- Generated on for OpenMD by
1.17.0
|
OpenMD 3.2
Molecular Dynamics in the Open
|
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 | 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 | 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 | tcorr_arg |
| Correlation time (length of each window) in fs (default='100000.0'). | |
| char * | tcorr_orig |
| Correlation time (length of each window) in fs original value given at command line. | |
| const char * | tcorr_help |
| Correlation time (length of each window) in fs help description. | |
| int | nstart_arg |
| Number of frames to skip at start of trajectory (default='0'). | |
| char * | nstart_orig |
| Number of frames to skip at start of trajectory original value given at command line. | |
| const char * | nstart_help |
| Number of frames to skip at start of trajectory help description. | |
| double | tsep_arg |
| Separation time between correlation windows (0 = no gap) (default='0.0'). | |
| char * | tsep_orig |
| Separation time between correlation windows (0 = no gap) original value given at command line. | |
| const char * | tsep_help |
| Separation time between correlation windows (0 = no gap) help description. | |
| double | t_apod_arg |
| Apodization time (fs) [filters tcorr with exp(-t/t_apod) in Fourier-transformed spectroscopic functions] (default='0.0'). | |
| char * | t_apod_orig |
| Apodization time (fs) [filters tcorr with exp(-t/t_apod) in Fourier-transformed spectroscopic functions] original value given at command line. | |
| const char * | t_apod_help |
| Apodization time (fs) [filters tcorr with exp(-t/t_apod) in Fourier-transformed spectroscopic functions] help description. | |
| double | t_zerofill_arg |
| Zero-fill time (fs) [Pads time correlation functions with zeros from tcorr -> t_zerofill in Fourier-transformed spectroscopic functions] (default='0.0'). | |
| char * | t_zerofill_orig |
| Zero-fill time (fs) [Pads time correlation functions with zeros from tcorr -> t_zerofill in Fourier-transformed spectroscopic functions] original value given at command line. | |
| const char * | t_zerofill_help |
| Zero-fill time (fs) [Pads time correlation functions with zeros from tcorr -> t_zerofill in Fourier-transformed spectroscopic functions] 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. | |
| enum enum_selectionMode | selectionMode_arg |
| How to treat objects which leave a dynamic selection and then return later (default = survival) (default='survival'). | |
| char * | selectionMode_orig |
| How to treat objects which leave a dynamic selection and then return later (default = survival) original value given at command line. | |
| const char * | selectionMode_help |
| How to treat objects which leave a dynamic selection and then return later (default = survival) help description. | |
| char * | sfgPolarization_arg |
| SFG polarization combination: ssp, ppp, sps (default='ssp'). | |
| char * | sfgPolarization_orig |
| SFG polarization combination: ssp, ppp, sps original value given at command line. | |
| const char * | sfgPolarization_help |
| SFG polarization combination: ssp, ppp, sps help description. | |
| double | fermiCoupling_arg |
| Fermi coupling [cm-1] for stretch-bend coupling in SFG spectra (default='25'). | |
| char * | fermiCoupling_orig |
| Fermi coupling [cm-1] for stretch-bend coupling in SFG spectra original value given at command line. | |
| const char * | fermiCoupling_help |
| Fermi coupling [cm-1] for stretch-bend coupling in SFG spectra 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. | |
| const char * | sfg_help |
| SFG susceptibility spectrum (exciton model) - use molecular selections 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 | seleoffset_given |
| Whether seleoffset 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 | tcorr_given |
| Whether tcorr was given. | |
| unsigned int | nstart_given |
| Whether nstart was given. | |
| unsigned int | tsep_given |
| Whether tsep was given. | |
| unsigned int | t_apod_given |
| Whether t_apod was given. | |
| unsigned int | t_zerofill_given |
| Whether t_zerofill 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 | selectionMode_given |
| Whether selectionMode was given. | |
| unsigned int | sfgPolarization_given |
| Whether sfgPolarization was given. | |
| unsigned int | fermiCoupling_given |
| Whether fermiCoupling 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. | |
| unsigned int | sfg_given |
| Whether sfg 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. | |
| double | voxelSize_arg |
| voxel size for coarse graining (Angstroms) (default='2.0'). | |
| char * | voxelSize_orig |
| voxel size for coarse graining (Angstroms) original value given at command line. | |
| const char * | voxelSize_help |
| voxel size for coarse graining (Angstroms) help description. | |
| double | gaussWidth_arg |
| Gaussian width for coarse graining (Angstroms) (default='3.0'). | |
| char * | gaussWidth_orig |
| Gaussian width for coarse graining (Angstroms) original value given at command line. | |
| const char * | gaussWidth_help |
| Gaussian width for coarse graining (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 * | deltaCount_help |
| difference in counts between two selections help description. | |
| const char * | fluxOut_help |
| number flux out of a selection 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. | |
| const char * | qsurf_help |
| tetrahedrality Q field as OpenDX volumetric files 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 | voxelSize_given |
| Whether voxelSize was given. | |
| unsigned int | gaussWidth_given |
| Whether gaussWidth was given. | |
| unsigned int | com_given |
| Whether com was given. | |
| unsigned int | comvel_given |
| Whether comvel was given. | |
| unsigned int | deltaCount_given |
| Whether deltaCount was given. | |
| unsigned int | fluxOut_given |
| Whether fluxOut 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. | |
| unsigned int | qsurf_given |
| Whether qsurf 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 | 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. | |
| int | seleoffset3_arg |
| global index offset for a fourth object (used to define a vector between sites in molecule). | |
| char * | seleoffset3_orig |
| global index offset for a fourth object (used to define a vector between sites in molecule) original value given at command line. | |
| const char * | seleoffset3_help |
| global index offset for a fourth 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. | |
| 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. | |
| double | lorentzianWidth_arg |
| Lorentzian half-width [cm-1] applied to eigenstates in SFG spectra (default='5'). | |
| char * | lorentzianWidth_orig |
| Lorentzian half-width [cm-1] applied to eigenstates in SFG spectra original value given at command line. | |
| const char * | lorentzianWidth_help |
| Lorentzian half-width [cm-1] applied to eigenstates in SFG spectra 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_rangle_help |
| spatially-resolved tetrahedrality order parameter Qk(r,cos(theta)) 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 * | OHfreqmap_help |
| electrostatic field to OH frequency distribution based on the Corcelli frequency map 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 | seleoffset2_given |
| Whether seleoffset2 was given. | |
| unsigned int | seleoffset3_given |
| Whether seleoffset3 was given. | |
| unsigned int | molname_given |
| Whether molname was given. | |
| unsigned int | begin_given |
| Whether begin 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 | lorentzianWidth_given |
| Whether lorentzianWidth 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_rangle_given |
| Whether tet_param_rangle 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 | OHfreqmap_given |
| Whether OHfreqmap 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. | |
Where the command line options are stored.
Definition at line 38 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::angle_r_given |
Whether angle_r was given.
Definition at line 330 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::angle_r_help |
angle of R help description.
Definition at line 208 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::atom_name_arg |
name of atom for with average charge to be generated.
Definition at line 169 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::atom_name_given |
Whether atom_name was given.
Definition at line 299 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::atom_name_help |
name of atom for with average charge to be generated help description.
Definition at line 171 of file StaticPropsCmd.hpp.
| 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 170 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::bad_given |
Whether bad was given.
Definition at line 306 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::bad_help |
N(theta) bond angle density within (–rcut must be specified) help description.
Definition at line 184 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::basetype_flag |
Convert to base atom type (default=off).
Definition at line 79 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::basetype_given |
Whether basetype was given.
Definition at line 110 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::basetype_help |
Convert to base atom type help description.
Definition at line 80 of file Dump2XYZCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::beadSize_given |
Whether beadSize was given.
Definition at line 82 of file HydroCmd.hpp.
| 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.
| 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.
| int gengetopt_args_info::begin_arg |
begin internal index.
Definition at line 128 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::begin_given |
Whether begin was given.
Definition at line 285 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::begin_help |
begin internal index help description.
Definition at line 130 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::begin_orig |
begin internal index original value given at command line.
Definition at line 129 of file StaticPropsCmd.hpp.
| double gengetopt_args_info::binWidth_arg |
width of radial bins in angstroms (default='1.0').
Definition at line 71 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::binWidth_given |
Whether binWidth was given.
Definition at line 266 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::binWidth_help |
width of radial bins in angstroms help description.
Definition at line 73 of file StaticPropsCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::bo_given |
Whether bo was given.
Definition at line 303 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::bo_help |
bond order parameter (–rcut must be specified) help description.
Definition at line 181 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::bondcorr_given |
Whether bondcorr was given.
Definition at line 213 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::bondcorr_help |
Bond extension correlation function help description.
Definition at line 143 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::box_flag |
Optimize box geometry before performing calculation (default=off).
Definition at line 45 of file elasticConstantsCmd.hpp.
| unsigned int gengetopt_args_info::box_given |
Whether box was given.
Definition at line 63 of file elasticConstantsCmd.hpp.
| const char* gengetopt_args_info::box_help |
Optimize box geometry before performing calculation help description.
Definition at line 46 of file elasticConstantsCmd.hpp.
| double gengetopt_args_info::bufferLength_arg |
Buffer length in angstroms.
Definition at line 80 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::bufferLength_given |
Whether bufferLength was given.
Definition at line 116 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::bufferLength_help |
Buffer length in angstroms help description.
Definition at line 82 of file SequentialPropsCmd.hpp.
| char* gengetopt_args_info::bufferLength_orig |
Buffer length in angstroms original value given at command line.
Definition at line 81 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::ca1_given |
Whether ca1 was given.
Definition at line 124 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::ca1_help |
contact angle of selection (using center of mass) help description.
Definition at line 96 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::ca2_given |
Whether ca2 was given.
Definition at line 125 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::ca2_help |
contact angle of selection (using density profile) help description.
Definition at line 97 of file SequentialPropsCmd.hpp.
| double gengetopt_args_info::centroidX_arg |
Location of droplet centroid in x.
Definition at line 65 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::centroidX_given |
Whether centroidX was given.
Definition at line 111 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::centroidX_help |
Location of droplet centroid in x help description.
Definition at line 67 of file SequentialPropsCmd.hpp.
| char* gengetopt_args_info::centroidX_orig |
Location of droplet centroid in x original value given at command line.
Definition at line 66 of file SequentialPropsCmd.hpp.
| double gengetopt_args_info::centroidY_arg |
Location of droplet centroid in y.
Definition at line 68 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::centroidY_given |
Whether centroidY was given.
Definition at line 112 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::centroidY_help |
Location of droplet centroid in y help description.
Definition at line 70 of file SequentialPropsCmd.hpp.
| char* gengetopt_args_info::centroidY_orig |
Location of droplet centroid in y original value given at command line.
Definition at line 69 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::charge_density_z_given |
Whether charge_density_z was given.
Definition at line 371 of file StaticPropsCmd.hpp.
| 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 249 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::charger_given |
Whether charger was given.
Definition at line 366 of file StaticPropsCmd.hpp.
| 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 244 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::charges_flag |
Print charges in xyz file (default=off).
Definition at line 87 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::charges_given |
Whether charges was given.
Definition at line 114 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::charges_help |
Print charges in xyz file help description.
Definition at line 88 of file Dump2XYZCmd.hpp.
| double gengetopt_args_info::chargetemperature_arg |
charge temperature (K).
Definition at line 54 of file thermalizerCmd.hpp.
| unsigned int gengetopt_args_info::chargetemperature_given |
Whether chargetemperature was given.
Definition at line 64 of file thermalizerCmd.hpp.
| const char* gengetopt_args_info::chargetemperature_help |
charge temperature (K) help description.
Definition at line 56 of file thermalizerCmd.hpp.
| char* gengetopt_args_info::chargetemperature_orig |
charge temperature (K) original value given at command line.
Definition at line 55 of file thermalizerCmd.hpp.
| unsigned int gengetopt_args_info::chargez_given |
Whether chargez was given.
Definition at line 365 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::chargez_help |
computes the charge distribution along selected axis and selected atom help description.
Definition at line 243 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::ckcorr_given |
Whether ckcorr was given.
Definition at line 221 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::ckcorr_help |
Charge - Kinetic energy cross correlation function help description.
Definition at line 151 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::clusterShape_group_counter |
Counter for group clusterShape.
Definition at line 94 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::cn_given |
Whether cn was given.
Definition at line 347 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::cn_help |
Coordination Number Distribution help description.
Definition at line 225 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::cohZ_given |
Whether cohZ was given.
Definition at line 207 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::cohZ_help |
Lengendre correlation function for OH bond vectors binned by Z help description.
Definition at line 137 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::columnAtoms_arg |
Number of atoms along central column (Decahedron only).
Definition at line 54 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::columnAtoms_given |
Whether columnAtoms was given.
Definition at line 80 of file icosahedralBuilderCmd.hpp.
| 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.
| 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.
| unsigned int gengetopt_args_info::com_given |
Whether com was given.
Definition at line 120 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::com_help |
selection center of mass help description.
Definition at line 92 of file SequentialPropsCmd.hpp.
| enum enum_component gengetopt_args_info::component_arg |
component of momentum for the momemtum distribution (default = z axis) (default='z').
Definition at line 152 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::component_given |
Whether component was given.
Definition at line 293 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::component_help |
component of momentum for the momemtum distribution (default = z axis) help description.
Definition at line 154 of file StaticPropsCmd.hpp.
| 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 153 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::comsele_arg |
select stunt doubles for center-of-mass reference point.
Definition at line 113 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::comsele_given |
Whether comsele was given.
Definition at line 280 of file StaticPropsCmd.hpp.
| 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.
| 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.
| unsigned int gengetopt_args_info::comvel_given |
Whether comvel was given.
Definition at line 121 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::comvel_help |
selection center of mass velocity help description.
Definition at line 93 of file SequentialPropsCmd.hpp.
| int gengetopt_args_info::correlation_function_group_counter |
Counter for group correlation_function.
Definition at line 237 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::count_given |
Whether count was given.
Definition at line 307 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::count_help |
count of objects matching selection criteria (and associated statistics) help description.
Definition at line 185 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::countz_given |
Whether countz was given.
Definition at line 372 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::countz_help |
computes the number of selected atoms along selected axis help description.
Definition at line 250 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::cscorr_given |
Whether cscorr was given.
Definition at line 222 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::cscorr_help |
Charge - Orientation order parameter (Cos\theta) cross correlation function help description.
Definition at line 152 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::cuboctahedron_given |
Whether cuboctahedron was given.
Definition at line 89 of file icosahedralBuilderCmd.hpp.
| const char* gengetopt_args_info::cuboctahedron_help |
Create a regular Cuboctahedron (requires lattice) help description.
Definition at line 71 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::current_density_given |
Whether current_density was given.
Definition at line 364 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::current_density_help |
computes the current density for the selected atom help description.
Definition at line 242 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::current_given |
Whether current was given.
Definition at line 228 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::current_help |
Current density auto correlation function help description.
Definition at line 158 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::dcorr_given |
Whether dcorr was given.
Definition at line 204 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::dcorr_help |
dipole correlation function help description.
Definition at line 134 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::ddisp_given |
Whether ddisp was given.
Definition at line 230 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::ddisp_help |
Collective Dipole displacement function (Helfand moment of Current Density) help description.
Definition at line 160 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::deca_given |
Whether deca was given.
Definition at line 85 of file icosahedralBuilderCmd.hpp.
| const char* gengetopt_args_info::deca_help |
Create a regualar Decahedral cluster help description.
Definition at line 67 of file icosahedralBuilderCmd.hpp.
| double gengetopt_args_info::delta_arg |
size of relative volume changes for strains.
Definition at line 56 of file elasticConstantsCmd.hpp.
| unsigned int gengetopt_args_info::delta_given |
Whether delta was given.
Definition at line 66 of file elasticConstantsCmd.hpp.
| const char* gengetopt_args_info::delta_help |
size of relative volume changes for strains help description.
Definition at line 58 of file elasticConstantsCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::deltaCount_given |
Whether deltaCount was given.
Definition at line 122 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::deltaCount_help |
difference in counts between two selections help description.
Definition at line 94 of file SequentialPropsCmd.hpp.
| double gengetopt_args_info::density_arg |
density (g/cm^3).
Definition at line 45 of file randomBuilderCmd.hpp.
| unsigned int gengetopt_args_info::density_given |
Whether density was given.
Definition at line 69 of file randomBuilderCmd.hpp.
| 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.
| char * gengetopt_args_info::density_orig |
density (g/cm^3) original value given at command line.
Definition at line 46 of file randomBuilderCmd.hpp.
| unsigned int gengetopt_args_info::densityfield_given |
Whether densityfield was given.
Definition at line 359 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::densityfield_help |
computes an average density field help description.
Definition at line 237 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::dipole_orientation_given |
Whether dipole_orientation was given.
Definition at line 374 of file StaticPropsCmd.hpp.
| 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 252 of file StaticPropsCmd.hpp.
| 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 105 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::dipoleX_given |
Whether dipoleX was given.
Definition at line 187 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::dipoleX_help |
X-component of the dipole with respect to body frame help description.
Definition at line 107 of file DynamicPropsCmd.hpp.
| 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 106 of file DynamicPropsCmd.hpp.
| 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 108 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::dipoleY_given |
Whether dipoleY was given.
Definition at line 188 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::dipoleY_help |
Y-component of the dipole with respect to body frame help description.
Definition at line 110 of file DynamicPropsCmd.hpp.
| 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 109 of file DynamicPropsCmd.hpp.
| 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 111 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::dipoleZ_given |
Whether dipoleZ was given.
Definition at line 189 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::dipoleZ_help |
Z-component of the dipole with respect to body frame help description.
Definition at line 113 of file DynamicPropsCmd.hpp.
| 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 112 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::disp_given |
Whether disp was given.
Definition at line 226 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::disp_help |
Displacement correlation function help description.
Definition at line 156 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::dispZ_given |
Whether dispZ was given.
Definition at line 227 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::dispZ_help |
Displacement correlation function binned by Z help description.
Definition at line 157 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::drcorr_given |
Whether drcorr was given.
Definition at line 211 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::drcorr_help |
Directional msd for particles with unit vectors help description.
Definition at line 141 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::dropletR_arg |
Droplet radius in angstroms.
Definition at line 74 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::dropletR_given |
Whether dropletR was given.
Definition at line 114 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::dropletR_help |
Droplet radius in angstroms help description.
Definition at line 76 of file SequentialPropsCmd.hpp.
| char* gengetopt_args_info::dropletR_orig |
Droplet radius in angstroms original value given at command line.
Definition at line 75 of file SequentialPropsCmd.hpp.
| double gengetopt_args_info::dz_arg |
slab width (dz).
Definition at line 89 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::dz_given |
Whether dz was given.
Definition at line 272 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::dz_help |
slab width (dz) help description.
Definition at line 91 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::dz_orig |
slab width (dz) original value given at command line.
Definition at line 90 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::eam_density_given |
Whether eam_density was given.
Definition at line 362 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::eam_density_help |
computes an average eam density profile of the selected atom help description.
Definition at line 240 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::efield_flag |
Print electric field vector in xyz file (default=off).
Definition at line 89 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::efield_given |
Whether efield was given.
Definition at line 115 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::efield_help |
Print electric field vector in xyz file help description.
Definition at line 90 of file Dump2XYZCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::elements_given |
Whether elements was given.
Definition at line 83 of file HydroCmd.hpp.
| 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.
| int gengetopt_args_info::ellipsoid_flag |
Build an Ellipsoid instead of a rod.
(default=off).
Definition at line 54 of file nanorodBuilderCmd.hpp.
| unsigned int gengetopt_args_info::ellipsoid_given |
Whether ellipsoid was given.
Definition at line 82 of file nanorodBuilderCmd.hpp.
| const char* gengetopt_args_info::ellipsoid_help |
Build an Ellipsoid instead of a rod.
help description.
Definition at line 55 of file nanorodBuilderCmd.hpp.
| double gengetopt_args_info::end_arg |
ending affine scale (default='1.2').
Definition at line 51 of file equationofstateCmd.hpp.
| int gengetopt_args_info::end_arg |
end internal index.
Definition at line 131 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::end_given |
Whether end was given.
Definition at line 63 of file equationofstateCmd.hpp.
| 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.
| 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.
| double gengetopt_args_info::energy_arg |
energy (kcal/mol).
Definition at line 51 of file thermalizerCmd.hpp.
| unsigned int gengetopt_args_info::energy_given |
Whether energy was given.
Definition at line 63 of file thermalizerCmd.hpp.
| const char* gengetopt_args_info::energy_help |
energy (kcal/mol) help description.
Definition at line 53 of file thermalizerCmd.hpp.
| char* gengetopt_args_info::energy_orig |
energy (kcal/mol) original value given at command line.
Definition at line 52 of file thermalizerCmd.hpp.
| unsigned int gengetopt_args_info::facorr_given |
Whether facorr was given.
Definition at line 223 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::facorr_help |
Force - Force auto correlation function help description.
Definition at line 153 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::fermiCoupling_arg |
Fermi coupling [cm-1] for stretch-bend coupling in SFG spectra (default='25').
Definition at line 120 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::fermiCoupling_given |
Whether fermiCoupling was given.
Definition at line 192 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::fermiCoupling_help |
Fermi coupling [cm-1] for stretch-bend coupling in SFG spectra help description.
Definition at line 122 of file DynamicPropsCmd.hpp.
| char * gengetopt_args_info::fermiCoupling_orig |
Fermi coupling [cm-1] for stretch-bend coupling in SFG spectra original value given at command line.
Definition at line 121 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::fluxOut_given |
Whether fluxOut was given.
Definition at line 123 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::fluxOut_help |
number flux out of a selection help description.
Definition at line 95 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::for_given |
Whether for was given.
Definition at line 305 of file StaticPropsCmd.hpp.
| 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 183 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::forces_flag |
Print forces xyz file (default=off).
Definition at line 83 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::forces_given |
Whether forces was given.
Definition at line 112 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::forces_help |
Print forces xyz file help description.
Definition at line 84 of file Dump2XYZCmd.hpp.
| int gengetopt_args_info::frame_arg |
print every n frame (default='1').
Definition at line 48 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::frame_given |
Whether frame was given.
Definition at line 98 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::frame_help |
print every n frame help description.
Definition at line 50 of file Dump2XYZCmd.hpp.
| 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().
| unsigned int gengetopt_args_info::freqfluccorr_given |
Whether freqfluccorr was given.
Definition at line 214 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::freqfluccorr_help |
Frequency Fluctuation correlation function help description.
Definition at line 144 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::ftcorr_given |
Whether ftcorr was given.
Definition at line 220 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::ftcorr_help |
Force - Torque cross correlation function help description.
Definition at line 150 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::gaussWidth_arg |
Gaussian width for coarse graining (Angstroms) (default='3.0').
Gaussian width (angstroms).
Definition at line 89 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::gaussWidth_given |
Whether gaussWidth was given.
Definition at line 119 of file SequentialPropsCmd.hpp.
| const char * gengetopt_args_info::gaussWidth_help |
Gaussian width for coarse graining (Angstroms) help description.
Gaussian width (angstroms) help description.
Definition at line 91 of file SequentialPropsCmd.hpp.
| char * gengetopt_args_info::gaussWidth_orig |
Gaussian width for coarse graining (Angstroms) original value given at command line.
Gaussian width (angstroms) original value given at command line.
Definition at line 90 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::gcn_given |
Whether gcn was given.
Definition at line 126 of file SequentialPropsCmd.hpp.
| const char * gengetopt_args_info::gcn_help |
Generalized Coordinate Number help description.
Generalized Coordination Number Distribution help description.
Definition at line 98 of file SequentialPropsCmd.hpp.
| int gengetopt_args_info::gen_xyz_flag |
generates xyz file (default=off).
Definition at line 167 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::gen_xyz_given |
Whether gen_xyz was given.
Definition at line 298 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::gen_xyz_help |
generates xyz file help description.
Definition at line 168 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::globalID_flag |
Print global ID in xyz file (default=off).
Definition at line 91 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::globalID_given |
Whether globalID was given.
Definition at line 116 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::globalID_help |
Print global ID in xyz file help description.
Definition at line 92 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::gofr_given |
Whether gofr was given.
Definition at line 309 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::gofr_help |
g(r) help description.
Definition at line 187 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::gofz_given |
Whether gofz was given.
Definition at line 310 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::gofz_help |
g(z) help description.
Definition at line 188 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::gxyz_given |
Whether gxyz was given.
Definition at line 316 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::gxyz_help |
g(x, y, z) help description.
Definition at line 194 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::hbond_given |
Whether hbond was given.
Definition at line 350 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::hbond_help |
Hydrogen Bonding statistics using geometric criteria (rcut and thetacut must be specified) help description.
Definition at line 228 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::hbondr_given |
Whether hbondr was given.
Definition at line 353 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::hbondr_help |
Hydrogen Bonding density binned by r (rcut and thetacut must be specified) help description.
Definition at line 231 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::hbondrvol_given |
Whether hbondrvol was given.
Definition at line 354 of file StaticPropsCmd.hpp.
| 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 232 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::hbondz_given |
Whether hbondz was given.
Definition at line 351 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::hbondz_help |
Hydrogen Bonding density binned by z (rcut and thetacut must be specified) help description.
Definition at line 229 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::hbondzvol_given |
Whether hbondzvol was given.
Definition at line 352 of file StaticPropsCmd.hpp.
| 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 230 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::help_given |
Whether help was given.
Definition at line 94 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char * gengetopt_args_info::help_help |
Print help and exit help description.
Definition at line 40 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::hullvol_given |
Whether hullvol was given.
Definition at line 331 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::hullvol_help |
hull volume of nanoparticle help description.
Definition at line 209 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::hxy_given |
Whether hxy was given.
Definition at line 328 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::hxy_help |
hxy help description.
Definition at line 206 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::ico_given |
Whether ico was given.
Definition at line 84 of file icosahedralBuilderCmd.hpp.
| const char* gengetopt_args_info::ico_help |
Create an Icosahedral cluster help description.
Definition at line 66 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::ino_given |
Whether ino was given.
Definition at line 86 of file icosahedralBuilderCmd.hpp.
| const char* gengetopt_args_info::ino_help |
Create an Ino Decahedral cluster help description.
Definition at line 68 of file icosahedralBuilderCmd.hpp.
| 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.
| int gengetopt_args_info::input_file_group_counter |
Counter for group input_file.
Definition at line 89 of file HydroCmd.hpp.
| unsigned int gengetopt_args_info::input_given |
Whether input was given.
Definition at line 96 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| 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.
| 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().
| 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().
| 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().
| unsigned int gengetopt_args_info::ior_given |
Whether ior was given.
Definition at line 304 of file StaticPropsCmd.hpp.
| 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 182 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::jumptime_given |
Whether jumptime was given.
Definition at line 215 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::jumptime_help |
Hydrogen bond jump time correlation function help description.
Definition at line 145 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::jumptimeR_given |
Whether jumptimeR was given.
Definition at line 217 of file DynamicPropsCmd.hpp.
| 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 147 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::jumptimeZ_given |
Whether jumptimeZ was given.
Definition at line 216 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::jumptimeZ_help |
Hydrogen bond jump time correlation function binned by Z help description.
Definition at line 146 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::kirkwood_buff_given |
Whether kirkwood_buff was given.
Definition at line 318 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::kirkwood_buff_help |
Kirkwood-Buff integrals (–sele1 and –sele2 must both be specified) help description.
Definition at line 196 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::kirkwood_given |
Whether kirkwood was given.
Definition at line 357 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::kirkwood_help |
distance-dependent Kirkwood factor help description.
Definition at line 235 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::kirkwoodQ_given |
Whether kirkwoodQ was given.
Definition at line 358 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::kirkwoodQ_help |
distance-dependent Kirkwood factor for quadrupoles help description.
Definition at line 236 of file StaticPropsCmd.hpp.
| char * gengetopt_args_info::lattice_arg |
Lattice Type.
Definition at line 51 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::lattice_given |
Whether lattice was given.
Definition at line 79 of file icosahedralBuilderCmd.hpp.
| const char * gengetopt_args_info::lattice_help |
Lattice Type help description.
Definition at line 53 of file icosahedralBuilderCmd.hpp.
| char * gengetopt_args_info::lattice_orig |
Lattice Type original value given at command line.
Definition at line 52 of file icosahedralBuilderCmd.hpp.
| double gengetopt_args_info::latticeConstant_arg |
Lattice spacing in Angstroms for cubic lattice.
Definition at line 48 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::latticeConstant_given |
Whether latticeConstant was given.
Definition at line 78 of file icosahedralBuilderCmd.hpp.
| const char * gengetopt_args_info::latticeConstant_help |
Lattice spacing in Angstroms for cubic lattice.
help description.
Definition at line 50 of file icosahedralBuilderCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::lcorr_given |
Whether lcorr was given.
Definition at line 205 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::lcorr_help |
Lengendre correlation function help description.
Definition at line 135 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::lcorrZ_given |
Whether lcorrZ was given.
Definition at line 206 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::lcorrZ_help |
Lengendre correlation function binned by Z help description.
Definition at line 136 of file DynamicPropsCmd.hpp.
| 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 102 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::length_given |
Whether length was given.
Definition at line 186 of file DynamicPropsCmd.hpp.
| 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 104 of file DynamicPropsCmd.hpp.
| 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 103 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::lorentzianWidth_arg |
Lorentzian half-width [cm-1] applied to eigenstates in SFG spectra (default='5').
Definition at line 175 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::lorentzianWidth_given |
Whether lorentzianWidth was given.
Definition at line 301 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::lorentzianWidth_help |
Lorentzian half-width [cm-1] applied to eigenstates in SFG spectra help description.
Definition at line 177 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::lorentzianWidth_orig |
Lorentzian half-width [cm-1] applied to eigenstates in SFG spectra original value given at command line.
Definition at line 176 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::marks_given |
Whether marks was given.
Definition at line 87 of file icosahedralBuilderCmd.hpp.
| const char* gengetopt_args_info::marks_help |
Create a Marks Decahedral cluster help description.
Definition at line 69 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::massdensityr_given |
Whether massdensityr was given.
Definition at line 368 of file StaticPropsCmd.hpp.
| 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 246 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::massdensityz_given |
Whether massdensityz was given.
Definition at line 367 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::massdensityz_help |
computes the mass density of the selection along selected axis help description.
Definition at line 245 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::mcount_given |
Whether mcount was given.
Definition at line 308 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::mcount_help |
count of molecules matching selection criteria (and associated statistics) help description.
Definition at line 186 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::meandisp_given |
Whether meandisp was given.
Definition at line 232 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::meandisp_help |
mean displacement help description.
Definition at line 162 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::method_arg |
Calculation Method.
Definition at line 47 of file elasticConstantsCmd.hpp.
| unsigned int gengetopt_args_info::method_given |
Whether method was given.
Definition at line 64 of file elasticConstantsCmd.hpp.
| const char* gengetopt_args_info::method_help |
Calculation Method help description.
Definition at line 49 of file elasticConstantsCmd.hpp.
| char* gengetopt_args_info::method_orig |
Calculation Method original value given at command line.
Definition at line 48 of file elasticConstantsCmd.hpp.
| enum enum_model gengetopt_args_info::model_arg |
hydrodynamics model.
Definition at line 59 of file HydroCmd.hpp.
| unsigned int gengetopt_args_info::model_given |
Whether model was given.
Definition at line 81 of file HydroCmd.hpp.
| const char* gengetopt_args_info::model_help |
hydrodynamics model help description.
Definition at line 61 of file HydroCmd.hpp.
| char* gengetopt_args_info::model_orig |
hydrodynamics model original value given at command line.
Definition at line 60 of file HydroCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::molFraction_given |
Whether molFraction was given.
Definition at line 77 of file nanoparticleBuilderCmd.hpp.
| 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.
| 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.
| 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.
| 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.
| char* gengetopt_args_info::molname_arg |
molecule name.
Definition at line 125 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::molname_given |
Whether molname was given.
Definition at line 284 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::molname_help |
molecule name help description.
Definition at line 127 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::molname_orig |
molecule name original value given at command line.
Definition at line 126 of file StaticPropsCmd.hpp.
| enum enum_momentum gengetopt_args_info::momentum_arg |
Type of momentum whose distribtution is required (default = Liner Momentum) (default='P').
Definition at line 149 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::momentum_distribution_given |
Whether momentum_distribution was given.
Definition at line 373 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::momentum_distribution_help |
computes the momentum distribution for the selected atom help description.
Definition at line 251 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::momentum_given |
Whether momentum was given.
Definition at line 292 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::momentum_help |
Type of momentum whose distribtution is required (default = Liner Momentum) help description.
Definition at line 151 of file StaticPropsCmd.hpp.
| 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 150 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::msms_arg |
filename root for MSMS .vert and .face files.
Definition at line 53 of file HydroCmd.hpp.
| unsigned int gengetopt_args_info::msms_given |
Whether msms was given.
Definition at line 79 of file HydroCmd.hpp.
| 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.
| 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.
| unsigned int gengetopt_args_info::multipole_given |
Whether multipole was given.
Definition at line 345 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::multipole_help |
average multipole moments contained within cutoff spheres as a function of radius help description.
Definition at line 223 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::nanglebins_arg |
number of bins for cos(angle) (default='50').
Definition at line 74 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::nanglebins_given |
Whether nanglebins was given.
Definition at line 267 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::nanglebins_help |
number of bins for cos(angle) help description.
Definition at line 76 of file StaticPropsCmd.hpp.
| 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.
| int gengetopt_args_info::nbins_arg |
Number of bins (default='100').
number of bins (general purpose) (default='100').
Definition at line 66 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::nbins_given |
Whether nbins was given.
Definition at line 174 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::nbins_help |
Number of bins help description.
number of bins (general purpose) help description.
Definition at line 68 of file DynamicPropsCmd.hpp.
| 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 67 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::nbins_x_arg |
number of bins in x axis (default='100').
Definition at line 59 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::nbins_x_given |
Whether nbins_x was given.
Definition at line 262 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::nbins_x_help |
number of bins in x axis help description.
Definition at line 61 of file StaticPropsCmd.hpp.
| 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.
| int gengetopt_args_info::nbins_y_arg |
number of bins in y axis (default='100').
Definition at line 62 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::nbins_y_given |
Whether nbins_y was given.
Definition at line 263 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::nbins_y_help |
number of bins in y axis help description.
Definition at line 64 of file StaticPropsCmd.hpp.
| 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.
| int gengetopt_args_info::nbins_z_arg |
number of bins in z axis (default='100').
Definition at line 59 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::nbins_z_given |
Whether nbins_z was given.
Definition at line 109 of file SequentialPropsCmd.hpp.
| const char * gengetopt_args_info::nbins_z_help |
number of bins in z axis help description.
Definition at line 61 of file SequentialPropsCmd.hpp.
| char * gengetopt_args_info::nbins_z_orig |
number of bins in z axis original value given at command line.
Definition at line 60 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::net_charge_given |
Whether net_charge was given.
Definition at line 363 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::net_charge_help |
computes an average charge profile of the selected atom help description.
Definition at line 241 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::nitrile_given |
Whether nitrile was given.
Definition at line 343 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::nitrile_help |
electrostatic potential to frequency map based on the Cho nitrile fits help description.
Definition at line 221 of file StaticPropsCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::noCOM_given |
Whether noCOM was given.
Definition at line 98 of file omd2omdCmd.hpp.
| 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.
| int gengetopt_args_info::noWrap_flag |
do not rewrap coordinates into the box (default=off).
Definition at line 78 of file omd2omdCmd.hpp.
| unsigned int gengetopt_args_info::noWrap_given |
Whether noWrap was given.
Definition at line 97 of file omd2omdCmd.hpp.
| const char* gengetopt_args_info::noWrap_help |
do not rewrap coordinates into the box help description.
Definition at line 79 of file omd2omdCmd.hpp.
| int gengetopt_args_info::npoints_arg |
number of points for fitting stress-strain relationship (default='25').
Definition at line 50 of file elasticConstantsCmd.hpp.
| unsigned int gengetopt_args_info::npoints_given |
Whether npoints was given.
Definition at line 65 of file elasticConstantsCmd.hpp.
| 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.
| 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.
| 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.
| unsigned int gengetopt_args_info::nrbins_given |
Whether nrbins was given.
Definition at line 265 of file StaticPropsCmd.hpp.
| 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.
| 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.
| int gengetopt_args_info::nstart_arg |
Number of frames to skip at start of trajectory (default='0').
Definition at line 75 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::nstart_given |
Whether nstart was given.
Definition at line 177 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::nstart_help |
Number of frames to skip at start of trajectory help description.
Definition at line 77 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::nstart_orig |
Number of frames to skip at start of trajectory original value given at command line.
Definition at line 76 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::number_arg |
number of data points (default='50').
Definition at line 54 of file equationofstateCmd.hpp.
| unsigned int gengetopt_args_info::number_given |
Whether number was given.
Definition at line 64 of file equationofstateCmd.hpp.
| const char* gengetopt_args_info::number_help |
number of data points help description.
Definition at line 56 of file equationofstateCmd.hpp.
| char* gengetopt_args_info::number_orig |
number of data points original value given at command line.
Definition at line 55 of file equationofstateCmd.hpp.
| unsigned int gengetopt_args_info::numberr_given |
Whether numberr was given.
Definition at line 370 of file StaticPropsCmd.hpp.
| 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 248 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::numberz_given |
Whether numberz was given.
Definition at line 369 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::numberz_help |
computes the number density along selected axis and selected molcule help description.
Definition at line 247 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::nx_arg |
number of unit cells in x.
Definition at line 48 of file randomBuilderCmd.hpp.
| unsigned int gengetopt_args_info::nx_given |
Whether nx was given.
Definition at line 70 of file randomBuilderCmd.hpp.
| const char * gengetopt_args_info::nx_help |
number of unit cells in x help description.
Definition at line 50 of file randomBuilderCmd.hpp.
| 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.
| int gengetopt_args_info::ny_arg |
number of unit cells in y.
Definition at line 51 of file randomBuilderCmd.hpp.
| unsigned int gengetopt_args_info::ny_given |
Whether ny was given.
Definition at line 71 of file randomBuilderCmd.hpp.
| const char * gengetopt_args_info::ny_help |
number of unit cells in y help description.
Definition at line 53 of file randomBuilderCmd.hpp.
| 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.
| int gengetopt_args_info::nz_arg |
number of unit cells in z.
Definition at line 54 of file randomBuilderCmd.hpp.
| unsigned int gengetopt_args_info::nz_given |
Whether nz was given.
Definition at line 72 of file randomBuilderCmd.hpp.
| const char * gengetopt_args_info::nz_help |
number of unit cells in z help description.
Definition at line 56 of file randomBuilderCmd.hpp.
| 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.
| int gengetopt_args_info::nzbins_arg |
Number of Z bins (default='100').
Definition at line 69 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::nzbins_given |
Whether nzbins was given.
Definition at line 175 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::nzbins_help |
Number of Z bins help description.
Definition at line 71 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::nzbins_orig |
Number of Z bins original value given at command line.
Definition at line 70 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::OHcut_arg |
Oxygen-Hydrogen cutoff radius (angstroms) (default='2.45').
Definition at line 96 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::OHcut_given |
Whether OHcut was given.
Definition at line 184 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::OHcut_help |
Oxygen-Hydrogen cutoff radius (angstroms) help description.
Definition at line 98 of file DynamicPropsCmd.hpp.
| char * gengetopt_args_info::OHcut_orig |
Oxygen-Hydrogen cutoff radius (angstroms) original value given at command line.
Definition at line 97 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::OHfreqmap_given |
Whether OHfreqmap was given.
Definition at line 344 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::OHfreqmap_help |
electrostatic field to OH frequency distribution based on the Corcelli frequency map help description.
Definition at line 222 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::onsager_given |
Whether onsager was given.
Definition at line 229 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::onsager_help |
Onsager coefficient correlation functions help description.
Definition at line 159 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::OOcut_arg |
Oxygen-Oxygen cutoff radius (angstroms) (default='3.5').
Definition at line 90 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::OOcut_given |
Whether OOcut was given.
Definition at line 182 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::OOcut_help |
Oxygen-Oxygen cutoff radius (angstroms) help description.
Definition at line 92 of file DynamicPropsCmd.hpp.
| char * gengetopt_args_info::OOcut_orig |
Oxygen-Oxygen cutoff radius (angstroms) original value given at command line.
Definition at line 91 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::order_arg |
Lengendre Polynomial Order.
Definition at line 63 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::order_given |
Whether order was given.
Definition at line 173 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::order_help |
Lengendre Polynomial Order help description.
Definition at line 65 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::order_orig |
Lengendre Polynomial Order original value given at command line.
Definition at line 64 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::order_prob_given |
Whether order_prob was given.
Definition at line 375 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::order_prob_help |
probability of order parameter for given selection help description.
Definition at line 253 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::originsele_arg |
select origin.
Definition at line 64 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::originsele_given |
Whether originsele was given.
Definition at line 105 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::originsele_help |
select origin help description.
Definition at line 66 of file Dump2XYZCmd.hpp.
| 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().
| 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.
| unsigned int gengetopt_args_info::output_given |
Whether output was given.
Definition at line 97 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| 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.
| 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().
| unsigned int gengetopt_args_info::p2_given |
Whether p2 was given.
Definition at line 319 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::p2_help |
p2 order parameter (–sele1 must be specified, –sele2 is optional) help description.
Definition at line 197 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::p2r_given |
Whether p2r was given.
Definition at line 320 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::p2r_help |
p2 order parameter using r as director axis help description.
Definition at line 198 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::p2z_given |
Whether p2z was given.
Definition at line 321 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::p2z_help |
p2 order parameter using z (or privilegedAxis) as director axis help description.
Definition at line 199 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::p_angle_given |
Whether p_angle was given.
Definition at line 327 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::p_angle_help |
p(cos(theta)) (–sele1 must be specified, –sele2 is optional) help description.
Definition at line 205 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::periodicBox_flag |
map to the periodic box (default=off).
Definition at line 53 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::periodicBox_given |
Whether periodicBox was given.
Definition at line 100 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::periodicBox_help |
map to the periodic box help description.
Definition at line 54 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::persistence_given |
Whether persistence was given.
Definition at line 218 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::persistence_help |
Hydrogen bond persistence correlation function help description.
Definition at line 148 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::pipe_density_given |
Whether pipe_density was given.
Definition at line 326 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::pipe_density_help |
pipe density, rho(axis1, axis2) help description.
Definition at line 204 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::pjcorr_given |
Whether pjcorr was given.
Definition at line 219 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::pjcorr_help |
Momentum - Angular Momentum cross correlation function help description.
Definition at line 149 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::potDiff_given |
Whether potDiff was given.
Definition at line 355 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::potDiff_help |
potential energy difference when charge on selection is set to zero help description.
Definition at line 233 of file StaticPropsCmd.hpp.
| enum enum_privilegedAxis2 gengetopt_args_info::privilegedAxis2_arg |
which axis is special for spatial analysis (default = x axis) (default='x').
Definition at line 146 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::privilegedAxis2_given |
Whether privilegedAxis2 was given.
Definition at line 291 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::privilegedAxis2_help |
which axis is special for spatial analysis (default = x axis) help description.
Definition at line 148 of file StaticPropsCmd.hpp.
| 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 147 of file StaticPropsCmd.hpp.
| enum enum_privilegedAxis gengetopt_args_info::privilegedAxis_arg |
which axis is special for spatial analysis (default = z axis) (default='z').
Definition at line 99 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::privilegedAxis_given |
Whether privilegedAxis was given.
Definition at line 185 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::privilegedAxis_help |
which axis is special for spatial analysis (default = z axis) help description.
Definition at line 101 of file DynamicPropsCmd.hpp.
| 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 100 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::qsurf_given |
Whether qsurf was given.
Definition at line 128 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::qsurf_help |
tetrahedrality Q field as OpenDX volumetric files help description.
Definition at line 100 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::r_omega_given |
Whether r_omega was given.
Definition at line 312 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::r_omega_help |
g(r, cos(omega)) help description.
Definition at line 190 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::r_rcorr_given |
Whether r_rcorr was given.
Definition at line 209 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::r_rcorr_help |
Radial msd help description.
Definition at line 139 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::r_theta_given |
Whether r_theta was given.
Definition at line 311 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::r_theta_help |
g(r, cos(theta)) help description.
Definition at line 189 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::r_theta_omega_given |
Whether r_theta_omega was given.
Definition at line 315 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::r_theta_omega_help |
g(r, cos(theta), cos(omega)) help description.
Definition at line 193 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::r_z_given |
Whether r_z was given.
Definition at line 313 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::r_z_help |
g(r, z) help description.
Definition at line 191 of file StaticPropsCmd.hpp.
| double gengetopt_args_info::radius_arg |
Nanoparticle radius in Angstroms.
nanoparticle radius.
Nanorod radius in Angstroms.
Definition at line 48 of file nanoparticleBuilderCmd.hpp.
| unsigned int gengetopt_args_info::radius_given |
Whether radius was given.
Definition at line 75 of file nanoparticleBuilderCmd.hpp.
| 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.
| 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.
| unsigned int gengetopt_args_info::rcorr_given |
Whether rcorr was given.
Definition at line 194 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::rcorr_help |
mean squared displacement help description.
Definition at line 124 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::rcorrZ_given |
Whether rcorrZ was given.
Definition at line 195 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::rcorrZ_help |
mean squared displacement binned by Z help description.
Definition at line 125 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::rcut_arg |
| unsigned int gengetopt_args_info::rcut_given |
Whether rcut was given.
Definition at line 181 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::rcut_help |
cutoff radius (angstroms) help description.
cutoff radius (rcut) help description.
Definition at line 89 of file DynamicPropsCmd.hpp.
| 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 88 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::referenceZ_arg |
Reference z-height of solid surface.
Definition at line 71 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::referenceZ_given |
Whether referenceZ was given.
Definition at line 113 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::referenceZ_help |
Reference z-height of solid surface help description.
Definition at line 73 of file SequentialPropsCmd.hpp.
| char* gengetopt_args_info::referenceZ_orig |
Reference z-height of solid surface original value given at command line.
Definition at line 72 of file SequentialPropsCmd.hpp.
| char * gengetopt_args_info::refsele_arg |
select reference.
select reference (use and only use with –gxyz).
Definition at line 67 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::refsele_given |
Whether refsele was given.
Definition at line 106 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| 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.
| 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().
| int gengetopt_args_info::repairMolecules_arg |
rewrap molecules around the molecular center of mass (default='1').
Definition at line 75 of file omd2omdCmd.hpp.
| unsigned int gengetopt_args_info::repairMolecules_given |
Whether repairMolecules was given.
Definition at line 96 of file omd2omdCmd.hpp.
| 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.
| 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.
| 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.
| unsigned int gengetopt_args_info::repeatX_given |
Whether repeatX was given.
Definition at line 107 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| 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.
| 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().
| 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.
| unsigned int gengetopt_args_info::repeatY_given |
Whether repeatY was given.
Definition at line 108 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| 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.
| 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().
| 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.
| unsigned int gengetopt_args_info::repeatZ_given |
Whether repeatZ was given.
Definition at line 109 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| 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.
| 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().
| unsigned int gengetopt_args_info::rho_r_given |
Whether rho_r was given.
Definition at line 329 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::rho_r_help |
rho(R) help description.
Definition at line 207 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::rigidbody_flag |
add a pseudo COM atom to rigidbody (default=off).
Definition at line 57 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::rigidbody_given |
Whether rigidbody was given.
Definition at line 102 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::rigidbody_help |
add a pseudo COM atom to rigidbody help description.
Definition at line 58 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::rnemdr_given |
Whether rnemdr was given.
Definition at line 341 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::rnemdr_help |
shell-resolved RNEMD statistics (temperature, density, angular velocity) help description.
Definition at line 219 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::rnemdrt_given |
Whether rnemdrt was given.
Definition at line 342 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::rnemdrt_help |
shell and angle-resolved RNEMD statistics (temperature, density, angular velocity) help description.
Definition at line 220 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::rnemdz_given |
Whether rnemdz was given.
Definition at line 340 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::rnemdz_help |
slab-resolved RNEMD statistics (temperature, density, velocity) help description.
Definition at line 218 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::rodlength_given |
Whether rodlength was given.
Definition at line 332 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::rodlength_help |
length of nanorod help description.
Definition at line 210 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::rotAngleDisp_given |
Whether rotAngleDisp was given.
Definition at line 231 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::rotAngleDisp_help |
Displacement correlation function for rotation angles help description.
Definition at line 161 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::rotatePhi_arg |
rotate all coordinates Euler angle Phi (default='0.0').
Definition at line 66 of file omd2omdCmd.hpp.
| unsigned int gengetopt_args_info::rotatePhi_given |
Whether rotatePhi was given.
Definition at line 93 of file omd2omdCmd.hpp.
| const char* gengetopt_args_info::rotatePhi_help |
rotate all coordinates Euler angle Phi help description.
Definition at line 68 of file omd2omdCmd.hpp.
| 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.
| double gengetopt_args_info::rotatePsi_arg |
rotate all coordinates Euler angle Psi (default='0.0').
Definition at line 72 of file omd2omdCmd.hpp.
| unsigned int gengetopt_args_info::rotatePsi_given |
Whether rotatePsi was given.
Definition at line 95 of file omd2omdCmd.hpp.
| const char* gengetopt_args_info::rotatePsi_help |
rotate all coordinates Euler angle Psi help description.
Definition at line 74 of file omd2omdCmd.hpp.
| 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.
| double gengetopt_args_info::rotateTheta_arg |
rotate all coordinates Euler angle Theta (default='0.0').
Definition at line 69 of file omd2omdCmd.hpp.
| unsigned int gengetopt_args_info::rotateTheta_given |
Whether rotateTheta was given.
Definition at line 94 of file omd2omdCmd.hpp.
| const char* gengetopt_args_info::rotateTheta_help |
rotate all coordinates Euler angle Theta help description.
Definition at line 71 of file omd2omdCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::rp2_given |
Whether rp2 was given.
Definition at line 322 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::rp2_help |
rp2 order parameter (–sele1 and –sele2 must be specified) help description.
Definition at line 200 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::scd_given |
Whether scd was given.
Definition at line 323 of file StaticPropsCmd.hpp.
| 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 201 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::scn_given |
Whether scn was given.
Definition at line 348 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::scn_help |
Secondary Coordination Number Distribution help description.
Definition at line 226 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::sdcorr_given |
Whether sdcorr was given.
Definition at line 208 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::sdcorr_help |
System dipole correlation function help description.
Definition at line 138 of file DynamicPropsCmd.hpp.
| char * gengetopt_args_info::sele1_arg |
select first stuntdouble set.
select the first stuntdouble set.
Definition at line 51 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::sele1_given |
Whether sele1 was given.
Definition at line 169 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::sele1_help |
select first stuntdouble set help description.
select the first stuntdouble set help description.
Definition at line 53 of file DynamicPropsCmd.hpp.
| 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 52 of file DynamicPropsCmd.hpp.
| 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 54 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::sele2_given |
Whether sele2 was given.
Definition at line 170 of file DynamicPropsCmd.hpp.
| 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 56 of file DynamicPropsCmd.hpp.
| 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 55 of file DynamicPropsCmd.hpp.
| char * gengetopt_args_info::sele3_arg |
select third stuntdouble set.
select the third stuntdouble set.
Definition at line 57 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::sele3_given |
Whether sele3 was given.
Definition at line 171 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::sele3_help |
select third stuntdouble set help description.
select the third stuntdouble set help description.
Definition at line 59 of file DynamicPropsCmd.hpp.
| 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 58 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::selecorr_given |
Whether selecorr was given.
Definition at line 193 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::selecorr_help |
selection correlation function help description.
Definition at line 123 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::selection_arg |
general selection syntax.
Definition at line 61 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::selection_given |
Whether selection was given.
Definition at line 104 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::selection_help |
general selection syntax help description.
Definition at line 63 of file Dump2XYZCmd.hpp.
| 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().
| enum enum_selectionMode gengetopt_args_info::selectionMode_arg |
How to treat objects which leave a dynamic selection and then return later (default = survival) (default='survival').
Definition at line 114 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::selectionMode_given |
Whether selectionMode was given.
Definition at line 190 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::selectionMode_help |
How to treat objects which leave a dynamic selection and then return later (default = survival) help description.
Definition at line 116 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::selectionMode_orig |
How to treat objects which leave a dynamic selection and then return later (default = survival) original value given at command line.
Definition at line 115 of file DynamicPropsCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::seleoffset2_given |
Whether seleoffset2 was given.
Definition at line 282 of file StaticPropsCmd.hpp.
| 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.
| 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.
| int gengetopt_args_info::seleoffset3_arg |
global index offset for a fourth object (used to define a vector between sites in molecule).
Definition at line 122 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::seleoffset3_given |
Whether seleoffset3 was given.
Definition at line 283 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::seleoffset3_help |
global index offset for a fourth object (used to define a vector between sites in molecule) help description.
Definition at line 124 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::seleoffset3_orig |
global index offset for a fourth object (used to define a vector between sites in molecule) original value given at command line.
Definition at line 123 of file StaticPropsCmd.hpp.
| 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 60 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::seleoffset_given |
Whether seleoffset was given.
Definition at line 172 of file DynamicPropsCmd.hpp.
| 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 62 of file DynamicPropsCmd.hpp.
| 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 61 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::sequentialProps_group_counter |
Counter for group sequentialProps.
Definition at line 132 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::sfg_given |
Whether sfg was given.
Definition at line 233 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::sfg_help |
SFG susceptibility spectrum (exciton model) - use molecular selections help description.
SFG susceptibility spectrum (time averaging approximation) - uses molecular selections help description.
Definition at line 163 of file DynamicPropsCmd.hpp.
| char * gengetopt_args_info::sfgPolarization_arg |
SFG polarization combination: ssp, ppp, sps (default='ssp').
Definition at line 117 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::sfgPolarization_given |
Whether sfgPolarization was given.
Definition at line 191 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::sfgPolarization_help |
SFG polarization combination: ssp, ppp, sps help description.
Definition at line 119 of file DynamicPropsCmd.hpp.
| char * gengetopt_args_info::sfgPolarization_orig |
SFG polarization combination: ssp, ppp, sps original value given at command line.
Definition at line 118 of file DynamicPropsCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::shellRadius_given |
Whether shellRadius was given.
Definition at line 76 of file nanoparticleBuilderCmd.hpp.
| 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.
| 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.
| 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.
| 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.
| int gengetopt_args_info::shells_arg |
Nanoparticle shells.
Definition at line 45 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::shells_given |
Whether shells was given.
Definition at line 77 of file icosahedralBuilderCmd.hpp.
| const char* gengetopt_args_info::shells_help |
Nanoparticle shells help description.
Definition at line 47 of file icosahedralBuilderCmd.hpp.
| char* gengetopt_args_info::shells_orig |
Nanoparticle shells original value given at command line.
Definition at line 46 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::slab_density_given |
Whether slab_density was given.
Definition at line 325 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::slab_density_help |
slab density, rho(z) help description.
Definition at line 203 of file StaticPropsCmd.hpp.
| double gengetopt_args_info::start_arg |
starting affine scale (default='0.8').
Definition at line 48 of file equationofstateCmd.hpp.
| unsigned int gengetopt_args_info::start_given |
Whether start was given.
Definition at line 62 of file equationofstateCmd.hpp.
| const char* gengetopt_args_info::start_help |
starting affine scale help description.
Definition at line 50 of file equationofstateCmd.hpp.
| char* gengetopt_args_info::start_orig |
starting affine scale original value given at command line.
Definition at line 49 of file equationofstateCmd.hpp.
| int gengetopt_args_info::staticProps_group_counter |
Counter for group staticProps.
Definition at line 380 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::step_arg |
process every n frame (default='1').
Definition at line 53 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::step_given |
Whether step was given.
Definition at line 260 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::step_help |
process every n frame help description.
Definition at line 55 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::step_orig |
process every n frame original value given at command line.
Definition at line 54 of file StaticPropsCmd.hpp.
| char* gengetopt_args_info::stl_arg |
stl file for BoundaryElement model.
Definition at line 50 of file HydroCmd.hpp.
| unsigned int gengetopt_args_info::stl_given |
Whether stl was given.
Definition at line 78 of file HydroCmd.hpp.
| const char* gengetopt_args_info::stl_help |
stl file for BoundaryElement model help description.
Definition at line 52 of file HydroCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::stone_given |
Whether stone was given.
Definition at line 88 of file icosahedralBuilderCmd.hpp.
| const char* gengetopt_args_info::stone_help |
Create a Curling-stone Decahedral cluster help description.
Definition at line 70 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::stresscorr_given |
Whether stresscorr was given.
Definition at line 212 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::stresscorr_help |
Stress tensor correlation function help description.
Definition at line 142 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::surfDiffusion_given |
Whether surfDiffusion was given.
Definition at line 346 of file StaticPropsCmd.hpp.
| 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 224 of file StaticPropsCmd.hpp.
| double gengetopt_args_info::t_apod_arg |
Apodization time (fs) [filters tcorr with exp(-t/t_apod) in Fourier-transformed spectroscopic functions] (default='0.0').
Definition at line 81 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::t_apod_given |
Whether t_apod was given.
Definition at line 179 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::t_apod_help |
Apodization time (fs) [filters tcorr with exp(-t/t_apod) in Fourier-transformed spectroscopic functions] help description.
Definition at line 83 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::t_apod_orig |
Apodization time (fs) [filters tcorr with exp(-t/t_apod) in Fourier-transformed spectroscopic functions] original value given at command line.
Definition at line 82 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::t_zerofill_arg |
Zero-fill time (fs) [Pads time correlation functions with zeros from tcorr -> t_zerofill in Fourier-transformed spectroscopic functions] (default='0.0').
Definition at line 84 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::t_zerofill_given |
Whether t_zerofill was given.
Definition at line 180 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::t_zerofill_help |
Zero-fill time (fs) [Pads time correlation functions with zeros from tcorr -> t_zerofill in Fourier-transformed spectroscopic functions] help description.
Definition at line 86 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::t_zerofill_orig |
Zero-fill time (fs) [Pads time correlation functions with zeros from tcorr -> t_zerofill in Fourier-transformed spectroscopic functions] original value given at command line.
Definition at line 85 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::tacorr_given |
Whether tacorr was given.
Definition at line 225 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::tacorr_help |
Torque auto correlation function help description.
Definition at line 155 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::tcorr_arg |
Correlation time (length of each window) in fs (default='100000.0').
Definition at line 72 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::tcorr_given |
Whether tcorr was given.
Definition at line 176 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::tcorr_help |
Correlation time (length of each window) in fs help description.
Definition at line 74 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::tcorr_orig |
Correlation time (length of each window) in fs original value given at command line.
Definition at line 73 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::temperature_arg |
temperature (in Kelvin (default='300').
temperature (K).
Definition at line 70 of file HydroCmd.hpp.
| unsigned int gengetopt_args_info::temperature_given |
Whether temperature was given.
Definition at line 85 of file HydroCmd.hpp.
| const char * gengetopt_args_info::temperature_help |
temperature (in Kelvin help description.
temperature (K) help description.
Definition at line 72 of file HydroCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::testequi_given |
Whether testequi was given.
Definition at line 127 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::testequi_help |
Temperature using all componets of linear and angular momentum help description.
Definition at line 99 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::tet_hb_given |
Whether tet_hb was given.
Definition at line 356 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::tet_hb_help |
hydrogen bond statistics binned by tetrahedrality of donor and acceptor molecules help description.
Definition at line 234 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::tet_param_dens_given |
Whether tet_param_dens was given.
Definition at line 337 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::tet_param_dens_help |
computes density of the tetrahedrality order parameter Qk help description.
Definition at line 215 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::tet_param_given |
Whether tet_param was given.
Definition at line 333 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::tet_param_help |
tetrahedrality order parameter (Qk) help description.
Definition at line 211 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::tet_param_r_given |
Whether tet_param_r was given.
Definition at line 335 of file StaticPropsCmd.hpp.
| 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 213 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::tet_param_rangle_given |
Whether tet_param_rangle was given.
Definition at line 336 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::tet_param_rangle_help |
spatially-resolved tetrahedrality order parameter Qk(r,cos(theta)) around a third selection help description.
Definition at line 214 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::tet_param_xyz_given |
Whether tet_param_xyz was given.
Definition at line 338 of file StaticPropsCmd.hpp.
| 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 216 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::tet_param_z_given |
Whether tet_param_z was given.
Definition at line 334 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::tet_param_z_help |
spatially-resolved tetrahedrality order parameter Qk(z) help description.
Definition at line 212 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::tfcorr_given |
Whether tfcorr was given.
Definition at line 224 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::tfcorr_help |
Torque - Force Cross correlation function help description.
Definition at line 154 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::thermalizer_group_counter |
Counter for group thermalizer.
Definition at line 68 of file thermalizerCmd.hpp.
| unsigned int gengetopt_args_info::theta_omega_given |
Whether theta_omega was given.
Definition at line 314 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::theta_omega_help |
g(cos(theta), cos(omega)) help description.
Definition at line 192 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::thetacorr_given |
Whether thetacorr was given.
Definition at line 210 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::thetacorr_help |
Angular msd help description.
Definition at line 140 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::thetacut_arg |
HOO cutoff angle (degrees) (default='30').
Definition at line 93 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::thetacut_given |
Whether thetacut was given.
Definition at line 183 of file DynamicPropsCmd.hpp.
| const char * gengetopt_args_info::thetacut_help |
HOO cutoff angle (degrees) help description.
Definition at line 95 of file DynamicPropsCmd.hpp.
| char * gengetopt_args_info::thetacut_orig |
HOO cutoff angle (degrees) original value given at command line.
Definition at line 94 of file DynamicPropsCmd.hpp.
| double gengetopt_args_info::threshDens_arg |
Threshold Density in g/cm^3.
Definition at line 77 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::threshDens_given |
Whether threshDens was given.
Definition at line 115 of file SequentialPropsCmd.hpp.
| const char* gengetopt_args_info::threshDens_help |
Threshold Density in g/cm^3 help description.
Definition at line 79 of file SequentialPropsCmd.hpp.
| char* gengetopt_args_info::threshDens_orig |
Threshold Density in g/cm^3 original value given at command line.
Definition at line 78 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::trans_param_z_given |
Whether trans_param_z was given.
Definition at line 339 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::trans_param_z_help |
spatially-resolved translational order parameter t(z) help description.
Definition at line 217 of file StaticPropsCmd.hpp.
| double gengetopt_args_info::translateX_arg |
translate all x coordinates by some amount (default='0.0').
Definition at line 57 of file omd2omdCmd.hpp.
| unsigned int gengetopt_args_info::translateX_given |
Whether translateX was given.
Definition at line 90 of file omd2omdCmd.hpp.
| const char* gengetopt_args_info::translateX_help |
translate all x coordinates by some amount help description.
Definition at line 59 of file omd2omdCmd.hpp.
| 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.
| double gengetopt_args_info::translateY_arg |
translate all y coordinates by some amount (default='0.0').
Definition at line 60 of file omd2omdCmd.hpp.
| unsigned int gengetopt_args_info::translateY_given |
Whether translateY was given.
Definition at line 91 of file omd2omdCmd.hpp.
| const char* gengetopt_args_info::translateY_help |
translate all y coordinates by some amount help description.
Definition at line 62 of file omd2omdCmd.hpp.
| 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.
| double gengetopt_args_info::translateZ_arg |
translate all z coordinates by some amount (default='0.0').
Definition at line 63 of file omd2omdCmd.hpp.
| unsigned int gengetopt_args_info::translateZ_given |
Whether translateZ was given.
Definition at line 92 of file omd2omdCmd.hpp.
| const char* gengetopt_args_info::translateZ_help |
translate all z coordinates by some amount help description.
Definition at line 65 of file omd2omdCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::truncatedCube_given |
Whether truncatedCube was given.
Definition at line 90 of file icosahedralBuilderCmd.hpp.
| const char* gengetopt_args_info::truncatedCube_help |
Create a Truncated Cube (requires lattice) help description.
Definition at line 72 of file icosahedralBuilderCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::truncatedPlanes_given |
Whether truncatedPlanes was given.
Definition at line 82 of file icosahedralBuilderCmd.hpp.
| 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.
| 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.
| double gengetopt_args_info::tsep_arg |
Separation time between correlation windows (0 = no gap) (default='0.0').
Definition at line 78 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::tsep_given |
Whether tsep was given.
Definition at line 178 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::tsep_help |
Separation time between correlation windows (0 = no gap) help description.
Definition at line 80 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::tsep_orig |
Separation time between correlation windows (0 = no gap) original value given at command line.
Definition at line 79 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::twinAtoms_arg |
Number of atoms along twin boundary (Decahedron only).
Definition at line 57 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::twinAtoms_given |
Whether twinAtoms was given.
Definition at line 81 of file icosahedralBuilderCmd.hpp.
| 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.
| 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.
| unsigned int gengetopt_args_info::twodgofr_given |
Whether twodgofr was given.
Definition at line 317 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::twodgofr_help |
2D g(r) (Slab width –dz must be specified) help description.
Definition at line 195 of file StaticPropsCmd.hpp.
| int gengetopt_args_info::unitCells_arg |
Number of unit cell (Cuboctahedron and Truncated Cube only).
Definition at line 63 of file icosahedralBuilderCmd.hpp.
| unsigned int gengetopt_args_info::unitCells_given |
Whether unitCells was given.
Definition at line 83 of file icosahedralBuilderCmd.hpp.
| 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.
| 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.
| 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 164 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::v_radius_given |
Whether v_radius was given.
Definition at line 297 of file StaticPropsCmd.hpp.
| 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 166 of file StaticPropsCmd.hpp.
| 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 165 of file StaticPropsCmd.hpp.
| double gengetopt_args_info::vacancyInnerRadius_arg |
Radius arround core-shell where vacancies should be located.
Definition at line 64 of file nanoparticleBuilderCmd.hpp.
| unsigned int gengetopt_args_info::vacancyInnerRadius_given |
Whether vacancyInnerRadius was given.
Definition at line 79 of file nanoparticleBuilderCmd.hpp.
| 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.
| 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.
| double gengetopt_args_info::vacancyOuterRadius_arg |
Radius arround core-shell where vacancies should be located.
Definition at line 67 of file nanoparticleBuilderCmd.hpp.
| unsigned int gengetopt_args_info::vacancyOuterRadius_given |
Whether vacancyOuterRadius was given.
Definition at line 80 of file nanoparticleBuilderCmd.hpp.
| 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.
| 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.
| double gengetopt_args_info::vacancyPercent_arg |
Percentage of atoms to remove from within vacancy range.
Definition at line 61 of file nanoparticleBuilderCmd.hpp.
| unsigned int gengetopt_args_info::vacancyPercent_given |
Whether vacancyPercent was given.
Definition at line 78 of file nanoparticleBuilderCmd.hpp.
| 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.
| 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.
| unsigned int gengetopt_args_info::vaOutProdcorr_given |
Whether vaOutProdcorr was given.
Definition at line 199 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::vaOutProdcorr_help |
Velocity - Velocity auto outer product correlation function help description.
Definition at line 129 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::vcorr_given |
Whether vcorr was given.
Definition at line 196 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::vcorr_help |
velocity correlation function help description.
Definition at line 126 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::vcorrR_given |
Whether vcorrR was given.
Definition at line 198 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::vcorrR_help |
velocity correlation function projected radially help description.
Definition at line 128 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::vcorrZ_given |
Whether vcorrZ was given.
Definition at line 197 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::vcorrZ_help |
velocity correlation function along z-axis help description.
Definition at line 127 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::vectors_flag |
Print vectors (dipoles, etc) in xyz file (default=off).
Definition at line 85 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::vectors_given |
Whether vectors was given.
Definition at line 113 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::vectors_help |
Print vectors (dipoles, etc) in xyz file help description.
Definition at line 86 of file Dump2XYZCmd.hpp.
| int gengetopt_args_info::velocities_flag |
Print velocities in xyz file (default=off).
Definition at line 81 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::velocities_given |
Whether velocities was given.
Definition at line 111 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::velocities_help |
Print velocities in xyz file help description.
Definition at line 82 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::velocityfield_given |
Whether velocityfield was given.
Definition at line 360 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::velocityfield_help |
computes an average velocity field help description.
Definition at line 238 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::velocityZ_given |
Whether velocityZ was given.
Definition at line 361 of file StaticPropsCmd.hpp.
| const char* gengetopt_args_info::velocityZ_help |
computes an average two-dimensional velocity map help description.
Definition at line 239 of file StaticPropsCmd.hpp.
| unsigned int gengetopt_args_info::version_given |
Whether version was given.
Definition at line 95 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char * gengetopt_args_info::version_help |
Print version and exit help description.
Definition at line 41 of file Dump2XYZCmd.hpp.
| double gengetopt_args_info::viscosity_arg |
viscosity (in poise) (default='0.01').
Definition at line 67 of file HydroCmd.hpp.
| unsigned int gengetopt_args_info::viscosity_given |
Whether viscosity was given.
Definition at line 84 of file HydroCmd.hpp.
| const char* gengetopt_args_info::viscosity_help |
viscosity (in poise) help description.
Definition at line 69 of file HydroCmd.hpp.
| char* gengetopt_args_info::viscosity_orig |
viscosity (in poise) original value given at command line.
Definition at line 68 of file HydroCmd.hpp.
| double gengetopt_args_info::voxelSize_arg |
voxel size for coarse graining (Angstroms) (default='2.0').
voxel size (angstroms).
Definition at line 86 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::voxelSize_given |
Whether voxelSize was given.
Definition at line 118 of file SequentialPropsCmd.hpp.
| const char * gengetopt_args_info::voxelSize_help |
voxel size for coarse graining (Angstroms) help description.
voxel size (angstroms) help description.
Definition at line 88 of file SequentialPropsCmd.hpp.
| char * gengetopt_args_info::voxelSize_orig |
voxel size for coarse graining (Angstroms) original value given at command line.
voxel size (angstroms) original value given at command line.
Definition at line 87 of file SequentialPropsCmd.hpp.
| unsigned int gengetopt_args_info::vwOutProdcorr_given |
Whether vwOutProdcorr was given.
Definition at line 201 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::vwOutProdcorr_help |
Velocity - Angular Velocity outer product correlation function help description.
Definition at line 131 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::waOutProdcorr_given |
Whether waOutProdcorr was given.
Definition at line 200 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::waOutProdcorr_help |
Angular Velocity - Angular Velocity auto outer product correlation function help description.
Definition at line 130 of file DynamicPropsCmd.hpp.
| int gengetopt_args_info::water_flag |
skip the the waters (default=off).
Definition at line 51 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::water_given |
Whether water was given.
Definition at line 99 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::water_help |
skip the the waters help description.
Definition at line 52 of file Dump2XYZCmd.hpp.
| int gengetopt_args_info::watertype_flag |
replace the atom type of water model (default=on).
Definition at line 59 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::watertype_given |
Whether watertype was given.
Definition at line 103 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::watertype_help |
replace the atom type of water model help description.
Definition at line 60 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::wcorr_given |
Whether wcorr was given.
Definition at line 203 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::wcorr_help |
charge velocity correlation function help description.
Definition at line 133 of file DynamicPropsCmd.hpp.
| unsigned int gengetopt_args_info::wvOutProdcorr_given |
Whether wvOutProdcorr was given.
Definition at line 202 of file DynamicPropsCmd.hpp.
| const char* gengetopt_args_info::wvOutProdcorr_help |
Angular Velocity - Velocity outer product correlation function help description.
Definition at line 132 of file DynamicPropsCmd.hpp.
| char* gengetopt_args_info::xyz_arg |
xyz file for AtomicBead model.
Definition at line 47 of file HydroCmd.hpp.
| unsigned int gengetopt_args_info::xyz_given |
Whether xyz was given.
Definition at line 77 of file HydroCmd.hpp.
| const char* gengetopt_args_info::xyz_help |
xyz file for AtomicBead model help description.
Definition at line 49 of file HydroCmd.hpp.
| 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.
| int gengetopt_args_info::zconstraint_flag |
replace the atom types of zconstraint molecules (default=off).
Definition at line 55 of file Dump2XYZCmd.hpp.
| unsigned int gengetopt_args_info::zconstraint_given |
Whether zconstraint was given.
Definition at line 101 of file Dump2XYZCmd.hpp.
Referenced by cmdline_parser_dump().
| const char* gengetopt_args_info::zconstraint_help |
replace the atom types of zconstraint molecules help description.
Definition at line 56 of file Dump2XYZCmd.hpp.
| 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.
| unsigned int gengetopt_args_info::zlength_given |
Whether zlength was given.
Definition at line 274 of file StaticPropsCmd.hpp.
| 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.
| 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.
| 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.
| unsigned int gengetopt_args_info::zoffset_given |
Whether zoffset was given.
Definition at line 275 of file StaticPropsCmd.hpp.
| 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.
| 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.
1.17.0