#include <assert.h>
#include <errno.h>
#include <stdarg.h>
#include <stdbool.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <regex.h>
#include <time.h>
#include <unistd.h>
#include <gsl/gsl_histogram.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_multifit_nlinear.h>
#include <gsl/gsl_spline.h>
#include <gsl/gsl_fft_real.h>
#include <gsl/gsl_fft_complex.h>
#include <gsl/gsl_fft_halfcomplex.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <math.h>
#include <complex.h>
#include "mtwist.h"
#include <cvode/cvode.h>
#include <nvector/nvector_serial.h>
#include "array.h"
#include "constants.h"
#include "arena.h"

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Classes
struct	StoredHistogram
struct	Monomer
	Monomer represents a monomer in a pair with associated dynamic variables. The order of variables in the qp array is specified by the following indices: More...
struct	MoleculeSystem
	Angular variables and conjugated momenta are stored within the MoleculeSystem struct in the same order as within the qp of Monomer struct. More...
struct	CalcParams
struct	CFnc
struct	CFncs
struct	CFncArray
struct	SFnc
struct	Spectrum
struct	Spectra
struct	WingParams
struct	WingData
struct	Tracker
struct	String_Builder

Macros
#define	OMPI_SKIP_MPICXX
#define	_GNU_SOURCE
#define	MT_GENERATE_CODE_IN_HEADER 0
#define	IPHI 0
	= 0
#define	IPPHI 1
	= 1
#define	ITHETA 2
	= 2
#define	IPTHETA 3
	= 3
#define	IR 4
	= 4
#define	IPR 5
	= 5
#define	IPSI 4
	= 4
#define	IPPSI 5
	= 5
#define	UNUSED(x)
#define	TODO(message)
#define	UNREACHABLE(message)
#define	return_defer(value)
#define	DA_INIT_CAP 256
#define	da_append(da, item)
#define	da_insert(da, i, item)
#define	da_last(da)
#define	INIT_WRANK
#define	INIT_WSIZE
#define	INFO(...)
#define	WARNING(...)
#define	ERROR(...)
#define	PRINT0(...)
#define	MONOMER_COUNT 6
#define	MODULO_BASE 100
#define	average_correlation_functions_ext(average, ...)

Typedefs
typedef void(*	dipolePtr) (double *, double[3])
typedef void(*	dipoleFree) (void)
typedef double(*	pesPtr) (double *)
typedef void(*	dpesPtr) (double , double )

Enumerations
enum	MonomerType { ATOM = 0 , LINEAR_MOLECULE = 4 , LINEAR_MOLECULE_REQ_INTEGER = MODULO_BASE + 4 , LINEAR_MOLECULE_REQ_HALFINTEGER = 2*MODULO_BASE + 4 , ROTOR = 6 , ROTOR_REQUANTIZED_ROTATION = MODULO_BASE + 6 }
	MonomerType enum is used to distinguish between systems of different types and stores the phase point size. More...
enum	PairState { PAIR_STATE_NONE , PAIR_STATE_FREE_AND_METASTABLE , PAIR_STATE_BOUND , PAIR_STATE_ALL , PAIR_STATE_COUNT }
	PairState is an enumeration representing the possible states of a pair. More...
enum	CalculationType { CALCULATION_NONE , CALCULATION_PR_MU , CALCULATION_CORRELATION_SINGLE , CALCULATION_CORRELATION_ARRAY , CALCULATION_PROCESSING , CALCULATION_PHASE_SPACE_M0 , CALCULATION_PHASE_SPACE_M2 , CALCULATION_TYPES_COUNT }
enum	SamplingType { REJECT , MCMC }

Functions
void	sincos (double, double , double )
int	syncfs (int)
MoleculeSystem	init_ms (double mu, MonomerType t1, MonomerType t2, double I1, double I2, size_t seed)
	Function init_ms prepares the MoleculeSystem based on the specified monomer types, sets up memory buffers and initializes random number generator.
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.
void	free_ms (MoleculeSystem *ms)
const char *	display_monomer_type (MonomerType t)
void	put_qp_into_ms (MoleculeSystem *ms, Array qp)
void	get_qp_from_ms (MoleculeSystem ms, Array qp)
void	extract_q_and_write_into_ms (MoleculeSystem *ms)
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.
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.
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
double	kinetic_energy (MoleculeSystem *ms)
	Function kinetic_energy computes the kinetic energy at the phase-point stored in MoleculeSystem.
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	try_applying_requantization_for_monomer (Monomer *m, size_t step_counter)
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.
double	find_closest_integer (double j)
	find_closest_integer
double	find_closest_half_integer (double j)
	find_closest_half_integer
void	invert_momenta (MoleculeSystem *ms)
	invert_momenta
double	analytic_full_partition_function_by_V (MoleculeSystem *ms, double Temperature)
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)
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
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)
void	send_histogram_and_reset (gsl_histogram *h)
void	recv_histogram_and_append (Arena a, int source, gsl_histogram *h)
gsl_histogram *	gsl_histogram_extend_right (gsl_histogram *h, size_t add_bins)
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_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 seconds)
void	sb_reset (String_Builder *sb)
void	sb_free (String_Builder *sb)
CFnc	copy_cfnc (CFnc cf)
SFnc	copy_sfnc (SFnc sf)
Spectrum	copy_spectrum (Spectrum sp)
void	normalize_cfnc (CFnc *cf)
void	free_cfnc (CFnc cf)
void	free_cfnc_array (CFncArray ca)
void	free_sfnc (SFnc cf)
void	free_spectrum (Spectrum sp)
bool	writetxt (const char filename, double x, double y, size_t len, const char header)
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)
bool	write_spectrum (const char *filename, Spectrum sp)
int	write_spectrum_ext (FILE *fp, Spectrum sp)
bool	parse_number_of_trajectories_from_header (const char header, double ntraj)
bool	parse_temperature_from_header (const char header, double Temperature)
bool	read_correlation_function (const char filename, String_Builder sb, CFnc *cf)
bool	read_spectral_function (const char filename, String_Builder sb, SFnc *sf)
bool	read_spectrum (const char filename, String_Builder sb, Spectrum *sp)
bool	average_correlation_functions (CFnc *average, CFncs cfncs)
int	average_correlation_functions__impl (CFnc *average, int arg_count,...)
void	connes_apodization (Array a, double sampling_time)
double *	dct (double *v, size_t len)
double *	idct (double *v, size_t len)
CFnc	dct_sf_to_cf (SFnc sf)
SFnc	idct_cf_to_sf (CFnc cf)
Spectrum	compute_alpha (SFnc sf)
SFnc	desymmetrize_d1 (SFnc sf)
SFnc	desymmetrize_d2_sf (SFnc sf)
Spectrum	desymmetrize_d2_sp (Spectrum sp)
SFnc	desymmetrize_schofield_sf (SFnc sf)
Spectrum	desymmetrize_schofield_sp (Spectrum sp)
SFnc	desymmetrize_egelstaff (SFnc sf)
SFnc	desymmetrize_egelstaff_from_cf (CFnc cf)
SFnc	desymmetrize_frommhold (SFnc sf)
SFnc	desymmetrize_frommhold_from_cf (CFnc cf)
CFnc	egelstaff_time_transform (CFnc cf, bool frommhold_renormalization)
Spectrum	inv_desymmetrize_schofield (Spectrum sp)
Spectrum	inv_desymmetrize_d2 (Spectrum sp)
double *	pad_to_power_of_two (double v, size_t len, size_t padded_len)
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_nonlinear_opt (size_t n, double x, double y, WingParams *wing_params)
WingParams	fit_baseline (CFnc *cf, size_t EXT_RANGE_MIN)

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

Macro Definition Documentation

◆ _GNU_SOURCE

#define _GNU_SOURCE

◆ average_correlation_functions_ext

#define average_correlation_functions_ext	(		average,
			... )

Value:

average_correlation_functions__impl(average, sizeof((CFnc[]){__VA_ARGS__}) / sizeof(CFnc), __VA_ARGS__)

average_correlation_functions__impl

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

Definition hawaii.c:4897

CFnc

Definition hawaii.h:385

◆ da_append

#define da_append	(		da,
			item )

Value:

    do {                                                                             \
        if ((da)->count >= (da)->capacity) {                                         \
            (da)->capacity = (da)->capacity == 0 ? DA_INIT_CAP : (da)->capacity*2;   \
            (da)->items = realloc((da)->items, (da)->capacity*sizeof(*(da)->items)); \
            assert((da)->items != NULL && "ASSERT: not enough memory\n");            \
        }                                                                            \
                                                                                     \
        (da)->items[(da)->count++] = (item);                                         \
    } while (0)

◆ DA_INIT_CAP

#define DA_INIT_CAP 256

◆ da_insert

#define da_insert	(	da,
		i,
		item )

Value:

    do {                                 \
        if ((i < 0) || ((i) > (da)->count)) { \
            assert(0 && "ASSERT: index out of bounds\n"); \
        } \
        if ((da)->count >= (da)->capacity) { \
            (da)->capacity = (da)->capacity == 0 ? DA_INIT_CAP : (da)->capacity*2; \
            (da)->items = realloc((da)->items, (da)->capacity*sizeof(*(da)->items)); \
            assert((da)->items != NULL && "ASSERT: not enough memory\n"); \
        } \
        memmove((da)->items + (i) + 1, (da)->items + (i), ((da)->count - (i))*sizeof(*(da)->items)); \
        (da)->items[(i)] = (item); \
        (da)->count++; \
    } while(0)

◆ da_last

#define da_last ( da )

Value:

(da)->items[(da)->count - 1]

◆ ERROR

#define ERROR ( ... )

Value:

if (_print0_margin > 0) printf("%*s", _print0_margin, " "); \

printf("ERROR: "); printf(__VA_ARGS__); \

_print0_margin

int _print0_margin

Definition hawaii.c:42

◆ INFO

#define INFO ( ... )

Value:

    if (!_print0_suppress_info) {                                   \
        if (_print0_margin > 0) printf("%*s", _print0_margin, " "); \
        printf(__VA_ARGS__);                                        \
    }

◆ INIT_WRANK

#define INIT_WRANK

◆ INIT_WSIZE

#define INIT_WSIZE

◆ IPHI

#define IPHI 0

= 0

◆ IPPHI

#define IPPHI 1

= 1

◆ IPPSI

#define IPPSI 5

= 5

◆ IPR

#define IPR 5

= 5

◆ IPSI

#define IPSI 4

= 4

◆ IPTHETA

#define IPTHETA 3

= 3

◆ IR

#define IR 4

= 4

◆ ITHETA

#define ITHETA 2

= 2

◆ MODULO_BASE

#define MODULO_BASE 100

◆ MONOMER_COUNT

#define MONOMER_COUNT 6

◆ MT_GENERATE_CODE_IN_HEADER

#define MT_GENERATE_CODE_IN_HEADER 0

◆ OMPI_SKIP_MPICXX

#define OMPI_SKIP_MPICXX

◆ PRINT0

#define PRINT0 ( ... )

Value:

if (_print0_margin > 0) printf("%*s", _print0_margin, " "); \

printf(__VA_ARGS__);

◆ return_defer

#define return_defer ( value )

Value:

do { result = (value); goto defer; } while(0)

◆ TODO

#define TODO ( message )

Value:

do { fprintf(stderr, "%s:%d: TODO: %s\n", __FILE__, __LINE__, message); abort(); } while(0)

◆ UNREACHABLE

#define UNREACHABLE ( message )

Value:

do { fprintf(stderr, "%s:%d: UNREACHABLE: %s\n", __FILE__, __LINE__, message); abort(); } while(0)

◆ UNUSED

#define UNUSED ( x )

Value:

(void)(x)

◆ WARNING

#define WARNING ( ... )

Value:

if (_print0_margin > 0) printf("%*s", _print0_margin, " "); \

printf("WARNING: "); printf(__VA_ARGS__); \

Typedef Documentation

◆ dipoleFree

typedef void(* dipoleFree) (void)

◆ dipolePtr

typedef void(* dipolePtr) (double *, double[3])

dipolePtr

◆ dpesPtr

typedef void(* dpesPtr) (double *, double *)

dpes function accepts an array of Q_SIZE variables. MoleculeSystem describes the order of variables. The pointer to dpes is a global variable in hawaii.c file. The derivative of potential energy function is loaded from the dynamic library (see keyword SO_POTENTIAL in Input File Description). Intermolecular distance measured in Bohrs, while angles are measured in radians. The function is expected to return an array of derivatives of energy in units of Hartree/Bohr of length Q_SIZE.

◆ pesPtr

typedef double(* pesPtr) (double *)

pes function accepts an array of Q_SIZE variables. MoleculeSystem describes the order of variables. The pointer to pes is a global variable in hawaii.c file. The potential energy function is loaded from the dynamic library (see keyword SO_POTENTIAL in Input File Description). Intermolecular distance is measured in Bohrs, while angles are measured in radians. The function is expected to return energy in units of Hartree.

Enumeration Type Documentation

◆ CalculationType

enum CalculationType

Enumerator
CALCULATION_NONE
CALCULATION_PR_MU
CALCULATION_CORRELATION_SINGLE
CALCULATION_CORRELATION_ARRAY
CALCULATION_PROCESSING
CALCULATION_PHASE_SPACE_M0
CALCULATION_PHASE_SPACE_M2
CALCULATION_TYPES_COUNT

◆ MonomerType

enum MonomerType

MonomerType enum is used to distinguish between systems of different types and stores the phase point size.

The size of phase point is calculated as size(phase_point) = MonomerType % MODULO_BASE, where MODULO_BASE is defined to 100 by default.

Enumerator
ATOM	Represents an atom with phase point size 0.
LINEAR_MOLECULE	Represents a linear molecule with phase point size 4.
LINEAR_MOLECULE_REQ_INTEGER	Represents a linear molecule with integer angular momentum with phase point size 4.
LINEAR_MOLECULE_REQ_HALFINTEGER	Represents a linear molecule with half-integer angular momentum with phase point size 4.
ROTOR	Represents a rotor with phase point size 6.
ROTOR_REQUANTIZED_ROTATION	Represents a rotor with requantized rotation with phase point size 6.

◆ PairState

enum PairState

PairState is an enumeration representing the possible states of a pair.

Enumerator
PAIR_STATE_NONE	Default/uninitialized state.
PAIR_STATE_FREE_AND_METASTABLE	Free and metastable states (TODO: automatically separate the contributions based on the number of turning points).
PAIR_STATE_BOUND	Bound states.
PAIR_STATE_ALL	Represents the totality of all possible states (aggregate value).
PAIR_STATE_COUNT	Enum counter value (not a valid state). Used for array sizing.

◆ SamplingType

enum SamplingType

Enumerator
REJECT
MCMC

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_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

◆ 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 )

◆ 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_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 cf )

◆ free_spectrum()

void free_spectrum ( Spectrum sp )

◆ generate_normal()

double generate_normal ( double sigma )

◆ get_qp_from_ms()

void get_qp_from_ms	(	MoleculeSystem *	ms,
		Array *	qp )

◆ gsl_histogram_extend_right()

gsl_histogram * gsl_histogram_extend_right	(	gsl_histogram *	h,
		size_t	add_bins )

◆ 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 )

◆ 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.

◆ 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	seconds )

◆ 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 )

◆ sincos()

void sincos	(	double	,
		double *	,
		double *	)

◆ syncfs()

int syncfs ( int )

◆ 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.

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

◆ 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

extern

◆ _print0_suppress_info

bool _print0_suppress_info

extern

◆ _wrank

int _wrank

extern

◆ _wsize

int _wsize

extern

◆ CALCULATION_TYPES

const char* CALCULATION_TYPES[CALCULATION_TYPES_COUNT]

extern

◆ dipole_1

dipolePtr dipole_1

extern

◆ dipole_2

dipolePtr dipole_2

extern

◆ dpes

dpesPtr dpes

extern

◆ free_dipole_1

dipoleFree free_dipole_1

extern

◆ free_dipole_2

dipoleFree free_dipole_2

extern

◆ INIT_WP

WingParams INIT_WP

extern

◆ MONOMER_TYPES

MonomerType MONOMER_TYPES[MONOMER_COUNT]

extern

◆ PAIR_STATES

const char* PAIR_STATES[PAIR_STATE_COUNT]

extern

◆ pes

pesPtr pes

extern

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Macro Definition Documentation

◆ _GNU_SOURCE

◆ average_correlation_functions_ext

◆ da_append

◆ DA_INIT_CAP

◆ da_insert

◆ da_last

◆ ERROR

◆ INFO

◆ INIT_WRANK

◆ INIT_WSIZE

◆ IPHI

◆ IPPHI

◆ IPPSI

◆ IPR

◆ IPSI

◆ IPTHETA

◆ IR

◆ ITHETA

◆ MODULO_BASE

◆ MONOMER_COUNT

◆ MT_GENERATE_CODE_IN_HEADER

◆ OMPI_SKIP_MPICXX

◆ PRINT0

◆ return_defer

◆ TODO

◆ UNREACHABLE

◆ UNUSED

◆ WARNING

Typedef Documentation

◆ dipoleFree

◆ dipolePtr

◆ dpesPtr

◆ pesPtr

Enumeration Type Documentation

◆ CalculationType

◆ MonomerType

◆ PairState

◆ SamplingType

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_M0()

◆ calculate_M2()

◆ 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()

◆ 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()