#include "hawaii.h"
#include "arena.h"
#include "trajectory.h"
#include "hep_hawaii.h"
#include "angles_handler.hpp"

Include dependency graph for hawaii.c:

Macros
#define	ARENA_REGION_DEFAULT_CAPACITY (8*1024)
#define	HISTOGRAM_MAX_TPS 50
#define	R_HISTOGRAM_BINS 100
#define	R_HISTOGRAM_MAX 10000000.0
#define	DEFAULT_JINI_HISTOGRAM_FILENAME1 "jini.dat.1"
#define	DEFAULT_JINI_HISTOGRAM_FILENAME2 "jini.dat.2"
#define	DEFAULT_JINI_HISTOGRAM_BINS 352
#define	DEFAULT_JINI_HISTOGRAM_MAX 35.0
#define	DEFAULT_JFIN_HISTOGRAM_FILENAME1 "jfin.dat.1"
#define	DEFAULT_JFIN_HISTOGRAM_FILENAME2 "jfin.dat.2"
#define	DEFAULT_JFIN_HISTOGRAM_BINS 352
#define	DEFAULT_JFIN_HISTOGRAM_MAX 35.0
#define	DEFAULT_NSWITCH_HISTOGRAM_FILENAME1 "nswitch.dat.1"
#define	DEFAULT_NSWITCH_HISTOGRAM_FILENAME2 "nswitch.dat.2"
#define	DEFAULT_NSWITCH_HISTOGRAM_BINS 20
#define	DEFAULT_NSWITCH_HISTOGRAM_MAX 20.0
#define	ARENA_IMPLEMENTATION
#define	nparams 3
#define	REAL(z, i)
#define	IMAG(z, i)

Functions
MoleculeSystem	init_ms_from_monomers (double mu, Monomer m1, Monomer m2, size_t seed)
	Function init_ms_from_monomers prepares the MoleculeSystem based on the provided Monomer structs, sets up memory buffers and initializes random number generator.
MoleculeSystem	init_ms (double mu, MonomerType t1, MonomerType t2, double II1, double II2, size_t seed)
	Function init_ms prepares the MoleculeSystem based on the specified monomer types, sets up memory buffers and initializes random number generator.
void	free_stored_histogram (StoredHistogram *sh)
void	free_ms (MoleculeSystem *ms)
const char *	display_monomer_type (MonomerType t)
double	find_closest_integer (double j)
	find_closest_integer
double	find_closest_half_integer (double j)
	find_closest_half_integer
void	j_monomer (Monomer *m, double j[3])
	j_monomer computes the magnitude of angular momentum of passed-in monomer. Currently, implemented only for linear molecules.
double	torque_monomer (Monomer *m)
	torque_monomer computes the magnitude of torque (time-derivative of angular momentum) of passed-in monomer. Requires the derivative of potential Monomer::dVdq to be set within the monomer. Currently, implemented only for linear molecules.
void	rhsMonomer (Monomer m, double deriv)
	rhsMonomer dispatches between computing the right-hand side of Hamilton's equations of motion depending on the type of monomer. In addition to differentiating the kinetic energy, the derivatives of potential energy, which are taken from Monomer::dVdq, are also added to compute the right-hand side. rhsMonomer does not account for requantization which should happen after this function has been called.
void	extract_dVdq_and_write_into_monomers (MoleculeSystem *ms)
int	rhs (realtype t, N_Vector y, N_Vector ydot, void *data)
	rhs function is passed to CVode library to propagate the trajectory. First, the phase-point coordinates are stored into MoleculeSystem struct. A contiguous vector of coordinates is assembled via extract_q_and_write_into_ms. Next, by calling the external function dpes, the derivatives of potential energy are computed and stored into MoleculeSystem::dVdq field. The components of derivative vector are then copied into the field Monomer::dVdq of the corresponding Monomer via the call to extract_dVdq_and_write_into_monomers. The right-hand side of Hamilton's equations with respect to intermolecular degrees of freedom are readily obtained and filled into output ydot, while the derivatives with respect to monomer's coordinates are handled by rhsMonomer function.
gsl_matrix *	compute_numerical_jac (void(transform_angles)(double qlab, double qmol), double qlab, size_t ninput_coordinates, size_t noutput_coordinates, size_t order)
	compute_numerical_jac
Array	compute_numerical_derivatives (double(f)(double q), double *q, size_t len, size_t order)
	compute_numerical_derivatives
Array	compute_numerical_rhs (MoleculeSystem *ms, size_t order)
	compute_numerical_rhs Computes the right-hand side of Hamilton's equations of motion using finite-difference formulas. The returned Array contains derivatives whose order corresponds to variable ordering employed in the MoleculeSystem structure.
double	kinetic_energy (MoleculeSystem *ms)
	Function kinetic_energy computes the kinetic energy at the phase-point stored in MoleculeSystem.
void	put_qp_into_ms (MoleculeSystem *ms, Array qp)
void	get_qp_from_ms (MoleculeSystem ms, Array qp)
void	extract_q (double qp, double q, size_t QP_SIZE)
void	extract_q_and_write_into_ms (MoleculeSystem *ms)
void	invert_momenta (MoleculeSystem *ms)
	invert_momenta
double	Hamiltonian (MoleculeSystem *ms)
	Function Hamiltonian calls kinetic_energy function to compute kinetic energy, assembles a contiguous vector of coordinates via calling extract_q_and_write_into_ms and passes it to external pes function. The obtained values are added and returned.
double	generate_normal (double sigma)
void	q_generator (MoleculeSystem ms, CalcParams params)
	Function q_generator generates with density $\rho \sim R^2$ in the range [params.sampler_Rmin, params.sampler_Rmax]. The distributions of $\varphi, \psi$ are $\varphi, \psi \sim U[0, 2\pi]$ and for $\theta$ is $\cos \theta \sim U[0, 1]$ . Implemented for intermolecular degrees of freedom, linear molecule and rotor.
void	p_generator (MoleculeSystem *ms, double Temperature)
	Function p_generator samples momenta from distribution $\rho \sim e^{-K/kT}$ at given temperature.
bool	reject (MoleculeSystem *ms, double Temperature, double pesmin)
	reject applies the rejection step to the phase-point that is stored in the MoleculeSystem. It presupposes that the provided phase-point is sampled from $\rho \sim e^{-K/kT}$ using q_generator and p_generator functions. The random variable $u \sim U[0, 1]$ is chosen, to determine whether the current phase-point is to be accepted with probability $\rho \sim \exp(-H/kT)$ .
void	calculate_M0 (MoleculeSystem ms, CalcParams params, double Temperature, double m, double q)
	calculate_M0 Running mean/variance formulas taken from GSL 1.15 https://github.com/ampl/gsl/blob/master/monte/plain.c
void	compute_dHdp (MoleculeSystem ms, gsl_matrix dHdp)
	compute_dHdp
void	calculate_M2 (MoleculeSystem ms, CalcParams params, double Temperature, double m, double q)
	calculate_M2 Running mean/variance formulas taken from GSL 1.15 https://github.com/ampl/gsl/blob/master/monte/plain.c
void	mpi_calculate_M0 (MoleculeSystem ms, CalcParams params, double Temperature, double m, double q)
	mpi_calculate_M0
void	mpi_calculate_M2 (MoleculeSystem ms, CalcParams params, double Temperature, double m, double q)
	mpi_calculate_M2
void	track_turning_points (Tracker *tr, double R)
int	correlation_eval_zimmerman_trick (MoleculeSystem ms, Trajectory traj, CalcParams params, double crln, size_t *tps)
	correlation_eval_zimmerman_trick
void	try_applying_requantization_for_monomer (Monomer *m, size_t step_counter)
int	correlation_eval (MoleculeSystem ms, Trajectory traj, CalcParams params, double crln, size_t *tps)
	correlation_eval
void	gsl_fft_square (double *farr, size_t N)
CFncArray	calculate_correlation_array_and_save (MoleculeSystem ms, CalcParams params, double base_temperature)
	calculate_correlation_array_and_save
void	setup_nswitch_histogram_for_monomer (Monomer *m)
void	setup_jini_histogram_for_monomer (Monomer *m)
void	setup_jfin_histogram_for_monomer (Monomer *m)
void	send_histogram_and_reset (gsl_histogram *h)
void	normalize_cfnc (CFnc *cf)
CFnc	calculate_correlation_and_save (MoleculeSystem ms, CalcParams params, double Temperature)
	calculate_correlation_and_save
void	recv_histogram_and_append (Arena a, int source, gsl_histogram *h)
SFnc	calculate_spectral_function_using_prmu_representation_and_save (MoleculeSystem ms, CalcParams params, double Temperature)
	calculate_spectral_function_using_prmu_representation_and_save
int	assert_float_is_equal_to (double estimate, double true_value, double abs_tolerance)
double *	linspace (double start, double end, size_t n)
double *	arena_linspace (Arena *a, double start, double end, size_t n)
size_t *	arena_linspace_size_t (Arena *a, size_t start, size_t end, size_t n)
bool	write_spectrum (const char *filename, Spectrum sp)
int	write_spectrum_ext (FILE *fp, Spectrum sp)
bool	write_correlation_function (const char *filename, CFnc cf)
int	write_correlation_function_ext (FILE *fp, CFnc cf)
bool	write_spectral_function (const char *filename, SFnc sf)
int	write_spectral_function_ext (FILE *fp, SFnc sf)
int	write_histogram_ext (FILE fp, gsl_histogram h, int count)
void	sb_reserve (String_Builder *sb, size_t n)
void	sb_append (String_Builder sb, const char line, size_t n)
void	sb_append_null (String_Builder *sb)
void	sb_reset (String_Builder *sb)
void	sb_append_cstring (String_Builder sb, const char line)
void	sb_append_format (String_Builder sb, const char format,...)
void	sb_append_seconds_as_datetime_string (String_Builder *sb, int s)
void	sb_free (String_Builder *sb)
bool	read_correlation_function (const char filename, String_Builder sb, CFnc *cf)
bool	average_correlation_functions (CFnc *average, CFncs cfncs)
int	average_correlation_functions__impl (CFnc *average, int arg_count,...)
bool	read_spectral_function (const char filename, String_Builder sb, SFnc *sf)
bool	parse_temperature_from_header (const char header, double Temperature)
bool	parse_number_of_trajectories_from_header (const char header, double ntraj)
bool	read_spectrum (const char filename, String_Builder sb, Spectrum *sp)
bool	writetxt (const char filename, double x, double y, size_t len, const char header)
double	analytic_full_partition_function_by_V (MoleculeSystem *ms, double Temperature)
gsl_histogram *	gsl_histogram_extend_right (gsl_histogram *h, size_t add_bins)
void	free_cfnc (CFnc cf)
void	free_cfnc_array (CFncArray ca)
void	free_sfnc (SFnc sf)
void	free_spectrum (Spectrum sp)
double	wingmodel (WingParams *wp, double t)
double	wingmodel_image (WingParams *wp, double nu)
int	wingmodel_f (const gsl_vector x, void data, gsl_vector *f)
int	wingmodel_df (const gsl_vector x, void data, gsl_matrix *J)
void	gsl_multifit_callback (const size_t iter, void params, const gsl_multifit_nlinear_workspace w)
void	gsl_nonlinear_opt (size_t n, double x, double y, WingParams *wing_params)
WingParams	fit_baseline (CFnc *cf, size_t EXT_RANGE_MIN)
void	connes_apodization (Array a, double sampling_time)
double *	dct (double *v, size_t len)
double *	idct (double *v, size_t len)
double *	pad_to_power_of_two (double v, size_t len, size_t padded_len)
SFnc	idct_cf_to_sf (CFnc cf)
CFnc	dct_sf_to_cf (SFnc sf)
SFnc	desymmetrize_schofield_sf (SFnc sf)
Spectrum	desymmetrize_schofield_sp (Spectrum sp)
Spectrum	inv_desymmetrize_schofield (Spectrum sp)
SFnc	desymmetrize_d2_sf (SFnc sf)
Spectrum	desymmetrize_d2_sp (Spectrum sp)
Spectrum	inv_desymmetrize_d2 (Spectrum sp)
SFnc	desymmetrize_d1 (SFnc sf)
CFnc	egelstaff_time_transform (CFnc cf, bool frommhold_renormalization)
SFnc	desymmetrize_frommhold (SFnc sf)
SFnc	desymmetrize_egelstaff_from_cf (CFnc cf)
SFnc	desymmetrize_frommhold_from_cf (CFnc cf)
SFnc	desymmetrize_egelstaff (SFnc sf)
Spectrum	compute_alpha (SFnc sf)
double	integrate_composite_simpson (double x, double y, size_t len)
bool	compute_Mn_from_cf_using_classical_detailed_balance (CFnc cf, size_t n, double *result)
double	compute_Mn_from_sf_using_classical_detailed_balance (SFnc sf, size_t n)
double	compute_Mn_from_sf_using_quantum_detailed_balance (SFnc sf, size_t n)
CFnc	copy_cfnc (CFnc cf)
SFnc	copy_sfnc (SFnc sf)
Spectrum	copy_spectrum (Spectrum sp)

Variables
dipolePtr	dipole_1 = NULL
dipoleFree	free_dipole_1 = NULL
dipolePtr	dipole_2 = NULL
dipoleFree	free_dipole_2 = NULL
pesPtr	pes = NULL
dpesPtr	dpes = NULL
int	_wrank = 0
int	_wsize = 1
bool	_print0_suppress_info = false
int	_print0_margin = 0
const char *	PAIR_STATES [PAIR_STATE_COUNT]
const char *	CALCULATION_TYPES [CALCULATION_TYPES_COUNT]
MonomerType	MONOMER_TYPES [MONOMER_COUNT]
WingParams	INIT_WP

Macro Definition Documentation

◆ ARENA_IMPLEMENTATION

#define ARENA_IMPLEMENTATION

◆ ARENA_REGION_DEFAULT_CAPACITY

#define ARENA_REGION_DEFAULT_CAPACITY (8*1024)

◆ DEFAULT_JFIN_HISTOGRAM_BINS

#define DEFAULT_JFIN_HISTOGRAM_BINS 352

◆ DEFAULT_JFIN_HISTOGRAM_FILENAME1

#define DEFAULT_JFIN_HISTOGRAM_FILENAME1 "jfin.dat.1"

◆ DEFAULT_JFIN_HISTOGRAM_FILENAME2

#define DEFAULT_JFIN_HISTOGRAM_FILENAME2 "jfin.dat.2"

◆ DEFAULT_JFIN_HISTOGRAM_MAX

#define DEFAULT_JFIN_HISTOGRAM_MAX 35.0

◆ DEFAULT_JINI_HISTOGRAM_BINS

#define DEFAULT_JINI_HISTOGRAM_BINS 352

◆ DEFAULT_JINI_HISTOGRAM_FILENAME1

#define DEFAULT_JINI_HISTOGRAM_FILENAME1 "jini.dat.1"

◆ DEFAULT_JINI_HISTOGRAM_FILENAME2

#define DEFAULT_JINI_HISTOGRAM_FILENAME2 "jini.dat.2"

◆ DEFAULT_JINI_HISTOGRAM_MAX

#define DEFAULT_JINI_HISTOGRAM_MAX 35.0

◆ DEFAULT_NSWITCH_HISTOGRAM_BINS

#define DEFAULT_NSWITCH_HISTOGRAM_BINS 20

◆ DEFAULT_NSWITCH_HISTOGRAM_FILENAME1

#define DEFAULT_NSWITCH_HISTOGRAM_FILENAME1 "nswitch.dat.1"

◆ DEFAULT_NSWITCH_HISTOGRAM_FILENAME2

#define DEFAULT_NSWITCH_HISTOGRAM_FILENAME2 "nswitch.dat.2"

◆ DEFAULT_NSWITCH_HISTOGRAM_MAX

#define DEFAULT_NSWITCH_HISTOGRAM_MAX 20.0

◆ HISTOGRAM_MAX_TPS

#define HISTOGRAM_MAX_TPS 50

◆ IMAG

#define IMAG	(		z,
			i )

Value:

((z)[2*(i) + 1])

◆ nparams

#define nparams 3

◆ R_HISTOGRAM_BINS

#define R_HISTOGRAM_BINS 100

◆ R_HISTOGRAM_MAX

#define R_HISTOGRAM_MAX 10000000.0

◆ REAL

#define REAL	(		z,
			i )

Value:

((z)[2*(i)])

Function Documentation

◆ analytic_full_partition_function_by_V()

double analytic_full_partition_function_by_V	(	MoleculeSystem *	ms,
		double	Temperature )

◆ arena_linspace()

double * arena_linspace	(	Arena *	a,
		double	start,
		double	end,
		size_t	n )

◆ arena_linspace_size_t()

size_t * arena_linspace_size_t	(	Arena *	a,
		size_t	start,
		size_t	end,
		size_t	n )

◆ assert_float_is_equal_to()

int assert_float_is_equal_to	(	double	estimate,
		double	true_value,
		double	abs_tolerance )

◆ average_correlation_functions()

bool average_correlation_functions	(	CFnc *	average,
		CFncs	cfncs )

◆ average_correlation_functions__impl()

int average_correlation_functions__impl	(	CFnc *	average,
		int	arg_count,
			... )

◆ calculate_correlation_and_save()

CFnc calculate_correlation_and_save	(	MoleculeSystem *	ms,
		CalcParams *	params,
		double	Temperature )

calculate_correlation_and_save

TODO: check 'sampler_Rmin': we want to catch the situation when it's too low for given Temperature

◆ calculate_correlation_array_and_save()

CFncArray calculate_correlation_array_and_save	(	MoleculeSystem *	ms,
		CalcParams *	params,
		double	base_temperature )

calculate_correlation_array_and_save

◆ calculate_M0()

void calculate_M0	(	MoleculeSystem *	ms,
		CalcParams *	params,
		double	Temperature,
		double *	m,
		double *	q )

calculate_M0 Running mean/variance formulas taken from GSL 1.15 https://github.com/ampl/gsl/blob/master/monte/plain.c

◆ calculate_M2()

void calculate_M2	(	MoleculeSystem *	ms,
		CalcParams *	params,
		double	Temperature,
		double *	m,
		double *	q )

calculate_M2 Running mean/variance formulas taken from GSL 1.15 https://github.com/ampl/gsl/blob/master/monte/plain.c

◆ calculate_spectral_function_using_prmu_representation_and_save()

SFnc calculate_spectral_function_using_prmu_representation_and_save	(	MoleculeSystem *	ms,
		CalcParams *	params,
		double	Temperature )

calculate_spectral_function_using_prmu_representation_and_save

◆ compute_alpha()

Spectrum compute_alpha ( SFnc sf )

◆ compute_dHdp()

void compute_dHdp	(	MoleculeSystem *	ms,
		gsl_matrix *	dHdp )

compute_dHdp

◆ compute_Mn_from_cf_using_classical_detailed_balance()

bool compute_Mn_from_cf_using_classical_detailed_balance	(	CFnc	cf,
		size_t	n,
		double *	result )

◆ compute_Mn_from_sf_using_classical_detailed_balance()

double compute_Mn_from_sf_using_classical_detailed_balance	(	SFnc	sf,
		size_t	n )

◆ compute_Mn_from_sf_using_quantum_detailed_balance()

double compute_Mn_from_sf_using_quantum_detailed_balance	(	SFnc	sf,
		size_t	n )

◆ compute_numerical_derivatives()

Array compute_numerical_derivatives	(	double(*	f )(double *q),
		double *	q,
		size_t	len,
		size_t	order )

compute_numerical_derivatives

◆ compute_numerical_jac()

gsl_matrix * compute_numerical_jac	(	void(*	transform_angles )(double qlab, double qmol),
		double *	qlab,
		size_t	ninput_coordinates,
		size_t	noutput_coordinates,
		size_t	order )

compute_numerical_jac

◆ compute_numerical_rhs()

Array compute_numerical_rhs	(	MoleculeSystem *	ms,
		size_t	order )

compute_numerical_rhs Computes the right-hand side of Hamilton's equations of motion using finite-difference formulas. The returned Array contains derivatives whose order corresponds to variable ordering employed in the MoleculeSystem structure.

Parameters

ms	Pointer to the MoleculeSystem for which to compute the derivatives.
order	Order of the finite-difference formula to employ for calculation.

◆ connes_apodization()

void connes_apodization	(	Array	a,
		double	sampling_time )

◆ copy_cfnc()

CFnc copy_cfnc ( CFnc cf )

◆ copy_sfnc()

SFnc copy_sfnc ( SFnc sf )

◆ copy_spectrum()

Spectrum copy_spectrum ( Spectrum sp )

◆ correlation_eval()

int correlation_eval	(	MoleculeSystem *	ms,
		Trajectory *	traj,
		CalcParams *	params,
		double *	crln,
		size_t *	tps )

correlation_eval

◆ correlation_eval_zimmerman_trick()

int correlation_eval_zimmerman_trick	(	MoleculeSystem *	ms,
		Trajectory *	traj,
		CalcParams *	params,
		double *	crln,
		size_t *	tps )

correlation_eval_zimmerman_trick

◆ dct()

double * dct	(	double *	v,
		size_t	len )

◆ dct_sf_to_cf()

CFnc dct_sf_to_cf ( SFnc sf )

◆ desymmetrize_d1()

SFnc desymmetrize_d1 ( SFnc sf )

◆ desymmetrize_d2_sf()

SFnc desymmetrize_d2_sf ( SFnc sf )

◆ desymmetrize_d2_sp()

Spectrum desymmetrize_d2_sp ( Spectrum sp )

◆ desymmetrize_egelstaff()

SFnc desymmetrize_egelstaff ( SFnc sf )

◆ desymmetrize_egelstaff_from_cf()

SFnc desymmetrize_egelstaff_from_cf ( CFnc cf )

◆ desymmetrize_frommhold()

SFnc desymmetrize_frommhold ( SFnc sf )

◆ desymmetrize_frommhold_from_cf()

SFnc desymmetrize_frommhold_from_cf ( CFnc cf )

◆ desymmetrize_schofield_sf()

SFnc desymmetrize_schofield_sf ( SFnc sf )

◆ desymmetrize_schofield_sp()

Spectrum desymmetrize_schofield_sp ( Spectrum sp )

◆ display_monomer_type()

const char * display_monomer_type ( MonomerType t )

◆ egelstaff_time_transform()

CFnc egelstaff_time_transform	(	CFnc	cf,
		bool	frommhold_renormalization )

◆ extract_dVdq_and_write_into_monomers()

void extract_dVdq_and_write_into_monomers ( MoleculeSystem * ms )

◆ extract_q()

void extract_q	(	double *	qp,
		double *	q,
		size_t	QP_SIZE )

◆ extract_q_and_write_into_ms()

void extract_q_and_write_into_ms ( MoleculeSystem * ms )

◆ find_closest_half_integer()

double find_closest_half_integer ( double j )

find_closest_half_integer

requantization to: 0.0, 0.5, 1.5, 2.5, 3.5 ...

◆ find_closest_integer()

double find_closest_integer ( double j )

find_closest_integer

requantization to: 0.0, 1.0, 2.0, 3.0 ...

◆ fit_baseline()

WingParams fit_baseline	(	CFnc *	cf,
		size_t	EXT_RANGE_MIN )

◆ free_cfnc()

void free_cfnc ( CFnc cf )

◆ free_cfnc_array()

void free_cfnc_array ( CFncArray ca )

◆ free_ms()

void free_ms ( MoleculeSystem * ms )

◆ free_sfnc()

void free_sfnc ( SFnc sf )

◆ free_spectrum()

void free_spectrum ( Spectrum sp )

◆ free_stored_histogram()

void free_stored_histogram ( StoredHistogram * sh )

◆ generate_normal()

double generate_normal ( double sigma )

◆ get_qp_from_ms()

void get_qp_from_ms	(	MoleculeSystem *	ms,
		Array *	qp )

◆ gsl_fft_square()

void gsl_fft_square	(	double *	farr,
		size_t	N )

◆ gsl_histogram_extend_right()

gsl_histogram * gsl_histogram_extend_right	(	gsl_histogram *	h,
		size_t	add_bins )

◆ gsl_multifit_callback()

void gsl_multifit_callback	(	const size_t	iter,
		void *	params,
		const gsl_multifit_nlinear_workspace *	w )

◆ gsl_nonlinear_opt()

void gsl_nonlinear_opt	(	size_t	n,
		double *	x,
		double *	y,
		WingParams *	wing_params )

◆ Hamiltonian()

double Hamiltonian ( MoleculeSystem * ms )

Function Hamiltonian calls kinetic_energy function to compute kinetic energy, assembles a contiguous vector of coordinates via calling extract_q_and_write_into_ms and passes it to external pes function. The obtained values are added and returned.

◆ idct()

double * idct	(	double *	v,
		size_t	len )

◆ idct_cf_to_sf()

SFnc idct_cf_to_sf ( CFnc cf )

◆ init_ms()

MoleculeSystem init_ms	(	double	mu,
		MonomerType	t1,
		MonomerType	t2,
		double *	II1,
		double *	II2,
		size_t	seed )

Function init_ms prepares the MoleculeSystem based on the specified monomer types, sets up memory buffers and initializes random number generator.

Parameters

mu	Reduced mass of the molecule pair
t1	Type of the first monomer
t2	Type of the second monomer
I1	Inertia tensor values for the first monomer. If the monomer is MonomerType::ATOM, no values will be read from the pointer, so NULL can be passed. Two and three values are expected for linear molecule (MonomerType::LINEAR_MOLECULE, MonomerType::LINEAR_MOLECULE_REQ_INTEGER and MonomerType::LINEAR_MOLECULE_REQ_HALFINTEGER) and rotor (MonomerType::ROTOR and MonomerType::ROTOR_REQUANTIZED_ROTATION).
I2	Inertia tensor values for the second monomer.
seed	Seed to set up random number generator (Mersenne Twister). A unique seed will be produced if 0 value is passed.

◆ init_ms_from_monomers()

MoleculeSystem init_ms_from_monomers	(	double	mu,
		Monomer *	m1,
		Monomer *	m2,
		size_t	seed )

Function init_ms_from_monomers prepares the MoleculeSystem based on the provided Monomer structs, sets up memory buffers and initializes random number generator.

◆ integrate_composite_simpson()

double integrate_composite_simpson	(	double *	x,
		double *	y,
		size_t	len )

◆ inv_desymmetrize_d2()

Spectrum inv_desymmetrize_d2 ( Spectrum sp )

◆ inv_desymmetrize_schofield()

Spectrum inv_desymmetrize_schofield ( Spectrum sp )

◆ invert_momenta()

void invert_momenta ( MoleculeSystem * ms )

invert_momenta

◆ j_monomer()

void j_monomer	(	Monomer *	m,
		double	j[3] )

j_monomer computes the magnitude of angular momentum of passed-in monomer. Currently, implemented only for linear molecules.

$[\textrm{linear molecule}]: j = \begin{bmatrix} - p_\theta \sin \varphi - p_\varphi \cos \varphi / \tan \theta \\ p_\theta \cos \varphi - p_\varphi \sin \varphi / \tan \theta \\ p_\varphi \end{bmatrix}$

◆ kinetic_energy()

double kinetic_energy ( MoleculeSystem * ms )

Function kinetic_energy computes the kinetic energy at the phase-point stored in MoleculeSystem.

The kinetic energy in the laboratory frame of reference is calculated in parts. The part corresponding to intermolecular degrees of freedom:

$T_\textrm{int} = \frac{p_R^2}{2 \mu} + \frac{p_\Theta^2}{2 \mu R^2} + \frac{p_\Phi^2}{2\mu R^2 \sin^2 \Theta};$

to linear molecule:

$T_\textrm{lin} = \frac{p_\theta^2}{2 I} + \frac{p_\varphi^2}{2 I \sin^2 \theta};$

and to rotor:

$T_\textrm{rotor} = \frac{1}{2 I_1 \sin^2 \theta_2} \Big[ \left( p_\varphi - p_\psi \cos \theta \right) \sin \psi + p_\theta \sin \theta \cos \psi \Big]^2 \\ + \frac{1}{2 I_2 \sin^2 \theta} \Big[ \left( p_\varphi - p_\psi \cos \theta \right) \cos \psi - p_\theta \sin \theta \sin \psi \Big]^2 \\ + \frac{1}{2 I_3} \left( p_\psi \right)^2.$

◆ linspace()

double * linspace	(	double	start,
		double	end,
		size_t	n )

◆ mpi_calculate_M0()

void mpi_calculate_M0	(	MoleculeSystem *	ms,
		CalcParams *	params,
		double	Temperature,
		double *	m,
		double *	q )

mpi_calculate_M0

◆ mpi_calculate_M2()

void mpi_calculate_M2	(	MoleculeSystem *	ms,
		CalcParams *	params,
		double	Temperature,
		double *	m,
		double *	q )

mpi_calculate_M2

◆ normalize_cfnc()

void normalize_cfnc ( CFnc * cf )

◆ p_generator()

void p_generator	(	MoleculeSystem *	ms,
		double	Temperature )

Function p_generator samples momenta from distribution $\rho \sim e^{-K/kT}$ at given temperature.

◆ pad_to_power_of_two()

double * pad_to_power_of_two	(	double *	v,
		size_t	len,
		size_t *	padded_len )

◆ parse_number_of_trajectories_from_header()

bool parse_number_of_trajectories_from_header	(	const char *	header,
		double *	ntraj )

◆ parse_temperature_from_header()

bool parse_temperature_from_header	(	const char *	header,
		double *	Temperature )

◆ put_qp_into_ms()

void put_qp_into_ms	(	MoleculeSystem *	ms,
		Array	qp )

◆ q_generator()

void q_generator	(	MoleculeSystem *	ms,
		CalcParams *	params )

Function q_generator generates with density $\rho \sim R^2$ in the range [params.sampler_Rmin, params.sampler_Rmax]. The distributions of $\varphi, \psi$ are $\varphi, \psi \sim U[0, 2\pi]$ and for $\theta$ is $\cos \theta \sim U[0, 1]$ . Implemented for intermolecular degrees of freedom, linear molecule and rotor.

◆ read_correlation_function()

bool read_correlation_function	(	const char *	filename,
		String_Builder *	sb,
		CFnc *	cf )

◆ read_spectral_function()

bool read_spectral_function	(	const char *	filename,
		String_Builder *	sb,
		SFnc *	sf )

◆ read_spectrum()

bool read_spectrum	(	const char *	filename,
		String_Builder *	sb,
		Spectrum *	sp )

◆ recv_histogram_and_append()

void recv_histogram_and_append	(	Arena *	a,
		int	source,
		gsl_histogram **	h )

◆ reject()

bool reject	(	MoleculeSystem *	ms,
		double	Temperature,
		double	pesmin )

reject applies the rejection step to the phase-point that is stored in the MoleculeSystem. It presupposes that the provided phase-point is sampled from $\rho \sim e^{-K/kT}$ using q_generator and p_generator functions. The random variable $u \sim U[0, 1]$ is chosen, to determine whether the current phase-point is to be accepted with probability $\rho \sim \exp(-H/kT)$ .

◆ rhs()

int rhs	(	realtype	t,
		N_Vector	y,
		N_Vector	ydot,
		void *	data )

rhs function is passed to CVode library to propagate the trajectory. First, the phase-point coordinates are stored into MoleculeSystem struct. A contiguous vector of coordinates is assembled via extract_q_and_write_into_ms. Next, by calling the external function dpes, the derivatives of potential energy are computed and stored into MoleculeSystem::dVdq field. The components of derivative vector are then copied into the field Monomer::dVdq of the corresponding Monomer via the call to extract_dVdq_and_write_into_monomers. The right-hand side of Hamilton's equations with respect to intermolecular degrees of freedom are readily obtained and filled into output ydot, while the derivatives with respect to monomer's coordinates are handled by rhsMonomer function.

◆ rhsMonomer()

void rhsMonomer	(	Monomer *	m,
		double *	deriv )

rhsMonomer dispatches between computing the right-hand side of Hamilton's equations of motion depending on the type of monomer. In addition to differentiating the kinetic energy, the derivatives of potential energy, which are taken from Monomer::dVdq, are also added to compute the right-hand side.
rhsMonomer does not account for requantization which should happen after this function has been called.

◆ sb_append()

void sb_append	(	String_Builder *	sb,
		const char *	line,
		size_t	n )

◆ sb_append_cstring()

void sb_append_cstring	(	String_Builder *	sb,
		const char *	line )

◆ sb_append_format()

void sb_append_format	(	String_Builder *	sb,
		const char *	format,
			... )

◆ sb_append_null()

void sb_append_null ( String_Builder * sb )

◆ sb_append_seconds_as_datetime_string()

void sb_append_seconds_as_datetime_string	(	String_Builder *	sb,
		int	s )

◆ sb_free()

void sb_free ( String_Builder * sb )

◆ sb_reserve()

void sb_reserve	(	String_Builder *	sb,
		size_t	n )

◆ sb_reset()

void sb_reset ( String_Builder * sb )

◆ send_histogram_and_reset()

void send_histogram_and_reset ( gsl_histogram * h )

◆ setup_jfin_histogram_for_monomer()

void setup_jfin_histogram_for_monomer ( Monomer * m )

◆ setup_jini_histogram_for_monomer()

void setup_jini_histogram_for_monomer ( Monomer * m )

◆ setup_nswitch_histogram_for_monomer()

void setup_nswitch_histogram_for_monomer ( Monomer * m )

◆ torque_monomer()

double torque_monomer ( Monomer * m )

torque_monomer computes the magnitude of torque (time-derivative of angular momentum) of passed-in monomer. Requires the derivative of potential Monomer::dVdq to be set within the monomer. Currently, implemented only for linear molecules.

$[\textrm{linear molecule}]: \tau = \begin{bmatrix} \displaystyle \sin \varphi \frac{\diff{V}}{\diff{\theta}} + \cos \varphi / \tan \theta \frac{\diff{V}}{\diff{\varphi}} \\ \displaystyle -\cos \varphi \frac{\diff{V}}{\diff{\theta}} + \sin \varphi / \tan \theta \frac{\diff{V}}{\diff{\varphi}} \\ \displaystyle -\frac{\diff{V}}{\diff{\varphi}} \end{bmatrix}$

◆ track_turning_points()

void track_turning_points	(	Tracker *	tr,
		double	R )

◆ try_applying_requantization_for_monomer()

void try_applying_requantization_for_monomer	(	Monomer *	m,
		size_t	step_counter )

◆ wingmodel()

double wingmodel	(	WingParams *	wp,
		double	t )

◆ wingmodel_df()

int wingmodel_df	(	const gsl_vector *	x,
		void *	data,
		gsl_matrix *	J )

◆ wingmodel_f()

int wingmodel_f	(	const gsl_vector *	x,
		void *	data,
		gsl_vector *	f )

◆ wingmodel_image()

double wingmodel_image	(	WingParams *	wp,
		double	nu )

◆ write_correlation_function()

bool write_correlation_function	(	const char *	filename,
		CFnc	cf )

◆ write_correlation_function_ext()

int write_correlation_function_ext	(	FILE *	fp,
		CFnc	cf )

◆ write_histogram_ext()

int write_histogram_ext	(	FILE *	fp,
		gsl_histogram *	h,
		int	count )

◆ write_spectral_function()

bool write_spectral_function	(	const char *	filename,
		SFnc	sf )

◆ write_spectral_function_ext()

int write_spectral_function_ext	(	FILE *	fp,
		SFnc	sf )

◆ write_spectrum()

bool write_spectrum	(	const char *	filename,
		Spectrum	sp )

◆ write_spectrum_ext()

int write_spectrum_ext	(	FILE *	fp,
		Spectrum	sp )

◆ writetxt()

bool writetxt	(	const char *	filename,
		double *	x,
		double *	y,
		size_t	len,
		const char *	header )

Variable Documentation

◆ _print0_margin

int _print0_margin = 0

◆ _print0_suppress_info

bool _print0_suppress_info = false

◆ _wrank

int _wrank = 0

◆ _wsize

int _wsize = 1

◆ CALCULATION_TYPES

const char* CALCULATION_TYPES[CALCULATION_TYPES_COUNT]

Initial value:

= {
    "NONE",
    "PR_MU",
    "CORRELATION_SINGLE",
    "CORRELATION_ARRAY",
    "PROCESSING",
    "CALCULATE_PHASE_SPACE_M0", 
    "CALCULATE_PHASE_SPACE_M2", 
}

◆ dipole_1

dipolePtr dipole_1 = NULL

◆ dipole_2

dipolePtr dipole_2 = NULL

◆ dpes

dpesPtr dpes = NULL

◆ free_dipole_1

dipoleFree free_dipole_1 = NULL

◆ free_dipole_2

dipoleFree free_dipole_2 = NULL

◆ INIT_WP

WingParams INIT_WP

Initial value:

= {
  .A = 0.1, 
  .B = 0.1, 
  .C = 1.0,
}

◆ MONOMER_TYPES

MonomerType MONOMER_TYPES[MONOMER_COUNT]

Initial value:

= {
    ATOM, 
    LINEAR_MOLECULE, 
    LINEAR_MOLECULE_REQ_INTEGER, 
    LINEAR_MOLECULE_REQ_HALFINTEGER, 
    ROTOR, 
    ROTOR_REQUANTIZED_ROTATION,
}

◆ PAIR_STATES

const char* PAIR_STATES[PAIR_STATE_COUNT]

Initial value:

= {
    "NONE",
    "FREE_AND_METASTABLE",
    "BOUND",
    "ALL",
}

◆ pes

pesPtr pes = NULL

Macros

Functions

Variables

Macro Definition Documentation

◆ ARENA_IMPLEMENTATION

◆ ARENA_REGION_DEFAULT_CAPACITY

◆ DEFAULT_JFIN_HISTOGRAM_BINS

◆ DEFAULT_JFIN_HISTOGRAM_FILENAME1

◆ DEFAULT_JFIN_HISTOGRAM_FILENAME2

◆ DEFAULT_JFIN_HISTOGRAM_MAX

◆ DEFAULT_JINI_HISTOGRAM_BINS

◆ DEFAULT_JINI_HISTOGRAM_FILENAME1

◆ DEFAULT_JINI_HISTOGRAM_FILENAME2

◆ DEFAULT_JINI_HISTOGRAM_MAX

◆ DEFAULT_NSWITCH_HISTOGRAM_BINS

◆ DEFAULT_NSWITCH_HISTOGRAM_FILENAME1

◆ DEFAULT_NSWITCH_HISTOGRAM_FILENAME2

◆ DEFAULT_NSWITCH_HISTOGRAM_MAX

◆ HISTOGRAM_MAX_TPS

◆ IMAG

◆ nparams

◆ R_HISTOGRAM_BINS

◆ R_HISTOGRAM_MAX

◆ REAL

Function Documentation

◆ analytic_full_partition_function_by_V()

◆ arena_linspace()

◆ arena_linspace_size_t()

◆ assert_float_is_equal_to()

◆ average_correlation_functions()

◆ average_correlation_functions__impl()

◆ calculate_correlation_and_save()

◆ calculate_correlation_array_and_save()

◆ calculate_M0()

◆ calculate_M2()

◆ calculate_spectral_function_using_prmu_representation_and_save()

◆ compute_alpha()

◆ compute_dHdp()

◆ compute_Mn_from_cf_using_classical_detailed_balance()

◆ compute_Mn_from_sf_using_classical_detailed_balance()

◆ compute_Mn_from_sf_using_quantum_detailed_balance()

◆ compute_numerical_derivatives()

◆ compute_numerical_jac()

◆ compute_numerical_rhs()

◆ connes_apodization()

◆ copy_cfnc()

◆ copy_sfnc()

◆ copy_spectrum()

◆ correlation_eval()

◆ correlation_eval_zimmerman_trick()

◆ dct()

◆ dct_sf_to_cf()

◆ desymmetrize_d1()

◆ desymmetrize_d2_sf()

◆ desymmetrize_d2_sp()

◆ desymmetrize_egelstaff()

◆ desymmetrize_egelstaff_from_cf()

◆ desymmetrize_frommhold()

◆ desymmetrize_frommhold_from_cf()

◆ desymmetrize_schofield_sf()

◆ desymmetrize_schofield_sp()

◆ display_monomer_type()

◆ egelstaff_time_transform()

◆ extract_dVdq_and_write_into_monomers()

◆ extract_q()

◆ extract_q_and_write_into_ms()

◆ find_closest_half_integer()

◆ find_closest_integer()

◆ fit_baseline()

◆ free_cfnc()

◆ free_cfnc_array()

◆ free_ms()

◆ free_sfnc()

◆ free_spectrum()

◆ free_stored_histogram()

◆ generate_normal()

◆ get_qp_from_ms()

◆ gsl_fft_square()

◆ gsl_histogram_extend_right()

◆ gsl_multifit_callback()