND_CONSTRAINT
 #define NPT
 #define DPD

samples/chamber_game.py

@@ -32,7 +32,7 @@
 from espressomd.visualization_opengl import openGLLive, KeyboardButtonEvent, KeyboardFireEvent
 
 required_features = ["LENNARD_JONES", "WCA", "MASS",
-                     "EXTERNAL_FORCES", "LANGEVIN_PER_PARTICLE"]
+                     "EXTERNAL_FORCES", "THERMOSTAT_PER_PARTICLE"]
 espressomd.assert_features(required_features)
 
 print("""THE CHAMBER GAME

samples/drude_bmimpf6.py

@@ -27,7 +27,7 @@
 import espressomd
 required_features = ["LENNARD_JONES", "P3M", "MASS", "ROTATION",
                      "ROTATIONAL_INERTIA", "VIRTUAL_SITES_RELATIVE",
-                     "THOLE", "LANGEVIN_PER_PARTICLE"]
+                     "THOLE", "THERMOSTAT_PER_PARTICLE"]
 espressomd.assert_features(required_features)
 
 import espressomd.observables

src/config/features.def

@@ -18,8 +18,7 @@ EXTERNAL_FORCES
 MASS
 EXCLUSIONS
 BOND_CONSTRAINT
-LANGEVIN_PER_PARTICLE
-BROWNIAN_PER_PARTICLE
+THERMOSTAT_PER_PARTICLE
 COLLISION_DETECTION
 NPT
 ENGINE                          implies ROTATION, EXTERNAL_FORCES

src/config/myconfig-default.hpp

@@ -32,8 +32,7 @@
 #define MASS
 #define PARTICLE_ANISOTROPY
 #define EXTERNAL_FORCES
-#define LANGEVIN_PER_PARTICLE
-#define BROWNIAN_PER_PARTICLE
+#define THERMOSTAT_PER_PARTICLE
 #define BOND_CONSTRAINT
 #define NPT
 #define DPD

src/core/Particle.hpp

@@ -146,7 +146,7 @@ struct ParticleProperties {
   static constexpr bool is_virtual = false;
 #endif /* VIRTUAL_SITES */
 
-#if defined(LANGEVIN_PER_PARTICLE) || defined(BROWNIAN_PER_PARTICLE)
+#ifdef THERMOSTAT_PER_PARTICLE
 #ifndef PARTICLE_ANISOTROPY
   double gamma = -1.;
 #else
@@ -160,7 +160,7 @@ struct ParticleProperties {
   Utils::Vector3d gamma_rot = {-1., -1., -1.};
 #endif // ROTATIONAL_INERTIA
 #endif // ROTATION
-#endif // LANGEVIN_PER_PARTICLE || BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
 #ifdef EXTERNAL_FORCES
   /** flag whether to fix a particle in space.
@@ -219,12 +219,12 @@ struct ParticleProperties {
 #endif
 #endif /* VIRTUAL_SITES */
 
-#if defined(LANGEVIN_PER_PARTICLE) || defined(BROWNIAN_PER_PARTICLE)
+#ifdef THERMOSTAT_PER_PARTICLE
     ar γ
 #ifdef ROTATION
     ar &gamma_rot;
 #endif
-#endif // LANGEVIN_PER_PARTICLE || BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 #ifdef EXTERNAL_FORCES
     ar &ext_flag;
     ar &ext_force;

src/core/particle_data.cpp

@@ -121,7 +121,7 @@ using UpdatePropertyMessage = boost::variant
                          &Prop::vs_relative>
 #endif
 #endif
-#if defined(LANGEVIN_PER_PARTICLE) || defined(BROWNIAN_PER_PARTICLE)
+#ifdef THERMOSTAT_PER_PARTICLE
 #ifndef PARTICLE_ANISOTROPY
         , UpdateProperty<double, &Prop::gamma>
 #else
@@ -134,7 +134,7 @@ using UpdatePropertyMessage = boost::variant
         , UpdateProperty<Utils::Vector3d, &Prop::gamma_rot>
 #endif // PARTICLE_ANISOTROPY
 #endif // ROTATION
-#endif // LANGEVIN_PER_PARTICLE || BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 #ifdef EXTERNAL_FORCES
         , UpdateProperty<uint8_t, &Prop::ext_flag>
         , UpdateProperty<Utils::Vector3d, &Prop::ext_force>
@@ -865,8 +865,7 @@ void set_particle_torque_lab(int part, const Utils::Vector3d &torque_lab) {
 }
 #endif
 
-#if defined(LANGEVIN_PER_PARTICLE) || defined(BROWNIAN_PER_PARTICLE)
-
+#ifdef THERMOSTAT_PER_PARTICLE
 #ifndef PARTICLE_ANISOTROPY
 void set_particle_gamma(int part, double gamma) {
   mpi_update_particle_property<double, &ParticleProperties::gamma>(part, gamma);
@@ -891,7 +890,7 @@ void set_particle_gamma_rot(int part, Utils::Vector3d gamma_rot) {
 }
 #endif // PARTICLE_ANISOTROPY
 #endif // ROTATION
-#endif // LANGEVIN_PER_PARTICLE || BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
 #ifdef EXTERNAL_FORCES
 #ifdef ROTATION
@@ -1241,7 +1240,7 @@ void pointer_to_fix(Particle const *p, const uint8_t *&res) {
 }
 #endif
 
-#if defined(LANGEVIN_PER_PARTICLE) || defined(BROWNIAN_PER_PARTICLE)
+#ifdef THERMOSTAT_PER_PARTICLE
 void pointer_to_gamma(Particle const *p, double const *&res) {
 #ifndef PARTICLE_ANISOTROPY
   res = &(p->p.gamma);
@@ -1260,7 +1259,7 @@ void pointer_to_gamma_rot(Particle const *p, double const *&res) {
 }
 #endif // ROTATION
 
-#endif // LANGEVIN_PER_PARTICLE || BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
 #ifdef ENGINE
 void pointer_to_swimming(Particle const *p,

src/core/particle_data.hpp

@@ -242,7 +242,7 @@ void set_particle_vs_relative(int part, int vs_relative_to, double vs_distance,
                               Utils::Quaternion<double> const &rel_ori);
 #endif
 
-#if defined(LANGEVIN_PER_PARTICLE) || defined(BROWNIAN_PER_PARTICLE)
+#ifdef THERMOSTAT_PER_PARTICLE
 /** Call only on the master node: set particle frictional coefficient.
  *  @param part the particle.
  *  @param gamma its new frictional coefficient.
@@ -259,7 +259,7 @@ void set_particle_gamma_rot(int part, double gamma);
 void set_particle_gamma_rot(int part, Utils::Vector3d gamma_rot);
 #endif
 #endif
-#endif // LANGEVIN_PER_PARTICLE || BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
 #ifdef EXTERNAL_FORCES
 #ifdef ROTATION
@@ -385,12 +385,12 @@ void pointer_to_ext_torque(Particle const *p, double const *&res2);
 void pointer_to_fix(Particle const *p, const uint8_t *&res);
 #endif
 
-#if defined(LANGEVIN_PER_PARTICLE) || defined(BROWNIAN_PER_PARTICLE)
+#ifdef THERMOSTAT_PER_PARTICLE
 void pointer_to_gamma(Particle const *p, double const *&res);
 #ifdef ROTATION
 void pointer_to_gamma_rot(Particle const *p, double const *&res);
 #endif
-#endif // LANGEVIN_PER_PARTICLE || BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
 #ifdef ENGINE
 void pointer_to_swimming(Particle const *p,

src/core/thermostats/brownian_inline.hpp

@@ -44,7 +44,7 @@ inline Utils::Vector3d bd_drag(Thermostat::GammaType const &brownian_gamma,
   // The friction tensor Z from the Eq. (14.31) of Schlick2010:
   Thermostat::GammaType gamma;
 
-#ifdef BROWNIAN_PER_PARTICLE
+#ifdef THERMOSTAT_PER_PARTICLE
   if (p.p.gamma >= Thermostat::GammaType{}) {
     gamma = p.p.gamma;
   } else
@@ -106,7 +106,7 @@ inline Utils::Vector3d bd_drag_vel(Thermostat::GammaType const &brownian_gamma,
   // The friction tensor Z from the eq. (14.31) of Schlick2010:
   Thermostat::GammaType gamma;
 
-#ifdef BROWNIAN_PER_PARTICLE
+#ifdef THERMOSTAT_PER_PARTICLE
   if (p.p.gamma >= Thermostat::GammaType{}) {
     gamma = p.p.gamma;
   } else
@@ -172,7 +172,7 @@ inline Utils::Vector3d bd_random_walk(BrownianThermostat const &brownian,
     return {};
 
   Thermostat::GammaType sigma_pos = brownian.sigma_pos;
-#ifdef BROWNIAN_PER_PARTICLE
+#ifdef THERMOSTAT_PER_PARTICLE
   // override default if particle-specific gamma
   if (p.p.gamma >= Thermostat::GammaType{}) {
     if (temperature > 0.0) {
@@ -181,7 +181,7 @@ inline Utils::Vector3d bd_random_walk(BrownianThermostat const &brownian,
       sigma_pos = Thermostat::GammaType{};
     }
   }
-#endif // BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
   // Eq. (14.37) is factored by the Gaussian noise (12.22) with its squared
   // magnitude defined in the second eq. (14.38), Schlick2010.
@@ -280,7 +280,7 @@ bd_drag_rot(Thermostat::GammaType const &brownian_gamma_rotation, Particle &p,
             double dt) {
   Thermostat::GammaType gamma;
 
-#ifdef BROWNIAN_PER_PARTICLE
+#ifdef THERMOSTAT_PER_PARTICLE
   if (p.p.gamma_rot >= Thermostat::GammaType{}) {
     gamma = p.p.gamma_rot;
   } else
@@ -322,7 +322,7 @@ bd_drag_vel_rot(Thermostat::GammaType const &brownian_gamma_rotation,
                 Particle const &p) {
   Thermostat::GammaType gamma;
 
-#ifdef BROWNIAN_PER_PARTICLE
+#ifdef THERMOSTAT_PER_PARTICLE
   if (p.p.gamma_rot >= Thermostat::GammaType{}) {
     gamma = p.p.gamma_rot;
   } else
@@ -359,7 +359,7 @@ bd_random_walk_rot(BrownianThermostat const &brownian, Particle const &p,
                    double dt) {
 
   Thermostat::GammaType sigma_pos = brownian.sigma_pos_rotation;
-#ifdef BROWNIAN_PER_PARTICLE
+#ifdef THERMOSTAT_PER_PARTICLE
   // override default if particle-specific gamma
   if (p.p.gamma_rot >= Thermostat::GammaType{}) {
     if (temperature > 0.) {
@@ -368,7 +368,7 @@ bd_random_walk_rot(BrownianThermostat const &brownian, Particle const &p,
       sigma_pos = {}; // just an indication of the infinity
     }
   }
-#endif // BROWNIAN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
   Utils::Vector3d dphi = {};
   auto const noise = Random::noise_gaussian<RNGSalt::BROWNIAN_ROT_INC>(

src/core/thermostats/langevin_inline.hpp

@@ -34,7 +34,7 @@
 /** Langevin thermostat for particle translational velocities.
  *  Collects the particle velocity (different for ENGINE, PARTICLE_ANISOTROPY).
  *  Collects the langevin parameters kT, gamma (different for
- *  LANGEVIN_PER_PARTICLE). Applies the noise and friction term.
+ *  THERMOSTAT_PER_PARTICLE). Applies the noise and friction term.
  *  @param[in]     langevin       Parameters
  *  @param[in]     p              %Particle
  *  @param[in]     time_step      Time step
@@ -50,15 +50,15 @@ friction_thermo_langevin(LangevinThermostat const &langevin, Particle const &p,
   // Determine prefactors for the friction and the noise term
   Thermostat::GammaType pref_friction = langevin.pref_friction;
   Thermostat::GammaType pref_noise = langevin.pref_noise;
-#ifdef LANGEVIN_PER_PARTICLE
+#ifdef THERMOSTAT_PER_PARTICLE
   // override default if particle-specific gamma
   if (p.p.gamma >= Thermostat::GammaType{}) {
     auto const gamma =
         p.p.gamma >= Thermostat::GammaType{} ? p.p.gamma : langevin.gamma;
     pref_friction = -gamma;
     pref_noise = LangevinThermostat::sigma(temperature, time_step, gamma);
   }
-#endif // LANGEVIN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
   // Get effective velocity in the thermostatting
 #ifdef ENGINE
@@ -94,7 +94,7 @@ friction_thermo_langevin(LangevinThermostat const &langevin, Particle const &p,
 /** Langevin thermostat for particle angular velocities.
  *  Collects the particle velocity (different for PARTICLE_ANISOTROPY).
  *  Collects the langevin parameters kT, gamma_rot (different for
- *  LANGEVIN_PER_PARTICLE). Applies the noise and friction term.
+ *  THERMOSTAT_PER_PARTICLE). Applies the noise and friction term.
  *  @param[in]     langevin       Parameters
  *  @param[in]     p              %Particle
  *  @param[in]     time_step      Time step
@@ -106,7 +106,7 @@ friction_thermo_langevin_rotation(LangevinThermostat const &langevin,
   auto pref_friction = -langevin.gamma_rotation;
   auto pref_noise = langevin.pref_noise_rotation;
 
-#ifdef LANGEVIN_PER_PARTICLE
+#ifdef THERMOSTAT_PER_PARTICLE
   // override default if particle-specific gamma
   if (p.p.gamma_rot >= Thermostat::GammaType{}) {
     auto const gamma = p.p.gamma_rot >= Thermostat::GammaType{}
@@ -115,7 +115,7 @@ friction_thermo_langevin_rotation(LangevinThermostat const &langevin,
     pref_friction = -gamma;
     pref_noise = LangevinThermostat::sigma(temperature, time_step, gamma);
   }
-#endif // LANGEVIN_PER_PARTICLE
+#endif // THERMOSTAT_PER_PARTICLE
 
   auto const noise = Random::noise_uniform<RNGSalt::LANGEVIN_ROT>(
       langevin.rng_counter(), langevin.rng_seed(), p.p.identity);

src/python/espressomd/particle_data.pxd

@@ -129,7 +129,7 @@ cdef extern from "particle_data.hpp":
         void set_particle_virtual(int part, int isVirtual)
         void pointer_to_virtual(const particle * P, const bint * & res)
 
-    IF LANGEVIN_PER_PARTICLE or BROWNIAN_PER_PARTICLE:
+    IF THERMOSTAT_PER_PARTICLE:
         IF PARTICLE_ANISOTROPY:
             void set_particle_gamma(int part, Vector3d gamma)
         ELSE: