Parameters.h¶

Input parameters and parsing functions for the Lotus input file.

See Lotus Input File for a description of the Lotus input file. Public member variables of Options are valid keys.

Typedefs

typedef map<string, vector<string>> StrVecMap¶

class Options¶

#include <Parameters.h>

Options from Lotus input file.

This object is passed to most other objects to inform their behavior.

Public Functions

void readConfig(const char *configPath)¶

void printOptions()¶

Public Members

string dumpfile¶

Path to the LAMMPS dumpfile.

Required.

See: DumpfileReader

string datafile¶

Path to the LAMMPS datafile.

Required.

See: DatafileReader

string outLoc¶

Path to output directory.

Required.

See: Output Files

int stepsPerFrame¶

Number of Timesteps averaged for each frame.

Required.

In order to increase the number of atoms in each histogram bin, several timesteps are averaged together in each frame. If the number of steps in the dumpfile is not divisible by stepsPerFrame, then the last frame will have more steps than the rest.

See: Time.h

vector<int> liquidTypes¶

List of liquid atom types.

Required.

These are the types whose masses contribute towards the density calculations for the droplet.

Lists in YAML can be specified in either of the following ways. Both options are equivalent for use in the Lotus input file.

Option 1:

liquidTypes:
  - 1
  - 2
  - 3

Option 2:

liquidTypes: [1, 2, 3]

See: Droplet::fill
See: Monolayer::fill

vector<int> solidTypes¶

List of susbtrate atom types.

Required.

These are the types whose masses contribute towards the density calculations for the substrate. However, if substrate is false, feel free to supply an empty list (though the option must be present).

Lists in YAML can be specified in either of the following ways. Both options are equivalent for use in the Lotus input file.

Option 1:

substrateTypes:
- 1
- 2
- 3

Option 2:

substrateTypes: [1, 2, 3]

See: Substrate::fill

int numAtoms¶

Number of atoms in the LAMMPS dumpfile.

Optional. Default: 0

By default, this is read from the LAMMPS datafile. In the case that not all atoms from the datafile are present in the dumpfile (e.g. some are frozen), it is currently necessary to manually specify the number of atoms in the dumpfile via this option.

string geometry¶

Droplet geometry (spherical or cylindrical).

Optional. Default: “spherical” Acceptable values: “spherical”, “cylindrical”.

If “spherical” is chosen, then the droplet is assumed to be symmetric about the \(z\) axis, and distance to the \(z\) axis is used as the horizontal axis in the 2D density histogram of Figure 5.

If “cylindrical” is chosen, then the droplet is assumed to be periodic in \(y\), and symmetric about the \(y-z\) plane. In this case, distance to the \(y-z\) plane is used as the horizontal axis in Figure 5.

See: Monolayer::fillOne
See: Droplet::fillOne

bool saveImages¶

Whether to save .png images of figures.

Optional. Default: true

See: See Image Directory.

bool saveROOT¶

Whether to save .C ROOT macros of figures.

Optional. Default: false

See: See ROOT Directory.

bool verbose¶

Whether to print verbose output to stdout.

Optional. Default: false

This may include debugging information and other values which are not necessary for routine use.

int waterBondType¶

LAMMPS bond type for O-H bonds in water molecules.

Optional. Default: 2

This is useful if the droplet is water, and the orientation of water molecules is calculated.

Note: Molecule orientation is currently not calculated.
See: DatafileReader::readWaterBonds

double dz¶

\( z \) width of 1D and 2D histogram bins.

Optional. Default: 1.0

Units are angstroms.

See: Grid

double dv¶

Volume of 2D histogram bins.

Optional. Default: 250.0

Units are cubic angstroms.

See: Grid

double dens_min¶

Minimum density for TanhFigure and DensFigure.

Optional. Defaut: 0.0

Units are g/cm^2

TODO: Should be set to 0.0 everywhere, option is unnecessary.

double dens_max¶

Maximum density for TanhFigure and DensFigure.

Optional. Default: 5.0

Units are g/cm^3.

TODO: Should be combined with Options::densMax. The only reason not to combine them is that DensFigure (Figure 1) includes the substrate, while DropletFigure (Figure 5) does not. Since the substrate is generally more dense than the liquid, this suggests the use of different scales for the two figures.

double densMax¶

Maximum density for DropletFigure (Figure 5).

Optional. Default: 1.5

Units are g/cm^3.

double plot_rmax¶

Maximum \( r \) value for DropletFigure.

Optional. Default: 150.0

This option is not only relevant to the figure produced, but specifies the limits of the figure itself and therefore the maximum droplet size that can be correctly analyzed.

double plot_zmax¶

Maximum \( z \) value for DropletFigure.

Optional. Default: 100.0

This option is not only relevant to the figure produced, but specifies the limits of the figure itself and therefore the maximum droplet size that can be correctly analyzed.

double plot_aspect¶

Aspect ratio of figures.

Optional. Default: 1.0

Plot width is specified by plot_width, so this option is used to implicitly determine plot height.

int plot_width¶

Width of plots in pixels.

Optional. Default: 800

double expectedLiquidDensity¶

Theoretical density of the bulk liquid droplet.

Optional. Default: 1.0

Units are g/cm^3. This is useful for estimating the hyperbolic tangent fits before actually performing the fits.

Note: This is not actually used, although it would be a good idea and easy to implement.
See: TanhFit::guessTanhFit

bool monolayer¶

Whether to perform monolayer calculations.

Optional. Default: true

By default, the droplet’s base radius and contact angle are calculated by intersecting the fitted boundary circle with the \( z \) plane defining the top of the monolayer. In the case that this option is false, that plane may be manually specified through monoTop.

Note: monoTop is relative to the top of the substrate.
See: substrate
See: substrateTop
See: Monolayer

bool substrate¶

Whether to perform substrate calculations.

Optional. Default: true

By default, all \( z \) coordinates (including monoTop) are given relative to the top of the substrate. In the case that this option is false, the reference plane may be specified via substrateTop.

See: Substrate

bool fitCircle¶

Whether to fit a circle to the boundary points.

Optional. Default: true

As described in Calculation of Geometric Quantities of Interest, calculation of the bulk radius, contact angle, and bulk height require a circle to be fit to the boundary points. Therefore, these quantities will not be calculated if this option is false.

See: CircleFit
See: CircularBulk

double monoTop¶

\( z \) coordinate with which to intersect fitted circle.

Optional. Default: true

This option is only necessary if monolayer is false.

double substrateTop¶

\( z \) coordinate which is taken to be \( z=0 \).

Optional. Default: true

This option is only necessary if substrate is false.

double rDensCyl¶

Radius of cylinder used for 1D droplet density calculations.

Optional. Default: 10.0

Units are angstroms.

In order to calculate a density, we must select a volume over which to count atoms and sum their masses. For spherical droplets, a thin cylinder around the \( z \) axis is chosen. This parameter is the radius of that cylinder.