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Remove Langevin noise correlation #3355

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merged 7 commits into from
Dec 7, 2019
Merged

Remove Langevin noise correlation #3355

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ef964aa
Update RNG and thermostat docs
jngrad Dec 4, 2019
1d9806e
Remove correlation in Langevin noise
jngrad Dec 4, 2019
b7b0255
Add test for Langevin noise correlation
jngrad Dec 4, 2019
9993715
Fix feature guards
jngrad Dec 4, 2019
a30edc8
Produce more descriptive error messages
jngrad Dec 5, 2019
c0a3306
Reduce test temperature
jngrad Dec 5, 2019
f81e7b0
testsuite: dpd: Script momentum conservation check for dpd + langevin
fweik Dec 5, 2019
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20 changes: 8 additions & 12 deletions src/core/random.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,8 @@
#define RANDOM_H

/** \file

A random generator
*/
* Random number generation using Philox.
*/

#include "errorhandling.hpp"

Expand All @@ -50,6 +49,7 @@ enum class RNGSalt : uint64_t {
FLUID = 0,
PARTICLES,
LANGEVIN,
LANGEVIN_ROT,
SALT_DPD,
THERMALIZED_BOND
};
Expand Down Expand Up @@ -96,8 +96,7 @@ inline void unseeded_error() {

/**
* @brief checks the seeded state and throws error if unseeded
*
**/
*/
inline void check_user_has_seeded() {
static bool unseeded_error_thrown = false;
if (!user_has_seeded && !unseeded_error_thrown) {
Expand All @@ -111,26 +110,24 @@ inline void check_user_has_seeded() {
*
* @param cnt Unused.
* @param seeds A vector of seeds, must be at least n_nodes long.
**/
*/
void mpi_random_seed(int cnt, std::vector<int> &seeds);

/**
* @brief Gets a string representation of the state of all
* the nodes.
* @brief Gets a string representation of the state of all the nodes.
*/
std::string mpi_random_get_stat();

/**
* @brief Set the seeds on all the node to the state represented
* by the string.
* The string representation must be one that was returned by
* mpi_random_get_stat.
* @ref mpi_random_get_stat.
*/
void mpi_random_set_stat(const std::vector<std::string> &stat);

/**
* @brief
* Get the state size of the random number generator
* @brief Get the state size of the random number generator
*/
int get_state_size_of_generator();

Expand All @@ -152,7 +149,6 @@ void init_random_seed(int seed);
* @brief Draws a random real number from the uniform distribution in the range
* [0,1)
*/

inline double d_random() {
using namespace Random;
check_user_has_seeded();
Expand Down
10 changes: 1 addition & 9 deletions src/core/thermostat.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -35,18 +35,14 @@
#include <iostream>
#include <unistd.h>

/** thermostat switch */
int thermo_switch = THERMO_OFF;
/** Temperature */
double temperature = 0.0;

/** True if the thermostat should act on virtual particles. */
bool thermo_virtual = true;

using Thermostat::GammaType;

namespace {
/** @name Langevin parameters sentinel
/** @name Langevin parameters sentinels.
* These functions return the sentinel value for the Langevin
* parameters, indicating that they have not been set yet.
*/
Expand All @@ -56,11 +52,7 @@ Utils::Vector3d sentinel(Utils::Vector3d) { return {-1.0, -1.0, -1.0}; }
/*@}*/
} // namespace

/* LANGEVIN THERMOSTAT */

/** Langevin friction coefficient gamma for translation. */
GammaType langevin_gamma = sentinel(GammaType{});
/** Friction coefficient gamma for rotation. */
GammaType langevin_gamma_rotation = sentinel(GammaType{});
GammaType langevin_pref1;
GammaType langevin_pref2;
Expand Down
79 changes: 43 additions & 36 deletions src/core/thermostat.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
#ifndef CORE_THERMOSTAT_HPP
#define CORE_THERMOSTAT_HPP
/** \file
* Implementation in \ref thermostat.cpp.
*/

#include "config.hpp"
Expand All @@ -38,7 +39,6 @@
#include <tuple>

/** \name Thermostat switches */
/************************************************************/
/*@{*/
#define THERMO_OFF 0
#define THERMO_LANGEVIN 1
Expand All @@ -62,55 +62,60 @@ using GammaType = double;
* exported variables
************************************************/

/** Switch determining which thermostat to use. This is a or'd value
of the different possible thermostats (defines: \ref THERMO_OFF,
\ref THERMO_LANGEVIN, \ref THERMO_DPD \ref THERMO_NPT_ISO). If it
is zero all thermostats are switched off and the temperature is
set to zero. */
/** Switch determining which thermostat(s) to use. This is a or'd value
* of the different possible thermostats (defines: \ref THERMO_OFF,
* \ref THERMO_LANGEVIN, \ref THERMO_DPD \ref THERMO_NPT_ISO). If it
* is zero all thermostats are switched off and the temperature is
* set to zero.
*/
extern int thermo_switch;

/** temperature. */
/** Temperature of the thermostat. */
extern double temperature;

/** True if the thermostat should act on virtual particles. */
extern bool thermo_virtual;

/** Langevin friction coefficient gamma. */
/** Langevin friction coefficient gamma for translation. */
extern Thermostat::GammaType langevin_gamma;
/** Langevin friction coefficient gamma. */
/** Langevin friction coefficient gamma for rotation. */
extern Thermostat::GammaType langevin_gamma_rotation;

/** Friction coefficient for nptiso-thermostat's inline-function
* friction_therm0_nptiso */
/** Friction coefficient for nptiso-thermostat's function
* @ref friction_therm0_nptiso
*/
extern double nptiso_gamma0;
/** Friction coefficient for nptiso-thermostat's inline-function
* friction_thermV_nptiso */
/** Friction coefficient for nptiso-thermostat's function
* @ref friction_thermV_nptiso
*/
extern double nptiso_gammav;

/** Langevin RNG counter, used for both translation and rotation. */
extern std::unique_ptr<Utils::Counter<uint64_t>> langevin_rng_counter;

/************************************************
* functions
************************************************/

/** only require seed if rng is not initialized */
/** Only require seed if rng is not initialized. */
bool langevin_is_seed_required();

/** philox functionality: increment, get/set */
/** @name philox functionality: increment, get/set */
/*@{*/
void langevin_rng_counter_increment();
void langevin_set_rng_state(uint64_t counter);
uint64_t langevin_get_rng_state();
/*@}*/

/** initialize constants of the thermostat on
start of integration */
/** Initialize constants of the thermostat at the start of integration */
void thermo_init();

#ifdef NPT
/** add velocity-dependent noise and friction for NpT-sims to the particle's
velocity
@param vj j-component of the velocity
@return j-component of the noise added to the velocity, also scaled by
dt (contained in prefactors)
/** Add velocity-dependent noise and friction for NpT-sims to the particle's
* velocity
* @param vj j-component of the velocity
* @return j-component of the noise added to the velocity, also scaled by
* dt (contained in prefactors)
*/
inline double friction_therm0_nptiso(double vj) {
extern double nptiso_pref1, nptiso_pref2;
Expand All @@ -123,8 +128,9 @@ inline double friction_therm0_nptiso(double vj) {
return 0.0;
}

/** add p_diff-dependent noise and friction for NpT-sims to \ref
* nptiso_struct::p_diff */
/** Add p_diff-dependent noise and friction for NpT-sims to \ref
* nptiso_struct::p_diff
*/
inline double friction_thermV_nptiso(double p_diff) {
extern double nptiso_pref3, nptiso_pref4;
if (thermo_switch & THERMO_NPT_ISO) {
Expand All @@ -137,11 +143,11 @@ inline double friction_thermV_nptiso(double p_diff) {
}
#endif

/** Langevin thermostat core function.
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.
*/
/** 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.
*/
inline Utils::Vector3d friction_thermo_langevin(Particle const &p) {
// Early exit for virtual particles without thermostat
if (p.p.is_virtual && !thermo_virtual) {
Expand All @@ -167,7 +173,7 @@ inline Utils::Vector3d friction_thermo_langevin(Particle const &p) {
}
#endif /* LANGEVIN_PER_PARTICLE */

// Get velocity effective in the thermostatting
// Get effective velocity in the thermostatting
#ifdef ENGINE
auto const &velocity = (p.p.swim.v_swim != 0)
? p.m.v - p.p.swim.v_swim * p.r.calc_director()
Expand Down Expand Up @@ -201,10 +207,11 @@ inline Utils::Vector3d friction_thermo_langevin(Particle const &p) {
}

#ifdef ROTATION
/** set the particle torques to the friction term, i.e. \f$\tau_i=-\gamma w_i +
\xi_i\f$.
The same friction coefficient \f$\gamma\f$ is used as that for translation.
*/
/** 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.
*/
inline Utils::Vector3d friction_thermo_langevin_rotation(const Particle &p) {
extern Thermostat::GammaType langevin_pref2_rotation;

Expand All @@ -228,8 +235,8 @@ inline Utils::Vector3d friction_thermo_langevin_rotation(const Particle &p) {
using Random::v_noise;

// Here the thermostats happens
auto const noise =
v_noise<RNGSalt::LANGEVIN>(langevin_rng_counter->value(), p.p.identity);
auto const noise = v_noise<RNGSalt::LANGEVIN_ROT>(
langevin_rng_counter->value(), p.p.identity);
#ifdef PARTICLE_ANISOTROPY
return hadamard_product(langevin_pref_friction_buf, p.m.omega) +
hadamard_product(langevin_pref_noise_buf, noise);
Expand Down
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