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update docs for cell model

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This commit is contained in:
James McClure 2023-01-16 13:29:58 -05:00
parent 57736ced88
commit 7e286f16f1
6 changed files with 114 additions and 66 deletions
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19
docs/source/examples/membrane/cellModel.rst
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@ -9,6 +9,14 @@ file ``Bacterium.swc``, which specifies an oblong cell shape, relying on the ``.
is commonly used to approximate neuron structures. The case considered is the four ion membrane transport
problem considered in Figure 4 from McClure & Li
The cell simulation is performed by the executable ``lbpm_nernst_planck_cell_simulator``, which is launched
in the same way as other parallel tools
.. code:: bash
mpirun -np 2 $LBPM_BIN/lbpm_nernst_planck_cell_simulator Bacterium.db
The input file ``Bacterium.db`` specifies the following
.. code:: c
@ -85,16 +93,13 @@ The input file ``Bacterium.db`` specifies the following
ThresholdMassFractionIn = 1e-1, 1.0, 5e-3, 0.0
ThresholdMassFractionOut = 1e-1, 1.0, 5e-3, 0.0
}
Once this has been set, we launch ``lbpm_nernst_planck_simulator`` in the same way as other parallel tools
.. code:: bash
mpirun -np 2 $LBPM_BIN/lbpm_nernst_planck_simulator bacterium.db
*******************
Example Output
*******************
Successful output looks like the following
.. code:: bash
********************************************************

30
docs/source/userGuide/models/cell/cell.rst
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@ -3,6 +3,7 @@ Cell model
=============================================
LBPM includes a whole-cell simulator based on a coupled solution of the Nernst-Planck equations with Gauss's law.
The lattice Boltzmann formulation is described below.
*********************
Nernst-Planck model
@ -157,6 +158,27 @@ The local value of the potential is then updated based on a relaxation scheme, w
The algorithm can then proceed to the next timestep.
***************************
Membrane Model
***************************
The LBPM membrane model provides the basis to model cellular dynamics. There are currently two supported ways
to specify the membrane location:
1. provide a segemented image that is labeled to differentiate the cell
interior and exterior. See the script ``NaCl-cell.py`` and input file ``NaCl.db`` as a reference for how to use labeled images.
- ``IonConcentrationFile`` -- list of files that specify the initial concentration for each ion
- ``Filename`` -- 8-bit binary file provided in the ``Domain`` section of the input database
- ``ReadType`` -- this should be ``"8bit"`` (this is the default)
2. provide a ``.swc`` file that specifies the geometry (see example input file below).
- ``Filename`` -- swc file name should be provided in the ``Domain`` section of the input database
- ``ReadType`` -- this should be ``"swc"`` (required since ``"8bit"`` is the internal default)
Both examples are stored within the LBPM repository, located at ``example/SingleCell/``
****************************
Example Input File
****************************
@ -170,13 +192,9 @@ Example Input File
tolerance = 1.0e-9
visualization_interval = 1000 // Frequency to write visualization data
}
Stokes {
tau = 1.0
F = 0, 0, 0
ElectricField = 0, 0, 0 //body electric field; user-input unit: [V/m]
nu_phys = 0.889e-6 //fluid kinematic viscosity; user-input unit: [m^2/sec]
}
Ions {
use_membrane = true
Restart = false
MembraneIonConcentrationList = 150.0e-3, 10.0e-3, 15.0e-3, 155.0e-3 //user-input unit: [mol/m^3]
temperature = 293.15 //unit [K]
number_ion_species = 4 //number of ions

4
docs/source/userGuide/models/index.rst
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@ -12,9 +12,7 @@ Currently supported lattice Boltzmann models
mrt/*
nernstPlanck/*
PoissonBoltzmann/*
cell/*
greyscale/*

39
example/SingleCell/NaCl-cell.py
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@ -1,41 +1,38 @@
import numpy as np
import matplotlib.pylab as plt
Nx = 64
Ny = 64
Nz = 64
cx = Nx/2
cy = Ny/2
cz = Nz/2
radius = 12
D=np.ones((40,40,40),dtype="uint8")
D=np.ones((Nx,Ny,Nz),dtype="uint8")
cx = 20
cy = 20
cz = 20
radius = 8
for i in range(0, Nx):
for j in range (0, Ny):
for k in range (0,Nz):
for i in range(0, 40):
for j in range (0, 40):
for k in range (0,40):
dist = np.sqrt((i-cx)*(i-cx) + (j-cx)*(j-cx) + (k-cz)*(k-cz))
if (dist < radius ) :
D[i,j,k] = 2
D.tofile("cell_64x64x64.raw")
D.tofile("cell_40x40x40.raw")
C1=np.zeros((Nx,Ny,Nz),dtype="double")
C2=np.zeros((Nx,Ny,Nz),dtype="double")
C1=np.zeros((40,40,40),dtype="double")
C2=np.zeros((40,40,40),dtype="double")
for i in range(0, Nx):
for j in range (0, Ny):
for k in range (0,Nz):
for i in range(0, 40):
for j in range (0, 40):
for k in range (0,40):
#outside the cell
C1[i,j,k] = 125.0e-6 # Na
C2[i,j,k] = 125.0e-6 # Cl
dist = np.sqrt((i-cx)*(i-cx) + (j-cx)*(j-cx) + (k-cz)*(k-cz))
# inside the cell
if (dist < radius ) :
C1[i,j,k] = 110.0e-6
C2[i,j,k] = 110.0e-6
C1[i,j,k] = 5.0e-6
C2[i,j,k] = 5.0e-6
C1.tofile("cell_concentration_Na_64x64x64.raw")
C2.tofile("cell_concentration_Cl_64x64x64.raw")
C1.tofile("cell_concentration_Na_40x40x40.raw")
C2.tofile("cell_concentration_Cl_40x40x40.raw")

38
example/SingleCell/NaCl.db
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@ -1,9 +1,10 @@
MultiphysController {
timestepMax = 2000
timestepMax = 20
num_iter_Ion_List = 2
analysis_interval = 40
analysis_interval = 50
tolerance = 1.0e-9
visualization_interval = 40 // Frequency to write visualization data
visualization_interval = 100 // Frequency to write visualization data
analysis_interval = 50 // Frequency to perform analysis
}
Stokes {
tau = 1.0
@ -12,7 +13,9 @@ Stokes {
nu_phys = 0.889e-6 //fluid kinematic viscosity; user-input unit: [m^2/sec]
}
Ions {
IonConcentrationFile = "cell_concentration_Na_64x64x64.raw", "double", "cell_concentration_Cl_64x64x64.raw", "double"
use_membrane = true
Restart = false
IonConcentrationFile = "cell_concentration_Na_40x40x40.raw", "double", "cell_concentration_Cl_40x40x40.raw", "double"
temperature = 293.15 //unit [K]
number_ion_species = 2 //number of ions
tauList = 1.0, 1.0
@ -25,6 +28,8 @@ Ions {
FluidVelDummy = 0.0, 0.0, 0.0 // dummy fluid velocity for debugging
}
Poisson {
lattice_scheme = "D3Q19"
Restart = false
epsilonR = 78.5 //fluid dielectric constant [dimensionless]
BC_Inlet = 0 // ->1: fixed electric potential; ->2: sine/cosine periodic electric potential
BC_Outlet = 0 // ->1: fixed electric potential; ->2: sine/cosine periodic electric potential
@ -41,16 +46,19 @@ Poisson {
TestPeriodicTimeConv = 0.01 //unit:[sec]
TestPeriodicSaveInterval = 0.2 //unit:[sec]
//------------------------------ advanced setting ------------------------------------
timestepMax = 4000 //max timestep for obtaining steady-state electrical potential
analysis_interval = 25 //timestep checking steady-state convergence
tolerance = 1.0e-10 //stopping criterion for steady-state solution
timestepMax = 100000 //max timestep for obtaining steady-state electrical potential
analysis_interval = 200 //timestep checking steady-state convergence
tolerance = 1.0e-6 //stopping criterion for steady-state solution
InitialValueLabels = 1, 2
InitialValues = 0.0, 0.0
}
Domain {
Filename = "cell_64x64x64.raw"
Filename = "cell_40x40x40.raw"
nproc = 1, 1, 1 // Number of processors (Npx,Npy,Npz)
n = 64, 64, 64 // Size of local domain (Nx,Ny,Nz)
N = 64, 64, 64 // size of the input image
voxel_length = 0.1 //resolution; user-input unit: [um]
n = 40, 40, 40 // Size of local domain (Nx,Ny,Nz)
N = 40, 40, 40 // size of the input image
voxel_length = 1.0 //resolution; user-input unit: [um]
BC = 0 // Boundary condition type
ReadType = "8bit"
ReadValues = 0, 1, 2
@ -72,9 +80,9 @@ Visualization {
Membrane {
MembraneLabels = 2
VoltageThreshold = 0.0, 0.0
MassFractionIn = 1e-2, 1e-8
MassFractionOut = 1e-2, 1e-8
ThresholdMassFractionIn = 1e-2, 1e-8
ThresholdMassFractionOut = 1e-2, 1e-8
MassFractionIn = 0e-2, 5e-2
MassFractionOut = 0e-2, 5e-2
ThresholdMassFractionIn = 0e-2, 5e-2
ThresholdMassFractionOut = 0e-2, 5e-2
}

50
models/IonModel.cpp
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@ -300,7 +300,7 @@ void ScaLBL_IonModel::ReadParams(string filename, vector<int> &num_iter) {
void ScaLBL_IonModel::ReadParams(string filename) {
//NOTE: the maximum iteration timesteps for ions are left unspecified
// it relies on the multiphys controller to compute the max timestep
USE_MEMBRANE = false;
USE_MEMBRANE = true;
Restart = false;
// read the input database
db = std::make_shared<Database>(filename);
@ -1081,20 +1081,42 @@ void ScaLBL_IonModel::Initialize() {
printf("LB Ion Solver: initializing D3Q7 distributions\n");
//USE_MEMBRANE = true;
if (USE_MEMBRANE){
double *Ci_host;
if (rank == 0)
printf(" ...initializing based on membrane list \n");
Ci_host = new double[number_ion_species * Np];
for (size_t ic = 0; ic < number_ion_species; ic++) {
AssignIonConcentrationMembrane( &Ci_host[ic * Np], ic);
}
ScaLBL_CopyToDevice(Ci, Ci_host, number_ion_species * sizeof(double) * Np);
comm.barrier();
for (size_t ic = 0; ic < number_ion_species; ic++) {
ScaLBL_D3Q7_Ion_Init_FromFile(&fq[ic * Np * 7], &Ci[ic * Np], Np);
}
delete[] Ci_host;
double *Ci_host;
Ci_host = new double[number_ion_species * Np];
if (ion_db->keyExists("IonConcentrationFile")) {
//NOTE: "IonConcentrationFile" is a vector, including "file_name, datatype"
auto File_ion = ion_db->getVector<std::string>("IonConcentrationFile");
if (File_ion.size() == 2*number_ion_species) {
for (size_t ic = 0; ic < number_ion_species; ic++) {
AssignIonConcentration_FromFile(&Ci_host[ic * Np], File_ion,
ic);
}
ScaLBL_CopyToDevice(Ci, Ci_host,
number_ion_species * sizeof(double) * Np);
comm.barrier();
for (size_t ic = 0; ic < number_ion_species; ic++) {
ScaLBL_D3Q7_Ion_Init_FromFile(&fq[ic * Np * 7], &Ci[ic * Np],
Np);
}
}
}
else{
if (rank == 0)
printf(" ...initializing based on membrane list \n");
for (size_t ic = 0; ic < number_ion_species; ic++) {
AssignIonConcentrationMembrane( &Ci_host[ic * Np], ic);
}
ScaLBL_CopyToDevice(Ci, Ci_host, number_ion_species * sizeof(double) * Np);
comm.barrier();
for (size_t ic = 0; ic < number_ion_species; ic++) {
ScaLBL_D3Q7_Ion_Init_FromFile(&fq[ic * Np * 7], &Ci[ic * Np], Np);
}
}
delete[] Ci_host;
}
else if (ion_db->keyExists("IonConcentrationFile")) {
//NOTE: "IonConcentrationFile" is a vector, including "file_name, datatype"
auto File_ion = ion_db->getVector<std::string>("IonConcentrationFile");