stormm::trajectory::ThermostatWriter< T > Struct Template Reference

Partially writeable abstract for the Thermostat object. As with the MMControlKit struct (see the library header mm_controls.h), the step member variable is modifiable so that it can be updated without setting it in the parent object and regenerating the entire abstract. More...

#include <thermostat.h>

Collaboration diagram for stormm::trajectory::ThermostatWriter< T >:

Public Member Functions
	ThermostatWriter (ThermostatKind kind_in, ThermostatPartition layout_in, int natom_in, size_t padded_natom_in, int npart_in, int step_in, int depth_in, int init_evolution_in, int end_evolution_in, T init_temperature_in, T final_temperature_in, T dt_in, bool csnt_geom_in, T rattle_tol_in, int rattle_iter_in, int andr_cyc_in, T gamma_ln_in, T ln_implicit_in, T ln_explicit_in, bool load_synthesis_forces_in, const int4 *partition_bounds_in, const T *init_temperatures_in, const T *final_temperatures_in, ullint2 *state_xy_in, ullint2 *state_zw_in, PrecisionModel rng_mode_in, double *cache_in, float *sp_cache_in)
	The constructor takes the usual list of parent object attributes with pointers applicable on either the CPU host or GPU device.
	ThermostatWriter (const ThermostatWriter &original)=default
	The copy and move assignment operators will be implicitly deleted due to the presence of const member variables.
	ThermostatWriter (ThermostatWriter &&original)=default

Public Attributes
const ThermostatKind	kind
	The type of this thermostat, i.e. Andersen.
const ThermostatPartition	layout
const int	natom
	Number of atoms controlled by this thermostat.
const size_t	padded_natom
	The number of atoms padded by the warp size.
const int	npart
int	step
	Current step number of the simulation.
const int	depth
const int	init_evolution
const int	end_evolution
const T	init_temperature
const T	final_temperature
	Final target temperature, common to all atoms.
const T	dt
	The time step, in units of femtoseconds.
const bool	cnst_geom
	Indicate whether to apply geometry constraints.
const T	rattle_tol
	Convergence criterion for RATTLE bond length constraints.
const int	rattle_iter
const int	andr_cyc
const T	gamma_ln
const T	ln_implicit
const T	ln_explicit
const bool	load_synthesis_forces
const int4 *	partition_bounds
const T *	init_temperatures
	Array of initial target temperatures for each atom.
const T *	final_temperatures
	Array of final target gemperatures for each atom.
ullint2 *	state_xy
	First 128 bits of each 256-bit state vector.
ullint2 *	state_zw
	Second 128 bits of each 256-bit state vector.
const PrecisionModel	rng_mode
double *	cache
float *	sp_cache

Detailed Description

template<typename T>
struct stormm::trajectory::ThermostatWriter< T >

Partially writeable abstract for the Thermostat object. As with the MMControlKit struct (see the library header mm_controls.h), the step member variable is modifiable so that it can be updated without setting it in the parent object and regenerating the entire abstract.

Member Data Documentation

andr_cyc

template<typename T>

const int stormm::trajectory::ThermostatWriter< T >::andr_cyc

The frequency of Andersen velocity resets, in terms of simulation steps. Multiply by the time step dt to get the inverse strength of the Andersen thermostat.

cache

template<typename T>

double* stormm::trajectory::ThermostatWriter< T >::cache

Cache of double-precision pre-computed random values (depth gives the number of such values for each atom)

depth

template<typename T>

const int stormm::trajectory::ThermostatWriter< T >::depth

Depth of the cache (the true depth will be three times higher, to serve each atom with Cartesian X, Y, and Z influences)

end_evolution

template<typename T>

const int stormm::trajectory::ThermostatWriter< T >::end_evolution

The first step at which the thermostat begins to target final_temperature(s)

gamma_ln

template<typename T>

const T stormm::trajectory::ThermostatWriter< T >::gamma_ln

The "Gamma" factor for the Langevin thermostat, giving the number of collisions per femtosecond scaled by the conversion factor for taking forces in kcal/mol-A into Angstroms per femtosecond.

init_evolution

template<typename T>

const int stormm::trajectory::ThermostatWriter< T >::init_evolution

Final step at which the thermostat target temperatures come from init_temperature or the eponymous array, and the first step at which temperature targets begin to shift linearly towards final_temperature(s)

init_temperature

template<typename T>

const T stormm::trajectory::ThermostatWriter< T >::init_temperature

Initial target temperature, common to all atoms (if it is applicable)

layout

template<typename T>

const ThermostatPartition stormm::trajectory::ThermostatWriter< T >::layout

The manner in which different atoms or systems are held to one or more heat baths

ln_explicit

template<typename T>

const T stormm::trajectory::ThermostatWriter< T >::ln_explicit

Explicit Langevin factor, applied in the second velocity Verlet update as new coordinates are determined

ln_implicit

template<typename T>

const T stormm::trajectory::ThermostatWriter< T >::ln_implicit

Implicit Langevin factor, applied in the first velocity Verlet update after new forces have been computed

load_synthesis_forces

template<typename T>

const bool stormm::trajectory::ThermostatWriter< T >::load_synthesis_forces

If set to TRUE, forces from the synthesis will be loaded when performing the initial velocity update.

npart

template<typename T>

const int stormm::trajectory::ThermostatWriter< T >::npart

Number of unique partitions in the thermostat, each being the atom index bounds on a distinct heat bath at a particular temperature

partition_bounds

template<typename T>

const int4* stormm::trajectory::ThermostatWriter< T >::partition_bounds

Bounds array on the atoms that this thermostat regulates. Also includes the number of degrees of freedom in each partition.

rattle_iter

template<typename T>

const int stormm::trajectory::ThermostatWriter< T >::rattle_iter

Number of iterations to allow when attempting to converge RATTLE

rng_mode

template<typename T>

const PrecisionModel stormm::trajectory::ThermostatWriter< T >::rng_mode

The mode in which random numbers are available for this thermostat. One of cache or sp_cache, below, will be valid as indicated by this member variable.

sp_cache

template<typename T>

float* stormm::trajectory::ThermostatWriter< T >::sp_cache

Cache of single-precision pre-computed random values (depth gives the number of such values for each atom)

---

The documentation for this struct was generated from the following file:

• src/Trajectory/thermostat.h