Angular variables and conjugated momenta are stored within the MoleculeSystem struct in the same order as within the qp of Monomer struct. More...

#include <hawaii.h>

Collaboration diagram for MoleculeSystem:

[legend]

Public Attributes
double	intermolecular_qp [6]
	Coordinates and conjugated momenta that correspond to the intermolecular motion ( $\Phi$ , $p_\Phi$ , $\Theta$ , $p_\Theta$ , , ) .
Monomer	m1
	First monomer.
Monomer	m2
	Second monomer.
double	mu
	Reduced mass of molecule pair.
size_t	Q_SIZE
	Total number of coordinates for molecule pair.
size_t	QP_SIZE
	Total number of coordinates and momenta for molecular pair (phase point size).
double *	intermediate_q
	Contiguous vector of coordinates.
double *	dVdq
	Contiguous vector of potential energy derivatives.
size_t	seed
time_t	init_rawtime
	Initialization time represented as the number of seconds since Unix Epoch; set in init_ms.
time_t	temp_rawtime
	A temporary time field for the time at which the previous iteration of the iterative algorithm was completed; used for tracking elapsed time between iterations.

Detailed Description

Angular variables and conjugated momenta are stored within the MoleculeSystem struct in the same order as within the qp of Monomer struct.

The variables' indices in the intermolecular_qp array are defined as follows:

IPHI = 0
IPPHI = 1
ITHETA = 2
IPTHETA = 3
IR = 4
IPR = 5

Keep in mind that intermolecular coordinates and monomer's coordinates are not stored contiguously (monomer's coordinates are stored within the Monomer structure). The contiguous vector of coordinates can be assembled by calling extract_q_and_write_into_ms function, which stores the coordinates in memory pointed at by intermediate_q. These coordinates are passed to external functions that compute the values of intermolecular energy, its derivatives with respect to coordinates and induced dipole. There is no guarantee that coordinates stored in Monomer's and coordinates in memory at intermediate_q are always in sync. The function extract_q_and_write_into_ms must be invoked if the contiguous vector of coordinates is desired at a certain point of the program execution.

Member Data Documentation

◆ dVdq

double* MoleculeSystem::dVdq

Contiguous vector of potential energy derivatives.

◆ init_rawtime

time_t MoleculeSystem::init_rawtime

Initialization time represented as the number of seconds since Unix Epoch; set in init_ms.

◆ intermediate_q

double* MoleculeSystem::intermediate_q

Contiguous vector of coordinates.

◆ intermolecular_qp

double MoleculeSystem::intermolecular_qp[6]

Coordinates and conjugated momenta that correspond to the intermolecular motion ( $\Phi$ , $p_\Phi$ , $\Theta$ , $p_\Theta$ , , ) .

◆ m1

Monomer MoleculeSystem::m1

First monomer.

◆ m2

Monomer MoleculeSystem::m2

Second monomer.

◆ mu

double MoleculeSystem::mu

Reduced mass of molecule pair.

◆ Q_SIZE

size_t MoleculeSystem::Q_SIZE

Total number of coordinates for molecule pair.

◆ QP_SIZE

size_t MoleculeSystem::QP_SIZE

Total number of coordinates and momenta for molecular pair (phase point size).

◆ seed

size_t MoleculeSystem::seed

◆ temp_rawtime

time_t MoleculeSystem::temp_rawtime

A temporary time field for the time at which the previous iteration of the iterative algorithm was completed; used for tracking elapsed time between iterations.

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

src/hawaii.h

Public Attributes