Where the command line options are stored. More...

#include <Dump2XYZCmd.hpp>

Public Attributes
const char *	help_help
	Print help and exit help description.

const char *	version_help
	Print version and exit help description.

char *	input_arg
	input dump file.

char *	input_orig
	input dump file original value given at command line.

const char *	input_help
	input dump file help description.

char *	output_arg
	output file name.

char *	output_orig
	output file name original value given at command line.

const char *	output_help
	output file name help description.

int	frame_arg
	print every n frame (default='1').

char *	frame_orig
	print every n frame original value given at command line.

const char *	frame_help
	print every n frame help description.

int	water_flag
	skip the the waters (default=off).

const char *	water_help
	skip the the waters help description.

int	periodicBox_flag
	map to the periodic box (default=off).

const char *	periodicBox_help
	map to the periodic box help description.

int	zconstraint_flag
	replace the atom types of zconstraint molecules (default=off).

const char *	zconstraint_help
	replace the atom types of zconstraint molecules help description.

int	rigidbody_flag
	add a pseudo COM atom to rigidbody (default=off).

const char *	rigidbody_help
	add a pseudo COM atom to rigidbody help description.

int	watertype_flag
	replace the atom type of water model (default=on).

const char *	watertype_help
	replace the atom type of water model help description.

char *	selection_arg
	general selection syntax.

char *	selection_orig
	general selection syntax original value given at command line.

const char *	selection_help
	general selection syntax help description.

char *	originsele_arg
	select origin.

char *	originsele_orig
	select origin original value given at command line.

const char *	originsele_help
	select origin help description.

char *	refsele_arg
	select reference.

char *	refsele_orig
	select reference original value given at command line.

const char *	refsele_help
	select reference help description.

int	repeatX_arg
	The number of images to repeat in the x direction (default='0').

char *	repeatX_orig
	The number of images to repeat in the x direction original value given at command line.

const char *	repeatX_help
	The number of images to repeat in the x direction help description.

int	repeatY_arg
	The number of images to repeat in the y direction (default='0').

char *	repeatY_orig
	The number of images to repeat in the y direction original value given at command line.

const char *	repeatY_help
	The number of images to repeat in the y direction help description.

int	repeatZ_arg
	The number of images to repeat in the z direction (default='0').

char *	repeatZ_orig
	The number of images to repeat in the z direction original value given at command line.

const char *	repeatZ_help
	The number of images to repeat in the z direction help description.

int	basetype_flag
	Convert to base atom type (default=off).

const char *	basetype_help
	Convert to base atom type help description.

int	velocities_flag
	Print velocities in xyz file (default=off).

const char *	velocities_help
	Print velocities in xyz file help description.

int	forces_flag
	Print forces xyz file (default=off).

const char *	forces_help
	Print forces xyz file help description.

int	vectors_flag
	Print vectors (dipoles, etc) in xyz file (default=off).

const char *	vectors_help
	Print vectors (dipoles, etc) in xyz file help description.

int	charges_flag
	Print charges in xyz file (default=off).

const char *	charges_help
	Print charges in xyz file help description.

int	efield_flag
	Print electric field vector in xyz file (default=off).

const char *	efield_help
	Print electric field vector in xyz file help description.

int	globalID_flag
	Print global ID in xyz file (default=off).

const char *	globalID_help
	Print global ID in xyz file help description.

unsigned int	help_given
	Whether help was given.

unsigned int	version_given
	Whether version was given.

unsigned int	input_given
	Whether input was given.

unsigned int	output_given
	Whether output was given.

unsigned int	frame_given
	Whether frame was given.

unsigned int	water_given
	Whether water was given.

unsigned int	periodicBox_given
	Whether periodicBox was given.

unsigned int	zconstraint_given
	Whether zconstraint was given.

unsigned int	rigidbody_given
	Whether rigidbody was given.

unsigned int	watertype_given
	Whether watertype was given.

unsigned int	selection_given
	Whether selection was given.

unsigned int	originsele_given
	Whether originsele was given.

unsigned int	refsele_given
	Whether refsele was given.

unsigned int	repeatX_given
	Whether repeatX was given.

unsigned int	repeatY_given
	Whether repeatY was given.

unsigned int	repeatZ_given
	Whether repeatZ was given.

unsigned int	basetype_given
	Whether basetype was given.

unsigned int	velocities_given
	Whether velocities was given.

unsigned int	forces_given
	Whether forces was given.

unsigned int	vectors_given
	Whether vectors was given.

unsigned int	charges_given
	Whether charges was given.

unsigned int	efield_given
	Whether efield was given.

unsigned int	globalID_given
	Whether globalID was given.

char **	inputs
	unamed options (options without names)

unsigned	inputs_num
	unamed options number

char *	sele1_arg
	select first stuntdouble set.

char *	sele1_orig
	select first stuntdouble set original value given at command line.

const char *	sele1_help
	select first stuntdouble set help description.

char *	sele2_arg
	select second stuntdouble set (if sele2 is not set, use script from sele1).

char *	sele2_orig
	select second stuntdouble set (if sele2 is not set, use script from sele1) original value given at command line.

const char *	sele2_help
	select second stuntdouble set (if sele2 is not set, use script from sele1) help description.

char *	sele3_arg
	select third stuntdouble set.

char *	sele3_orig
	select third stuntdouble set original value given at command line.

const char *	sele3_help
	select third stuntdouble set help description.

int	order_arg
	Lengendre Polynomial Order.

char *	order_orig
	Lengendre Polynomial Order original value given at command line.

const char *	order_help
	Lengendre Polynomial Order help description.

int	nbins_arg
	Number of bins (default='100').

char *	nbins_orig
	Number of bins original value given at command line.

const char *	nbins_help
	Number of bins help description.

int	nzbins_arg
	Number of Z bins (default='100').

char *	nzbins_orig
	Number of Z bins original value given at command line.

const char *	nzbins_help
	Number of Z bins help description.

double	rcut_arg
	cutoff radius (angstroms).

char *	rcut_orig
	cutoff radius (angstroms) original value given at command line.

const char *	rcut_help
	cutoff radius (angstroms) help description.

double	OOcut_arg
	Oxygen-Oxygen cutoff radius (angstroms) (default='3.5').

char *	OOcut_orig
	Oxygen-Oxygen cutoff radius (angstroms) original value given at command line.

const char *	OOcut_help
	Oxygen-Oxygen cutoff radius (angstroms) help description.

double	thetacut_arg
	HOO cutoff angle (degrees) (default='30').

char *	thetacut_orig
	HOO cutoff angle (degrees) original value given at command line.

const char *	thetacut_help
	HOO cutoff angle (degrees) help description.

double	OHcut_arg
	Oxygen-Hydrogen cutoff radius (angstroms) (default='2.45').

char *	OHcut_orig
	Oxygen-Hydrogen cutoff radius (angstroms) original value given at command line.

const char *	OHcut_help
	Oxygen-Hydrogen cutoff radius (angstroms) help description.

enum enum_privilegedAxis	privilegedAxis_arg
	which axis is special for spatial analysis (default = z axis) (default='z').

char *	privilegedAxis_orig
	which axis is special for spatial analysis (default = z axis) original value given at command line.

const char *	privilegedAxis_help
	which axis is special for spatial analysis (default = z axis) help description.

double	length_arg
	maximum length (default='100').

char *	length_orig
	maximum length original value given at command line.

const char *	length_help
	maximum length help description.

double	dipoleX_arg
	X-component of the dipole with respect to body frame (default='0.0').

char *	dipoleX_orig
	X-component of the dipole with respect to body frame original value given at command line.

const char *	dipoleX_help
	X-component of the dipole with respect to body frame help description.

double	dipoleY_arg
	Y-component of the dipole with respect to body frame (default='0.0').

char *	dipoleY_orig
	Y-component of the dipole with respect to body frame original value given at command line.

const char *	dipoleY_help
	Y-component of the dipole with respect to body frame help description.

double	dipoleZ_arg
	Z-component of the dipole with respect to body frame (default='-1.0').

char *	dipoleZ_orig
	Z-component of the dipole with respect to body frame original value given at command line.

const char *	dipoleZ_help
	Z-component of the dipole with respect to body frame help description.

const char *	selecorr_help
	selection correlation function help description.

const char *	rcorr_help
	mean squared displacement help description.

const char *	rcorrZ_help
	mean squared displacement binned by Z help description.

const char *	vcorr_help
	velocity correlation function help description.

const char *	vcorrZ_help
	velocity correlation function along z-axis help description.

const char *	vcorrR_help
	velocity correlation function projected radially help description.

const char *	vaOutProdcorr_help
	Velocity - Velocity auto outer product correlation function help description.

const char *	waOutProdcorr_help
	Angular Velocity - Angular Velocity auto outer product correlation function help description.

const char *	vwOutProdcorr_help
	Velocity - Angular Velocity outer product correlation function help description.

const char *	wvOutProdcorr_help
	Angular Velocity - Velocity outer product correlation function help description.

const char *	wcorr_help
	charge velocity correlation function help description.

const char *	dcorr_help
	dipole correlation function help description.

const char *	lcorr_help
	Lengendre correlation function help description.

const char *	lcorrZ_help
	Lengendre correlation function binned by Z help description.

const char *	cohZ_help
	Lengendre correlation function for OH bond vectors binned by Z help description.

const char *	sdcorr_help
	System dipole correlation function help description.

const char *	r_rcorr_help
	Radial msd help description.

const char *	thetacorr_help
	Angular msd help description.

const char *	drcorr_help
	Directional msd for particles with unit vectors help description.

const char *	stresscorr_help
	Stress tensor correlation function help description.

const char *	bondcorr_help
	Bond extension correlation function help description.

const char *	freqfluccorr_help
	Frequency Fluctuation correlation function help description.

const char *	jumptime_help
	Hydrogen bond jump time correlation function help description.

const char *	jumptimeZ_help
	Hydrogen bond jump time correlation function binned by Z help description.

const char *	jumptimeR_help
	Hydrogen bond jump time correlation function binned by R around a third selection help description.

const char *	persistence_help
	Hydrogen bond persistence correlation function help description.

const char *	pjcorr_help
	Momentum - Angular Momentum cross correlation function help description.

const char *	ftcorr_help
	Force - Torque cross correlation function help description.

const char *	ckcorr_help
	Charge - Kinetic energy cross correlation function help description.

const char *	cscorr_help
	Charge - Orientation order parameter (Cos\theta) cross correlation function help description.

const char *	facorr_help
	Force - Force auto correlation function help description.

const char *	tfcorr_help
	Torque - Force Cross correlation function help description.

const char *	tacorr_help
	Torque auto correlation function help description.

const char *	disp_help
	Displacement correlation function help description.

const char *	dispZ_help
	Displacement correlation function binned by Z help description.

const char *	current_help
	Current density auto correlation function help description.

const char *	onsager_help
	Onsager coefficient correlation functions help description.

const char *	ddisp_help
	Collective Dipole displacement function (Helfand moment of Current Density) help description.

const char *	rotAngleDisp_help
	Displacement correlation function for rotation angles help description.

const char *	meandisp_help
	mean displacement help description.

unsigned int	sele1_given
	Whether sele1 was given.

unsigned int	sele2_given
	Whether sele2 was given.

unsigned int	sele3_given
	Whether sele3 was given.

unsigned int	order_given
	Whether order was given.

unsigned int	nbins_given
	Whether nbins was given.

unsigned int	nzbins_given
	Whether nzbins was given.

unsigned int	rcut_given
	Whether rcut was given.

unsigned int	OOcut_given
	Whether OOcut was given.

unsigned int	thetacut_given
	Whether thetacut was given.

unsigned int	OHcut_given
	Whether OHcut was given.

unsigned int	privilegedAxis_given
	Whether privilegedAxis was given.

unsigned int	length_given
	Whether length was given.

unsigned int	dipoleX_given
	Whether dipoleX was given.

unsigned int	dipoleY_given
	Whether dipoleY was given.

unsigned int	dipoleZ_given
	Whether dipoleZ was given.

unsigned int	selecorr_given
	Whether selecorr was given.

unsigned int	rcorr_given
	Whether rcorr was given.

unsigned int	rcorrZ_given
	Whether rcorrZ was given.

unsigned int	vcorr_given
	Whether vcorr was given.

unsigned int	vcorrZ_given
	Whether vcorrZ was given.

unsigned int	vcorrR_given
	Whether vcorrR was given.

unsigned int	vaOutProdcorr_given
	Whether vaOutProdcorr was given.

unsigned int	waOutProdcorr_given
	Whether waOutProdcorr was given.

unsigned int	vwOutProdcorr_given
	Whether vwOutProdcorr was given.

unsigned int	wvOutProdcorr_given
	Whether wvOutProdcorr was given.

unsigned int	wcorr_given
	Whether wcorr was given.

unsigned int	dcorr_given
	Whether dcorr was given.

unsigned int	lcorr_given
	Whether lcorr was given.

unsigned int	lcorrZ_given
	Whether lcorrZ was given.

unsigned int	cohZ_given
	Whether cohZ was given.

unsigned int	sdcorr_given
	Whether sdcorr was given.

unsigned int	r_rcorr_given
	Whether r_rcorr was given.

unsigned int	thetacorr_given
	Whether thetacorr was given.

unsigned int	drcorr_given
	Whether drcorr was given.

unsigned int	stresscorr_given
	Whether stresscorr was given.

unsigned int	bondcorr_given
	Whether bondcorr was given.

unsigned int	freqfluccorr_given
	Whether freqfluccorr was given.

unsigned int	jumptime_given
	Whether jumptime was given.

unsigned int	jumptimeZ_given
	Whether jumptimeZ was given.

unsigned int	jumptimeR_given
	Whether jumptimeR was given.

unsigned int	persistence_given
	Whether persistence was given.

unsigned int	pjcorr_given
	Whether pjcorr was given.

unsigned int	ftcorr_given
	Whether ftcorr was given.

unsigned int	ckcorr_given
	Whether ckcorr was given.

unsigned int	cscorr_given
	Whether cscorr was given.

unsigned int	facorr_given
	Whether facorr was given.

unsigned int	tfcorr_given
	Whether tfcorr was given.

unsigned int	tacorr_given
	Whether tacorr was given.

unsigned int	disp_given
	Whether disp was given.

unsigned int	dispZ_given
	Whether dispZ was given.

unsigned int	current_given
	Whether current was given.

unsigned int	onsager_given
	Whether onsager was given.

unsigned int	ddisp_given
	Whether ddisp was given.

unsigned int	rotAngleDisp_given
	Whether rotAngleDisp was given.

unsigned int	meandisp_given
	Whether meandisp was given.

int	correlation_function_group_counter
	Counter for group correlation_function.

int	box_flag
	Optimize box geometry before performing calculation (default=off).

const char *	box_help
	Optimize box geometry before performing calculation help description.

char *	method_arg
	Calculation Method.

char *	method_orig
	Calculation Method original value given at command line.

const char *	method_help
	Calculation Method help description.

int	npoints_arg
	number of points for fitting stress-strain relationship (default='25').

char *	npoints_orig
	number of points for fitting stress-strain relationship original value given at command line.

const char *	npoints_help
	number of points for fitting stress-strain relationship help description.

double	delta_arg
	size of relative volume changes for strains.

char *	delta_orig
	size of relative volume changes for strains original value given at command line.

const char *	delta_help
	size of relative volume changes for strains help description.

unsigned int	box_given
	Whether box was given.

unsigned int	method_given
	Whether method was given.

unsigned int	npoints_given
	Whether npoints was given.

unsigned int	delta_given
	Whether delta was given.

double	start_arg
	starting affine scale (default='0.8').

char *	start_orig
	starting affine scale original value given at command line.

const char *	start_help
	starting affine scale help description.

double	end_arg
	ending affine scale (default='1.2').

char *	end_orig
	ending affine scale original value given at command line.

const char *	end_help
	ending affine scale help description.

int	number_arg
	number of data points (default='50').

char *	number_orig
	number of data points original value given at command line.

const char *	number_help
	number of data points help description.

unsigned int	start_given
	Whether start was given.

unsigned int	end_given
	Whether end was given.

unsigned int	number_given
	Whether number was given.

char *	xyz_arg
	xyz file for AtomicBead model.

char *	xyz_orig
	xyz file for AtomicBead model original value given at command line.

const char *	xyz_help
	xyz file for AtomicBead model help description.

char *	stl_arg
	stl file for BoundaryElement model.

char *	stl_orig
	stl file for BoundaryElement model original value given at command line.

const char *	stl_help
	stl file for BoundaryElement model help description.

char *	msms_arg
	filename root for MSMS .vert and .face files.

char *	msms_orig
	filename root for MSMS .vert and .face files original value given at command line.

const char *	msms_help
	filename root for MSMS .vert and .face files help description.

enum enum_model	model_arg
	hydrodynamics model.

char *	model_orig
	hydrodynamics model original value given at command line.

const char *	model_help
	hydrodynamics model help description.

double	beadSize_arg
	bead size (diameter) for RoughShell model (in angstroms) (default='0.2').

char *	beadSize_orig
	bead size (diameter) for RoughShell model (in angstroms) original value given at command line.

const char *	beadSize_help
	bead size (diameter) for RoughShell model (in angstroms) help description.

int	elements_flag
	output the hydrodynamic elements (beads or triangles) only, hydrodynamics calculation will not be performed (default=off).

const char *	elements_help
	output the hydrodynamic elements (beads or triangles) only, hydrodynamics calculation will not be performed help description.

double	viscosity_arg
	viscosity (in poise) (default='0.01').

char *	viscosity_orig
	viscosity (in poise) original value given at command line.

const char *	viscosity_help
	viscosity (in poise) help description.

double	temperature_arg
	temperature (in Kelvin (default='300').

char *	temperature_orig
	temperature (in Kelvin original value given at command line.

const char *	temperature_help
	temperature (in Kelvin help description.

unsigned int	xyz_given
	Whether xyz was given.

unsigned int	stl_given
	Whether stl was given.

unsigned int	msms_given
	Whether msms was given.

unsigned int	model_given
	Whether model was given.

unsigned int	beadSize_given
	Whether beadSize was given.

unsigned int	elements_given
	Whether elements was given.

unsigned int	viscosity_given
	Whether viscosity was given.

unsigned int	temperature_given
	Whether temperature was given.

int	input_file_group_counter
	Counter for group input_file.

int	shells_arg
	Nanoparticle shells.

char *	shells_orig
	Nanoparticle shells original value given at command line.

const char *	shells_help
	Nanoparticle shells help description.

double	latticeConstant_arg
	Lattice spacing in Angstroms for cubic lattice.

char *	latticeConstant_orig
	Lattice spacing in Angstroms for cubic lattice.

const char *	latticeConstant_help
	Lattice spacing in Angstroms for cubic lattice.

char *	lattice_arg
	Lattice Type.

char *	lattice_orig
	Lattice Type original value given at command line.

const char *	lattice_help
	Lattice Type help description.

int	columnAtoms_arg
	Number of atoms along central column (Decahedron only).

char *	columnAtoms_orig
	Number of atoms along central column (Decahedron only) original value given at command line.

const char *	columnAtoms_help
	Number of atoms along central column (Decahedron only) help description.

int	twinAtoms_arg
	Number of atoms along twin boundary (Decahedron only).

char *	twinAtoms_orig
	Number of atoms along twin boundary (Decahedron only) original value given at command line.

const char *	twinAtoms_help
	Number of atoms along twin boundary (Decahedron only) help description.

int	truncatedPlanes_arg
	Number of truncated planes (Curling-stone Decahedra and Truncated Cubes only).

char *	truncatedPlanes_orig
	Number of truncated planes (Curling-stone Decahedra and Truncated Cubes only) original value given at command line.

const char *	truncatedPlanes_help
	Number of truncated planes (Curling-stone Decahedra and Truncated Cubes only) help description.

int	unitCells_arg
	Number of unit cell (Cuboctahedron and Truncated Cube only).

char *	unitCells_orig
	Number of unit cell (Cuboctahedron and Truncated Cube only) original value given at command line.

const char *	unitCells_help
	Number of unit cell (Cuboctahedron and Truncated Cube only) help description.

const char *	ico_help
	Create an Icosahedral cluster help description.

const char *	deca_help
	Create a regualar Decahedral cluster help description.

const char *	ino_help
	Create an Ino Decahedral cluster help description.

const char *	marks_help
	Create a Marks Decahedral cluster help description.

const char *	stone_help
	Create a Curling-stone Decahedral cluster help description.

const char *	cuboctahedron_help
	Create a regular Cuboctahedron (requires lattice) help description.

const char *	truncatedCube_help
	Create a Truncated Cube (requires lattice) help description.

unsigned int	shells_given
	Whether shells was given.

unsigned int	latticeConstant_given
	Whether latticeConstant was given.

unsigned int	lattice_given
	Whether lattice was given.

unsigned int	columnAtoms_given
	Whether columnAtoms was given.

unsigned int	twinAtoms_given
	Whether twinAtoms was given.

unsigned int	truncatedPlanes_given
	Whether truncatedPlanes was given.

unsigned int	unitCells_given
	Whether unitCells was given.

unsigned int	ico_given
	Whether ico was given.

unsigned int	deca_given
	Whether deca was given.

unsigned int	ino_given
	Whether ino was given.

unsigned int	marks_given
	Whether marks was given.

unsigned int	stone_given
	Whether stone was given.

unsigned int	cuboctahedron_given
	Whether cuboctahedron was given.

unsigned int	truncatedCube_given
	Whether truncatedCube was given.

int	clusterShape_group_counter
	Counter for group clusterShape.

double	radius_arg
	Nanoparticle radius in Angstroms.

char *	radius_orig
	Nanoparticle radius in Angstroms original value given at command line.

const char *	radius_help
	Nanoparticle radius in Angstroms help description.

double *	shellRadius_arg
	Radius containing within it only molecules of a specific component.

char **	shellRadius_orig
	Radius containing within it only molecules of a specific component.

unsigned int	shellRadius_min
	Radius containing within it only molecules of a specific component.

unsigned int	shellRadius_max
	Radius containing within it only molecules of a specific component.

const char *	shellRadius_help
	Radius containing within it only molecules of a specific component.

double *	molFraction_arg
	Builds a multi-component random alloy nanoparticle.

char **	molFraction_orig
	Builds a multi-component random alloy nanoparticle.

unsigned int	molFraction_min
	Builds a multi-component random alloy nanoparticle.

unsigned int	molFraction_max
	Builds a multi-component random alloy nanoparticle.

const char *	molFraction_help
	Builds a multi-component random alloy nanoparticle.

double	vacancyPercent_arg
	Percentage of atoms to remove from within vacancy range.

char *	vacancyPercent_orig
	Percentage of atoms to remove from within vacancy range original value given at command line.

const char *	vacancyPercent_help
	Percentage of atoms to remove from within vacancy range help description.

double	vacancyInnerRadius_arg
	Radius arround core-shell where vacancies should be located.

char *	vacancyInnerRadius_orig
	Radius arround core-shell where vacancies should be located.

const char *	vacancyInnerRadius_help
	Radius arround core-shell where vacancies should be located.

double	vacancyOuterRadius_arg
	Radius arround core-shell where vacancies should be located.

char *	vacancyOuterRadius_orig
	Radius arround core-shell where vacancies should be located.

const char *	vacancyOuterRadius_help
	Radius arround core-shell where vacancies should be located.

unsigned int	radius_given
	Whether radius was given.

unsigned int	shellRadius_given
	Whether shellRadius was given.

unsigned int	molFraction_given
	Whether molFraction was given.

unsigned int	vacancyPercent_given
	Whether vacancyPercent was given.

unsigned int	vacancyInnerRadius_given
	Whether vacancyInnerRadius was given.

unsigned int	vacancyOuterRadius_given
	Whether vacancyOuterRadius was given.

int	ellipsoid_flag
	Build an Ellipsoid instead of a rod.

const char *	ellipsoid_help
	Build an Ellipsoid instead of a rod.

unsigned int	ellipsoid_given
	Whether ellipsoid was given.

double	translateX_arg
	translate all x coordinates by some amount (default='0.0').

char *	translateX_orig
	translate all x coordinates by some amount original value given at command line.

const char *	translateX_help
	translate all x coordinates by some amount help description.

double	translateY_arg
	translate all y coordinates by some amount (default='0.0').

char *	translateY_orig
	translate all y coordinates by some amount original value given at command line.

const char *	translateY_help
	translate all y coordinates by some amount help description.

double	translateZ_arg
	translate all z coordinates by some amount (default='0.0').

char *	translateZ_orig
	translate all z coordinates by some amount original value given at command line.

const char *	translateZ_help
	translate all z coordinates by some amount help description.

double	rotatePhi_arg
	rotate all coordinates Euler angle Phi (default='0.0').

char *	rotatePhi_orig
	rotate all coordinates Euler angle Phi original value given at command line.

const char *	rotatePhi_help
	rotate all coordinates Euler angle Phi help description.

double	rotateTheta_arg
	rotate all coordinates Euler angle Theta (default='0.0').

char *	rotateTheta_orig
	rotate all coordinates Euler angle Theta original value given at command line.

const char *	rotateTheta_help
	rotate all coordinates Euler angle Theta help description.

double	rotatePsi_arg
	rotate all coordinates Euler angle Psi (default='0.0').

char *	rotatePsi_orig
	rotate all coordinates Euler angle Psi original value given at command line.

const char *	rotatePsi_help
	rotate all coordinates Euler angle Psi help description.

int	repairMolecules_arg
	rewrap molecules around the molecular center of mass (default='1').

char *	repairMolecules_orig
	rewrap molecules around the molecular center of mass original value given at command line.

const char *	repairMolecules_help
	rewrap molecules around the molecular center of mass help description.

int	noWrap_flag
	do not rewrap coordinates into the box (default=off).

const char *	noWrap_help
	do not rewrap coordinates into the box help description.

int	noCOM_flag
	do not use Center of Mass as origin of the box (default=off).

const char *	noCOM_help
	do not use Center of Mass as origin of the box help description.

unsigned int	translateX_given
	Whether translateX was given.

unsigned int	translateY_given
	Whether translateY was given.

unsigned int	translateZ_given
	Whether translateZ was given.

unsigned int	rotatePhi_given
	Whether rotatePhi was given.

unsigned int	rotateTheta_given
	Whether rotateTheta was given.

unsigned int	rotatePsi_given
	Whether rotatePsi was given.

unsigned int	repairMolecules_given
	Whether repairMolecules was given.

unsigned int	noWrap_given
	Whether noWrap was given.

unsigned int	noCOM_given
	Whether noCOM was given.

double	density_arg
	density (g/cm^3).

char *	density_orig
	density (g/cm^3) original value given at command line.

const char *	density_help
	density (g/cm^3) help description.

int	nx_arg
	number of unit cells in x.

char *	nx_orig
	number of unit cells in x original value given at command line.

const char *	nx_help
	number of unit cells in x help description.

int	ny_arg
	number of unit cells in y.

char *	ny_orig
	number of unit cells in y original value given at command line.

const char *	ny_help
	number of unit cells in y help description.

int	nz_arg
	number of unit cells in z.

char *	nz_orig
	number of unit cells in z original value given at command line.

const char *	nz_help
	number of unit cells in z help description.

unsigned int	density_given
	Whether density was given.

unsigned int	nx_given
	Whether nx was given.

unsigned int	ny_given
	Whether ny was given.

unsigned int	nz_given
	Whether nz was given.

int	nbins_z_arg
	number of bins in z axis (default='100').

char *	nbins_z_orig
	number of bins in z axis original value given at command line.

const char *	nbins_z_help
	number of bins in z axis help description.

double	centroidX_arg
	Location of droplet centroid in x.

char *	centroidX_orig
	Location of droplet centroid in x original value given at command line.

const char *	centroidX_help
	Location of droplet centroid in x help description.

double	centroidY_arg
	Location of droplet centroid in y.

char *	centroidY_orig
	Location of droplet centroid in y original value given at command line.

const char *	centroidY_help
	Location of droplet centroid in y help description.

double	referenceZ_arg
	Reference z-height of solid surface.

char *	referenceZ_orig
	Reference z-height of solid surface original value given at command line.

const char *	referenceZ_help
	Reference z-height of solid surface help description.

double	dropletR_arg
	Droplet radius in angstroms.

char *	dropletR_orig
	Droplet radius in angstroms original value given at command line.

const char *	dropletR_help
	Droplet radius in angstroms help description.

double	threshDens_arg
	Threshold Density in g/cm^3.

char *	threshDens_orig
	Threshold Density in g/cm^3 original value given at command line.

const char *	threshDens_help
	Threshold Density in g/cm^3 help description.

double	bufferLength_arg
	Buffer length in angstroms.

char *	bufferLength_orig
	Buffer length in angstroms original value given at command line.

const char *	bufferLength_help
	Buffer length in angstroms help description.

const char *	com_help
	selection center of mass help description.

const char *	comvel_help
	selection center of mass velocity help description.

const char *	ca1_help
	contact angle of selection (using center of mass) help description.

const char *	ca2_help
	contact angle of selection (using density profile) help description.

const char *	gcn_help
	Generalized Coordinate Number help description.

const char *	testequi_help
	Temperature using all componets of linear and angular momentum help description.

unsigned int	nbins_z_given
	Whether nbins_z was given.

unsigned int	centroidX_given
	Whether centroidX was given.

unsigned int	centroidY_given
	Whether centroidY was given.

unsigned int	referenceZ_given
	Whether referenceZ was given.

unsigned int	dropletR_given
	Whether dropletR was given.

unsigned int	threshDens_given
	Whether threshDens was given.

unsigned int	bufferLength_given
	Whether bufferLength was given.

unsigned int	com_given
	Whether com was given.

unsigned int	comvel_given
	Whether comvel was given.

unsigned int	ca1_given
	Whether ca1 was given.

unsigned int	ca2_given
	Whether ca2 was given.

unsigned int	gcn_given
	Whether gcn was given.

unsigned int	testequi_given
	Whether testequi was given.

int	sequentialProps_group_counter
	Counter for group sequentialProps.

int	step_arg
	process every n frame (default='1').

char *	step_orig
	process every n frame original value given at command line.

const char *	step_help
	process every n frame help description.

int	nbins_x_arg
	number of bins in x axis (default='100').

char *	nbins_x_orig
	number of bins in x axis original value given at command line.

const char *	nbins_x_help
	number of bins in x axis help description.

int	nbins_y_arg
	number of bins in y axis (default='100').

char *	nbins_y_orig
	number of bins in y axis original value given at command line.

const char *	nbins_y_help
	number of bins in y axis help description.

int	nrbins_arg
	number of radial bins (usually duplicates functionality of nbins) (default='100').

char *	nrbins_orig
	number of radial bins (usually duplicates functionality of nbins) original value given at command line.

const char *	nrbins_help
	number of radial bins (usually duplicates functionality of nbins) help description.

double	binWidth_arg
	width of radial bins in angstroms (default='1.0').

char *	binWidth_orig
	width of radial bins in angstroms original value given at command line.

const char *	binWidth_help
	width of radial bins in angstroms help description.

int	nanglebins_arg
	number of bins for cos(angle) (default='50').

char *	nanglebins_orig
	number of bins for cos(angle) original value given at command line.

const char *	nanglebins_help
	number of bins for cos(angle) help description.

double	dz_arg
	slab width (dz).

char *	dz_orig
	slab width (dz) original value given at command line.

const char *	dz_help
	slab width (dz) help description.

double	zlength_arg
	maximum length (Defaults to 1/2 smallest length of first frame).

char *	zlength_orig
	maximum length (Defaults to 1/2 smallest length of first frame) original value given at command line.

const char *	zlength_help
	maximum length (Defaults to 1/2 smallest length of first frame) help description.

double	zoffset_arg
	Where to set the zero for the slab_density calculation (default='0').

char *	zoffset_orig
	Where to set the zero for the slab_density calculation original value given at command line.

const char *	zoffset_help
	Where to set the zero for the slab_density calculation help description.

char *	comsele_arg
	select stunt doubles for center-of-mass reference point.

char *	comsele_orig
	select stunt doubles for center-of-mass reference point original value given at command line.

const char *	comsele_help
	select stunt doubles for center-of-mass reference point help description.

int	seleoffset_arg
	global index offset for a second object (used to define a vector between sites in molecule).

char *	seleoffset_orig
	global index offset for a second object (used to define a vector between sites in molecule) original value given at command line.

const char *	seleoffset_help
	global index offset for a second object (used to define a vector between sites in molecule) help description.

int	seleoffset2_arg
	global index offset for a third object (used to define a vector between sites in molecule).

char *	seleoffset2_orig
	global index offset for a third object (used to define a vector between sites in molecule) original value given at command line.

const char *	seleoffset2_help
	global index offset for a third object (used to define a vector between sites in molecule) help description.

char *	molname_arg
	molecule name.

char *	molname_orig
	molecule name original value given at command line.

const char *	molname_help
	molecule name help description.

int	begin_arg
	begin internal index.

char *	begin_orig
	begin internal index original value given at command line.

const char *	begin_help
	begin internal index help description.

int	end_arg
	end internal index.

double	voxelSize_arg
	voxel size (angstroms).

char *	voxelSize_orig
	voxel size (angstroms) original value given at command line.

const char *	voxelSize_help
	voxel size (angstroms) help description.

double	gaussWidth_arg
	Gaussian width (angstroms).

char *	gaussWidth_orig
	Gaussian width (angstroms) original value given at command line.

const char *	gaussWidth_help
	Gaussian width (angstroms) help description.

enum enum_privilegedAxis2	privilegedAxis2_arg
	which axis is special for spatial analysis (default = x axis) (default='x').

char *	privilegedAxis2_orig
	which axis is special for spatial analysis (default = x axis) original value given at command line.

const char *	privilegedAxis2_help
	which axis is special for spatial analysis (default = x axis) help description.

enum enum_momentum	momentum_arg
	Type of momentum whose distribtution is required (default = Liner Momentum) (default='P').

char *	momentum_orig
	Type of momentum whose distribtution is required (default = Liner Momentum) original value given at command line.

const char *	momentum_help
	Type of momentum whose distribtution is required (default = Liner Momentum) help description.

enum enum_component	component_arg
	component of momentum for the momemtum distribution (default = z axis) (default='z').

char *	component_orig
	component of momentum for the momemtum distribution (default = z axis) original value given at command line.

const char *	component_help
	component of momentum for the momemtum distribution (default = z axis) help description.

double	v_radius_arg
	VanderWaals radiius for fictious atoms used in model eg.

char *	v_radius_orig
	VanderWaals radiius for fictious atoms used in model eg.

const char *	v_radius_help
	VanderWaals radiius for fictious atoms used in model eg.

int	gen_xyz_flag
	generates xyz file (default=off).

const char *	gen_xyz_help
	generates xyz file help description.

char *	atom_name_arg
	name of atom for with average charge to be generated.

char *	atom_name_orig
	name of atom for with average charge to be generated original value given at command line.

const char *	atom_name_help
	name of atom for with average charge to be generated help description.

const char *	bo_help
	bond order parameter (–rcut must be specified) help description.

const char *	ior_help
	icosahedral bond order parameter as a function of radius (–rcut must be specified) help description.

const char *	for_help
	FCC bond order parameter as a function of radius (–rcut must be specified) help description.

const char *	bad_help
	N(theta) bond angle density within (–rcut must be specified) help description.

const char *	count_help
	count of objects matching selection criteria (and associated statistics) help description.

const char *	mcount_help
	count of molecules matching selection criteria (and associated statistics) help description.

const char *	gofr_help
	g(r) help description.

const char *	gofz_help
	g(z) help description.

const char *	r_theta_help
	g(r, cos(theta)) help description.

const char *	r_omega_help
	g(r, cos(omega)) help description.

const char *	r_z_help
	g(r, z) help description.

const char *	theta_omega_help
	g(cos(theta), cos(omega)) help description.

const char *	r_theta_omega_help
	g(r, cos(theta), cos(omega)) help description.

const char *	gxyz_help
	g(x, y, z) help description.

const char *	twodgofr_help
	2D g(r) (Slab width –dz must be specified) help description.

const char *	kirkwood_buff_help
	Kirkwood-Buff integrals (–sele1 and –sele2 must both be specified) help description.

const char *	p2_help
	p2 order parameter (–sele1 must be specified, –sele2 is optional) help description.

const char *	p2r_help
	p2 order parameter using r as director axis help description.

const char *	p2z_help
	p2 order parameter using z (or privilegedAxis) as director axis help description.

const char *	rp2_help
	rp2 order parameter (–sele1 and –sele2 must be specified) help description.

const char *	scd_help
	scd order parameter (either –sele1, –sele2, –sele3 are specified or –molname, –begin, –end are specified) help description.

const char *	slab_density_help
	slab density, rho(z) help description.

const char *	pipe_density_help
	pipe density, rho(axis1, axis2) help description.

const char *	p_angle_help
	p(cos(theta)) (–sele1 must be specified, –sele2 is optional) help description.

const char *	hxy_help
	hxy help description.

const char *	rho_r_help
	rho(R) help description.

const char *	angle_r_help
	angle of R help description.

const char *	hullvol_help
	hull volume of nanoparticle help description.

const char *	rodlength_help
	length of nanorod help description.

const char *	tet_param_help
	tetrahedrality order parameter (Qk) help description.

const char *	tet_param_z_help
	spatially-resolved tetrahedrality order parameter Qk(z) help description.

const char *	tet_param_r_help
	spatially-resolved tetrahedrality order parameter Qk(r) around a third selection help description.

const char *	tet_param_dens_help
	computes density of the tetrahedrality order parameter Qk help description.

const char *	tet_param_xyz_help
	volume-resolved tetrahedrality order parameter Qk(x,y,z).

const char *	trans_param_z_help
	spatially-resolved translational order parameter t(z) help description.

const char *	rnemdz_help
	slab-resolved RNEMD statistics (temperature, density, velocity) help description.

const char *	rnemdr_help
	shell-resolved RNEMD statistics (temperature, density, angular velocity) help description.

const char *	rnemdrt_help
	shell and angle-resolved RNEMD statistics (temperature, density, angular velocity) help description.

const char *	nitrile_help
	electrostatic potential to frequency map based on the Cho nitrile fits help description.

const char *	multipole_help
	average multipole moments contained within cutoff spheres as a function of radius help description.

const char *	surfDiffusion_help
	X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion help description.

const char *	cn_help
	Coordination Number Distribution help description.

const char *	scn_help
	Secondary Coordination Number Distribution help description.

const char *	hbond_help
	Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified) help description.

const char *	hbondz_help
	Hydrogen Bonding density binned by z (rcut and thetacut must be specified) help description.

const char *	hbondzvol_help
	Hydrogen Bonding density binned by z and normalized by bin volume (rcut and thetacut must be specified) help description.

const char *	hbondr_help
	Hydrogen Bonding density binned by r (rcut and thetacut must be specified) help description.

const char *	hbondrvol_help
	Hydrogen Bonding density binned by r and normalized by bin volume (rcut and thetacut must be specified) help description.

const char *	potDiff_help
	potential energy difference when charge on selection is set to zero help description.

const char *	tet_hb_help
	hydrogen bond statistics binned by tetrahedrality of donor and acceptor molecules help description.

const char *	kirkwood_help
	distance-dependent Kirkwood factor help description.

const char *	kirkwoodQ_help
	distance-dependent Kirkwood factor for quadrupoles help description.

const char *	densityfield_help
	computes an average density field help description.

const char *	velocityfield_help
	computes an average velocity field help description.

const char *	velocityZ_help
	computes an average two-dimensional velocity map help description.

const char *	eam_density_help
	computes an average eam density profile of the selected atom help description.

const char *	net_charge_help
	computes an average charge profile of the selected atom help description.

const char *	current_density_help
	computes the current density for the selected atom help description.

const char *	chargez_help
	computes the charge distribution along selected axis and selected atom help description.

const char *	charger_help
	computes the charge density as a function of the radius and selected atom help description.

const char *	massdensityz_help
	computes the mass density of the selection along selected axis help description.

const char *	massdensityr_help
	computes the mass density of the selection as a function of the radius from the center of mass help description.

const char *	numberz_help
	computes the number density along selected axis and selected molcule help description.

const char *	numberr_help
	computes the number density as a function of the radius and selected molecule help description.

const char *	charge_density_z_help
	computes the continuous charge distribution along selected axis and selected atom help description.

const char *	countz_help
	computes the number of selected atoms along selected axis help description.

const char *	momentum_distribution_help
	computes the momentum distribution for the selected atom help description.

const char *	dipole_orientation_help
	spatially-resolved dipole order parameter S(z), S = (3 Cos^2\theta - 1)/2 help description.

const char *	order_prob_help
	probability of order parameter for given selection help description.

unsigned int	step_given
	Whether step was given.

unsigned int	nbins_x_given
	Whether nbins_x was given.

unsigned int	nbins_y_given
	Whether nbins_y was given.

unsigned int	nrbins_given
	Whether nrbins was given.

unsigned int	binWidth_given
	Whether binWidth was given.

unsigned int	nanglebins_given
	Whether nanglebins was given.

unsigned int	dz_given
	Whether dz was given.

unsigned int	zlength_given
	Whether zlength was given.

unsigned int	zoffset_given
	Whether zoffset was given.

unsigned int	comsele_given
	Whether comsele was given.

unsigned int	seleoffset_given
	Whether seleoffset was given.

unsigned int	seleoffset2_given
	Whether seleoffset2 was given.

unsigned int	molname_given
	Whether molname was given.

unsigned int	begin_given
	Whether begin was given.

unsigned int	voxelSize_given
	Whether voxelSize was given.

unsigned int	gaussWidth_given
	Whether gaussWidth was given.

unsigned int	privilegedAxis2_given
	Whether privilegedAxis2 was given.

unsigned int	momentum_given
	Whether momentum was given.

unsigned int	component_given
	Whether component was given.

unsigned int	v_radius_given
	Whether v_radius was given.

unsigned int	gen_xyz_given
	Whether gen_xyz was given.

unsigned int	atom_name_given
	Whether atom_name was given.

unsigned int	bo_given
	Whether bo was given.

unsigned int	ior_given
	Whether ior was given.

unsigned int	for_given
	Whether for was given.

unsigned int	bad_given
	Whether bad was given.

unsigned int	count_given
	Whether count was given.

unsigned int	mcount_given
	Whether mcount was given.

unsigned int	gofr_given
	Whether gofr was given.

unsigned int	gofz_given
	Whether gofz was given.

unsigned int	r_theta_given
	Whether r_theta was given.

unsigned int	r_omega_given
	Whether r_omega was given.

unsigned int	r_z_given
	Whether r_z was given.

unsigned int	theta_omega_given
	Whether theta_omega was given.

unsigned int	r_theta_omega_given
	Whether r_theta_omega was given.

unsigned int	gxyz_given
	Whether gxyz was given.

unsigned int	twodgofr_given
	Whether twodgofr was given.

unsigned int	kirkwood_buff_given
	Whether kirkwood_buff was given.

unsigned int	p2_given
	Whether p2 was given.

unsigned int	p2r_given
	Whether p2r was given.

unsigned int	p2z_given
	Whether p2z was given.

unsigned int	rp2_given
	Whether rp2 was given.

unsigned int	scd_given
	Whether scd was given.

unsigned int	slab_density_given
	Whether slab_density was given.

unsigned int	pipe_density_given
	Whether pipe_density was given.

unsigned int	p_angle_given
	Whether p_angle was given.

unsigned int	hxy_given
	Whether hxy was given.

unsigned int	rho_r_given
	Whether rho_r was given.

unsigned int	angle_r_given
	Whether angle_r was given.

unsigned int	hullvol_given
	Whether hullvol was given.

unsigned int	rodlength_given
	Whether rodlength was given.

unsigned int	tet_param_given
	Whether tet_param was given.

unsigned int	tet_param_z_given
	Whether tet_param_z was given.

unsigned int	tet_param_r_given
	Whether tet_param_r was given.

unsigned int	tet_param_dens_given
	Whether tet_param_dens was given.

unsigned int	tet_param_xyz_given
	Whether tet_param_xyz was given.

unsigned int	trans_param_z_given
	Whether trans_param_z was given.

unsigned int	rnemdz_given
	Whether rnemdz was given.

unsigned int	rnemdr_given
	Whether rnemdr was given.

unsigned int	rnemdrt_given
	Whether rnemdrt was given.

unsigned int	nitrile_given
	Whether nitrile was given.

unsigned int	multipole_given
	Whether multipole was given.

unsigned int	surfDiffusion_given
	Whether surfDiffusion was given.

unsigned int	cn_given
	Whether cn was given.

unsigned int	scn_given
	Whether scn was given.

unsigned int	hbond_given
	Whether hbond was given.

unsigned int	hbondz_given
	Whether hbondz was given.

unsigned int	hbondzvol_given
	Whether hbondzvol was given.

unsigned int	hbondr_given
	Whether hbondr was given.

unsigned int	hbondrvol_given
	Whether hbondrvol was given.

unsigned int	potDiff_given
	Whether potDiff was given.

unsigned int	tet_hb_given
	Whether tet_hb was given.

unsigned int	kirkwood_given
	Whether kirkwood was given.

unsigned int	kirkwoodQ_given
	Whether kirkwoodQ was given.

unsigned int	densityfield_given
	Whether densityfield was given.

unsigned int	velocityfield_given
	Whether velocityfield was given.

unsigned int	velocityZ_given
	Whether velocityZ was given.

unsigned int	eam_density_given
	Whether eam_density was given.

unsigned int	net_charge_given
	Whether net_charge was given.

unsigned int	current_density_given
	Whether current_density was given.

unsigned int	chargez_given
	Whether chargez was given.

unsigned int	charger_given
	Whether charger was given.

unsigned int	massdensityz_given
	Whether massdensityz was given.

unsigned int	massdensityr_given
	Whether massdensityr was given.

unsigned int	numberz_given
	Whether numberz was given.

unsigned int	numberr_given
	Whether numberr was given.

unsigned int	charge_density_z_given
	Whether charge_density_z was given.

unsigned int	countz_given
	Whether countz was given.

unsigned int	momentum_distribution_given
	Whether momentum_distribution was given.

unsigned int	dipole_orientation_given
	Whether dipole_orientation was given.

unsigned int	order_prob_given
	Whether order_prob was given.

int	staticProps_group_counter
	Counter for group staticProps.

double	energy_arg
	energy (kcal/mol).

char *	energy_orig
	energy (kcal/mol) original value given at command line.

const char *	energy_help
	energy (kcal/mol) help description.

double	chargetemperature_arg
	charge temperature (K).

char *	chargetemperature_orig
	charge temperature (K) original value given at command line.

const char *	chargetemperature_help
	charge temperature (K) help description.

unsigned int	energy_given
	Whether energy was given.

unsigned int	chargetemperature_given
	Whether chargetemperature was given.

int	thermalizer_group_counter
	Counter for group thermalizer.

Detailed Description

Where the command line options are stored.

Definition at line 38 of file Dump2XYZCmd.hpp.

Member Data Documentation

◆ angle_r_given

unsigned int gengetopt_args_info::angle_r_given

Whether angle_r was given.

Definition at line 311 of file StaticPropsCmd.hpp.

◆ angle_r_help

const char* gengetopt_args_info::angle_r_help

angle of R help description.

Definition at line 196 of file StaticPropsCmd.hpp.

◆ atom_name_arg

char* gengetopt_args_info::atom_name_arg

name of atom for with average charge to be generated.

Definition at line 166 of file StaticPropsCmd.hpp.

◆ atom_name_given

unsigned int gengetopt_args_info::atom_name_given

Whether atom_name was given.

Definition at line 283 of file StaticPropsCmd.hpp.

◆ atom_name_help

const char* gengetopt_args_info::atom_name_help

name of atom for with average charge to be generated help description.

Definition at line 168 of file StaticPropsCmd.hpp.

◆ atom_name_orig

char* gengetopt_args_info::atom_name_orig

name of atom for with average charge to be generated original value given at command line.

Definition at line 167 of file StaticPropsCmd.hpp.

◆ bad_given

unsigned int gengetopt_args_info::bad_given

Whether bad was given.

Definition at line 287 of file StaticPropsCmd.hpp.

◆ bad_help

const char* gengetopt_args_info::bad_help

N(theta) bond angle density within (–rcut must be specified) help description.

Definition at line 172 of file StaticPropsCmd.hpp.

◆ basetype_flag

int gengetopt_args_info::basetype_flag

Convert to base atom type (default=off).

Definition at line 79 of file Dump2XYZCmd.hpp.

◆ basetype_given

unsigned int gengetopt_args_info::basetype_given

Whether basetype was given.

Definition at line 110 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ basetype_help

const char* gengetopt_args_info::basetype_help

Convert to base atom type help description.

Definition at line 80 of file Dump2XYZCmd.hpp.

◆ beadSize_arg

double gengetopt_args_info::beadSize_arg

bead size (diameter) for RoughShell model (in angstroms) (default='0.2').

Definition at line 62 of file HydroCmd.hpp.

◆ beadSize_given

unsigned int gengetopt_args_info::beadSize_given

Whether beadSize was given.

Definition at line 82 of file HydroCmd.hpp.

◆ beadSize_help

const char* gengetopt_args_info::beadSize_help

bead size (diameter) for RoughShell model (in angstroms) help description.

Definition at line 64 of file HydroCmd.hpp.

◆ beadSize_orig

char* gengetopt_args_info::beadSize_orig

bead size (diameter) for RoughShell model (in angstroms) original value given at command line.

Definition at line 63 of file HydroCmd.hpp.

◆ begin_arg

int gengetopt_args_info::begin_arg

begin internal index.

Definition at line 125 of file StaticPropsCmd.hpp.

◆ begin_given

unsigned int gengetopt_args_info::begin_given

Whether begin was given.

Definition at line 269 of file StaticPropsCmd.hpp.

◆ begin_help

const char* gengetopt_args_info::begin_help

begin internal index help description.

Definition at line 127 of file StaticPropsCmd.hpp.

◆ begin_orig

char* gengetopt_args_info::begin_orig

begin internal index original value given at command line.

Definition at line 126 of file StaticPropsCmd.hpp.

◆ binWidth_arg

double gengetopt_args_info::binWidth_arg

width of radial bins in angstroms (default='1.0').

Definition at line 71 of file StaticPropsCmd.hpp.

◆ binWidth_given

unsigned int gengetopt_args_info::binWidth_given

Whether binWidth was given.

Definition at line 251 of file StaticPropsCmd.hpp.

◆ binWidth_help

const char* gengetopt_args_info::binWidth_help

width of radial bins in angstroms help description.

Definition at line 73 of file StaticPropsCmd.hpp.

◆ binWidth_orig

char* gengetopt_args_info::binWidth_orig

width of radial bins in angstroms original value given at command line.

Definition at line 72 of file StaticPropsCmd.hpp.

◆ bo_given

unsigned int gengetopt_args_info::bo_given

Whether bo was given.

Definition at line 284 of file StaticPropsCmd.hpp.

◆ bo_help

const char* gengetopt_args_info::bo_help

bond order parameter (–rcut must be specified) help description.

Definition at line 169 of file StaticPropsCmd.hpp.

◆ bondcorr_given

unsigned int gengetopt_args_info::bondcorr_given

Whether bondcorr was given.

Definition at line 175 of file DynamicPropsCmd.hpp.

◆ bondcorr_help

const char* gengetopt_args_info::bondcorr_help

Bond extension correlation function help description.

Definition at line 115 of file DynamicPropsCmd.hpp.

◆ box_flag

int gengetopt_args_info::box_flag

Optimize box geometry before performing calculation (default=off).

Definition at line 45 of file elasticConstantsCmd.hpp.

◆ box_given

unsigned int gengetopt_args_info::box_given

Whether box was given.

Definition at line 63 of file elasticConstantsCmd.hpp.

◆ box_help

const char* gengetopt_args_info::box_help

Optimize box geometry before performing calculation help description.

Definition at line 46 of file elasticConstantsCmd.hpp.

◆ bufferLength_arg

double gengetopt_args_info::bufferLength_arg

Buffer length in angstroms.

Definition at line 75 of file SequentialPropsCmd.hpp.

◆ bufferLength_given

unsigned int gengetopt_args_info::bufferLength_given

Whether bufferLength was given.

Definition at line 101 of file SequentialPropsCmd.hpp.

◆ bufferLength_help

const char* gengetopt_args_info::bufferLength_help

Buffer length in angstroms help description.

Definition at line 77 of file SequentialPropsCmd.hpp.

◆ bufferLength_orig

char* gengetopt_args_info::bufferLength_orig

Buffer length in angstroms original value given at command line.

Definition at line 76 of file SequentialPropsCmd.hpp.

◆ ca1_given

unsigned int gengetopt_args_info::ca1_given

Whether ca1 was given.

Definition at line 105 of file SequentialPropsCmd.hpp.

◆ ca1_help

const char* gengetopt_args_info::ca1_help

contact angle of selection (using center of mass) help description.

Definition at line 83 of file SequentialPropsCmd.hpp.

◆ ca2_given

unsigned int gengetopt_args_info::ca2_given

Whether ca2 was given.

Definition at line 106 of file SequentialPropsCmd.hpp.

◆ ca2_help

const char* gengetopt_args_info::ca2_help

contact angle of selection (using density profile) help description.

Definition at line 84 of file SequentialPropsCmd.hpp.

◆ centroidX_arg

double gengetopt_args_info::centroidX_arg

Location of droplet centroid in x.

Definition at line 60 of file SequentialPropsCmd.hpp.

◆ centroidX_given

unsigned int gengetopt_args_info::centroidX_given

Whether centroidX was given.

Definition at line 96 of file SequentialPropsCmd.hpp.

◆ centroidX_help

const char* gengetopt_args_info::centroidX_help

Location of droplet centroid in x help description.

Definition at line 62 of file SequentialPropsCmd.hpp.

◆ centroidX_orig

char* gengetopt_args_info::centroidX_orig

Location of droplet centroid in x original value given at command line.

Definition at line 61 of file SequentialPropsCmd.hpp.

◆ centroidY_arg

double gengetopt_args_info::centroidY_arg

Location of droplet centroid in y.

Definition at line 63 of file SequentialPropsCmd.hpp.

◆ centroidY_given

unsigned int gengetopt_args_info::centroidY_given

Whether centroidY was given.

Definition at line 97 of file SequentialPropsCmd.hpp.

◆ centroidY_help

const char* gengetopt_args_info::centroidY_help

Location of droplet centroid in y help description.

Definition at line 65 of file SequentialPropsCmd.hpp.

◆ centroidY_orig

char* gengetopt_args_info::centroidY_orig

Location of droplet centroid in y original value given at command line.

Definition at line 64 of file SequentialPropsCmd.hpp.

◆ charge_density_z_given

unsigned int gengetopt_args_info::charge_density_z_given

Whether charge_density_z was given.

Definition at line 350 of file StaticPropsCmd.hpp.

◆ charge_density_z_help

const char* gengetopt_args_info::charge_density_z_help

computes the continuous charge distribution along selected axis and selected atom help description.

Definition at line 235 of file StaticPropsCmd.hpp.

◆ charger_given

unsigned int gengetopt_args_info::charger_given

Whether charger was given.

Definition at line 345 of file StaticPropsCmd.hpp.

◆ charger_help

const char* gengetopt_args_info::charger_help

computes the charge density as a function of the radius and selected atom help description.

Definition at line 230 of file StaticPropsCmd.hpp.

◆ charges_flag

int gengetopt_args_info::charges_flag

Print charges in xyz file (default=off).

Definition at line 87 of file Dump2XYZCmd.hpp.

◆ charges_given

unsigned int gengetopt_args_info::charges_given

Whether charges was given.

Definition at line 114 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ charges_help

const char* gengetopt_args_info::charges_help

Print charges in xyz file help description.

Definition at line 88 of file Dump2XYZCmd.hpp.

◆ chargetemperature_arg

double gengetopt_args_info::chargetemperature_arg

charge temperature (K).

Definition at line 54 of file thermalizerCmd.hpp.

◆ chargetemperature_given

unsigned int gengetopt_args_info::chargetemperature_given

Whether chargetemperature was given.

Definition at line 64 of file thermalizerCmd.hpp.

◆ chargetemperature_help

const char* gengetopt_args_info::chargetemperature_help

charge temperature (K) help description.

Definition at line 56 of file thermalizerCmd.hpp.

◆ chargetemperature_orig

char* gengetopt_args_info::chargetemperature_orig

charge temperature (K) original value given at command line.

Definition at line 55 of file thermalizerCmd.hpp.

◆ chargez_given

unsigned int gengetopt_args_info::chargez_given

Whether chargez was given.

Definition at line 344 of file StaticPropsCmd.hpp.

◆ chargez_help

const char* gengetopt_args_info::chargez_help

computes the charge distribution along selected axis and selected atom help description.

Definition at line 229 of file StaticPropsCmd.hpp.

◆ ckcorr_given

unsigned int gengetopt_args_info::ckcorr_given

Whether ckcorr was given.

Definition at line 183 of file DynamicPropsCmd.hpp.

◆ ckcorr_help

const char* gengetopt_args_info::ckcorr_help

Charge - Kinetic energy cross correlation function help description.

Definition at line 123 of file DynamicPropsCmd.hpp.

◆ clusterShape_group_counter

int gengetopt_args_info::clusterShape_group_counter

Counter for group clusterShape.

Definition at line 94 of file icosahedralBuilderCmd.hpp.

◆ cn_given

unsigned int gengetopt_args_info::cn_given

Whether cn was given.

Definition at line 326 of file StaticPropsCmd.hpp.

◆ cn_help

const char* gengetopt_args_info::cn_help

Coordination Number Distribution help description.

Definition at line 211 of file StaticPropsCmd.hpp.

◆ cohZ_given

unsigned int gengetopt_args_info::cohZ_given

Whether cohZ was given.

Definition at line 169 of file DynamicPropsCmd.hpp.

◆ cohZ_help

const char* gengetopt_args_info::cohZ_help

Lengendre correlation function for OH bond vectors binned by Z help description.

Definition at line 109 of file DynamicPropsCmd.hpp.

◆ columnAtoms_arg

int gengetopt_args_info::columnAtoms_arg

Number of atoms along central column (Decahedron only).

Definition at line 54 of file icosahedralBuilderCmd.hpp.

◆ columnAtoms_given

unsigned int gengetopt_args_info::columnAtoms_given

Whether columnAtoms was given.

Definition at line 80 of file icosahedralBuilderCmd.hpp.

◆ columnAtoms_help

const char* gengetopt_args_info::columnAtoms_help

Number of atoms along central column (Decahedron only) help description.

Definition at line 56 of file icosahedralBuilderCmd.hpp.

◆ columnAtoms_orig

char* gengetopt_args_info::columnAtoms_orig

Number of atoms along central column (Decahedron only) original value given at command line.

Definition at line 55 of file icosahedralBuilderCmd.hpp.

◆ com_given

unsigned int gengetopt_args_info::com_given

Whether com was given.

Definition at line 103 of file SequentialPropsCmd.hpp.

◆ com_help

const char* gengetopt_args_info::com_help

selection center of mass help description.

Definition at line 81 of file SequentialPropsCmd.hpp.

◆ component_arg

enum enum_component gengetopt_args_info::component_arg

component of momentum for the momemtum distribution (default = z axis) (default='z').

Definition at line 149 of file StaticPropsCmd.hpp.

◆ component_given

unsigned int gengetopt_args_info::component_given

Whether component was given.

Definition at line 277 of file StaticPropsCmd.hpp.

◆ component_help

const char* gengetopt_args_info::component_help

component of momentum for the momemtum distribution (default = z axis) help description.

Definition at line 151 of file StaticPropsCmd.hpp.

◆ component_orig

char* gengetopt_args_info::component_orig

component of momentum for the momemtum distribution (default = z axis) original value given at command line.

Definition at line 150 of file StaticPropsCmd.hpp.

◆ comsele_arg

char* gengetopt_args_info::comsele_arg

select stunt doubles for center-of-mass reference point.

Definition at line 113 of file StaticPropsCmd.hpp.

◆ comsele_given

unsigned int gengetopt_args_info::comsele_given

Whether comsele was given.

Definition at line 265 of file StaticPropsCmd.hpp.

◆ comsele_help

const char* gengetopt_args_info::comsele_help

select stunt doubles for center-of-mass reference point help description.

Definition at line 115 of file StaticPropsCmd.hpp.

◆ comsele_orig

char* gengetopt_args_info::comsele_orig

select stunt doubles for center-of-mass reference point original value given at command line.

Definition at line 114 of file StaticPropsCmd.hpp.

◆ comvel_given

unsigned int gengetopt_args_info::comvel_given

Whether comvel was given.

Definition at line 104 of file SequentialPropsCmd.hpp.

◆ comvel_help

const char* gengetopt_args_info::comvel_help

selection center of mass velocity help description.

Definition at line 82 of file SequentialPropsCmd.hpp.

◆ correlation_function_group_counter

int gengetopt_args_info::correlation_function_group_counter

Counter for group correlation_function.

Definition at line 198 of file DynamicPropsCmd.hpp.

◆ count_given

unsigned int gengetopt_args_info::count_given

Whether count was given.

Definition at line 288 of file StaticPropsCmd.hpp.

◆ count_help

const char* gengetopt_args_info::count_help

count of objects matching selection criteria (and associated statistics) help description.

Definition at line 173 of file StaticPropsCmd.hpp.

◆ countz_given

unsigned int gengetopt_args_info::countz_given

Whether countz was given.

Definition at line 351 of file StaticPropsCmd.hpp.

◆ countz_help

const char* gengetopt_args_info::countz_help

computes the number of selected atoms along selected axis help description.

Definition at line 236 of file StaticPropsCmd.hpp.

◆ cscorr_given

unsigned int gengetopt_args_info::cscorr_given

Whether cscorr was given.

Definition at line 184 of file DynamicPropsCmd.hpp.

◆ cscorr_help

const char* gengetopt_args_info::cscorr_help

Charge - Orientation order parameter (Cos\theta) cross correlation function help description.

Definition at line 124 of file DynamicPropsCmd.hpp.

◆ cuboctahedron_given

unsigned int gengetopt_args_info::cuboctahedron_given

Whether cuboctahedron was given.

Definition at line 89 of file icosahedralBuilderCmd.hpp.

◆ cuboctahedron_help

const char* gengetopt_args_info::cuboctahedron_help

Create a regular Cuboctahedron (requires lattice) help description.

Definition at line 71 of file icosahedralBuilderCmd.hpp.

◆ current_density_given

unsigned int gengetopt_args_info::current_density_given

Whether current_density was given.

Definition at line 343 of file StaticPropsCmd.hpp.

◆ current_density_help

const char* gengetopt_args_info::current_density_help

computes the current density for the selected atom help description.

Definition at line 228 of file StaticPropsCmd.hpp.

◆ current_given

unsigned int gengetopt_args_info::current_given

Whether current was given.

Definition at line 190 of file DynamicPropsCmd.hpp.

◆ current_help

const char* gengetopt_args_info::current_help

Current density auto correlation function help description.

Definition at line 130 of file DynamicPropsCmd.hpp.

◆ dcorr_given

unsigned int gengetopt_args_info::dcorr_given

Whether dcorr was given.

Definition at line 166 of file DynamicPropsCmd.hpp.

◆ dcorr_help

const char* gengetopt_args_info::dcorr_help

dipole correlation function help description.

Definition at line 106 of file DynamicPropsCmd.hpp.

◆ ddisp_given

unsigned int gengetopt_args_info::ddisp_given

Whether ddisp was given.

Definition at line 192 of file DynamicPropsCmd.hpp.

◆ ddisp_help

const char* gengetopt_args_info::ddisp_help

Collective Dipole displacement function (Helfand moment of Current Density) help description.

Definition at line 132 of file DynamicPropsCmd.hpp.

◆ deca_given

unsigned int gengetopt_args_info::deca_given

Whether deca was given.

Definition at line 85 of file icosahedralBuilderCmd.hpp.

◆ deca_help

const char* gengetopt_args_info::deca_help

Create a regualar Decahedral cluster help description.

Definition at line 67 of file icosahedralBuilderCmd.hpp.

◆ delta_arg

double gengetopt_args_info::delta_arg

size of relative volume changes for strains.

Definition at line 56 of file elasticConstantsCmd.hpp.

◆ delta_given

unsigned int gengetopt_args_info::delta_given

Whether delta was given.

Definition at line 66 of file elasticConstantsCmd.hpp.

◆ delta_help

const char* gengetopt_args_info::delta_help

size of relative volume changes for strains help description.

Definition at line 58 of file elasticConstantsCmd.hpp.

◆ delta_orig

char* gengetopt_args_info::delta_orig

size of relative volume changes for strains original value given at command line.

Definition at line 57 of file elasticConstantsCmd.hpp.

◆ density_arg

double gengetopt_args_info::density_arg

density (g/cm^3).

Definition at line 45 of file randomBuilderCmd.hpp.

◆ density_given

unsigned int gengetopt_args_info::density_given

Whether density was given.

Definition at line 69 of file randomBuilderCmd.hpp.

◆ density_help

const char * gengetopt_args_info::density_help

density (g/cm^3) help description.

density plot help description.

Definition at line 47 of file randomBuilderCmd.hpp.

◆ density_orig

char * gengetopt_args_info::density_orig

density (g/cm^3) original value given at command line.

Definition at line 46 of file randomBuilderCmd.hpp.

◆ densityfield_given

unsigned int gengetopt_args_info::densityfield_given

Whether densityfield was given.

Definition at line 338 of file StaticPropsCmd.hpp.

◆ densityfield_help

const char* gengetopt_args_info::densityfield_help

computes an average density field help description.

Definition at line 223 of file StaticPropsCmd.hpp.

◆ dipole_orientation_given

unsigned int gengetopt_args_info::dipole_orientation_given

Whether dipole_orientation was given.

Definition at line 353 of file StaticPropsCmd.hpp.

◆ dipole_orientation_help

const char* gengetopt_args_info::dipole_orientation_help

spatially-resolved dipole order parameter S(z), S = (3 Cos^2\theta - 1)/2 help description.

Definition at line 238 of file StaticPropsCmd.hpp.

◆ dipoleX_arg

double gengetopt_args_info::dipoleX_arg

X-component of the dipole with respect to body frame (default='0.0').

X-component of the dipole with respect to body frame.

Definition at line 86 of file DynamicPropsCmd.hpp.

◆ dipoleX_given

unsigned int gengetopt_args_info::dipoleX_given

Whether dipoleX was given.

Definition at line 152 of file DynamicPropsCmd.hpp.

◆ dipoleX_help

const char * gengetopt_args_info::dipoleX_help

X-component of the dipole with respect to body frame help description.

Definition at line 88 of file DynamicPropsCmd.hpp.

◆ dipoleX_orig

char * gengetopt_args_info::dipoleX_orig

X-component of the dipole with respect to body frame original value given at command line.

Definition at line 87 of file DynamicPropsCmd.hpp.

◆ dipoleY_arg

double gengetopt_args_info::dipoleY_arg

Y-component of the dipole with respect to body frame (default='0.0').

Y-component of the dipole with respect to body frame.

Definition at line 89 of file DynamicPropsCmd.hpp.

◆ dipoleY_given

unsigned int gengetopt_args_info::dipoleY_given

Whether dipoleY was given.

Definition at line 153 of file DynamicPropsCmd.hpp.

◆ dipoleY_help

const char * gengetopt_args_info::dipoleY_help

Y-component of the dipole with respect to body frame help description.

Definition at line 91 of file DynamicPropsCmd.hpp.

◆ dipoleY_orig

char * gengetopt_args_info::dipoleY_orig

Y-component of the dipole with respect to body frame original value given at command line.

Definition at line 90 of file DynamicPropsCmd.hpp.

◆ dipoleZ_arg

double gengetopt_args_info::dipoleZ_arg

Z-component of the dipole with respect to body frame (default='-1.0').

Z-component of the dipole with respect to body frame.

Definition at line 92 of file DynamicPropsCmd.hpp.

◆ dipoleZ_given

unsigned int gengetopt_args_info::dipoleZ_given

Whether dipoleZ was given.

Definition at line 154 of file DynamicPropsCmd.hpp.

◆ dipoleZ_help

const char * gengetopt_args_info::dipoleZ_help

Z-component of the dipole with respect to body frame help description.

Definition at line 94 of file DynamicPropsCmd.hpp.

◆ dipoleZ_orig

char * gengetopt_args_info::dipoleZ_orig

Z-component of the dipole with respect to body frame original value given at command line.

Definition at line 93 of file DynamicPropsCmd.hpp.

◆ disp_given

unsigned int gengetopt_args_info::disp_given

Whether disp was given.

Definition at line 188 of file DynamicPropsCmd.hpp.

◆ disp_help

const char* gengetopt_args_info::disp_help

Displacement correlation function help description.

Definition at line 128 of file DynamicPropsCmd.hpp.

◆ dispZ_given

unsigned int gengetopt_args_info::dispZ_given

Whether dispZ was given.

Definition at line 189 of file DynamicPropsCmd.hpp.

◆ dispZ_help

const char* gengetopt_args_info::dispZ_help

Displacement correlation function binned by Z help description.

Definition at line 129 of file DynamicPropsCmd.hpp.

◆ drcorr_given

unsigned int gengetopt_args_info::drcorr_given

Whether drcorr was given.

Definition at line 173 of file DynamicPropsCmd.hpp.

◆ drcorr_help

const char* gengetopt_args_info::drcorr_help

Directional msd for particles with unit vectors help description.

Definition at line 113 of file DynamicPropsCmd.hpp.

◆ dropletR_arg

double gengetopt_args_info::dropletR_arg

Droplet radius in angstroms.

Definition at line 69 of file SequentialPropsCmd.hpp.

◆ dropletR_given

unsigned int gengetopt_args_info::dropletR_given

Whether dropletR was given.

Definition at line 99 of file SequentialPropsCmd.hpp.

◆ dropletR_help

const char* gengetopt_args_info::dropletR_help

Droplet radius in angstroms help description.

Definition at line 71 of file SequentialPropsCmd.hpp.

◆ dropletR_orig

char* gengetopt_args_info::dropletR_orig

Droplet radius in angstroms original value given at command line.

Definition at line 70 of file SequentialPropsCmd.hpp.

◆ dz_arg

double gengetopt_args_info::dz_arg

slab width (dz).

Definition at line 89 of file StaticPropsCmd.hpp.

◆ dz_given

unsigned int gengetopt_args_info::dz_given

Whether dz was given.

Definition at line 257 of file StaticPropsCmd.hpp.

◆ dz_help

const char* gengetopt_args_info::dz_help

slab width (dz) help description.

Definition at line 91 of file StaticPropsCmd.hpp.

◆ dz_orig

char* gengetopt_args_info::dz_orig

slab width (dz) original value given at command line.

Definition at line 90 of file StaticPropsCmd.hpp.

◆ eam_density_given

unsigned int gengetopt_args_info::eam_density_given

Whether eam_density was given.

Definition at line 341 of file StaticPropsCmd.hpp.

◆ eam_density_help

const char* gengetopt_args_info::eam_density_help

computes an average eam density profile of the selected atom help description.

Definition at line 226 of file StaticPropsCmd.hpp.

◆ efield_flag

int gengetopt_args_info::efield_flag

Print electric field vector in xyz file (default=off).

Definition at line 89 of file Dump2XYZCmd.hpp.

◆ efield_given

unsigned int gengetopt_args_info::efield_given

Whether efield was given.

Definition at line 115 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ efield_help

const char* gengetopt_args_info::efield_help

Print electric field vector in xyz file help description.

Definition at line 90 of file Dump2XYZCmd.hpp.

◆ elements_flag

int gengetopt_args_info::elements_flag

output the hydrodynamic elements (beads or triangles) only, hydrodynamics calculation will not be performed (default=off).

Definition at line 65 of file HydroCmd.hpp.

◆ elements_given

unsigned int gengetopt_args_info::elements_given

Whether elements was given.

Definition at line 83 of file HydroCmd.hpp.

◆ elements_help

const char* gengetopt_args_info::elements_help

output the hydrodynamic elements (beads or triangles) only, hydrodynamics calculation will not be performed help description.

Definition at line 66 of file HydroCmd.hpp.

◆ ellipsoid_flag

int gengetopt_args_info::ellipsoid_flag

Build an Ellipsoid instead of a rod.

(default=off).

Definition at line 54 of file nanorodBuilderCmd.hpp.

◆ ellipsoid_given

unsigned int gengetopt_args_info::ellipsoid_given

Whether ellipsoid was given.

Definition at line 82 of file nanorodBuilderCmd.hpp.

◆ ellipsoid_help

const char* gengetopt_args_info::ellipsoid_help

Build an Ellipsoid instead of a rod.

help description.

Definition at line 55 of file nanorodBuilderCmd.hpp.

◆ end_arg [1/2]

double gengetopt_args_info::end_arg

ending affine scale (default='1.2').

Definition at line 51 of file equationofstateCmd.hpp.

◆ end_arg [2/2]

int gengetopt_args_info::end_arg

end internal index.

Definition at line 128 of file StaticPropsCmd.hpp.

◆ end_given

unsigned int gengetopt_args_info::end_given

Whether end was given.

Definition at line 63 of file equationofstateCmd.hpp.

◆ end_help

const char * gengetopt_args_info::end_help

ending affine scale help description.

end internal index help description.

Definition at line 53 of file equationofstateCmd.hpp.

◆ end_orig

char * gengetopt_args_info::end_orig

ending affine scale original value given at command line.

end internal index original value given at command line.

Definition at line 52 of file equationofstateCmd.hpp.

◆ energy_arg

double gengetopt_args_info::energy_arg

energy (kcal/mol).

Definition at line 51 of file thermalizerCmd.hpp.

◆ energy_given

unsigned int gengetopt_args_info::energy_given

Whether energy was given.

Definition at line 63 of file thermalizerCmd.hpp.

◆ energy_help

const char* gengetopt_args_info::energy_help

energy (kcal/mol) help description.

Definition at line 53 of file thermalizerCmd.hpp.

◆ energy_orig

char* gengetopt_args_info::energy_orig

energy (kcal/mol) original value given at command line.

Definition at line 52 of file thermalizerCmd.hpp.

◆ facorr_given

unsigned int gengetopt_args_info::facorr_given

Whether facorr was given.

Definition at line 185 of file DynamicPropsCmd.hpp.

◆ facorr_help

const char* gengetopt_args_info::facorr_help

Force - Force auto correlation function help description.

Definition at line 125 of file DynamicPropsCmd.hpp.

◆ for_given

unsigned int gengetopt_args_info::for_given

Whether for was given.

Definition at line 286 of file StaticPropsCmd.hpp.

◆ for_help

const char* gengetopt_args_info::for_help

FCC bond order parameter as a function of radius (–rcut must be specified) help description.

Definition at line 171 of file StaticPropsCmd.hpp.

◆ forces_flag

int gengetopt_args_info::forces_flag

Print forces xyz file (default=off).

Definition at line 83 of file Dump2XYZCmd.hpp.

◆ forces_given

unsigned int gengetopt_args_info::forces_given

Whether forces was given.

Definition at line 112 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ forces_help

const char* gengetopt_args_info::forces_help

Print forces xyz file help description.

Definition at line 84 of file Dump2XYZCmd.hpp.

◆ frame_arg

int gengetopt_args_info::frame_arg

print every n frame (default='1').

Definition at line 48 of file Dump2XYZCmd.hpp.

◆ frame_given

unsigned int gengetopt_args_info::frame_given

Whether frame was given.

Definition at line 98 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ frame_help

const char* gengetopt_args_info::frame_help

print every n frame help description.

Definition at line 50 of file Dump2XYZCmd.hpp.

◆ frame_orig

char* gengetopt_args_info::frame_orig

print every n frame original value given at command line.

Definition at line 49 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ freqfluccorr_given

unsigned int gengetopt_args_info::freqfluccorr_given

Whether freqfluccorr was given.

Definition at line 176 of file DynamicPropsCmd.hpp.

◆ freqfluccorr_help

const char* gengetopt_args_info::freqfluccorr_help

Frequency Fluctuation correlation function help description.

Definition at line 116 of file DynamicPropsCmd.hpp.

◆ ftcorr_given

unsigned int gengetopt_args_info::ftcorr_given

Whether ftcorr was given.

Definition at line 182 of file DynamicPropsCmd.hpp.

◆ ftcorr_help

const char* gengetopt_args_info::ftcorr_help

Force - Torque cross correlation function help description.

Definition at line 122 of file DynamicPropsCmd.hpp.

◆ gaussWidth_arg

double gengetopt_args_info::gaussWidth_arg

Gaussian width (angstroms).

Definition at line 137 of file StaticPropsCmd.hpp.

◆ gaussWidth_given

unsigned int gengetopt_args_info::gaussWidth_given

Whether gaussWidth was given.

Definition at line 273 of file StaticPropsCmd.hpp.

◆ gaussWidth_help

const char* gengetopt_args_info::gaussWidth_help

Gaussian width (angstroms) help description.

Definition at line 139 of file StaticPropsCmd.hpp.

◆ gaussWidth_orig

char* gengetopt_args_info::gaussWidth_orig

Gaussian width (angstroms) original value given at command line.

Definition at line 138 of file StaticPropsCmd.hpp.

◆ gcn_given

unsigned int gengetopt_args_info::gcn_given

Whether gcn was given.

Definition at line 107 of file SequentialPropsCmd.hpp.

◆ gcn_help

const char * gengetopt_args_info::gcn_help

Generalized Coordinate Number help description.

Generalized Coordination Number Distribution help description.

Definition at line 85 of file SequentialPropsCmd.hpp.

◆ gen_xyz_flag

int gengetopt_args_info::gen_xyz_flag

generates xyz file (default=off).

Definition at line 164 of file StaticPropsCmd.hpp.

◆ gen_xyz_given

unsigned int gengetopt_args_info::gen_xyz_given

Whether gen_xyz was given.

Definition at line 282 of file StaticPropsCmd.hpp.

◆ gen_xyz_help

const char* gengetopt_args_info::gen_xyz_help

generates xyz file help description.

Definition at line 165 of file StaticPropsCmd.hpp.

◆ globalID_flag

int gengetopt_args_info::globalID_flag

Print global ID in xyz file (default=off).

Definition at line 91 of file Dump2XYZCmd.hpp.

◆ globalID_given

unsigned int gengetopt_args_info::globalID_given

Whether globalID was given.

Definition at line 116 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ globalID_help

const char* gengetopt_args_info::globalID_help

Print global ID in xyz file help description.

Definition at line 92 of file Dump2XYZCmd.hpp.

◆ gofr_given

unsigned int gengetopt_args_info::gofr_given

Whether gofr was given.

Definition at line 290 of file StaticPropsCmd.hpp.

◆ gofr_help

const char* gengetopt_args_info::gofr_help

g(r) help description.

Definition at line 175 of file StaticPropsCmd.hpp.

◆ gofz_given

unsigned int gengetopt_args_info::gofz_given

Whether gofz was given.

Definition at line 291 of file StaticPropsCmd.hpp.

◆ gofz_help

const char* gengetopt_args_info::gofz_help

g(z) help description.

Definition at line 176 of file StaticPropsCmd.hpp.

◆ gxyz_given

unsigned int gengetopt_args_info::gxyz_given

Whether gxyz was given.

Definition at line 297 of file StaticPropsCmd.hpp.

◆ gxyz_help

const char* gengetopt_args_info::gxyz_help

g(x, y, z) help description.

Definition at line 182 of file StaticPropsCmd.hpp.

◆ hbond_given

unsigned int gengetopt_args_info::hbond_given

Whether hbond was given.

Definition at line 329 of file StaticPropsCmd.hpp.

◆ hbond_help

const char* gengetopt_args_info::hbond_help

Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified) help description.

Definition at line 214 of file StaticPropsCmd.hpp.

◆ hbondr_given

unsigned int gengetopt_args_info::hbondr_given

Whether hbondr was given.

Definition at line 332 of file StaticPropsCmd.hpp.

◆ hbondr_help

const char* gengetopt_args_info::hbondr_help

Hydrogen Bonding density binned by r (rcut and thetacut must be specified) help description.

Definition at line 217 of file StaticPropsCmd.hpp.

◆ hbondrvol_given

unsigned int gengetopt_args_info::hbondrvol_given

Whether hbondrvol was given.

Definition at line 333 of file StaticPropsCmd.hpp.

◆ hbondrvol_help

const char* gengetopt_args_info::hbondrvol_help

Hydrogen Bonding density binned by r and normalized by bin volume (rcut and thetacut must be specified) help description.

Definition at line 218 of file StaticPropsCmd.hpp.

◆ hbondz_given

unsigned int gengetopt_args_info::hbondz_given

Whether hbondz was given.

Definition at line 330 of file StaticPropsCmd.hpp.

◆ hbondz_help

const char* gengetopt_args_info::hbondz_help

Hydrogen Bonding density binned by z (rcut and thetacut must be specified) help description.

Definition at line 215 of file StaticPropsCmd.hpp.

◆ hbondzvol_given

unsigned int gengetopt_args_info::hbondzvol_given

Whether hbondzvol was given.

Definition at line 331 of file StaticPropsCmd.hpp.

◆ hbondzvol_help

const char* gengetopt_args_info::hbondzvol_help

Hydrogen Bonding density binned by z and normalized by bin volume (rcut and thetacut must be specified) help description.

Definition at line 216 of file StaticPropsCmd.hpp.

◆ help_given

unsigned int gengetopt_args_info::help_given

Whether help was given.

Definition at line 94 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ help_help

const char * gengetopt_args_info::help_help

Print help and exit help description.

Definition at line 40 of file Dump2XYZCmd.hpp.

◆ hullvol_given

unsigned int gengetopt_args_info::hullvol_given

Whether hullvol was given.

Definition at line 312 of file StaticPropsCmd.hpp.

◆ hullvol_help

const char* gengetopt_args_info::hullvol_help

hull volume of nanoparticle help description.

Definition at line 197 of file StaticPropsCmd.hpp.

◆ hxy_given

unsigned int gengetopt_args_info::hxy_given

Whether hxy was given.

Definition at line 309 of file StaticPropsCmd.hpp.

◆ hxy_help

const char* gengetopt_args_info::hxy_help

hxy help description.

Definition at line 194 of file StaticPropsCmd.hpp.

◆ ico_given

unsigned int gengetopt_args_info::ico_given

Whether ico was given.

Definition at line 84 of file icosahedralBuilderCmd.hpp.

◆ ico_help

const char* gengetopt_args_info::ico_help

Create an Icosahedral cluster help description.

Definition at line 66 of file icosahedralBuilderCmd.hpp.

◆ ino_given

unsigned int gengetopt_args_info::ino_given

Whether ino was given.

Definition at line 86 of file icosahedralBuilderCmd.hpp.

◆ ino_help

const char* gengetopt_args_info::ino_help

Create an Ino Decahedral cluster help description.

Definition at line 68 of file icosahedralBuilderCmd.hpp.

◆ input_arg

char * gengetopt_args_info::input_arg

input dump file.

use specified input (.omd, .dump, .eor) file.

input MetaData (omd) file.

use specified input (.omd) file.

Input file name.

Definition at line 42 of file Dump2XYZCmd.hpp.

◆ input_file_group_counter

int gengetopt_args_info::input_file_group_counter

Counter for group input_file.

Definition at line 89 of file HydroCmd.hpp.

◆ input_given

unsigned int gengetopt_args_info::input_given

Whether input was given.

Definition at line 96 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ input_help

const char * gengetopt_args_info::input_help

input dump file help description.

use specified input (.omd, .dump, .eor) file help description.

input MetaData (omd) file help description.

use specified input (.omd) file help description.

Input file name help description.

Definition at line 44 of file Dump2XYZCmd.hpp.

◆ input_orig

char * gengetopt_args_info::input_orig

input dump file original value given at command line.

use specified input (.omd, .dump, .eor) file original value given at command line.

input MetaData (omd) file original value given at command line.

use specified input (.omd) file original value given at command line.

Input file name original value given at command line.

Definition at line 43 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ inputs

char ** gengetopt_args_info::inputs

unamed options (options without names)

unnamed options (options without names)

Definition at line 118 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_init().

◆ inputs_num

unsigned gengetopt_args_info::inputs_num

unamed options number

unnamed options number

Definition at line 119 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_init().

◆ ior_given

unsigned int gengetopt_args_info::ior_given

Whether ior was given.

Definition at line 285 of file StaticPropsCmd.hpp.

◆ ior_help

const char* gengetopt_args_info::ior_help

icosahedral bond order parameter as a function of radius (–rcut must be specified) help description.

Definition at line 170 of file StaticPropsCmd.hpp.

◆ jumptime_given

unsigned int gengetopt_args_info::jumptime_given

Whether jumptime was given.

Definition at line 177 of file DynamicPropsCmd.hpp.

◆ jumptime_help

const char* gengetopt_args_info::jumptime_help

Hydrogen bond jump time correlation function help description.

Definition at line 117 of file DynamicPropsCmd.hpp.

◆ jumptimeR_given

unsigned int gengetopt_args_info::jumptimeR_given

Whether jumptimeR was given.

Definition at line 179 of file DynamicPropsCmd.hpp.

◆ jumptimeR_help

const char* gengetopt_args_info::jumptimeR_help

Hydrogen bond jump time correlation function binned by R around a third selection help description.

Definition at line 119 of file DynamicPropsCmd.hpp.

◆ jumptimeZ_given

unsigned int gengetopt_args_info::jumptimeZ_given

Whether jumptimeZ was given.

Definition at line 178 of file DynamicPropsCmd.hpp.

◆ jumptimeZ_help

const char* gengetopt_args_info::jumptimeZ_help

Hydrogen bond jump time correlation function binned by Z help description.

Definition at line 118 of file DynamicPropsCmd.hpp.

◆ kirkwood_buff_given

unsigned int gengetopt_args_info::kirkwood_buff_given

Whether kirkwood_buff was given.

Definition at line 299 of file StaticPropsCmd.hpp.

◆ kirkwood_buff_help

const char* gengetopt_args_info::kirkwood_buff_help

Kirkwood-Buff integrals (–sele1 and –sele2 must both be specified) help description.

Definition at line 184 of file StaticPropsCmd.hpp.

◆ kirkwood_given

unsigned int gengetopt_args_info::kirkwood_given

Whether kirkwood was given.

Definition at line 336 of file StaticPropsCmd.hpp.

◆ kirkwood_help

const char* gengetopt_args_info::kirkwood_help

distance-dependent Kirkwood factor help description.

Definition at line 221 of file StaticPropsCmd.hpp.

◆ kirkwoodQ_given

unsigned int gengetopt_args_info::kirkwoodQ_given

Whether kirkwoodQ was given.

Definition at line 337 of file StaticPropsCmd.hpp.

◆ kirkwoodQ_help

const char* gengetopt_args_info::kirkwoodQ_help

distance-dependent Kirkwood factor for quadrupoles help description.

Definition at line 222 of file StaticPropsCmd.hpp.

◆ lattice_arg

char * gengetopt_args_info::lattice_arg

Lattice Type.

Definition at line 51 of file icosahedralBuilderCmd.hpp.

◆ lattice_given

unsigned int gengetopt_args_info::lattice_given

Whether lattice was given.

Definition at line 79 of file icosahedralBuilderCmd.hpp.

◆ lattice_help

const char * gengetopt_args_info::lattice_help

Lattice Type help description.

Definition at line 53 of file icosahedralBuilderCmd.hpp.

◆ lattice_orig

char * gengetopt_args_info::lattice_orig

Lattice Type original value given at command line.

Definition at line 52 of file icosahedralBuilderCmd.hpp.

◆ latticeConstant_arg

double gengetopt_args_info::latticeConstant_arg

Lattice spacing in Angstroms for cubic lattice.

Definition at line 48 of file icosahedralBuilderCmd.hpp.

◆ latticeConstant_given

unsigned int gengetopt_args_info::latticeConstant_given

Whether latticeConstant was given.

Definition at line 78 of file icosahedralBuilderCmd.hpp.

◆ latticeConstant_help

const char * gengetopt_args_info::latticeConstant_help

Lattice spacing in Angstroms for cubic lattice.

help description.

Definition at line 50 of file icosahedralBuilderCmd.hpp.

◆ latticeConstant_orig

char * gengetopt_args_info::latticeConstant_orig

Lattice spacing in Angstroms for cubic lattice.

original value given at command line.

Definition at line 49 of file icosahedralBuilderCmd.hpp.

◆ lcorr_given

unsigned int gengetopt_args_info::lcorr_given

Whether lcorr was given.

Definition at line 167 of file DynamicPropsCmd.hpp.

◆ lcorr_help

const char* gengetopt_args_info::lcorr_help

Lengendre correlation function help description.

Definition at line 107 of file DynamicPropsCmd.hpp.

◆ lcorrZ_given

unsigned int gengetopt_args_info::lcorrZ_given

Whether lcorrZ was given.

Definition at line 168 of file DynamicPropsCmd.hpp.

◆ lcorrZ_help

const char* gengetopt_args_info::lcorrZ_help

Lengendre correlation function binned by Z help description.

Definition at line 108 of file DynamicPropsCmd.hpp.

◆ length_arg

double gengetopt_args_info::length_arg

maximum length (default='100').

maximum length (Defaults to 1/2 smallest length of first frame).

Nanorod length in Angstroms.

Definition at line 83 of file DynamicPropsCmd.hpp.

◆ length_given

unsigned int gengetopt_args_info::length_given

Whether length was given.

Definition at line 151 of file DynamicPropsCmd.hpp.

◆ length_help

const char * gengetopt_args_info::length_help

maximum length help description.

maximum length (Defaults to 1/2 smallest length of first frame) help description.

Nanorod length in Angstroms help description.

Definition at line 85 of file DynamicPropsCmd.hpp.

◆ length_orig

char * gengetopt_args_info::length_orig

maximum length original value given at command line.

maximum length (Defaults to 1/2 smallest length of first frame) original value given at command line.

Nanorod length in Angstroms original value given at command line.

Definition at line 84 of file DynamicPropsCmd.hpp.

◆ marks_given

unsigned int gengetopt_args_info::marks_given

Whether marks was given.

Definition at line 87 of file icosahedralBuilderCmd.hpp.

◆ marks_help

const char* gengetopt_args_info::marks_help

Create a Marks Decahedral cluster help description.

Definition at line 69 of file icosahedralBuilderCmd.hpp.

◆ massdensityr_given

unsigned int gengetopt_args_info::massdensityr_given

Whether massdensityr was given.

Definition at line 347 of file StaticPropsCmd.hpp.

◆ massdensityr_help

const char* gengetopt_args_info::massdensityr_help

computes the mass density of the selection as a function of the radius from the center of mass help description.

Definition at line 232 of file StaticPropsCmd.hpp.

◆ massdensityz_given

unsigned int gengetopt_args_info::massdensityz_given

Whether massdensityz was given.

Definition at line 346 of file StaticPropsCmd.hpp.

◆ massdensityz_help

const char* gengetopt_args_info::massdensityz_help

computes the mass density of the selection along selected axis help description.

Definition at line 231 of file StaticPropsCmd.hpp.

◆ mcount_given

unsigned int gengetopt_args_info::mcount_given

Whether mcount was given.

Definition at line 289 of file StaticPropsCmd.hpp.

◆ mcount_help

const char* gengetopt_args_info::mcount_help

count of molecules matching selection criteria (and associated statistics) help description.

Definition at line 174 of file StaticPropsCmd.hpp.

◆ meandisp_given

unsigned int gengetopt_args_info::meandisp_given

Whether meandisp was given.

Definition at line 194 of file DynamicPropsCmd.hpp.

◆ meandisp_help

const char* gengetopt_args_info::meandisp_help

mean displacement help description.

Definition at line 134 of file DynamicPropsCmd.hpp.

◆ method_arg

char* gengetopt_args_info::method_arg

Calculation Method.

Definition at line 47 of file elasticConstantsCmd.hpp.

◆ method_given

unsigned int gengetopt_args_info::method_given

Whether method was given.

Definition at line 64 of file elasticConstantsCmd.hpp.

◆ method_help

const char* gengetopt_args_info::method_help

Calculation Method help description.

Definition at line 49 of file elasticConstantsCmd.hpp.

◆ method_orig

char* gengetopt_args_info::method_orig

Calculation Method original value given at command line.

Definition at line 48 of file elasticConstantsCmd.hpp.

◆ model_arg

enum enum_model gengetopt_args_info::model_arg

hydrodynamics model.

Definition at line 59 of file HydroCmd.hpp.

◆ model_given

unsigned int gengetopt_args_info::model_given

Whether model was given.

Definition at line 81 of file HydroCmd.hpp.

◆ model_help

const char* gengetopt_args_info::model_help

hydrodynamics model help description.

Definition at line 61 of file HydroCmd.hpp.

◆ model_orig

char* gengetopt_args_info::model_orig

hydrodynamics model original value given at command line.

Definition at line 60 of file HydroCmd.hpp.

◆ molFraction_arg

double * gengetopt_args_info::molFraction_arg

Builds a multi-component random alloy nanoparticle.

(Default) Builds a multi-component random mixed nanoparticle.

A mole Fraction must be specified for each component > 1 in the template file..

Mole Fraction must be specified for each componet > 1 in MD file..

Definition at line 56 of file nanoparticleBuilderCmd.hpp.

◆ molFraction_given

unsigned int gengetopt_args_info::molFraction_given

Whether molFraction was given.

Definition at line 77 of file nanoparticleBuilderCmd.hpp.

◆ molFraction_help

const char * gengetopt_args_info::molFraction_help

Builds a multi-component random alloy nanoparticle.

(Default) Builds a multi-component random mixed nanoparticle.

A mole Fraction must be specified for each component > 1 in the template file. help description.

Mole Fraction must be specified for each componet > 1 in MD file. help description.

Definition at line 60 of file nanoparticleBuilderCmd.hpp.

◆ molFraction_max

unsigned int gengetopt_args_info::molFraction_max

Builds a multi-component random alloy nanoparticle.

(Default) Builds a multi-component random mixed nanoparticle.

A mole Fraction must be specified for each component > 1 in the template file.'s maximum occurreces

Mole Fraction must be specified for each componet > 1 in MD file.'s maximum occurreces

Definition at line 59 of file nanoparticleBuilderCmd.hpp.

◆ molFraction_min

unsigned int gengetopt_args_info::molFraction_min

Builds a multi-component random alloy nanoparticle.

(Default) Builds a multi-component random mixed nanoparticle.

A mole Fraction must be specified for each component > 1 in the template file.'s minimum occurreces

Mole Fraction must be specified for each componet > 1 in MD file.'s minimum occurreces

Definition at line 58 of file nanoparticleBuilderCmd.hpp.

◆ molFraction_orig

char ** gengetopt_args_info::molFraction_orig

Builds a multi-component random alloy nanoparticle.

(Default) Builds a multi-component random mixed nanoparticle.

A mole Fraction must be specified for each component > 1 in the template file. original value given at command line.

Mole Fraction must be specified for each componet > 1 in MD file. original value given at command line.

Definition at line 57 of file nanoparticleBuilderCmd.hpp.

◆ molname_arg

char* gengetopt_args_info::molname_arg

molecule name.

Definition at line 122 of file StaticPropsCmd.hpp.

◆ molname_given

unsigned int gengetopt_args_info::molname_given

Whether molname was given.

Definition at line 268 of file StaticPropsCmd.hpp.

◆ molname_help

const char* gengetopt_args_info::molname_help

molecule name help description.

Definition at line 124 of file StaticPropsCmd.hpp.

◆ molname_orig

char* gengetopt_args_info::molname_orig

molecule name original value given at command line.

Definition at line 123 of file StaticPropsCmd.hpp.

◆ momentum_arg

enum enum_momentum gengetopt_args_info::momentum_arg

Type of momentum whose distribtution is required (default = Liner Momentum) (default='P').

Definition at line 146 of file StaticPropsCmd.hpp.

◆ momentum_distribution_given

unsigned int gengetopt_args_info::momentum_distribution_given

Whether momentum_distribution was given.

Definition at line 352 of file StaticPropsCmd.hpp.

◆ momentum_distribution_help

const char* gengetopt_args_info::momentum_distribution_help

computes the momentum distribution for the selected atom help description.

Definition at line 237 of file StaticPropsCmd.hpp.

◆ momentum_given

unsigned int gengetopt_args_info::momentum_given

Whether momentum was given.

Definition at line 276 of file StaticPropsCmd.hpp.

◆ momentum_help

const char* gengetopt_args_info::momentum_help

Type of momentum whose distribtution is required (default = Liner Momentum) help description.

Definition at line 148 of file StaticPropsCmd.hpp.

◆ momentum_orig

char* gengetopt_args_info::momentum_orig

Type of momentum whose distribtution is required (default = Liner Momentum) original value given at command line.

Definition at line 147 of file StaticPropsCmd.hpp.

◆ msms_arg

char* gengetopt_args_info::msms_arg

filename root for MSMS .vert and .face files.

Definition at line 53 of file HydroCmd.hpp.

◆ msms_given

unsigned int gengetopt_args_info::msms_given

Whether msms was given.

Definition at line 79 of file HydroCmd.hpp.

◆ msms_help

const char* gengetopt_args_info::msms_help

filename root for MSMS .vert and .face files help description.

Definition at line 55 of file HydroCmd.hpp.

◆ msms_orig

char* gengetopt_args_info::msms_orig

filename root for MSMS .vert and .face files original value given at command line.

Definition at line 54 of file HydroCmd.hpp.

◆ multipole_given

unsigned int gengetopt_args_info::multipole_given

Whether multipole was given.

Definition at line 324 of file StaticPropsCmd.hpp.

◆ multipole_help

const char* gengetopt_args_info::multipole_help

average multipole moments contained within cutoff spheres as a function of radius help description.

Definition at line 209 of file StaticPropsCmd.hpp.

◆ nanglebins_arg

int gengetopt_args_info::nanglebins_arg

number of bins for cos(angle) (default='50').

Definition at line 74 of file StaticPropsCmd.hpp.

◆ nanglebins_given

unsigned int gengetopt_args_info::nanglebins_given

Whether nanglebins was given.

Definition at line 252 of file StaticPropsCmd.hpp.

◆ nanglebins_help

const char* gengetopt_args_info::nanglebins_help

number of bins for cos(angle) help description.

Definition at line 76 of file StaticPropsCmd.hpp.

◆ nanglebins_orig

char* gengetopt_args_info::nanglebins_orig

number of bins for cos(angle) original value given at command line.

Definition at line 75 of file StaticPropsCmd.hpp.

◆ nbins_arg

int gengetopt_args_info::nbins_arg

Number of bins (default='100').

number of bins (general purpose) (default='100').

Definition at line 62 of file DynamicPropsCmd.hpp.

◆ nbins_given

unsigned int gengetopt_args_info::nbins_given

Whether nbins was given.

Definition at line 144 of file DynamicPropsCmd.hpp.

◆ nbins_help

const char * gengetopt_args_info::nbins_help

Number of bins help description.

number of bins (general purpose) help description.

Definition at line 64 of file DynamicPropsCmd.hpp.

◆ nbins_orig

char * gengetopt_args_info::nbins_orig

Number of bins original value given at command line.

number of bins (general purpose) original value given at command line.

Definition at line 63 of file DynamicPropsCmd.hpp.

◆ nbins_x_arg

int gengetopt_args_info::nbins_x_arg

number of bins in x axis (default='100').

Definition at line 59 of file StaticPropsCmd.hpp.

◆ nbins_x_given

unsigned int gengetopt_args_info::nbins_x_given

Whether nbins_x was given.

Definition at line 247 of file StaticPropsCmd.hpp.

◆ nbins_x_help

const char* gengetopt_args_info::nbins_x_help

number of bins in x axis help description.

Definition at line 61 of file StaticPropsCmd.hpp.

◆ nbins_x_orig

char* gengetopt_args_info::nbins_x_orig

number of bins in x axis original value given at command line.

Definition at line 60 of file StaticPropsCmd.hpp.

◆ nbins_y_arg

int gengetopt_args_info::nbins_y_arg

number of bins in y axis (default='100').

Definition at line 62 of file StaticPropsCmd.hpp.

◆ nbins_y_given

unsigned int gengetopt_args_info::nbins_y_given

Whether nbins_y was given.

Definition at line 248 of file StaticPropsCmd.hpp.

◆ nbins_y_help

const char* gengetopt_args_info::nbins_y_help

number of bins in y axis help description.

Definition at line 64 of file StaticPropsCmd.hpp.

◆ nbins_y_orig

char* gengetopt_args_info::nbins_y_orig

number of bins in y axis original value given at command line.

Definition at line 63 of file StaticPropsCmd.hpp.

◆ nbins_z_arg

int gengetopt_args_info::nbins_z_arg

number of bins in z axis (default='100').

Definition at line 57 of file SequentialPropsCmd.hpp.

◆ nbins_z_given

unsigned int gengetopt_args_info::nbins_z_given

Whether nbins_z was given.

Definition at line 95 of file SequentialPropsCmd.hpp.

◆ nbins_z_help

const char * gengetopt_args_info::nbins_z_help

number of bins in z axis help description.

Definition at line 59 of file SequentialPropsCmd.hpp.

◆ nbins_z_orig

char * gengetopt_args_info::nbins_z_orig

number of bins in z axis original value given at command line.

Definition at line 58 of file SequentialPropsCmd.hpp.

◆ net_charge_given

unsigned int gengetopt_args_info::net_charge_given

Whether net_charge was given.

Definition at line 342 of file StaticPropsCmd.hpp.

◆ net_charge_help

const char* gengetopt_args_info::net_charge_help

computes an average charge profile of the selected atom help description.

Definition at line 227 of file StaticPropsCmd.hpp.

◆ nitrile_given

unsigned int gengetopt_args_info::nitrile_given

Whether nitrile was given.

Definition at line 323 of file StaticPropsCmd.hpp.

◆ nitrile_help

const char* gengetopt_args_info::nitrile_help

electrostatic potential to frequency map based on the Cho nitrile fits help description.

Definition at line 208 of file StaticPropsCmd.hpp.

◆ noCOM_flag

int gengetopt_args_info::noCOM_flag

do not use Center of Mass as origin of the box (default=off).

Definition at line 80 of file omd2omdCmd.hpp.

◆ noCOM_given

unsigned int gengetopt_args_info::noCOM_given

Whether noCOM was given.

Definition at line 98 of file omd2omdCmd.hpp.

◆ noCOM_help

const char* gengetopt_args_info::noCOM_help

do not use Center of Mass as origin of the box help description.

Definition at line 81 of file omd2omdCmd.hpp.

◆ noWrap_flag

int gengetopt_args_info::noWrap_flag

do not rewrap coordinates into the box (default=off).

Definition at line 78 of file omd2omdCmd.hpp.

◆ noWrap_given

unsigned int gengetopt_args_info::noWrap_given

Whether noWrap was given.

Definition at line 97 of file omd2omdCmd.hpp.

◆ noWrap_help

const char* gengetopt_args_info::noWrap_help

do not rewrap coordinates into the box help description.

Definition at line 79 of file omd2omdCmd.hpp.

◆ npoints_arg

int gengetopt_args_info::npoints_arg

number of points for fitting stress-strain relationship (default='25').

Definition at line 50 of file elasticConstantsCmd.hpp.

◆ npoints_given

unsigned int gengetopt_args_info::npoints_given

Whether npoints was given.

Definition at line 65 of file elasticConstantsCmd.hpp.

◆ npoints_help

const char* gengetopt_args_info::npoints_help

number of points for fitting stress-strain relationship help description.

Definition at line 54 of file elasticConstantsCmd.hpp.

◆ npoints_orig

char* gengetopt_args_info::npoints_orig

number of points for fitting stress-strain relationship original value given at command line.

Definition at line 52 of file elasticConstantsCmd.hpp.

◆ nrbins_arg

int gengetopt_args_info::nrbins_arg

number of radial bins (usually duplicates functionality of nbins) (default='100').

Definition at line 68 of file StaticPropsCmd.hpp.

◆ nrbins_given

unsigned int gengetopt_args_info::nrbins_given

Whether nrbins was given.

Definition at line 250 of file StaticPropsCmd.hpp.

◆ nrbins_help

const char* gengetopt_args_info::nrbins_help

number of radial bins (usually duplicates functionality of nbins) help description.

Definition at line 70 of file StaticPropsCmd.hpp.

◆ nrbins_orig

char* gengetopt_args_info::nrbins_orig

number of radial bins (usually duplicates functionality of nbins) original value given at command line.

Definition at line 69 of file StaticPropsCmd.hpp.

◆ number_arg

int gengetopt_args_info::number_arg

number of data points (default='50').

Definition at line 54 of file equationofstateCmd.hpp.

◆ number_given

unsigned int gengetopt_args_info::number_given

Whether number was given.

Definition at line 64 of file equationofstateCmd.hpp.

◆ number_help

const char* gengetopt_args_info::number_help

number of data points help description.

Definition at line 56 of file equationofstateCmd.hpp.

◆ number_orig

char* gengetopt_args_info::number_orig

number of data points original value given at command line.

Definition at line 55 of file equationofstateCmd.hpp.

◆ numberr_given

unsigned int gengetopt_args_info::numberr_given

Whether numberr was given.

Definition at line 349 of file StaticPropsCmd.hpp.

◆ numberr_help

const char* gengetopt_args_info::numberr_help

computes the number density as a function of the radius and selected molecule help description.

Definition at line 234 of file StaticPropsCmd.hpp.

◆ numberz_given

unsigned int gengetopt_args_info::numberz_given

Whether numberz was given.

Definition at line 348 of file StaticPropsCmd.hpp.

◆ numberz_help

const char* gengetopt_args_info::numberz_help

computes the number density along selected axis and selected molcule help description.

Definition at line 233 of file StaticPropsCmd.hpp.

◆ nx_arg

int gengetopt_args_info::nx_arg

number of unit cells in x.

Definition at line 48 of file randomBuilderCmd.hpp.

◆ nx_given

unsigned int gengetopt_args_info::nx_given

Whether nx was given.

Definition at line 70 of file randomBuilderCmd.hpp.

◆ nx_help

const char * gengetopt_args_info::nx_help

number of unit cells in x help description.

Definition at line 50 of file randomBuilderCmd.hpp.

◆ nx_orig

char * gengetopt_args_info::nx_orig

number of unit cells in x original value given at command line.

Definition at line 49 of file randomBuilderCmd.hpp.

◆ ny_arg

int gengetopt_args_info::ny_arg

number of unit cells in y.

Definition at line 51 of file randomBuilderCmd.hpp.

◆ ny_given

unsigned int gengetopt_args_info::ny_given

Whether ny was given.

Definition at line 71 of file randomBuilderCmd.hpp.

◆ ny_help

const char * gengetopt_args_info::ny_help

number of unit cells in y help description.

Definition at line 53 of file randomBuilderCmd.hpp.

◆ ny_orig

char * gengetopt_args_info::ny_orig

number of unit cells in y original value given at command line.

Definition at line 52 of file randomBuilderCmd.hpp.

◆ nz_arg

int gengetopt_args_info::nz_arg

number of unit cells in z.

Definition at line 54 of file randomBuilderCmd.hpp.

◆ nz_given

unsigned int gengetopt_args_info::nz_given

Whether nz was given.

Definition at line 72 of file randomBuilderCmd.hpp.

◆ nz_help

const char * gengetopt_args_info::nz_help

number of unit cells in z help description.

Definition at line 56 of file randomBuilderCmd.hpp.

◆ nz_orig

char * gengetopt_args_info::nz_orig

number of unit cells in z original value given at command line.

Definition at line 55 of file randomBuilderCmd.hpp.

◆ nzbins_arg

int gengetopt_args_info::nzbins_arg

Number of Z bins (default='100').

Definition at line 65 of file DynamicPropsCmd.hpp.

◆ nzbins_given

unsigned int gengetopt_args_info::nzbins_given

Whether nzbins was given.

Definition at line 145 of file DynamicPropsCmd.hpp.

◆ nzbins_help

const char* gengetopt_args_info::nzbins_help

Number of Z bins help description.

Definition at line 67 of file DynamicPropsCmd.hpp.

◆ nzbins_orig

char* gengetopt_args_info::nzbins_orig

Number of Z bins original value given at command line.

Definition at line 66 of file DynamicPropsCmd.hpp.

◆ OHcut_arg

double gengetopt_args_info::OHcut_arg

Oxygen-Hydrogen cutoff radius (angstroms) (default='2.45').

Definition at line 77 of file DynamicPropsCmd.hpp.

◆ OHcut_given

unsigned int gengetopt_args_info::OHcut_given

Whether OHcut was given.

Definition at line 149 of file DynamicPropsCmd.hpp.

◆ OHcut_help

const char * gengetopt_args_info::OHcut_help

Oxygen-Hydrogen cutoff radius (angstroms) help description.

Definition at line 79 of file DynamicPropsCmd.hpp.

◆ OHcut_orig

char * gengetopt_args_info::OHcut_orig

Oxygen-Hydrogen cutoff radius (angstroms) original value given at command line.

Definition at line 78 of file DynamicPropsCmd.hpp.

◆ onsager_given

unsigned int gengetopt_args_info::onsager_given

Whether onsager was given.

Definition at line 191 of file DynamicPropsCmd.hpp.

◆ onsager_help

const char* gengetopt_args_info::onsager_help

Onsager coefficient correlation functions help description.

Definition at line 131 of file DynamicPropsCmd.hpp.

◆ OOcut_arg

double gengetopt_args_info::OOcut_arg

Oxygen-Oxygen cutoff radius (angstroms) (default='3.5').

Definition at line 71 of file DynamicPropsCmd.hpp.

◆ OOcut_given

unsigned int gengetopt_args_info::OOcut_given

Whether OOcut was given.

Definition at line 147 of file DynamicPropsCmd.hpp.

◆ OOcut_help

const char * gengetopt_args_info::OOcut_help

Oxygen-Oxygen cutoff radius (angstroms) help description.

Definition at line 73 of file DynamicPropsCmd.hpp.

◆ OOcut_orig

char * gengetopt_args_info::OOcut_orig

Oxygen-Oxygen cutoff radius (angstroms) original value given at command line.

Definition at line 72 of file DynamicPropsCmd.hpp.

◆ order_arg

int gengetopt_args_info::order_arg

Lengendre Polynomial Order.

Definition at line 59 of file DynamicPropsCmd.hpp.

◆ order_given

unsigned int gengetopt_args_info::order_given

Whether order was given.

Definition at line 143 of file DynamicPropsCmd.hpp.

◆ order_help

const char* gengetopt_args_info::order_help

Lengendre Polynomial Order help description.

Definition at line 61 of file DynamicPropsCmd.hpp.

◆ order_orig

char* gengetopt_args_info::order_orig

Lengendre Polynomial Order original value given at command line.

Definition at line 60 of file DynamicPropsCmd.hpp.

◆ order_prob_given

unsigned int gengetopt_args_info::order_prob_given

Whether order_prob was given.

Definition at line 354 of file StaticPropsCmd.hpp.

◆ order_prob_help

const char* gengetopt_args_info::order_prob_help

probability of order parameter for given selection help description.

Definition at line 239 of file StaticPropsCmd.hpp.

◆ originsele_arg

char* gengetopt_args_info::originsele_arg

select origin.

Definition at line 64 of file Dump2XYZCmd.hpp.

◆ originsele_given

unsigned int gengetopt_args_info::originsele_given

Whether originsele was given.

Definition at line 105 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ originsele_help

const char* gengetopt_args_info::originsele_help

select origin help description.

Definition at line 66 of file Dump2XYZCmd.hpp.

◆ originsele_orig

char* gengetopt_args_info::originsele_orig

select origin original value given at command line.

Definition at line 65 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ output_arg

char * gengetopt_args_info::output_arg

output file name.

Output file name.

output file prefix.

use specified output file.

Definition at line 45 of file Dump2XYZCmd.hpp.

◆ output_given

unsigned int gengetopt_args_info::output_given

Whether output was given.

Definition at line 97 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ output_help

const char * gengetopt_args_info::output_help

output file name help description.

Output file name help description.

output file prefix help description.

use specified output file help description.

Definition at line 47 of file Dump2XYZCmd.hpp.

◆ output_orig

char * gengetopt_args_info::output_orig

output file name original value given at command line.

Output file name original value given at command line.

output file prefix original value given at command line.

use specified output file original value given at command line.

Definition at line 46 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ p2_given

unsigned int gengetopt_args_info::p2_given

Whether p2 was given.

Definition at line 300 of file StaticPropsCmd.hpp.

◆ p2_help

const char* gengetopt_args_info::p2_help

p2 order parameter (–sele1 must be specified, –sele2 is optional) help description.

Definition at line 185 of file StaticPropsCmd.hpp.

◆ p2r_given

unsigned int gengetopt_args_info::p2r_given

Whether p2r was given.

Definition at line 301 of file StaticPropsCmd.hpp.

◆ p2r_help

const char* gengetopt_args_info::p2r_help

p2 order parameter using r as director axis help description.

Definition at line 186 of file StaticPropsCmd.hpp.

◆ p2z_given

unsigned int gengetopt_args_info::p2z_given

Whether p2z was given.

Definition at line 302 of file StaticPropsCmd.hpp.

◆ p2z_help

const char* gengetopt_args_info::p2z_help

p2 order parameter using z (or privilegedAxis) as director axis help description.

Definition at line 187 of file StaticPropsCmd.hpp.

◆ p_angle_given

unsigned int gengetopt_args_info::p_angle_given

Whether p_angle was given.

Definition at line 308 of file StaticPropsCmd.hpp.

◆ p_angle_help

const char* gengetopt_args_info::p_angle_help

p(cos(theta)) (–sele1 must be specified, –sele2 is optional) help description.

Definition at line 193 of file StaticPropsCmd.hpp.

◆ periodicBox_flag

int gengetopt_args_info::periodicBox_flag

map to the periodic box (default=off).

Definition at line 53 of file Dump2XYZCmd.hpp.

◆ periodicBox_given

unsigned int gengetopt_args_info::periodicBox_given

Whether periodicBox was given.

Definition at line 100 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ periodicBox_help

const char* gengetopt_args_info::periodicBox_help

map to the periodic box help description.

Definition at line 54 of file Dump2XYZCmd.hpp.

◆ persistence_given

unsigned int gengetopt_args_info::persistence_given

Whether persistence was given.

Definition at line 180 of file DynamicPropsCmd.hpp.

◆ persistence_help

const char* gengetopt_args_info::persistence_help

Hydrogen bond persistence correlation function help description.

Definition at line 120 of file DynamicPropsCmd.hpp.

◆ pipe_density_given

unsigned int gengetopt_args_info::pipe_density_given

Whether pipe_density was given.

Definition at line 307 of file StaticPropsCmd.hpp.

◆ pipe_density_help

const char* gengetopt_args_info::pipe_density_help

pipe density, rho(axis1, axis2) help description.

Definition at line 192 of file StaticPropsCmd.hpp.

◆ pjcorr_given

unsigned int gengetopt_args_info::pjcorr_given

Whether pjcorr was given.

Definition at line 181 of file DynamicPropsCmd.hpp.

◆ pjcorr_help

const char* gengetopt_args_info::pjcorr_help

Momentum - Angular Momentum cross correlation function help description.

Definition at line 121 of file DynamicPropsCmd.hpp.

◆ potDiff_given

unsigned int gengetopt_args_info::potDiff_given

Whether potDiff was given.

Definition at line 334 of file StaticPropsCmd.hpp.

◆ potDiff_help

const char* gengetopt_args_info::potDiff_help

potential energy difference when charge on selection is set to zero help description.

Definition at line 219 of file StaticPropsCmd.hpp.

◆ privilegedAxis2_arg

enum enum_privilegedAxis2 gengetopt_args_info::privilegedAxis2_arg

which axis is special for spatial analysis (default = x axis) (default='x').

Definition at line 143 of file StaticPropsCmd.hpp.

◆ privilegedAxis2_given

unsigned int gengetopt_args_info::privilegedAxis2_given

Whether privilegedAxis2 was given.

Definition at line 275 of file StaticPropsCmd.hpp.

◆ privilegedAxis2_help

const char* gengetopt_args_info::privilegedAxis2_help

which axis is special for spatial analysis (default = x axis) help description.

Definition at line 145 of file StaticPropsCmd.hpp.

◆ privilegedAxis2_orig

char* gengetopt_args_info::privilegedAxis2_orig

which axis is special for spatial analysis (default = x axis) original value given at command line.

Definition at line 144 of file StaticPropsCmd.hpp.

◆ privilegedAxis_arg

enum enum_privilegedAxis gengetopt_args_info::privilegedAxis_arg

which axis is special for spatial analysis (default = z axis) (default='z').

Definition at line 80 of file DynamicPropsCmd.hpp.

◆ privilegedAxis_given

unsigned int gengetopt_args_info::privilegedAxis_given

Whether privilegedAxis was given.

Definition at line 150 of file DynamicPropsCmd.hpp.

◆ privilegedAxis_help

const char * gengetopt_args_info::privilegedAxis_help

which axis is special for spatial analysis (default = z axis) help description.

Definition at line 82 of file DynamicPropsCmd.hpp.

◆ privilegedAxis_orig

char * gengetopt_args_info::privilegedAxis_orig

which axis is special for spatial analysis (default = z axis) original value given at command line.

Definition at line 81 of file DynamicPropsCmd.hpp.

◆ r_omega_given

unsigned int gengetopt_args_info::r_omega_given

Whether r_omega was given.

Definition at line 293 of file StaticPropsCmd.hpp.

◆ r_omega_help

const char* gengetopt_args_info::r_omega_help

g(r, cos(omega)) help description.

Definition at line 178 of file StaticPropsCmd.hpp.

◆ r_rcorr_given

unsigned int gengetopt_args_info::r_rcorr_given

Whether r_rcorr was given.

Definition at line 171 of file DynamicPropsCmd.hpp.

◆ r_rcorr_help

const char* gengetopt_args_info::r_rcorr_help

Radial msd help description.

Definition at line 111 of file DynamicPropsCmd.hpp.

◆ r_theta_given

unsigned int gengetopt_args_info::r_theta_given

Whether r_theta was given.

Definition at line 292 of file StaticPropsCmd.hpp.

◆ r_theta_help

const char* gengetopt_args_info::r_theta_help

g(r, cos(theta)) help description.

Definition at line 177 of file StaticPropsCmd.hpp.

◆ r_theta_omega_given

unsigned int gengetopt_args_info::r_theta_omega_given

Whether r_theta_omega was given.

Definition at line 296 of file StaticPropsCmd.hpp.

◆ r_theta_omega_help

const char* gengetopt_args_info::r_theta_omega_help

g(r, cos(theta), cos(omega)) help description.

Definition at line 181 of file StaticPropsCmd.hpp.

◆ r_z_given

unsigned int gengetopt_args_info::r_z_given

Whether r_z was given.

Definition at line 294 of file StaticPropsCmd.hpp.

◆ r_z_help

const char* gengetopt_args_info::r_z_help

g(r, z) help description.

Definition at line 179 of file StaticPropsCmd.hpp.

◆ radius_arg

double gengetopt_args_info::radius_arg

Nanoparticle radius in Angstroms.

nanoparticle radius.

Nanorod radius in Angstroms.

Definition at line 48 of file nanoparticleBuilderCmd.hpp.

◆ radius_given

unsigned int gengetopt_args_info::radius_given

Whether radius was given.

Definition at line 75 of file nanoparticleBuilderCmd.hpp.

◆ radius_help

const char * gengetopt_args_info::radius_help

Nanoparticle radius in Angstroms help description.

nanoparticle radius help description.

Nanorod radius in Angstroms help description.

Definition at line 50 of file nanoparticleBuilderCmd.hpp.

◆ radius_orig

char * gengetopt_args_info::radius_orig

Nanoparticle radius in Angstroms original value given at command line.

nanoparticle radius original value given at command line.

Nanorod radius in Angstroms original value given at command line.

Definition at line 49 of file nanoparticleBuilderCmd.hpp.

◆ rcorr_given

unsigned int gengetopt_args_info::rcorr_given

Whether rcorr was given.

Definition at line 156 of file DynamicPropsCmd.hpp.

◆ rcorr_help

const char* gengetopt_args_info::rcorr_help

mean squared displacement help description.

Definition at line 96 of file DynamicPropsCmd.hpp.

◆ rcorrZ_given

unsigned int gengetopt_args_info::rcorrZ_given

Whether rcorrZ was given.

Definition at line 157 of file DynamicPropsCmd.hpp.

◆ rcorrZ_help

const char* gengetopt_args_info::rcorrZ_help

mean squared displacement binned by Z help description.

Definition at line 97 of file DynamicPropsCmd.hpp.

◆ rcut_arg

double gengetopt_args_info::rcut_arg

cutoff radius (angstroms).

cutoff radius (rcut).

Definition at line 68 of file DynamicPropsCmd.hpp.

◆ rcut_given

unsigned int gengetopt_args_info::rcut_given

Whether rcut was given.

Definition at line 146 of file DynamicPropsCmd.hpp.

◆ rcut_help

const char * gengetopt_args_info::rcut_help

cutoff radius (angstroms) help description.

cutoff radius (rcut) help description.

Definition at line 70 of file DynamicPropsCmd.hpp.

◆ rcut_orig

char * gengetopt_args_info::rcut_orig

cutoff radius (angstroms) original value given at command line.

cutoff radius (rcut) original value given at command line.

Definition at line 69 of file DynamicPropsCmd.hpp.

◆ referenceZ_arg

double gengetopt_args_info::referenceZ_arg

Reference z-height of solid surface.

Definition at line 66 of file SequentialPropsCmd.hpp.

◆ referenceZ_given

unsigned int gengetopt_args_info::referenceZ_given

Whether referenceZ was given.

Definition at line 98 of file SequentialPropsCmd.hpp.

◆ referenceZ_help

const char* gengetopt_args_info::referenceZ_help

Reference z-height of solid surface help description.

Definition at line 68 of file SequentialPropsCmd.hpp.

◆ referenceZ_orig

char* gengetopt_args_info::referenceZ_orig

Reference z-height of solid surface original value given at command line.

Definition at line 67 of file SequentialPropsCmd.hpp.

◆ refsele_arg

char * gengetopt_args_info::refsele_arg

select reference.

select reference (use and only use with –gxyz).

Definition at line 67 of file Dump2XYZCmd.hpp.

◆ refsele_given

unsigned int gengetopt_args_info::refsele_given

Whether refsele was given.

Definition at line 106 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ refsele_help

const char * gengetopt_args_info::refsele_help

select reference help description.

select reference (use and only use with –gxyz) help description.

Definition at line 69 of file Dump2XYZCmd.hpp.

◆ refsele_orig

char * gengetopt_args_info::refsele_orig

select reference original value given at command line.

select reference (use and only use with –gxyz) original value given at command line.

Definition at line 68 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ repairMolecules_arg

int gengetopt_args_info::repairMolecules_arg

rewrap molecules around the molecular center of mass (default='1').

Definition at line 75 of file omd2omdCmd.hpp.

◆ repairMolecules_given

unsigned int gengetopt_args_info::repairMolecules_given

Whether repairMolecules was given.

Definition at line 96 of file omd2omdCmd.hpp.

◆ repairMolecules_help

const char* gengetopt_args_info::repairMolecules_help

rewrap molecules around the molecular center of mass help description.

Definition at line 77 of file omd2omdCmd.hpp.

◆ repairMolecules_orig

char* gengetopt_args_info::repairMolecules_orig

rewrap molecules around the molecular center of mass original value given at command line.

Definition at line 76 of file omd2omdCmd.hpp.

◆ repeatX_arg

int gengetopt_args_info::repeatX_arg

The number of images to repeat in the x direction (default='0').

make the system repeat in the x direction (default='1').

Definition at line 70 of file Dump2XYZCmd.hpp.

◆ repeatX_given

unsigned int gengetopt_args_info::repeatX_given

Whether repeatX was given.

Definition at line 107 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ repeatX_help

const char * gengetopt_args_info::repeatX_help

The number of images to repeat in the x direction help description.

make the system repeat in the x direction help description.

Definition at line 72 of file Dump2XYZCmd.hpp.

◆ repeatX_orig

char * gengetopt_args_info::repeatX_orig

The number of images to repeat in the x direction original value given at command line.

make the system repeat in the x direction original value given at command line.

Definition at line 71 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ repeatY_arg

int gengetopt_args_info::repeatY_arg

The number of images to repeat in the y direction (default='0').

make the system repeat in the y direction (default='1').

Definition at line 73 of file Dump2XYZCmd.hpp.

◆ repeatY_given

unsigned int gengetopt_args_info::repeatY_given

Whether repeatY was given.

Definition at line 108 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ repeatY_help

const char * gengetopt_args_info::repeatY_help

The number of images to repeat in the y direction help description.

make the system repeat in the y direction help description.

Definition at line 75 of file Dump2XYZCmd.hpp.

◆ repeatY_orig

char * gengetopt_args_info::repeatY_orig

The number of images to repeat in the y direction original value given at command line.

make the system repeat in the y direction original value given at command line.

Definition at line 74 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ repeatZ_arg

int gengetopt_args_info::repeatZ_arg

The number of images to repeat in the z direction (default='0').

make the system repeat in the z direction (default='1').

Definition at line 76 of file Dump2XYZCmd.hpp.

◆ repeatZ_given

unsigned int gengetopt_args_info::repeatZ_given

Whether repeatZ was given.

Definition at line 109 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ repeatZ_help

const char * gengetopt_args_info::repeatZ_help

The number of images to repeat in the z direction help description.

make the system repeat in the z direction help description.

Definition at line 78 of file Dump2XYZCmd.hpp.

◆ repeatZ_orig

char * gengetopt_args_info::repeatZ_orig

The number of images to repeat in the z direction original value given at command line.

make the system repeat in the z direction original value given at command line.

Definition at line 77 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ rho_r_given

unsigned int gengetopt_args_info::rho_r_given

Whether rho_r was given.

Definition at line 310 of file StaticPropsCmd.hpp.

◆ rho_r_help

const char* gengetopt_args_info::rho_r_help

rho(R) help description.

Definition at line 195 of file StaticPropsCmd.hpp.

◆ rigidbody_flag

int gengetopt_args_info::rigidbody_flag

add a pseudo COM atom to rigidbody (default=off).

Definition at line 57 of file Dump2XYZCmd.hpp.

◆ rigidbody_given

unsigned int gengetopt_args_info::rigidbody_given

Whether rigidbody was given.

Definition at line 102 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ rigidbody_help

const char* gengetopt_args_info::rigidbody_help

add a pseudo COM atom to rigidbody help description.

Definition at line 58 of file Dump2XYZCmd.hpp.

◆ rnemdr_given

unsigned int gengetopt_args_info::rnemdr_given

Whether rnemdr was given.

Definition at line 321 of file StaticPropsCmd.hpp.

◆ rnemdr_help

const char* gengetopt_args_info::rnemdr_help

shell-resolved RNEMD statistics (temperature, density, angular velocity) help description.

Definition at line 206 of file StaticPropsCmd.hpp.

◆ rnemdrt_given

unsigned int gengetopt_args_info::rnemdrt_given

Whether rnemdrt was given.

Definition at line 322 of file StaticPropsCmd.hpp.

◆ rnemdrt_help

const char* gengetopt_args_info::rnemdrt_help

shell and angle-resolved RNEMD statistics (temperature, density, angular velocity) help description.

Definition at line 207 of file StaticPropsCmd.hpp.

◆ rnemdz_given

unsigned int gengetopt_args_info::rnemdz_given

Whether rnemdz was given.

Definition at line 320 of file StaticPropsCmd.hpp.

◆ rnemdz_help

const char* gengetopt_args_info::rnemdz_help

slab-resolved RNEMD statistics (temperature, density, velocity) help description.

Definition at line 205 of file StaticPropsCmd.hpp.

◆ rodlength_given

unsigned int gengetopt_args_info::rodlength_given

Whether rodlength was given.

Definition at line 313 of file StaticPropsCmd.hpp.

◆ rodlength_help

const char* gengetopt_args_info::rodlength_help

length of nanorod help description.

Definition at line 198 of file StaticPropsCmd.hpp.

◆ rotAngleDisp_given

unsigned int gengetopt_args_info::rotAngleDisp_given

Whether rotAngleDisp was given.

Definition at line 193 of file DynamicPropsCmd.hpp.

◆ rotAngleDisp_help

const char* gengetopt_args_info::rotAngleDisp_help

Displacement correlation function for rotation angles help description.

Definition at line 133 of file DynamicPropsCmd.hpp.

◆ rotatePhi_arg

double gengetopt_args_info::rotatePhi_arg

rotate all coordinates Euler angle Phi (default='0.0').

Definition at line 66 of file omd2omdCmd.hpp.

◆ rotatePhi_given

unsigned int gengetopt_args_info::rotatePhi_given

Whether rotatePhi was given.

Definition at line 93 of file omd2omdCmd.hpp.

◆ rotatePhi_help

const char* gengetopt_args_info::rotatePhi_help

rotate all coordinates Euler angle Phi help description.

Definition at line 68 of file omd2omdCmd.hpp.

◆ rotatePhi_orig

char* gengetopt_args_info::rotatePhi_orig

rotate all coordinates Euler angle Phi original value given at command line.

Definition at line 67 of file omd2omdCmd.hpp.

◆ rotatePsi_arg

double gengetopt_args_info::rotatePsi_arg

rotate all coordinates Euler angle Psi (default='0.0').

Definition at line 72 of file omd2omdCmd.hpp.

◆ rotatePsi_given

unsigned int gengetopt_args_info::rotatePsi_given

Whether rotatePsi was given.

Definition at line 95 of file omd2omdCmd.hpp.

◆ rotatePsi_help

const char* gengetopt_args_info::rotatePsi_help

rotate all coordinates Euler angle Psi help description.

Definition at line 74 of file omd2omdCmd.hpp.

◆ rotatePsi_orig

char* gengetopt_args_info::rotatePsi_orig

rotate all coordinates Euler angle Psi original value given at command line.

Definition at line 73 of file omd2omdCmd.hpp.

◆ rotateTheta_arg

double gengetopt_args_info::rotateTheta_arg

rotate all coordinates Euler angle Theta (default='0.0').

Definition at line 69 of file omd2omdCmd.hpp.

◆ rotateTheta_given

unsigned int gengetopt_args_info::rotateTheta_given

Whether rotateTheta was given.

Definition at line 94 of file omd2omdCmd.hpp.

◆ rotateTheta_help

const char* gengetopt_args_info::rotateTheta_help

rotate all coordinates Euler angle Theta help description.

Definition at line 71 of file omd2omdCmd.hpp.

◆ rotateTheta_orig

char* gengetopt_args_info::rotateTheta_orig

rotate all coordinates Euler angle Theta original value given at command line.

Definition at line 70 of file omd2omdCmd.hpp.

◆ rp2_given

unsigned int gengetopt_args_info::rp2_given

Whether rp2 was given.

Definition at line 303 of file StaticPropsCmd.hpp.

◆ rp2_help

const char* gengetopt_args_info::rp2_help

rp2 order parameter (–sele1 and –sele2 must be specified) help description.

Definition at line 188 of file StaticPropsCmd.hpp.

◆ scd_given

unsigned int gengetopt_args_info::scd_given

Whether scd was given.

Definition at line 304 of file StaticPropsCmd.hpp.

◆ scd_help

const char* gengetopt_args_info::scd_help

scd order parameter (either –sele1, –sele2, –sele3 are specified or –molname, –begin, –end are specified) help description.

Definition at line 189 of file StaticPropsCmd.hpp.

◆ scn_given

unsigned int gengetopt_args_info::scn_given

Whether scn was given.

Definition at line 327 of file StaticPropsCmd.hpp.

◆ scn_help

const char* gengetopt_args_info::scn_help

Secondary Coordination Number Distribution help description.

Definition at line 212 of file StaticPropsCmd.hpp.

◆ sdcorr_given

unsigned int gengetopt_args_info::sdcorr_given

Whether sdcorr was given.

Definition at line 170 of file DynamicPropsCmd.hpp.

◆ sdcorr_help

const char* gengetopt_args_info::sdcorr_help

System dipole correlation function help description.

Definition at line 110 of file DynamicPropsCmd.hpp.

◆ sele1_arg

char * gengetopt_args_info::sele1_arg

select first stuntdouble set.

select the first stuntdouble set.

Definition at line 50 of file DynamicPropsCmd.hpp.

◆ sele1_given

unsigned int gengetopt_args_info::sele1_given

Whether sele1 was given.

Definition at line 140 of file DynamicPropsCmd.hpp.

◆ sele1_help

const char * gengetopt_args_info::sele1_help

select first stuntdouble set help description.

select the first stuntdouble set help description.

Definition at line 52 of file DynamicPropsCmd.hpp.

◆ sele1_orig

char * gengetopt_args_info::sele1_orig

select first stuntdouble set original value given at command line.

select the first stuntdouble set original value given at command line.

Definition at line 51 of file DynamicPropsCmd.hpp.

◆ sele2_arg

char * gengetopt_args_info::sele2_arg

select second stuntdouble set (if sele2 is not set, use script from sele1).

select the second stuntdouble set.

Definition at line 53 of file DynamicPropsCmd.hpp.

◆ sele2_given

unsigned int gengetopt_args_info::sele2_given

Whether sele2 was given.

Definition at line 141 of file DynamicPropsCmd.hpp.

◆ sele2_help

const char * gengetopt_args_info::sele2_help

select second stuntdouble set (if sele2 is not set, use script from sele1) help description.

select the second stuntdouble set help description.

Definition at line 55 of file DynamicPropsCmd.hpp.

◆ sele2_orig

char * gengetopt_args_info::sele2_orig

select second stuntdouble set (if sele2 is not set, use script from sele1) original value given at command line.

select the second stuntdouble set original value given at command line.

Definition at line 54 of file DynamicPropsCmd.hpp.

◆ sele3_arg

char * gengetopt_args_info::sele3_arg

select third stuntdouble set.

select the third stuntdouble set.

Definition at line 56 of file DynamicPropsCmd.hpp.

◆ sele3_given

unsigned int gengetopt_args_info::sele3_given

Whether sele3 was given.

Definition at line 142 of file DynamicPropsCmd.hpp.

◆ sele3_help

const char * gengetopt_args_info::sele3_help

select third stuntdouble set help description.

select the third stuntdouble set help description.

Definition at line 58 of file DynamicPropsCmd.hpp.

◆ sele3_orig

char * gengetopt_args_info::sele3_orig

select third stuntdouble set original value given at command line.

select the third stuntdouble set original value given at command line.

Definition at line 57 of file DynamicPropsCmd.hpp.

◆ selecorr_given

unsigned int gengetopt_args_info::selecorr_given

Whether selecorr was given.

Definition at line 155 of file DynamicPropsCmd.hpp.

◆ selecorr_help

const char* gengetopt_args_info::selecorr_help

selection correlation function help description.

Definition at line 95 of file DynamicPropsCmd.hpp.

◆ selection_arg

char* gengetopt_args_info::selection_arg

general selection syntax.

Definition at line 61 of file Dump2XYZCmd.hpp.

◆ selection_given

unsigned int gengetopt_args_info::selection_given

Whether selection was given.

Definition at line 104 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ selection_help

const char* gengetopt_args_info::selection_help

general selection syntax help description.

Definition at line 63 of file Dump2XYZCmd.hpp.

◆ selection_orig

char* gengetopt_args_info::selection_orig

general selection syntax original value given at command line.

Definition at line 62 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ seleoffset2_arg

int gengetopt_args_info::seleoffset2_arg

global index offset for a third object (used to define a vector between sites in molecule).

Definition at line 119 of file StaticPropsCmd.hpp.

◆ seleoffset2_given

unsigned int gengetopt_args_info::seleoffset2_given

Whether seleoffset2 was given.

Definition at line 267 of file StaticPropsCmd.hpp.

◆ seleoffset2_help

const char* gengetopt_args_info::seleoffset2_help

global index offset for a third object (used to define a vector between sites in molecule) help description.

Definition at line 121 of file StaticPropsCmd.hpp.

◆ seleoffset2_orig

char* gengetopt_args_info::seleoffset2_orig

global index offset for a third object (used to define a vector between sites in molecule) original value given at command line.

Definition at line 120 of file StaticPropsCmd.hpp.

◆ seleoffset_arg

int gengetopt_args_info::seleoffset_arg

global index offset for a second object (used to define a vector between sites in molecule).

Definition at line 116 of file StaticPropsCmd.hpp.

◆ seleoffset_given

unsigned int gengetopt_args_info::seleoffset_given

Whether seleoffset was given.

Definition at line 266 of file StaticPropsCmd.hpp.

◆ seleoffset_help

const char* gengetopt_args_info::seleoffset_help

global index offset for a second object (used to define a vector between sites in molecule) help description.

Definition at line 118 of file StaticPropsCmd.hpp.

◆ seleoffset_orig

char* gengetopt_args_info::seleoffset_orig

global index offset for a second object (used to define a vector between sites in molecule) original value given at command line.

Definition at line 117 of file StaticPropsCmd.hpp.

◆ sequentialProps_group_counter

int gengetopt_args_info::sequentialProps_group_counter

Counter for group sequentialProps.

Definition at line 112 of file SequentialPropsCmd.hpp.

◆ shellRadius_arg

double * gengetopt_args_info::shellRadius_arg

Radius containing within it only molecules of a specific component.

Specified for each component > 1 in the template file..

Definition at line 51 of file nanoparticleBuilderCmd.hpp.

◆ shellRadius_given

unsigned int gengetopt_args_info::shellRadius_given

Whether shellRadius was given.

Definition at line 76 of file nanoparticleBuilderCmd.hpp.

◆ shellRadius_help

const char * gengetopt_args_info::shellRadius_help

Radius containing within it only molecules of a specific component.

Specified for each component > 1 in the template file. help description.

Definition at line 55 of file nanoparticleBuilderCmd.hpp.

◆ shellRadius_max

unsigned int gengetopt_args_info::shellRadius_max

Radius containing within it only molecules of a specific component.

Specified for each component > 1 in the template file.'s maximum occurreces

Definition at line 54 of file nanoparticleBuilderCmd.hpp.

◆ shellRadius_min

unsigned int gengetopt_args_info::shellRadius_min

Radius containing within it only molecules of a specific component.

Specified for each component > 1 in the template file.'s minimum occurreces

Definition at line 53 of file nanoparticleBuilderCmd.hpp.

◆ shellRadius_orig

char ** gengetopt_args_info::shellRadius_orig

Radius containing within it only molecules of a specific component.

Specified for each component > 1 in the template file. original value given at command line.

Definition at line 52 of file nanoparticleBuilderCmd.hpp.

◆ shells_arg

int gengetopt_args_info::shells_arg

Nanoparticle shells.

Definition at line 45 of file icosahedralBuilderCmd.hpp.

◆ shells_given

unsigned int gengetopt_args_info::shells_given

Whether shells was given.

Definition at line 77 of file icosahedralBuilderCmd.hpp.

◆ shells_help

const char* gengetopt_args_info::shells_help

Nanoparticle shells help description.

Definition at line 47 of file icosahedralBuilderCmd.hpp.

◆ shells_orig

char* gengetopt_args_info::shells_orig

Nanoparticle shells original value given at command line.

Definition at line 46 of file icosahedralBuilderCmd.hpp.

◆ slab_density_given

unsigned int gengetopt_args_info::slab_density_given

Whether slab_density was given.

Definition at line 306 of file StaticPropsCmd.hpp.

◆ slab_density_help

const char* gengetopt_args_info::slab_density_help

slab density, rho(z) help description.

Definition at line 191 of file StaticPropsCmd.hpp.

◆ start_arg

double gengetopt_args_info::start_arg

starting affine scale (default='0.8').

Definition at line 48 of file equationofstateCmd.hpp.

◆ start_given

unsigned int gengetopt_args_info::start_given

Whether start was given.

Definition at line 62 of file equationofstateCmd.hpp.

◆ start_help

const char* gengetopt_args_info::start_help

starting affine scale help description.

Definition at line 50 of file equationofstateCmd.hpp.

◆ start_orig

char* gengetopt_args_info::start_orig

starting affine scale original value given at command line.

Definition at line 49 of file equationofstateCmd.hpp.

◆ staticProps_group_counter

int gengetopt_args_info::staticProps_group_counter

Counter for group staticProps.

Definition at line 358 of file StaticPropsCmd.hpp.

◆ step_arg

int gengetopt_args_info::step_arg

process every n frame (default='1').

Definition at line 53 of file StaticPropsCmd.hpp.

◆ step_given

unsigned int gengetopt_args_info::step_given

Whether step was given.

Definition at line 245 of file StaticPropsCmd.hpp.

◆ step_help

const char* gengetopt_args_info::step_help

process every n frame help description.

Definition at line 55 of file StaticPropsCmd.hpp.

◆ step_orig

char* gengetopt_args_info::step_orig

process every n frame original value given at command line.

Definition at line 54 of file StaticPropsCmd.hpp.

◆ stl_arg

char* gengetopt_args_info::stl_arg

stl file for BoundaryElement model.

Definition at line 50 of file HydroCmd.hpp.

◆ stl_given

unsigned int gengetopt_args_info::stl_given

Whether stl was given.

Definition at line 78 of file HydroCmd.hpp.

◆ stl_help

const char* gengetopt_args_info::stl_help

stl file for BoundaryElement model help description.

Definition at line 52 of file HydroCmd.hpp.

◆ stl_orig

char* gengetopt_args_info::stl_orig

stl file for BoundaryElement model original value given at command line.

Definition at line 51 of file HydroCmd.hpp.

◆ stone_given

unsigned int gengetopt_args_info::stone_given

Whether stone was given.

Definition at line 88 of file icosahedralBuilderCmd.hpp.

◆ stone_help

const char* gengetopt_args_info::stone_help

Create a Curling-stone Decahedral cluster help description.

Definition at line 70 of file icosahedralBuilderCmd.hpp.

◆ stresscorr_given

unsigned int gengetopt_args_info::stresscorr_given

Whether stresscorr was given.

Definition at line 174 of file DynamicPropsCmd.hpp.

◆ stresscorr_help

const char* gengetopt_args_info::stresscorr_help

Stress tensor correlation function help description.

Definition at line 114 of file DynamicPropsCmd.hpp.

◆ surfDiffusion_given

unsigned int gengetopt_args_info::surfDiffusion_given

Whether surfDiffusion was given.

Definition at line 325 of file StaticPropsCmd.hpp.

◆ surfDiffusion_help

const char* gengetopt_args_info::surfDiffusion_help

X, Y, and R (surface diffusion if Z exposed and bulk immobile) diffusion help description.

Definition at line 210 of file StaticPropsCmd.hpp.

◆ tacorr_given

unsigned int gengetopt_args_info::tacorr_given

Whether tacorr was given.

Definition at line 187 of file DynamicPropsCmd.hpp.

◆ tacorr_help

const char* gengetopt_args_info::tacorr_help

Torque auto correlation function help description.

Definition at line 127 of file DynamicPropsCmd.hpp.

◆ temperature_arg

double gengetopt_args_info::temperature_arg

temperature (in Kelvin (default='300').

temperature (K).

Definition at line 70 of file HydroCmd.hpp.

◆ temperature_given

unsigned int gengetopt_args_info::temperature_given

Whether temperature was given.

Definition at line 85 of file HydroCmd.hpp.

◆ temperature_help

const char * gengetopt_args_info::temperature_help

temperature (in Kelvin help description.

temperature (K) help description.

Definition at line 72 of file HydroCmd.hpp.

◆ temperature_orig

char * gengetopt_args_info::temperature_orig

temperature (in Kelvin original value given at command line.

temperature (K) original value given at command line.

Definition at line 71 of file HydroCmd.hpp.

◆ testequi_given

unsigned int gengetopt_args_info::testequi_given

Whether testequi was given.

Definition at line 108 of file SequentialPropsCmd.hpp.

◆ testequi_help

const char* gengetopt_args_info::testequi_help

Temperature using all componets of linear and angular momentum help description.

Definition at line 86 of file SequentialPropsCmd.hpp.

◆ tet_hb_given

unsigned int gengetopt_args_info::tet_hb_given

Whether tet_hb was given.

Definition at line 335 of file StaticPropsCmd.hpp.

◆ tet_hb_help

const char* gengetopt_args_info::tet_hb_help

hydrogen bond statistics binned by tetrahedrality of donor and acceptor molecules help description.

Definition at line 220 of file StaticPropsCmd.hpp.

◆ tet_param_dens_given

unsigned int gengetopt_args_info::tet_param_dens_given

Whether tet_param_dens was given.

Definition at line 317 of file StaticPropsCmd.hpp.

◆ tet_param_dens_help

const char* gengetopt_args_info::tet_param_dens_help

computes density of the tetrahedrality order parameter Qk help description.

Definition at line 202 of file StaticPropsCmd.hpp.

◆ tet_param_given

unsigned int gengetopt_args_info::tet_param_given

Whether tet_param was given.

Definition at line 314 of file StaticPropsCmd.hpp.

◆ tet_param_help

const char* gengetopt_args_info::tet_param_help

tetrahedrality order parameter (Qk) help description.

Definition at line 199 of file StaticPropsCmd.hpp.

◆ tet_param_r_given

unsigned int gengetopt_args_info::tet_param_r_given

Whether tet_param_r was given.

Definition at line 316 of file StaticPropsCmd.hpp.

◆ tet_param_r_help

const char* gengetopt_args_info::tet_param_r_help

spatially-resolved tetrahedrality order parameter Qk(r) around a third selection help description.

Definition at line 201 of file StaticPropsCmd.hpp.

◆ tet_param_xyz_given

unsigned int gengetopt_args_info::tet_param_xyz_given

Whether tet_param_xyz was given.

Definition at line 318 of file StaticPropsCmd.hpp.

◆ tet_param_xyz_help

const char* gengetopt_args_info::tet_param_xyz_help

volume-resolved tetrahedrality order parameter Qk(x,y,z).

(voxelSize, rcut, and gaussWidth must be specified) help description.

Definition at line 203 of file StaticPropsCmd.hpp.

◆ tet_param_z_given

unsigned int gengetopt_args_info::tet_param_z_given

Whether tet_param_z was given.

Definition at line 315 of file StaticPropsCmd.hpp.

◆ tet_param_z_help

const char* gengetopt_args_info::tet_param_z_help

spatially-resolved tetrahedrality order parameter Qk(z) help description.

Definition at line 200 of file StaticPropsCmd.hpp.

◆ tfcorr_given

unsigned int gengetopt_args_info::tfcorr_given

Whether tfcorr was given.

Definition at line 186 of file DynamicPropsCmd.hpp.

◆ tfcorr_help

const char* gengetopt_args_info::tfcorr_help

Torque - Force Cross correlation function help description.

Definition at line 126 of file DynamicPropsCmd.hpp.

◆ thermalizer_group_counter

int gengetopt_args_info::thermalizer_group_counter

Counter for group thermalizer.

Definition at line 68 of file thermalizerCmd.hpp.

◆ theta_omega_given

unsigned int gengetopt_args_info::theta_omega_given

Whether theta_omega was given.

Definition at line 295 of file StaticPropsCmd.hpp.

◆ theta_omega_help

const char* gengetopt_args_info::theta_omega_help

g(cos(theta), cos(omega)) help description.

Definition at line 180 of file StaticPropsCmd.hpp.

◆ thetacorr_given

unsigned int gengetopt_args_info::thetacorr_given

Whether thetacorr was given.

Definition at line 172 of file DynamicPropsCmd.hpp.

◆ thetacorr_help

const char* gengetopt_args_info::thetacorr_help

Angular msd help description.

Definition at line 112 of file DynamicPropsCmd.hpp.

◆ thetacut_arg

double gengetopt_args_info::thetacut_arg

HOO cutoff angle (degrees) (default='30').

Definition at line 74 of file DynamicPropsCmd.hpp.

◆ thetacut_given

unsigned int gengetopt_args_info::thetacut_given

Whether thetacut was given.

Definition at line 148 of file DynamicPropsCmd.hpp.

◆ thetacut_help

const char * gengetopt_args_info::thetacut_help

HOO cutoff angle (degrees) help description.

Definition at line 76 of file DynamicPropsCmd.hpp.

◆ thetacut_orig

char * gengetopt_args_info::thetacut_orig

HOO cutoff angle (degrees) original value given at command line.

Definition at line 75 of file DynamicPropsCmd.hpp.

◆ threshDens_arg

double gengetopt_args_info::threshDens_arg

Threshold Density in g/cm^3.

Definition at line 72 of file SequentialPropsCmd.hpp.

◆ threshDens_given

unsigned int gengetopt_args_info::threshDens_given

Whether threshDens was given.

Definition at line 100 of file SequentialPropsCmd.hpp.

◆ threshDens_help

const char* gengetopt_args_info::threshDens_help

Threshold Density in g/cm^3 help description.

Definition at line 74 of file SequentialPropsCmd.hpp.

◆ threshDens_orig

char* gengetopt_args_info::threshDens_orig

Threshold Density in g/cm^3 original value given at command line.

Definition at line 73 of file SequentialPropsCmd.hpp.

◆ trans_param_z_given

unsigned int gengetopt_args_info::trans_param_z_given

Whether trans_param_z was given.

Definition at line 319 of file StaticPropsCmd.hpp.

◆ trans_param_z_help

const char* gengetopt_args_info::trans_param_z_help

spatially-resolved translational order parameter t(z) help description.

Definition at line 204 of file StaticPropsCmd.hpp.

◆ translateX_arg

double gengetopt_args_info::translateX_arg

translate all x coordinates by some amount (default='0.0').

Definition at line 57 of file omd2omdCmd.hpp.

◆ translateX_given

unsigned int gengetopt_args_info::translateX_given

Whether translateX was given.

Definition at line 90 of file omd2omdCmd.hpp.

◆ translateX_help

const char* gengetopt_args_info::translateX_help

translate all x coordinates by some amount help description.

Definition at line 59 of file omd2omdCmd.hpp.

◆ translateX_orig

char* gengetopt_args_info::translateX_orig

translate all x coordinates by some amount original value given at command line.

Definition at line 58 of file omd2omdCmd.hpp.

◆ translateY_arg

double gengetopt_args_info::translateY_arg

translate all y coordinates by some amount (default='0.0').

Definition at line 60 of file omd2omdCmd.hpp.

◆ translateY_given

unsigned int gengetopt_args_info::translateY_given

Whether translateY was given.

Definition at line 91 of file omd2omdCmd.hpp.

◆ translateY_help

const char* gengetopt_args_info::translateY_help

translate all y coordinates by some amount help description.

Definition at line 62 of file omd2omdCmd.hpp.

◆ translateY_orig

char* gengetopt_args_info::translateY_orig

translate all y coordinates by some amount original value given at command line.

Definition at line 61 of file omd2omdCmd.hpp.

◆ translateZ_arg

double gengetopt_args_info::translateZ_arg

translate all z coordinates by some amount (default='0.0').

Definition at line 63 of file omd2omdCmd.hpp.

◆ translateZ_given

unsigned int gengetopt_args_info::translateZ_given

Whether translateZ was given.

Definition at line 92 of file omd2omdCmd.hpp.

◆ translateZ_help

const char* gengetopt_args_info::translateZ_help

translate all z coordinates by some amount help description.

Definition at line 65 of file omd2omdCmd.hpp.

◆ translateZ_orig

char* gengetopt_args_info::translateZ_orig

translate all z coordinates by some amount original value given at command line.

Definition at line 64 of file omd2omdCmd.hpp.

◆ truncatedCube_given

unsigned int gengetopt_args_info::truncatedCube_given

Whether truncatedCube was given.

Definition at line 90 of file icosahedralBuilderCmd.hpp.

◆ truncatedCube_help

const char* gengetopt_args_info::truncatedCube_help

Create a Truncated Cube (requires lattice) help description.

Definition at line 72 of file icosahedralBuilderCmd.hpp.

◆ truncatedPlanes_arg

int gengetopt_args_info::truncatedPlanes_arg

Number of truncated planes (Curling-stone Decahedra and Truncated Cubes only).

Definition at line 60 of file icosahedralBuilderCmd.hpp.

◆ truncatedPlanes_given

unsigned int gengetopt_args_info::truncatedPlanes_given

Whether truncatedPlanes was given.

Definition at line 82 of file icosahedralBuilderCmd.hpp.

◆ truncatedPlanes_help

const char* gengetopt_args_info::truncatedPlanes_help

Number of truncated planes (Curling-stone Decahedra and Truncated Cubes only) help description.

Definition at line 62 of file icosahedralBuilderCmd.hpp.

◆ truncatedPlanes_orig

char* gengetopt_args_info::truncatedPlanes_orig

Number of truncated planes (Curling-stone Decahedra and Truncated Cubes only) original value given at command line.

Definition at line 61 of file icosahedralBuilderCmd.hpp.

◆ twinAtoms_arg

int gengetopt_args_info::twinAtoms_arg

Number of atoms along twin boundary (Decahedron only).

Definition at line 57 of file icosahedralBuilderCmd.hpp.

◆ twinAtoms_given

unsigned int gengetopt_args_info::twinAtoms_given

Whether twinAtoms was given.

Definition at line 81 of file icosahedralBuilderCmd.hpp.

◆ twinAtoms_help

const char* gengetopt_args_info::twinAtoms_help

Number of atoms along twin boundary (Decahedron only) help description.

Definition at line 59 of file icosahedralBuilderCmd.hpp.

◆ twinAtoms_orig

char* gengetopt_args_info::twinAtoms_orig

Number of atoms along twin boundary (Decahedron only) original value given at command line.

Definition at line 58 of file icosahedralBuilderCmd.hpp.

◆ twodgofr_given

unsigned int gengetopt_args_info::twodgofr_given

Whether twodgofr was given.

Definition at line 298 of file StaticPropsCmd.hpp.

◆ twodgofr_help

const char* gengetopt_args_info::twodgofr_help

2D g(r) (Slab width –dz must be specified) help description.

Definition at line 183 of file StaticPropsCmd.hpp.

◆ unitCells_arg

int gengetopt_args_info::unitCells_arg

Number of unit cell (Cuboctahedron and Truncated Cube only).

Definition at line 63 of file icosahedralBuilderCmd.hpp.

◆ unitCells_given

unsigned int gengetopt_args_info::unitCells_given

Whether unitCells was given.

Definition at line 83 of file icosahedralBuilderCmd.hpp.

◆ unitCells_help

const char* gengetopt_args_info::unitCells_help

Number of unit cell (Cuboctahedron and Truncated Cube only) help description.

Definition at line 65 of file icosahedralBuilderCmd.hpp.

◆ unitCells_orig

char* gengetopt_args_info::unitCells_orig

Number of unit cell (Cuboctahedron and Truncated Cube only) original value given at command line.

Definition at line 64 of file icosahedralBuilderCmd.hpp.

◆ v_radius_arg

double gengetopt_args_info::v_radius_arg

VanderWaals radiius for fictious atoms used in model eg.

M site in TIP4P-FQ water model.

Definition at line 161 of file StaticPropsCmd.hpp.

◆ v_radius_given

unsigned int gengetopt_args_info::v_radius_given

Whether v_radius was given.

Definition at line 281 of file StaticPropsCmd.hpp.

◆ v_radius_help

const char* gengetopt_args_info::v_radius_help

VanderWaals radiius for fictious atoms used in model eg.

M site in TIP4P-FQ water model help description.

Definition at line 163 of file StaticPropsCmd.hpp.

◆ v_radius_orig

char* gengetopt_args_info::v_radius_orig

VanderWaals radiius for fictious atoms used in model eg.

M site in TIP4P-FQ water model original value given at command line.

Definition at line 162 of file StaticPropsCmd.hpp.

◆ vacancyInnerRadius_arg

double gengetopt_args_info::vacancyInnerRadius_arg

Radius arround core-shell where vacancies should be located.

Definition at line 64 of file nanoparticleBuilderCmd.hpp.

◆ vacancyInnerRadius_given

unsigned int gengetopt_args_info::vacancyInnerRadius_given

Whether vacancyInnerRadius was given.

Definition at line 79 of file nanoparticleBuilderCmd.hpp.

◆ vacancyInnerRadius_help

const char * gengetopt_args_info::vacancyInnerRadius_help

Radius arround core-shell where vacancies should be located.

help description.

Definition at line 66 of file nanoparticleBuilderCmd.hpp.

◆ vacancyInnerRadius_orig

char * gengetopt_args_info::vacancyInnerRadius_orig

Radius arround core-shell where vacancies should be located.

original value given at command line.

Definition at line 65 of file nanoparticleBuilderCmd.hpp.

◆ vacancyOuterRadius_arg

double gengetopt_args_info::vacancyOuterRadius_arg

Radius arround core-shell where vacancies should be located.

Definition at line 67 of file nanoparticleBuilderCmd.hpp.

◆ vacancyOuterRadius_given

unsigned int gengetopt_args_info::vacancyOuterRadius_given

Whether vacancyOuterRadius was given.

Definition at line 80 of file nanoparticleBuilderCmd.hpp.

◆ vacancyOuterRadius_help

const char * gengetopt_args_info::vacancyOuterRadius_help

Radius arround core-shell where vacancies should be located.

help description.

Definition at line 69 of file nanoparticleBuilderCmd.hpp.

◆ vacancyOuterRadius_orig

char * gengetopt_args_info::vacancyOuterRadius_orig

Radius arround core-shell where vacancies should be located.

original value given at command line.

Definition at line 68 of file nanoparticleBuilderCmd.hpp.

◆ vacancyPercent_arg

double gengetopt_args_info::vacancyPercent_arg

Percentage of atoms to remove from within vacancy range.

Definition at line 61 of file nanoparticleBuilderCmd.hpp.

◆ vacancyPercent_given

unsigned int gengetopt_args_info::vacancyPercent_given

Whether vacancyPercent was given.

Definition at line 78 of file nanoparticleBuilderCmd.hpp.

◆ vacancyPercent_help

const char * gengetopt_args_info::vacancyPercent_help

Percentage of atoms to remove from within vacancy range help description.

Definition at line 63 of file nanoparticleBuilderCmd.hpp.

◆ vacancyPercent_orig

char * gengetopt_args_info::vacancyPercent_orig

Percentage of atoms to remove from within vacancy range original value given at command line.

Definition at line 62 of file nanoparticleBuilderCmd.hpp.

◆ vaOutProdcorr_given

unsigned int gengetopt_args_info::vaOutProdcorr_given

Whether vaOutProdcorr was given.

Definition at line 161 of file DynamicPropsCmd.hpp.

◆ vaOutProdcorr_help

const char* gengetopt_args_info::vaOutProdcorr_help

Velocity - Velocity auto outer product correlation function help description.

Definition at line 101 of file DynamicPropsCmd.hpp.

◆ vcorr_given

unsigned int gengetopt_args_info::vcorr_given

Whether vcorr was given.

Definition at line 158 of file DynamicPropsCmd.hpp.

◆ vcorr_help

const char* gengetopt_args_info::vcorr_help

velocity correlation function help description.

Definition at line 98 of file DynamicPropsCmd.hpp.

◆ vcorrR_given

unsigned int gengetopt_args_info::vcorrR_given

Whether vcorrR was given.

Definition at line 160 of file DynamicPropsCmd.hpp.

◆ vcorrR_help

const char* gengetopt_args_info::vcorrR_help

velocity correlation function projected radially help description.

Definition at line 100 of file DynamicPropsCmd.hpp.

◆ vcorrZ_given

unsigned int gengetopt_args_info::vcorrZ_given

Whether vcorrZ was given.

Definition at line 159 of file DynamicPropsCmd.hpp.

◆ vcorrZ_help

const char* gengetopt_args_info::vcorrZ_help

velocity correlation function along z-axis help description.

Definition at line 99 of file DynamicPropsCmd.hpp.

◆ vectors_flag

int gengetopt_args_info::vectors_flag

Print vectors (dipoles, etc) in xyz file (default=off).

Definition at line 85 of file Dump2XYZCmd.hpp.

◆ vectors_given

unsigned int gengetopt_args_info::vectors_given

Whether vectors was given.

Definition at line 113 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ vectors_help

const char* gengetopt_args_info::vectors_help

Print vectors (dipoles, etc) in xyz file help description.

Definition at line 86 of file Dump2XYZCmd.hpp.

◆ velocities_flag

int gengetopt_args_info::velocities_flag

Print velocities in xyz file (default=off).

Definition at line 81 of file Dump2XYZCmd.hpp.

◆ velocities_given

unsigned int gengetopt_args_info::velocities_given

Whether velocities was given.

Definition at line 111 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ velocities_help

const char* gengetopt_args_info::velocities_help

Print velocities in xyz file help description.

Definition at line 82 of file Dump2XYZCmd.hpp.

◆ velocityfield_given

unsigned int gengetopt_args_info::velocityfield_given

Whether velocityfield was given.

Definition at line 339 of file StaticPropsCmd.hpp.

◆ velocityfield_help

const char* gengetopt_args_info::velocityfield_help

computes an average velocity field help description.

Definition at line 224 of file StaticPropsCmd.hpp.

◆ velocityZ_given

unsigned int gengetopt_args_info::velocityZ_given

Whether velocityZ was given.

Definition at line 340 of file StaticPropsCmd.hpp.

◆ velocityZ_help

const char* gengetopt_args_info::velocityZ_help

computes an average two-dimensional velocity map help description.

Definition at line 225 of file StaticPropsCmd.hpp.

◆ version_given

unsigned int gengetopt_args_info::version_given

Whether version was given.

Definition at line 95 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ version_help

const char * gengetopt_args_info::version_help

Print version and exit help description.

Definition at line 41 of file Dump2XYZCmd.hpp.

◆ viscosity_arg

double gengetopt_args_info::viscosity_arg

viscosity (in poise) (default='0.01').

Definition at line 67 of file HydroCmd.hpp.

◆ viscosity_given

unsigned int gengetopt_args_info::viscosity_given

Whether viscosity was given.

Definition at line 84 of file HydroCmd.hpp.

◆ viscosity_help

const char* gengetopt_args_info::viscosity_help

viscosity (in poise) help description.

Definition at line 69 of file HydroCmd.hpp.

◆ viscosity_orig

char* gengetopt_args_info::viscosity_orig

viscosity (in poise) original value given at command line.

Definition at line 68 of file HydroCmd.hpp.

◆ voxelSize_arg

double gengetopt_args_info::voxelSize_arg

voxel size (angstroms).

Definition at line 134 of file StaticPropsCmd.hpp.

◆ voxelSize_given

unsigned int gengetopt_args_info::voxelSize_given

Whether voxelSize was given.

Definition at line 272 of file StaticPropsCmd.hpp.

◆ voxelSize_help

const char* gengetopt_args_info::voxelSize_help

voxel size (angstroms) help description.

Definition at line 136 of file StaticPropsCmd.hpp.

◆ voxelSize_orig

char* gengetopt_args_info::voxelSize_orig

voxel size (angstroms) original value given at command line.

Definition at line 135 of file StaticPropsCmd.hpp.

◆ vwOutProdcorr_given

unsigned int gengetopt_args_info::vwOutProdcorr_given

Whether vwOutProdcorr was given.

Definition at line 163 of file DynamicPropsCmd.hpp.

◆ vwOutProdcorr_help

const char* gengetopt_args_info::vwOutProdcorr_help

Velocity - Angular Velocity outer product correlation function help description.

Definition at line 103 of file DynamicPropsCmd.hpp.

◆ waOutProdcorr_given

unsigned int gengetopt_args_info::waOutProdcorr_given

Whether waOutProdcorr was given.

Definition at line 162 of file DynamicPropsCmd.hpp.

◆ waOutProdcorr_help

const char* gengetopt_args_info::waOutProdcorr_help

Angular Velocity - Angular Velocity auto outer product correlation function help description.

Definition at line 102 of file DynamicPropsCmd.hpp.

◆ water_flag

int gengetopt_args_info::water_flag

skip the the waters (default=off).

Definition at line 51 of file Dump2XYZCmd.hpp.

◆ water_given

unsigned int gengetopt_args_info::water_given

Whether water was given.

Definition at line 99 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ water_help

const char* gengetopt_args_info::water_help

skip the the waters help description.

Definition at line 52 of file Dump2XYZCmd.hpp.

◆ watertype_flag

int gengetopt_args_info::watertype_flag

replace the atom type of water model (default=on).

Definition at line 59 of file Dump2XYZCmd.hpp.

◆ watertype_given

unsigned int gengetopt_args_info::watertype_given

Whether watertype was given.

Definition at line 103 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ watertype_help

const char* gengetopt_args_info::watertype_help

replace the atom type of water model help description.

Definition at line 60 of file Dump2XYZCmd.hpp.

◆ wcorr_given

unsigned int gengetopt_args_info::wcorr_given

Whether wcorr was given.

Definition at line 165 of file DynamicPropsCmd.hpp.

◆ wcorr_help

const char* gengetopt_args_info::wcorr_help

charge velocity correlation function help description.

Definition at line 105 of file DynamicPropsCmd.hpp.

◆ wvOutProdcorr_given

unsigned int gengetopt_args_info::wvOutProdcorr_given

Whether wvOutProdcorr was given.

Definition at line 164 of file DynamicPropsCmd.hpp.

◆ wvOutProdcorr_help

const char* gengetopt_args_info::wvOutProdcorr_help

Angular Velocity - Velocity outer product correlation function help description.

Definition at line 104 of file DynamicPropsCmd.hpp.

◆ xyz_arg

char* gengetopt_args_info::xyz_arg

xyz file for AtomicBead model.

Definition at line 47 of file HydroCmd.hpp.

◆ xyz_given

unsigned int gengetopt_args_info::xyz_given

Whether xyz was given.

Definition at line 77 of file HydroCmd.hpp.

◆ xyz_help

const char* gengetopt_args_info::xyz_help

xyz file for AtomicBead model help description.

Definition at line 49 of file HydroCmd.hpp.

◆ xyz_orig

char* gengetopt_args_info::xyz_orig

xyz file for AtomicBead model original value given at command line.

Definition at line 48 of file HydroCmd.hpp.

◆ zconstraint_flag

int gengetopt_args_info::zconstraint_flag

replace the atom types of zconstraint molecules (default=off).

Definition at line 55 of file Dump2XYZCmd.hpp.

◆ zconstraint_given

unsigned int gengetopt_args_info::zconstraint_given

Whether zconstraint was given.

Definition at line 101 of file Dump2XYZCmd.hpp.

Referenced by cmdline_parser_dump().

◆ zconstraint_help

const char* gengetopt_args_info::zconstraint_help

replace the atom types of zconstraint molecules help description.

Definition at line 56 of file Dump2XYZCmd.hpp.

◆ zlength_arg

double gengetopt_args_info::zlength_arg

maximum length (Defaults to 1/2 smallest length of first frame).

Definition at line 95 of file StaticPropsCmd.hpp.

◆ zlength_given

unsigned int gengetopt_args_info::zlength_given

Whether zlength was given.

Definition at line 259 of file StaticPropsCmd.hpp.

◆ zlength_help

const char* gengetopt_args_info::zlength_help

maximum length (Defaults to 1/2 smallest length of first frame) help description.

Definition at line 97 of file StaticPropsCmd.hpp.

◆ zlength_orig

char* gengetopt_args_info::zlength_orig

maximum length (Defaults to 1/2 smallest length of first frame) original value given at command line.

Definition at line 96 of file StaticPropsCmd.hpp.

◆ zoffset_arg

double gengetopt_args_info::zoffset_arg

Where to set the zero for the slab_density calculation (default='0').

Definition at line 98 of file StaticPropsCmd.hpp.

◆ zoffset_given

unsigned int gengetopt_args_info::zoffset_given

Whether zoffset was given.

Definition at line 260 of file StaticPropsCmd.hpp.

◆ zoffset_help

const char* gengetopt_args_info::zoffset_help

Where to set the zero for the slab_density calculation help description.

Definition at line 100 of file StaticPropsCmd.hpp.

◆ zoffset_orig

char* gengetopt_args_info::zoffset_orig

Where to set the zero for the slab_density calculation original value given at command line.

Definition at line 99 of file StaticPropsCmd.hpp.

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

applications/dump2Xyz/Dump2XYZCmd.hpp
applications/dynamicProps/DynamicPropsCmd.hpp
applications/elasticConstants/elasticConstantsCmd.hpp
applications/eos/equationofstateCmd.hpp
applications/hydrodynamics/HydroCmd.hpp
applications/nanoparticleBuilder/icosahedralBuilderCmd.hpp
applications/nanoparticleBuilder/nanoparticleBuilderCmd.hpp
applications/nanoparticleBuilder/nanorod_pentBuilderCmd.hpp
applications/nanoparticleBuilder/nanorodBuilderCmd.hpp
applications/omd2omd/omd2omdCmd.hpp
applications/randomBuilder/randomBuilderCmd.hpp
applications/recenter/recenterCmd.hpp
applications/sequentialProps/SequentialPropsCmd.hpp
applications/simpleBuilder/simpleBuilderCmd.hpp
applications/staticProps/StaticPropsCmd.hpp
applications/thermalizer/thermalizerCmd.hpp

Public Attributes

Detailed Description

Member Data Documentation

◆ angle_r_given

◆ angle_r_help

◆ atom_name_arg

◆ atom_name_given

◆ atom_name_help

◆ atom_name_orig

◆ bad_given

◆ bad_help

◆ basetype_flag

◆ basetype_given

◆ basetype_help

◆ beadSize_arg

◆ beadSize_given

◆ beadSize_help

◆ beadSize_orig

◆ begin_arg

◆ begin_given

◆ begin_help

◆ begin_orig

◆ binWidth_arg

◆ binWidth_given

◆ binWidth_help

◆ binWidth_orig

◆ bo_given

◆ bo_help

◆ bondcorr_given

◆ bondcorr_help

◆ box_flag

◆ box_given

◆ box_help

◆ bufferLength_arg

◆ bufferLength_given

◆ bufferLength_help

◆ bufferLength_orig

◆ ca1_given

◆ ca1_help

◆ ca2_given

◆ ca2_help

◆ centroidX_arg

◆ centroidX_given

◆ centroidX_help

◆ centroidX_orig

◆ centroidY_arg

◆ centroidY_given

◆ centroidY_help

◆ centroidY_orig

◆ charge_density_z_given

◆ charge_density_z_help

◆ charger_given

◆ charger_help

◆ charges_flag

◆ charges_given

◆ charges_help

◆ chargetemperature_arg

◆ chargetemperature_given

◆ chargetemperature_help

◆ chargetemperature_orig

◆ chargez_given

◆ chargez_help

◆ ckcorr_given

◆ ckcorr_help

◆ clusterShape_group_counter

◆ cn_given

◆ cn_help

◆ cohZ_given

◆ cohZ_help

◆ columnAtoms_arg

◆ columnAtoms_given

◆ columnAtoms_help

◆ columnAtoms_orig

◆ com_given

◆ com_help

◆ component_arg

◆ component_given

◆ component_help

◆ component_orig

◆ comsele_arg