espressopp.integrator.LatticeBoltzmann¶
Overview
espressopp.integrator.LatticeBoltzmann 
Details
The LatticeBoltzmann (LB) class controls fluid hydrodynamics and allows for hybrid
LB/MD simulations. It is implemented as espressopp.integrator.Extension
in ESPResSo++.

class
espressopp.integrator.
LatticeBoltzmann
(system, nodeGrid, a = 1., tau = 1., numDims = 3, numVels = 19)¶ Parameters:  system (shared_ptr) – system object
 nodeGrid (Int3D) – arrangement of CPUs in space
 a (real) – lattice spacing (in lattice units).
 tau (real) – time discretization (in lattice units)
 numDims (int) – dimensionality of the LB model
 numVels (int) – number of velocity vectors in the LB model
Returns: lb object
The LBfluid in ESPResSo++ is aiming at simulations of complex soft matter systems. They consist of MD particles (colloids, composite nanoparticles or polymer chains) that are solved in the LBfluid preserving hydrodynamic interactions.
The default lattice model is D3Q19 (
numDims = 3
,numVels = 19
) and both lattice spacinga
and timesteptau
are set to 1. If some other lattice model is needed feel free to modify the code: adding 3D ones is straightforward, for 2D cases one has to make more thouroughs changes.The parameters of the LBfluid are expected in LennardJones (LJ) units. This strategy helps users with MDbackground think of LBfluid in term of LJ liquid. One only has to specify its properties such as liquid density, \(\rho\), temperature, \(T\), and viscosity, \(\eta\).
Note
Standard LJ fluid can be characterized by \(\rho \sim 1 [\sigma^{3}]\), \(T \sim 1 [\epsilon]\), and \(\eta \sim 5 [\epsilon \tau / \sigma^3]\)
Example
>>> L = 20 >>> >>> # create cubic box >>> box = (L, L, L) >>> # The rc+skin= lattice_size >>> rc = 0.9 >>> skin= 0.1 >>> >>> # initialize empty default system with the created cubic box. >>> system, integrator = espressopp.standard_system.Default(box) >>> >>> # nodeGrid is determined based on the number of CPUs used for simulation among others >>> nodeGrid=espressopp.tools.decomp.nodeGrid(espressopp.MPI.COMM_WORLD.size,box,rc,skin) >>> >>> # initialize lb object. The dimensions of the lattice are obtained from the >>> # system's box dimensions employing lattice spacing 1. >>> lb = espressopp.integrator.LatticeBoltzmann(system, nodeGrid)
Methods

getLBMom
(node, moment)¶ Get hydrodynamic moment from a specific node
Parameters:  node (Int3D) – node index
 moment (int) – hydrodynamic moment to get
Use 0 to get density \(\rho\) and 13 for mass flux components \(j_x\), \(j_y\) and \(j_z\), correspondingly.

setLBMom
(node, moment, value)¶ Set hydrodynamic moment for a specific node
Parameters:  node (Int3D) – node index
 moment (int) – hydrodynamic moment to set
 value (real) – value to set

saveLBConf
()¶ Dumps LB configuration with separate files for coupling forces, LBfluid moments and populations (the last one is a bit overkill). The dump files are written for every CPU separately and are put in the dump folder

keepLBDump
()¶ Sets a flag to keep previously dumped LB configuration. Normally the previous dump is deleted after a new one is made.
Example
>>> # set bulk viscosity >>> for k in range (10): >>> integrator.run(50000) >>> >>> # output LB configuration >>> lb.keepLBDump() # flag to keep previously saved LB state >>> lb.saveLBConf() # saves current state of the LB fluid
Properties

Int3D nodeGrid
Array of CPUs in space
Example
>>> # it is advised to set nodeGrid by internal ESPResSo++ function >>> # based on the number of CPUs >>> nodeGrid=espressopp.tools.decomp.nodeGrid(espressopp.MPI.COMM_WORLD.size,box,rc,skin)

real a = 1.
Lattice spacing (lattice units)

real tau = 1.
Lattice time step (lattice units)

int numDims = 3
Number of dimensions of the LB model (D3Q19)

int numVels = 19
Number of velocity vectors of the LB model (D3Q19)

real visc_b
Bulk viscosity (LJ units), affects
gamma_b
.Example
>>> # set bulk viscosity >>> lb.visc_b = 5.

real visc_s
Shear viscosity (LJ units), affects
gamma_s
.Example
>>> # set shear viscosity >>> lb.visc_s = 5.

real gamma_b = 0.
Bulk gamma (for experienced LB users)

real gamma_s = 0.
Shear gamma (for experienced LB users)

real gamma_odd = 0.
Odd gamma (for experienced LB users)

real gamma_even = 0.
Even gamma (for experienced LB users)

real lbTemp = 0.
Temperature of the LB fluid (LJ units)
Example
>>> L = 20 >>> T = 1. >>> N = 200 >>> >>> # create cubic box >>> box = (L, L, L) >>> rc=0.9 >>> skin=0.1 >>> >>> # initialize Lennard Jones system with the created cubic box and given temperature. >>> system, integrator = espressopp.standard_system.LennardJones(N, box, temperature=T) >>> >>> # nodeGrid is determined based on the number of CPUs used for simulation >>> nodeGrid=espressopp.tools.decomp.nodeGrid(espressopp.MPI.COMM_WORLD.size,box,rc,skin) >>> >>> # initialize lb object. The dimensions of the lattice are obtained from the >>> # system's box dimensions employing lattice spacing 1. >>> lb = espressopp.integrator.LatticeBoltzmann(system, nodeGrid) >>> >>> # set LB temperature to T >>> lb.lbTemp = T

real fricCoeff=5.
Friction coefficient of the coupling (LJ units)
Example
>>> # set friction coefficient of the coupling >>> lb.fricCoeff = 20.

int nSteps = 1
Timescale contrast (ratio) between LB and MD
Example
>>> # set time step contrast between LB and MD >>> lb.nSteps = 10

int profStep = 10000
Frequency of time profiling
Example
>>> # set profiling frequency >>> lb.profStep = 5000

Int3D getMyNi
Number of real and halo nodes for the CPU