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Merge branch '9-add-easy-setting-of-boundary-conditions' into 'main'

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Resolve "Add simplified setting of boundary conditions"

Closes #9

See merge request mluebke/diffusion!20
This commit is contained in:
Max Lübke 2022-06-13 16:35:21 +02:00
commit c3a0188dac
17 changed files with 7401 additions and 164 deletions
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37
.gitlab-ci.yml
View File

@ -3,36 +3,51 @@ image: sobc/gitlab-ci
stages:
- build
- test
- run
- static_analyze
- dynamic_analyze
before_script:
- apt-get update && apt-get install -y libeigen3-dev
build:
build_debug:
stage: build
artifacts:
paths:
- debug/app/1D
- debug/app/2D
expire_in: 100s
script:
- mkdir debug && cd debug
- cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_TESTING=ON ..
- make -j$(nproc)
build_release:
stage: build
artifacts:
paths:
- build/app/1D
- build/app/2D
- build/app/Comp2D
- build/test/test
expire_in: 100s
script:
- mkdir build && cd build
- cmake -DCMAKE_BUILD_TYPE=Debug ..
- make
- cmake -DCMAKE_BUILD_TYPE=GenericOpt -DENABLE_TESTING=ON ..
- make -j$(nproc)
test:
stage: test
script:
- ./build/test/test
run_1D:
stage: test
dependencies:
- build
stage: run
script:
- ./build/app/1D
run_2D:
stage: test
dependencies:
- build
stage: run
script:
- ./build/app/2D
@ -46,11 +61,11 @@ lint:
memcheck_1D:
stage: dynamic_analyze
script:
- cd build/app
- cd debug/app
- valgrind --tool=memcheck --leak-check=full --show-leak-kinds=all --track-origins=yes ./1D 1>/dev/null
memcheck_2D:
stage: dynamic_analyze
script:
- cd build/app
- cd debug/app
- valgrind --tool=memcheck --leak-check=full --show-leak-kinds=all --track-origins=yes ./2D 1>/dev/null

8
CMakeLists.txt
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@ -29,5 +29,13 @@ if(USE_UNSAFE_MATH_OPT)
add_compile_options(-ffast-math)
endif()
option(ENABLE_TESTING
"Run tests after succesfull compilation"
OFF)
add_subdirectory(app)
add_subdirectory(src)
if(ENABLE_TESTING)
add_subdirectory(test)
endif()

10
app/main_1D.cpp
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@ -1,5 +1,5 @@
#include "diffusion/BTCSBoundaryCondition.hpp"
#include <diffusion/BTCSDiffusion.hpp>
#include <diffusion/BoundaryCondition.hpp>
#include <iomanip>
#include <iostream> // for std
@ -18,7 +18,8 @@ int main(int argc, char *argv[]) {
// create input + diffusion coefficients for each grid cell
std::vector<double> alpha(n, 1e-1);
std::vector<double> field(n, 1e-6);
std::vector<boundary_condition> bc(n + 2, {0, 0});
BTCSBoundaryCondition bc;
// create instance of diffusion module
BTCSDiffusion diffu(dim);
@ -26,7 +27,8 @@ int main(int argc, char *argv[]) {
diffu.setXDimensions(1, n);
// set the boundary condition for the left ghost cell to dirichlet
bc[0] = {Diffusion::BC_CONSTANT, 5e-6};
bc(BC_SIDE_LEFT) = {BC_TYPE_CONSTANT, 5e-6};
// bc[0] = {Diffusion::BC_CONSTANT, 5e-6};
// diffu.setBoundaryCondition(1, 0, BTCSDiffusion::BC_CONSTANT,
// 5. * std::pow(10, -6));
@ -38,7 +40,7 @@ int main(int argc, char *argv[]) {
// loop 100 times
// output is currently generated by the method itself
for (int i = 0; i < 100; i++) {
diffu.simulate(field.data(), alpha.data(), bc.data());
diffu.simulate(field.data(), alpha.data(), bc);
cout << "Iteration: " << i << "\n\n";

25
app/main_2D.cpp
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@ -1,5 +1,5 @@
#include "diffusion/BTCSBoundaryCondition.hpp"
#include <diffusion/BTCSDiffusion.hpp>
#include <diffusion/BoundaryCondition.hpp>
#include <iomanip>
#include <iostream> // for std
#include <vector> // for vector
@ -16,39 +16,42 @@ int main(int argc, char *argv[]) {
int m = 5;
// create input + diffusion coefficients for each grid cell
std::vector<double> alpha(n * m, 1e-1);
std::vector<double> field(n * m, 1e-6);
std::vector<boundary_condition> bc((n + 2) * (m + 2), {0, 0});
std::vector<double> alpha(n * m, 1e-6);
std::vector<double> field(n * m, 0);
BTCSBoundaryCondition bc(n, m);
// create instance of diffusion module
BTCSDiffusion diffu(dim);
diffu.setXDimensions(1, n);
diffu.setYDimensions(1, m);
diffu.setXDimensions(n, n);
diffu.setYDimensions(m, m);
// set inlet to higher concentration without setting bc
field[12] = 5e-3;
field[12] = 1;
// set timestep for simulation to 1 second
diffu.setTimestep(1.);
diffu.setTimestep(1);
cout << setprecision(12);
for (int t = 0; t < 10; t++) {
diffu.simulate(field.data(), alpha.data(), bc.data());
for (int t = 0; t < 1000; t++) {
diffu.simulate(field.data(), alpha.data(), bc);
cout << "Iteration: " << t << "\n\n";
double sum = 0;
// iterate through rows
for (int i = 0; i < m; i++) {
// iterate through columns
for (int j = 0; j < n; j++) {
cout << left << std::setw(20) << field[i * n + j];
sum += field[i * n + j];
}
cout << "\n";
}
cout << "\n" << endl;
cout << "sum: " << sum << "\n" << endl;
}
return 0;

16
app/main_2D_const.cpp
View File

@ -1,5 +1,5 @@
#include "diffusion/BTCSBoundaryCondition.hpp"
#include <diffusion/BTCSDiffusion.hpp>
#include <diffusion/BoundaryCondition.hpp>
#include <iomanip>
#include <iostream> // for std
#include <vector> // for vector
@ -18,7 +18,7 @@ int main(int argc, char *argv[]) {
// create input + diffusion coefficients for each grid cell
std::vector<double> alpha(n * m, 1e-1);
std::vector<double> field(n * m, 1e-6);
std::vector<boundary_condition> bc((n + 2) * (m + 2), {0, 0});
BTCSBoundaryCondition bc(n, m);
// create instance of diffusion module
BTCSDiffusion diffu(dim);
@ -26,16 +26,20 @@ int main(int argc, char *argv[]) {
diffu.setXDimensions(1, n);
diffu.setYDimensions(1, m);
for (int i = 1; i <= n; i++) {
bc[(n + 2) * i] = {Diffusion::BC_CONSTANT, 5e-6};
}
boundary_condition input = {Diffusion::BC_TYPE_CONSTANT, 5e-6};
bc.setSide(BC_SIDE_LEFT, input);
// for (int i = 1; i <= n; i++) {
// bc[(n + 2) * i] = {Diffusion::BC_CONSTANT, 5e-6};
// }
// set timestep for simulation to 1 second
diffu.setTimestep(1.);
cout << setprecision(12);
for (int t = 0; t < 10; t++) {
diffu.simulate(field.data(), alpha.data(), bc.data());
diffu.simulate(field.data(), alpha.data(), bc);
cout << "Iteration: " << t << "\n\n";

8
app/main_2D_mdl.cpp
View File

@ -1,5 +1,5 @@
#include "diffusion/BTCSBoundaryCondition.hpp"
#include <diffusion/BTCSDiffusion.hpp>
#include <diffusion/BoundaryCondition.hpp>
#include <iomanip>
#include <iostream> // for std
#include <vector> // for vector
@ -16,9 +16,9 @@ int main(int argc, char *argv[]) {
int m = 501;
// create input + diffusion coefficients for each grid cell
std::vector<double> alpha(n * m, 1e-1);
std::vector<double> alpha(n * m, 1e-3);
std::vector<double> field(n * m, 0.);
std::vector<boundary_condition> bc((n + 2) * (m + 2), {0, 0});
BTCSBoundaryCondition bc(n, m);
field[125500] = 1;
@ -51,7 +51,7 @@ int main(int argc, char *argv[]) {
// Now we simulate and output 8 steps à 1 sec
for (int t = 1; t < 6; t++) {
double time = diffu.simulate(field.data(), alpha.data(), bc.data());
double time = diffu.simulate(field.data(), alpha.data(), bc);
cerr << "time elapsed: " << time << " seconds" << endl;

186
include/diffusion/BTCSBoundaryCondition.hpp Normal file
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@ -0,0 +1,186 @@
#ifndef BOUNDARYCONDITION_H_
#define BOUNDARYCONDITION_H_
#include <array>
#include <bits/stdint-uintn.h>
#include <stdexcept>
#include <stdint.h>
#include <vector>
typedef uint8_t bctype;
namespace Diffusion {
/**
* Defines a closed/Neumann boundary condition.
*/
static const bctype BC_TYPE_CLOSED = 0;
/**
* Defines a flux/Cauchy boundary condition.
*/
static const bctype BC_TYPE_FLUX = 1;
/**
* Defines a constant/Dirichlet boundary condition.
*/
static const bctype BC_TYPE_CONSTANT = 2;
/**
* Defines boundary conditions for the left side of the grid.
*/
static const uint8_t BC_SIDE_LEFT = 0;
/**
* Defines boundary conditions for the right side of the grid.
*/
static const uint8_t BC_SIDE_RIGHT = 1;
/**
* Defines boundary conditions for the top of the grid.
*/
static const uint8_t BC_SIDE_TOP = 2;
/**
* Defines boundary conditions for the bottom of the grid.
*/
static const uint8_t BC_SIDE_BOTTOM = 3;
/**
* Defines the boundary condition type and according value.
*/
typedef struct boundary_condition_s {
bctype type; /**< Type of the boundary condition */
double value; /**< Value of the boundary condition. Either a concrete value of
concentration for BC_TYPE_CONSTANT or gradient when type is
BC_TYPE_FLUX. Unused if BC_TYPE_CLOSED.*/
} boundary_condition;
/**
* Internal use only.
*/
typedef std::array<boundary_condition, 2> bc_tuple;
/**
* Class to define the boundary condition of a grid.
*/
class BTCSBoundaryCondition {
public:
/**
* Creates a new instance with two elements. Used when defining boundary
* conditions of 1D grids.
*/
BTCSBoundaryCondition();
/**
* Creates a new instance with 4 * max(x,y) elements. Used to describe the
* boundary conditions for 2D grids. NOTE: On non-squared grids there are more
* elements than needed and no exception is thrown if some index exceeding
* grid limits.
*
* \param x Number of grid cells in x-direction
* \param y Number of grid cells in y-direction
*
*/
BTCSBoundaryCondition(int x, int y);
/**
* Sets the boundary condition for a specific side of the grid.
*
* \param side Side for which the given boundary condition should be set.
* \param input_bc Instance of struct boundary_condition with desired boundary
* condition.
*
* \throws std::invalid_argument Indicates wrong dimensions of the grid.
* \throws std::out_of_range Indicates a out of range value for side.
*/
void setSide(uint8_t side, boundary_condition &input_bc);
/**
* Get both boundary conditions of a given row (left and right).
*
* \param i Index of row
*
* \returns Left and right boundary values as an array (defined as data
* type bc_tuple).
*/
auto row(uint32_t i) const -> bc_tuple;
/**
* Get both boundary conditions of a given column (top and bottom).
*
* \param i Index of column
*
* \returns Top and bottom boundary values as an array (defined as data
* type bc_tuple).
*/
auto col(uint32_t i) const -> bc_tuple;
/**
* Create an instance of boundary_condition data type. Can be seen as a helper
* function.
*
* \param type Type of the boundary condition.
* \param value According value of condition.
*
* \returns Instance of boundary_condition
*/
static boundary_condition returnBoundaryCondition(bctype type, double value) {
return {type, value};
}
private:
std::vector<boundary_condition> bc_internal;
uint8_t dim;
uint32_t maxsize;
public:
boundary_condition operator()(uint8_t side) const {
if (dim != 1) {
throw std::invalid_argument(
"Only 1D grid support 1 parameter in operator");
}
if (side > 1) {
throw std::out_of_range("1D index out of range");
}
return bc_internal[side];
}
boundary_condition operator()(uint8_t side, uint32_t i) const {
if (dim != 2) {
throw std::invalid_argument(
"Only 2D grids support 2 parameters in operator");
}
if (side > 3) {
throw std::out_of_range("2D index out of range");
}
return bc_internal[side * maxsize + i];
}
boundary_condition &operator()(uint8_t side) {
if (dim != 1) {
throw std::invalid_argument("Explicit setting of bc value with 2 "
"parameters is only supported for 2D grids");
}
if (side > 1) {
throw std::out_of_range("2D index out of range");
}
return bc_internal[side];
}
boundary_condition &operator()(uint8_t side, uint32_t i) {
if (dim != 2) {
throw std::invalid_argument("Explicit setting of bc value with 2 "
"parameters is only supported for 2D grids");
}
if (side > 3) {
throw std::out_of_range("2D index out of range");
}
return bc_internal[side * maxsize + i];
}
};
} // namespace Diffusion
#endif // BOUNDARYCONDITION_H_

31
include/diffusion/BTCSDiffusion.hpp
View File

@ -1,7 +1,7 @@
#ifndef BTCSDIFFUSION_H_
#define BTCSDIFFUSION_H_
#include "BoundaryCondition.hpp"
#include "diffusion/BTCSBoundaryCondition.hpp"
#include <Eigen/Sparse>
#include <Eigen/src/Core/Map.h>
@ -93,11 +93,11 @@ public:
* state of each grid cell.
* \param alpha Pointer to memory area of diffusion coefficients for each grid
* element.
* \param bc Pointer to memory setting boundary conidition of each grid cell.
* \param bc Instance of boundary condition class with.
*
* \return Time in seconds [s] used to simulate one iteration.
*/
auto simulate(double *c, double *alpha, Diffusion::boundary_condition *bc)
auto simulate(double *c, double *alpha, const BTCSBoundaryCondition &bc)
-> double;
/*!
@ -112,38 +112,31 @@ private:
DMatrixRowMajor;
typedef Eigen::Matrix<double, 1, Eigen::Dynamic, Eigen::RowMajor>
DVectorRowMajor;
typedef Eigen::Matrix<Diffusion::boundary_condition, Eigen::Dynamic,
Eigen::Dynamic, Eigen::RowMajor>
BCMatrixRowMajor;
typedef Eigen::Matrix<Diffusion::boundary_condition, 1, Eigen::Dynamic,
Eigen::RowMajor>
BCVectorRowMajor;
void simulate_base(DVectorRowMajor &c, const BCVectorRowMajor &bc,
static void simulate_base(DVectorRowMajor &c, const bc_tuple &bc,
const DVectorRowMajor &alpha, double dx, double time_step,
int size, const DVectorRowMajor &d_ortho);
void simulate1D(Eigen::Map<DVectorRowMajor> &c,
Eigen::Map<const DVectorRowMajor> &alpha,
Eigen::Map<const BCVectorRowMajor> &bc);
const BTCSBoundaryCondition &bc);
void simulate2D(Eigen::Map<DMatrixRowMajor> &c,
Eigen::Map<const DMatrixRowMajor> &alpha,
Eigen::Map<const BCMatrixRowMajor> &bc);
const BTCSBoundaryCondition &bc);
auto calc_d_ortho(const DMatrixRowMajor &c, const DMatrixRowMajor &alpha,
const BCMatrixRowMajor &bc, double time_step, double dx)
-> DMatrixRowMajor;
static auto calc_d_ortho(const DMatrixRowMajor &c, const DMatrixRowMajor &alpha,
const BTCSBoundaryCondition &bc, bool transposed,
double time_step, double dx) -> DMatrixRowMajor;
static void fillMatrixFromRow(Eigen::SparseMatrix<double> &A_matrix,
const DVectorRowMajor &alpha,
const BCVectorRowMajor &bc, int size, double dx,
double time_step);
const DVectorRowMajor &alpha, int size,
double dx, double time_step);
static void fillVectorFromRow(Eigen::VectorXd &b_vector,
const DVectorRowMajor &c,
const DVectorRowMajor &alpha,
const BCVectorRowMajor &bc,
const bc_tuple &bc,
const DVectorRowMajor &d_ortho, int size,
double dx, double time_step);
void simulate3D(std::vector<double> &c);

33
include/diffusion/BoundaryCondition.hpp
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@ -1,33 +0,0 @@
#ifndef BOUNDARYCONDITION_H_
#define BOUNDARYCONDITION_H_
namespace Diffusion {
/*!
* Defines both types of boundary condition as a datatype.
*/
typedef int bctype;
/*!
* Defines a closed/Neumann boundary condition.
*/
static const bctype BC_CLOSED = 0;
/*!
* Defines a flux/Cauchy boundary condition.
*/
static const bctype BC_FLUX = 1;
/*!
* Defines a constant/Dirichlet boundary condition.
*/
static const bctype BC_CONSTANT = 2;
typedef struct boundary_condition {
bctype type;
double value;
} boundary_condition;
} // namespace Diffusion
#endif // BOUNDARYCONDITION_H_

56
src/BTCSBoundaryCondition.cpp Normal file
View File

@ -0,0 +1,56 @@
#include <bits/stdint-uintn.h>
#include <diffusion/BTCSBoundaryCondition.hpp>
#include <stdexcept>
constexpr uint8_t DIM_1D = 2;
constexpr uint8_t DIM_2D = 4;
Diffusion::BTCSBoundaryCondition::BTCSBoundaryCondition() {
this->bc_internal.resize(DIM_1D, {0, 0});
this->dim = 1;
// this value is actually unused
this->maxsize = 1;
}
Diffusion::BTCSBoundaryCondition::BTCSBoundaryCondition(int x, int y) {
this->maxsize = (x >= y ? x : y);
this->bc_internal.resize(DIM_2D * maxsize, {0, 0});
this->dim = 2;
}
void Diffusion::BTCSBoundaryCondition::setSide(
uint8_t side, Diffusion::boundary_condition &input_bc) {
if (this->dim == 1) {
throw std::invalid_argument("setSide requires at least a 2D grid");
}
if (side > 3) {
throw std::out_of_range("Invalid range for 2D grid");
}
for (int i = 0; i < maxsize; i++) {
this->bc_internal[side * maxsize + i] = input_bc;
}
}
auto Diffusion::BTCSBoundaryCondition::col(uint32_t i) const
-> Diffusion::bc_tuple {
if (this->dim == 1) {
throw std::invalid_argument("Access of column requires at least 2D grid");
}
if (i >= this->maxsize) {
throw std::out_of_range("Index out of range");
}
return {this->bc_internal[BC_SIDE_TOP * this->maxsize + i],
this->bc_internal[BC_SIDE_BOTTOM * this->maxsize + i]};
}
auto Diffusion::BTCSBoundaryCondition::row(uint32_t i) const
-> Diffusion::bc_tuple {
if (i >= this->maxsize) {
throw std::out_of_range("Index out of range");
}
return {this->bc_internal[BC_SIDE_LEFT * this->maxsize + i],
this->bc_internal[BC_SIDE_RIGHT * this->maxsize + i]};
}

119
src/BTCSDiffusion.cpp
View File

@ -1,5 +1,5 @@
#include "diffusion/BTCSDiffusion.hpp"
#include "diffusion/BoundaryCondition.hpp"
#include "diffusion/BTCSBoundaryCondition.hpp"
#include <Eigen/SparseLU>
@ -9,6 +9,7 @@
#include <Eigen/src/SparseCore/SparseMatrixBase.h>
#include <algorithm>
#include <array>
#include <bits/stdint-uintn.h>
#include <cassert>
#include <chrono>
#include <cstddef>
@ -25,7 +26,7 @@
#define omp_get_thread_num() 0
#endif
#define DOUBLE_MACHINE_EPSILON 1.93e-34
constexpr double DOUBLE_MACHINE_EPSILON = 1.93e-34;
constexpr int BTCS_MAX_DEP_PER_CELL = 3;
constexpr int BTCS_2D_DT_SIZE = 2;
@ -87,7 +88,7 @@ void Diffusion::BTCSDiffusion::updateInternals() {
}
}
void Diffusion::BTCSDiffusion::simulate_base(DVectorRowMajor &c,
const BCVectorRowMajor &bc,
const Diffusion::bc_tuple &bc,
const DVectorRowMajor &alpha,
double dx, double time_step,
int size,
@ -103,7 +104,7 @@ void Diffusion::BTCSDiffusion::simulate_base(DVectorRowMajor &c,
b_vector.resize(size + 2);
x_vector.resize(size + 2);
fillMatrixFromRow(A_matrix, alpha, bc, size, dx, time_step);
fillMatrixFromRow(A_matrix, alpha, size, dx, time_step);
fillVectorFromRow(b_vector, c, alpha, bc, d_ortho, size, dx, time_step);
// start to solve
@ -120,7 +121,7 @@ void Diffusion::BTCSDiffusion::simulate_base(DVectorRowMajor &c,
void Diffusion::BTCSDiffusion::simulate1D(
Eigen::Map<DVectorRowMajor> &c, Eigen::Map<const DVectorRowMajor> &alpha,
Eigen::Map<const BCVectorRowMajor> &bc) {
const Diffusion::BTCSBoundaryCondition &bc) {
int size = this->grid_cells[0];
double dx = this->deltas[0];
@ -128,7 +129,7 @@ void Diffusion::BTCSDiffusion::simulate1D(
DVectorRowMajor input_field = c.row(0);
simulate_base(input_field, bc, alpha, dx, time_step, size,
simulate_base(input_field, bc.row(0), alpha, dx, time_step, size,
Eigen::VectorXd::Constant(size, 0));
c.row(0) << input_field;
@ -136,7 +137,7 @@ void Diffusion::BTCSDiffusion::simulate1D(
void Diffusion::BTCSDiffusion::simulate2D(
Eigen::Map<DMatrixRowMajor> &c, Eigen::Map<const DMatrixRowMajor> &alpha,
Eigen::Map<const BCMatrixRowMajor> &bc) {
const Diffusion::BTCSBoundaryCondition &bc) {
int n_rows = this->grid_cells[1];
int n_cols = this->grid_cells[0];
@ -144,35 +145,37 @@ void Diffusion::BTCSDiffusion::simulate2D(
double local_dt = this->time_step / BTCS_2D_DT_SIZE;
DMatrixRowMajor d_ortho = calc_d_ortho(c, alpha, bc, local_dt, dx);
DMatrixRowMajor d_ortho = calc_d_ortho(c, alpha, bc, false, local_dt, dx);
#pragma omp parallel for schedule(dynamic)
for (int i = 0; i < n_rows; i++) {
DVectorRowMajor input_field = c.row(i);
simulate_base(input_field, bc.row(i + 1), alpha.row(i), dx, local_dt,
n_cols, d_ortho.row(i));
simulate_base(input_field, bc.row(i), alpha.row(i), dx, local_dt, n_cols,
d_ortho.row(i));
c.row(i) << input_field;
}
dx = this->deltas[1];
d_ortho = calc_d_ortho(c.transpose(), alpha.transpose(), bc.transpose(),
local_dt, dx);
d_ortho =
calc_d_ortho(c.transpose(), alpha.transpose(), bc, true, local_dt, dx);
#pragma omp parallel for schedule(dynamic)
for (int i = 0; i < n_cols; i++) {
DVectorRowMajor input_field = c.col(i);
simulate_base(input_field, bc.col(i + 1), alpha.col(i), dx, local_dt,
n_rows, d_ortho.row(i));
simulate_base(input_field, bc.col(i), alpha.col(i), dx, local_dt, n_rows,
d_ortho.row(i));
c.col(i) << input_field.transpose();
}
}
auto Diffusion::BTCSDiffusion::calc_d_ortho(const DMatrixRowMajor &c,
const DMatrixRowMajor &alpha,
const BCMatrixRowMajor &bc,
double time_step, double dx)
-> DMatrixRowMajor {
auto Diffusion::BTCSDiffusion::calc_d_ortho(
const DMatrixRowMajor &c, const DMatrixRowMajor &alpha,
const Diffusion::BTCSBoundaryCondition &bc, bool transposed,
double time_step, double dx) -> DMatrixRowMajor {
uint8_t upper = (transposed ? Diffusion::BC_SIDE_LEFT : Diffusion::BC_SIDE_TOP);
uint8_t lower = (transposed ? Diffusion::BC_SIDE_RIGHT : Diffusion::BC_SIDE_BOTTOM);
int n_rows = c.rows();
int n_cols = c.cols();
@ -183,10 +186,10 @@ auto Diffusion::BTCSDiffusion::calc_d_ortho(const DMatrixRowMajor &c,
// first, iterate over first row
for (int j = 0; j < n_cols; j++) {
boundary_condition tmp_bc = bc(0, j + 1);
boundary_condition tmp_bc = bc(upper, j);
double sy = (time_step * alpha(0, j)) / (dx * dx);
y_values[0] = (tmp_bc.type == Diffusion::BC_CONSTANT
y_values[0] = (tmp_bc.type == Diffusion::BC_TYPE_CONSTANT
? tmp_bc.value
: getBCFromFlux(tmp_bc, c(0, j), alpha(0, j)));
y_values[1] = c(0, j);
@ -213,12 +216,12 @@ auto Diffusion::BTCSDiffusion::calc_d_ortho(const DMatrixRowMajor &c,
// and finally over last row
for (int j = 0; j < n_cols; j++) {
boundary_condition tmp_bc = bc(end + 1, j + 1);
boundary_condition tmp_bc = bc(lower, j);
double sy = (time_step * alpha(end, j)) / (dx * dx);
y_values[0] = c(end - 1, j);
y_values[1] = c(end, j);
y_values[2] = (tmp_bc.type == Diffusion::BC_CONSTANT
y_values[2] = (tmp_bc.type == Diffusion::BC_TYPE_CONSTANT
? tmp_bc.value
: getBCFromFlux(tmp_bc, c(end, j), alpha(end, j)));
@ -230,73 +233,49 @@ auto Diffusion::BTCSDiffusion::calc_d_ortho(const DMatrixRowMajor &c,
void Diffusion::BTCSDiffusion::fillMatrixFromRow(
Eigen::SparseMatrix<double> &A_matrix, const DVectorRowMajor &alpha,
const BCVectorRowMajor &bc, int size, double dx, double time_step) {
int size, double dx, double time_step) {
Diffusion::boundary_condition left = bc[1];
Diffusion::boundary_condition right = bc[size];
bool left_constant = (left.type == Diffusion::BC_CONSTANT);
bool right_constant = (right.type == Diffusion::BC_CONSTANT);
double sx = 0;
int A_size = A_matrix.cols();
A_matrix.insert(0, 0) = 1;
if (left_constant) {
A_matrix.insert(1, 1) = 1;
} else {
double sx = (alpha[0] * time_step) / (dx * dx);
A_matrix.insert(1, 1) = -1. - 3. * sx;
A_matrix.insert(1, 0) = 2. * sx;
A_matrix.insert(1, 2) = sx;
}
sx = (alpha[0] * time_step) / (dx * dx);
A_matrix.insert(1, 1) = -1. - 3. * sx;
A_matrix.insert(1, 0) = 2. * sx;
A_matrix.insert(1, 2) = sx;
for (int j = 2, k = j - 1; k < size - 1; j++, k++) {
double sx = (alpha[k] * time_step) / (dx * dx);
if (bc[k + 1].type == Diffusion::BC_CONSTANT) {
A_matrix.insert(j, j) = 1;
continue;
}
sx = (alpha[k] * time_step) / (dx * dx);
A_matrix.insert(j, j) = -1. - 2. * sx;
A_matrix.insert(j, (j - 1)) = sx;
A_matrix.insert(j, (j + 1)) = sx;
}
if (right_constant) {
A_matrix.insert(A_size - 2, A_size - 2) = 1;
} else {
double sx = (alpha[size - 1] * time_step) / (dx * dx);
A_matrix.insert(A_size - 2, A_size - 2) = -1. - 3. * sx;
A_matrix.insert(A_size - 2, A_size - 3) = sx;
A_matrix.insert(A_size - 2, A_size - 1) = 2. * sx;
}
sx = (alpha[size - 1] * time_step) / (dx * dx);
A_matrix.insert(A_size - 2, A_size - 2) = -1. - 3. * sx;
A_matrix.insert(A_size - 2, A_size - 3) = sx;
A_matrix.insert(A_size - 2, A_size - 1) = 2. * sx;
A_matrix.insert(A_size - 1, A_size - 1) = 1;
}
void Diffusion::BTCSDiffusion::fillVectorFromRow(
Eigen::VectorXd &b_vector, const DVectorRowMajor &c,
const DVectorRowMajor &alpha, const BCVectorRowMajor &bc,
const DVectorRowMajor &alpha, const bc_tuple &bc,
const DVectorRowMajor &d_ortho, int size, double dx, double time_step) {
Diffusion::boundary_condition left = bc[0];
Diffusion::boundary_condition right = bc[size + 1];
Diffusion::boundary_condition right = bc[1];
bool left_constant = (left.type == Diffusion::BC_CONSTANT);
bool right_constant = (right.type == Diffusion::BC_CONSTANT);
bool left_constant = (left.type == Diffusion::BC_TYPE_CONSTANT);
bool right_constant = (right.type == Diffusion::BC_TYPE_CONSTANT);
int b_size = b_vector.size();
for (int j = 0; j < size; j++) {
boundary_condition tmp_bc = bc[j + 1];
if (tmp_bc.type == Diffusion::BC_CONSTANT) {
b_vector[j + 1] = tmp_bc.value;
continue;
}
b_vector[j + 1] = -c[j] + d_ortho[j];
}
@ -314,8 +293,8 @@ void Diffusion::BTCSDiffusion::setTimestep(double time_step) {
this->time_step = time_step;
}
auto Diffusion::BTCSDiffusion::simulate(double *c, double *alpha,
Diffusion::boundary_condition *bc)
auto Diffusion::BTCSDiffusion::simulate(
double *c, double *alpha, const Diffusion::BTCSBoundaryCondition &bc)
-> double {
std::chrono::high_resolution_clock::time_point start =
@ -324,9 +303,8 @@ auto Diffusion::BTCSDiffusion::simulate(double *c, double *alpha,
if (this->grid_dim == 1) {
Eigen::Map<DVectorRowMajor> c_in(c, this->grid_cells[0]);
Eigen::Map<const DVectorRowMajor> alpha_in(alpha, this->grid_cells[0]);
Eigen::Map<const BCVectorRowMajor> bc_in(bc, this->grid_cells[0] + 2);
simulate1D(c_in, alpha_in, bc_in);
simulate1D(c_in, alpha_in, bc);
}
if (this->grid_dim == 2) {
Eigen::Map<DMatrixRowMajor> c_in(c, this->grid_cells[1],
@ -335,10 +313,7 @@ auto Diffusion::BTCSDiffusion::simulate(double *c, double *alpha,
Eigen::Map<const DMatrixRowMajor> alpha_in(alpha, this->grid_cells[1],
this->grid_cells[0]);
Eigen::Map<const BCMatrixRowMajor> bc_in(bc, this->grid_cells[1] + 2,
this->grid_cells[0] + 2);
simulate2D(c_in, alpha_in, bc_in);
simulate2D(c_in, alpha_in, bc);
}
std::chrono::high_resolution_clock::time_point end =
@ -357,9 +332,9 @@ inline auto Diffusion::BTCSDiffusion::getBCFromFlux(boundary_condition bc,
double val = 0;
if (bc.type == Diffusion::BC_CLOSED) {
if (bc.type == Diffusion::BC_TYPE_CLOSED) {
val = neighbor_c;
} else if (bc.type == Diffusion::BC_FLUX) {
} else if (bc.type == Diffusion::BC_TYPE_FLUX) {
// TODO
// val = bc[index].value;
} else {

5
src/CMakeLists.txt
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@ -1,7 +1,4 @@
set(HEADER_LIST "${BTCSDiffusion_SOURCE_DIR}/include/diffusion/BTCSDiffusion.hpp"
"${BTCSDiffusion_SOURCE_DIR}/include/diffusion/BoundaryCondition.hpp")
add_library(BTCSDiffusion STATIC BTCSDiffusion.cpp ${HEADER_LIST})
add_library(BTCSDiffusion STATIC BTCSDiffusion.cpp BTCSBoundaryCondition.cpp)
target_link_libraries(BTCSDiffusion Eigen3::Eigen)

5
test/CMakeLists.txt Normal file
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@ -0,0 +1,5 @@
add_library(doctest INTERFACE)
target_include_directories(doctest INTERFACE doctest)
add_executable(test setup.cpp testBoundaryCondition.cpp testDiffusion.cpp)
target_link_libraries(test doctest BTCSDiffusion)

6816
test/doctest/doctest.h Normal file
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File diff suppressed because it is too large Load Diff

2
test/setup.cpp Normal file
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@ -0,0 +1,2 @@
#define DOCTEST_CONFIG_IMPLEMENT_WITH_MAIN
#include "doctest.h"

83
test/testBoundaryCondition.cpp Normal file
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@ -0,0 +1,83 @@
#include <diffusion/BTCSBoundaryCondition.hpp>
#include <doctest.h>
using namespace Diffusion;
#define BC_CONST_VALUE 1e-5
TEST_CASE("1D Boundary Condition") {
BTCSBoundaryCondition bc;
boundary_condition bc_set = {BC_TYPE_CONSTANT, BC_CONST_VALUE};
SUBCASE("valid get") { CHECK_EQ(bc(BC_SIDE_LEFT).value, 0); }
SUBCASE("invalid get") {
CHECK_THROWS(bc(BC_SIDE_TOP));
CHECK_THROWS(bc(BC_SIDE_LEFT, 1));
}
SUBCASE("valid set") {
CHECK_NOTHROW(bc(BC_SIDE_LEFT) = bc_set);
CHECK_EQ(bc(BC_SIDE_LEFT).value, bc_set.value);
CHECK_EQ(bc(BC_SIDE_LEFT).type, bc_set.type);
}
SUBCASE("invalid set") {
CHECK_THROWS(bc(BC_SIDE_TOP) = bc_set);
CHECK_THROWS(bc(BC_SIDE_LEFT, 0) = bc_set);
}
SUBCASE("valid row getter") {
bc(BC_SIDE_LEFT) = bc_set;
bc_tuple tup = bc.row(0);
CHECK_EQ(tup[0].value, BC_CONST_VALUE);
CHECK_EQ(tup[1].value, 0);
}
SUBCASE("invalid row and col getter") {
CHECK_THROWS(bc.row(1));
CHECK_THROWS(bc.col(0));
}
}
TEST_CASE("2D Boundary Condition") {
BTCSBoundaryCondition bc(5, 5);
boundary_condition bc_set = {BC_TYPE_CONSTANT, BC_CONST_VALUE};
SUBCASE("valid get") { CHECK_EQ(bc(BC_SIDE_LEFT, 0).value, 0); }
SUBCASE("invalid get") {
CHECK_THROWS(bc(4, 0));
CHECK_THROWS(bc(BC_SIDE_LEFT));
}
SUBCASE("valid set") {
CHECK_NOTHROW(bc(BC_SIDE_LEFT, 0) = bc_set);
CHECK_EQ(bc(BC_SIDE_LEFT, 0).value, bc_set.value);
CHECK_EQ(bc(BC_SIDE_LEFT, 0).type, bc_set.type);
}
SUBCASE("invalid set") {
CHECK_THROWS(bc(BC_SIDE_LEFT) = bc_set);
CHECK_THROWS(bc(4, 0) = bc_set);
}
SUBCASE("call of setSide") {
CHECK_NOTHROW(bc.setSide(BC_SIDE_BOTTOM, bc_set));
CHECK_EQ(bc(BC_SIDE_BOTTOM, 1).value, bc_set.value);
CHECK_EQ(bc(BC_SIDE_BOTTOM, 1).type, bc_set.type);
}
}
TEST_CASE("Boundary Condition helpers") {
boundary_condition bc_set = {BC_TYPE_CONSTANT, BC_CONST_VALUE};
SUBCASE("return boundary condition skeleton") {
boundary_condition bc_test = BTCSBoundaryCondition::returnBoundaryCondition(bc_set.type, bc_set.value);
CHECK_EQ(bc_test.value, bc_set.value);
CHECK_EQ(bc_test.type, bc_set.type);
}
}

125
test/testDiffusion.cpp Normal file
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@ -0,0 +1,125 @@
#include <bits/stdint-uintn.h>
#include <diffusion/BTCSBoundaryCondition.hpp>
#include <diffusion/BTCSDiffusion.hpp>
#include <doctest.h>
#include <vector>
using namespace Diffusion;
#define DIMENSION 2
#define N 51
#define M 51
#define MID 1300
static std::vector<double> alpha(N *M, 1e-3);
static BTCSDiffusion setupDiffu(uint32_t n, uint32_t m) {
BTCSDiffusion diffu(DIMENSION);
diffu.setXDimensions(n, n);
diffu.setYDimensions(m, m);
diffu.setTimestep(1.);
return diffu;
}
TEST_CASE("closed boundaries - 1 concentration to 1 - rest 0") {
std::vector<double> field(N * M, 0);
field[MID] = 1;
BTCSDiffusion diffu = setupDiffu(N, M);
BTCSBoundaryCondition bc(N, M);
uint32_t iterations = 1000;
double sum = 0;
for (int t = 0; t < iterations; t++) {
diffu.simulate(field.data(), alpha.data(), bc);
if (t == iterations - 1) {
// iterate through rows
for (int i = 0; i < M; i++) {
// iterate through columns
for (int j = 0; j < N; j++) {
sum += field[i * N + j];
}
}
}
}
CAPTURE(sum);
// epsilon of 1e-8
CHECK(sum == doctest::Approx(1).epsilon(1e-6));
}
TEST_CASE("constant boundaries (0) - 1 concentration to 1 - rest 0") {
std::vector<double> field(N * M, 0);
field[MID] = 1;
BTCSDiffusion diffu = setupDiffu(N, M);
BTCSBoundaryCondition bc(N, M);
boundary_condition input = {BC_TYPE_CONSTANT, 0};
bc.setSide(BC_SIDE_LEFT, input);
bc.setSide(BC_SIDE_RIGHT, input);
bc.setSide(BC_SIDE_TOP, input);
bc.setSide(BC_SIDE_BOTTOM, input);
uint32_t max_iterations = 20000;
bool reached = false;
int t = 0;
for (t = 0; t < max_iterations; t++) {
diffu.simulate(field.data(), alpha.data(), bc);
if (field[N * M - 1] > 1e-15) {
reached = true;
break;
}
}
if (!reached) {
CAPTURE(field[N * M - 1]);
FAIL_CHECK(
"Concentration did not reach boundaries after count of iterations: ",
t);
}
}
TEST_CASE(
"constant top and bottom (1 and 0) - left and right closed - 0 inlet") {
std::vector<double> field(N * M, 0);
BTCSDiffusion diffu = setupDiffu(N, M);
BTCSBoundaryCondition bc(N, M);
boundary_condition top =
BTCSBoundaryCondition::returnBoundaryCondition(BC_TYPE_CONSTANT, 1);
boundary_condition bottom =
BTCSBoundaryCondition::returnBoundaryCondition(BC_TYPE_CONSTANT, 0);
bc.setSide(BC_SIDE_TOP, top);
bc.setSide(BC_SIDE_BOTTOM, bottom);
uint32_t max_iterations = 100;
for (int t = 0; t < max_iterations; t++) {
diffu.simulate(field.data(), alpha.data(), bc);
}
for (int i = 0; i < N; i++) {
double above = field[i];
for (int j = 1; j < M; j++) {
double curr = field[j * N + i];
if (curr > above) {
CAPTURE(curr);
CAPTURE(above);
FAIL("Concentration below is greater than above @ cell ", j * N + i);
}
}
}
}