statistics_molecule.c File Reference

see statistics_molecule.h More...

#include "statistics_molecule.h"
#include "errorhandling.h"
#include "grid.h"

Include dependency graph for statistics_molecule.c:

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Functions
int	analyze_fold_molecules (float *coord, double shift[3])
	Using the topology information stored in topology::topology this routine foldes all particles belonging to a molecule such that the center of mass of the molecule is inside the simulation box.
double	calc_mol_hydro_radius (Molecule mol)
void	calc_mol_center_of_mass (Molecule mol, double com[3])
	Incorporates mass of each particle.
double	calc_mol_gyr_radius2 (Molecule mol)
	Incorporates mass of each particle.

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Detailed Description

see statistics_molecule.h

Definition in file statistics_molecule.c.

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Function Documentation

int analyze_fold_molecules	(	float *	coord,
		double	shift[3]
	)

Using the topology information stored in topology::topology this routine foldes all particles belonging to a molecule such that the center of mass of the molecule is inside the simulation box.

Parameters:

coord	is an array specifying the full coordinates of all particles. Particles must be stored in particle ID order in this array.
shift	is a vector specifying a shift for the entire system coordinates that is applied prior to folding: This is used for visualization purposes.

Definition at line 30 of file statistics_molecule.c.

References box_l, box_l_i, calc_mol_center_of_mass(), IntList::e, ERROR_SPRINTF, ES_DOUBLE_SPACE, ES_ERROR, ES_INTEGER_SPACE, ES_OK, i, IntList::n, n_molecules, Molecule::part, PERIODIC, runtime_error(), sortPartCfg(), and topology.

Referenced by tclcommand_analyze_parse_get_folded_positions(), and tclcommand_imd_parse_pos().

void calc_mol_center_of_mass	(	Molecule	mol,
		double	com[3]
	)

Incorporates mass of each particle.

Definition at line 97 of file statistics_molecule.c.

References IntList::e, i, IntList::n, Particle::p, Molecule::part, partCfg, and PMASS.

Referenced by analyze_fold_molecules(), and calc_mol_gyr_radius2().

double calc_mol_gyr_radius2

(

Molecule

mol

)

Incorporates mass of each particle.

Definition at line 113 of file statistics_molecule.c.

References calc_mol_center_of_mass(), IntList::e, i, IntList::n, Particle::p, Molecule::part, partCfg, PMASS, sqrlen(), and vecsub().

double calc_mol_hydro_radius

(

Molecule

mol

)

Definition at line 79 of file statistics_molecule.c.

References IntList::e, i, IntList::n, ParticlePosition::p, Particle::p, Molecule::part, partCfg, Particle::r, sqrlen(), and vecsub().