MDBase.h¶

Basic quantities related to the MD simulation.

Contains time-independent data such as grid and atom information, as well as time-dependent information such as the substrate and monolayer extents.

struct BoxBounds¶

#include <MDBase.h>

Simulation box bounds, as defined in the LAMMPS dumpfile.

This data is updated each timestep.

See: DumpfileReader

Public Members

double xlo¶

double xhi¶

double ylo¶

double yhi¶

double zlo¶

double zhi¶

struct SimData¶

#include <MDBase.h>

Source of truth for general MD variables.

Variables are set here, and a pointer to this object is passed around and read elsewhere.

Public Functions

SimData(Options options)¶

~SimData()¶

void deleteWaterBonds()¶

Since water bonds are stored as a map from int to int*, those int*s must be allocated upon storage in the map. So we delete them here.

See: DatafileReader::readWaterBonds

void setOptions(Options options)¶

Copy a few important options directly to this object.

See: liquidTypes
See: solidTypes
See: stepsPerFrame
See: monoTop
See: substrateTop
See: numAtoms

void setNumSteps(int _numSteps)¶: Set numsteps and call setStepsPerFrame using value from Options::stepsPerFrame.

void setStepsPerFrame(int _stepsPerFrame)¶

Set the number of steps per frame and determine how many steps are in the last frame. Must be called after numSteps is defined. This function is called by setNumSteps.

See: LastFrame::setSteps

Public Members

Options options¶

int numAtoms¶

int numSteps¶

int numFrames¶

int stepsPerFrame¶

LastFrame lastFrame¶

vector<int> liquidTypes¶: Which atom types correspond to liquid.

vector<int> solidTypes¶: Which atom types correspond to substrate.

map<int, double> masses¶: Mass for each atom type.

map<int, int *> waterBonds¶

Maps oxygen atom id to two hydrogen atom ids.

See: DatafileReader::readWaterBonds

BoxBounds simBounds¶

double substrateTop¶

z coordinate of the top of the substrate.

If the substrate option is disabled, this can be manually specified via Options::substrateTop.

See: Substrate::findLimits

double monoTop¶

z coordinate of the top of the monolayer.

If the monolayer option is disabled, this can be manually specified in Options::monoTop.

See: Droplet::findMonolayer
See: Monolayer::findMonoLimits

Frame *framePtr¶

struct Grid¶

#include <MDBase.h>

Grid to use for 2D histogram.

Each bin in the grid has the same volume. dz and dv are specified by Options::dz and Options::dv, and determine the size of the bins. dr is determined automatically for each bin from the other two.

Public Functions