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Add math function from file #692 #701

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Add math function from file #692 #701

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13f5194
:art: add math function from file
Nov 27, 2020
a413321
:wrench: refactor declaration of variables
Nov 27, 2020
46853d0
:art: refactor and change input data to csv
Dec 3, 2020
3d10bf6
:mechanic: add csv.h
Dec 3, 2020
322e0f5
:wrench: move csv and add license
Dec 16, 2020
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5 changes: 5 additions & 0 deletions include/io/io_mesh.h
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,11 @@ class IOMesh {
virtual std::vector<std::tuple<mpm::Index, unsigned, double>> read_forces(
const std::string& forces_file) = 0;

//! Read math function file
//! \param[in] math function file name with values of x and fx
virtual std::vector<std::tuple<double, double>> read_math_function(
const std::string& math_function_file) = 0;

}; // IOMesh class
} // namespace mpm

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5 changes: 5 additions & 0 deletions include/io/io_mesh_ascii.h
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,11 @@ class IOMeshAscii : public IOMesh<Tdim> {
std::vector<std::tuple<mpm::Index, unsigned, double>> read_forces(
const std::string& forces_file) override;

//! Read math function file
//! \param[in] math function file name with values of x and fx
std::vector<std::tuple<double, double>> read_math_function(
const std::string& math_function_file) override;

private:
//! Logger
std::shared_ptr<spdlog::logger> console_;
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104 changes: 74 additions & 30 deletions include/io/io_mesh_ascii.tcc
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Expand Up @@ -270,12 +270,12 @@ std::map<mpm::Index, Eigen::Matrix<double, Tdim, 1>>
// ignore comment lines (# or !) or blank lines
if ((line.find('#') == std::string::npos) &&
(line.find('!') == std::string::npos) && (line != "")) {
// ID and read stream
mpm::Index id;
// Angles and ream stream
Eigen::Matrix<double, Tdim, 1> angles;
while (istream.good()) {
// ID and read stream
mpm::Index id;
istream >> id;
// Angles and ream stream
Eigen::Matrix<double, Tdim, 1> angles;
for (unsigned i = 0; i < Tdim; ++i) istream >> angles[i];
euler_angles.emplace(std::make_pair(id, angles));
}
Expand Down Expand Up @@ -314,11 +314,11 @@ std::vector<std::tuple<mpm::Index, double>>
// ignore comment lines (# or !) or blank lines
if ((line.find('#') == std::string::npos) &&
(line.find('!') == std::string::npos) && (line != "")) {
// ID
mpm::Index id;
// Volume
double volume;
while (istream.good()) {
// ID
mpm::Index id;
// Volume
double volume;
// Read stream
istream >> id >> volume;
volumes.emplace_back(std::make_tuple(id, volume));
Expand Down Expand Up @@ -358,9 +358,9 @@ std::vector<std::array<mpm::Index, 2>>
// ignore comment lines (# or !) or blank lines
if ((line.find('#') == std::string::npos) &&
(line.find('!') == std::string::npos) && (line != "")) {
// ID
mpm::Index pid, cid;
while (istream.good()) {
// ID
mpm::Index pid, cid;
// Read stream
istream >> pid >> cid;
particles_cells.emplace_back(std::array<mpm::Index, 2>({pid, cid}));
Expand Down Expand Up @@ -416,13 +416,13 @@ std::vector<std::tuple<mpm::Index, unsigned, double>>
// ignore comment lines (# or !) or blank lines
if ((line.find('#') == std::string::npos) &&
(line.find('!') == std::string::npos) && (line != "")) {
// ID
mpm::Index id;
// Direction
unsigned dir;
// Velocity
double velocity;
while (istream.good()) {
// ID
mpm::Index id;
// Direction
unsigned dir;
// Velocity
double velocity;
// Read stream
istream >> id >> dir >> velocity;
constraints.emplace_back(std::make_tuple(id, dir, velocity));
Expand Down Expand Up @@ -462,15 +462,15 @@ std::vector<std::tuple<mpm::Index, unsigned, int, double>>
// ignore comment lines (# or !) or blank lines
if ((line.find('#') == std::string::npos) &&
(line.find('!') == std::string::npos) && (line != "")) {
// ID
mpm::Index id;
// Direction
unsigned dir;
// Sign
int sign;
// Friction
double friction;
while (istream.good()) {
// ID
mpm::Index id;
// Direction
unsigned dir;
// Sign
int sign;
// Friction
double friction;
// Read stream
istream >> id >> dir >> sign >> friction;
constraints.emplace_back(std::make_tuple(id, dir, sign, friction));
Expand Down Expand Up @@ -509,13 +509,13 @@ std::vector<std::tuple<mpm::Index, unsigned, double>>
// ignore comment lines (# or !) or blank lines
if ((line.find('#') == std::string::npos) &&
(line.find('!') == std::string::npos) && (line != "")) {
// ID
mpm::Index id;
// Direction
unsigned dir;
// Force
double force;
while (istream.good()) {
// ID
mpm::Index id;
// Direction
unsigned dir;
// Force
double force;
// Read stream
istream >> id >> dir >> force;
forces.emplace_back(std::make_tuple(id, dir, force));
Expand All @@ -530,3 +530,47 @@ std::vector<std::tuple<mpm::Index, unsigned, double>>
}
return forces;
}

//! Return math function
template <unsigned Tdim>
std::vector<std::tuple<double, double>>
mpm::IOMeshAscii<Tdim>::read_math_function(
const std::string& math_function_file) {

// initialize math function
std::vector<std::tuple<double, double>> math_function;
math_function.clear();

// input file stream
std::fstream file;
file.open(math_function_file.c_str(), std::ios::in);

try {
if (file.is_open() && file.good()) {
// Line
std::string line;
while (std::getline(file, line)) {
boost::algorithm::trim(line);
std::istringstream istream(line);
// ignore comment lines (# or !) or blank lines
if ((line.find('#') == std::string::npos) &&
(line.find('!') == std::string::npos) && (line != "")) {
// x value
double x_value;
// fx value
double fx_value;
while (istream.good()) {
// Read stream
istream >> x_value >> fx_value;
math_function.emplace_back(std::make_tuple(x_value, fx_value));
}
}
}
}
file.close();
} catch (std::exception& exception) {
console_->error("Read math function : {}", exception.what());
file.close();
}
return math_function;
}
31 changes: 29 additions & 2 deletions include/solvers/mpm_base.tcc
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Expand Up @@ -762,16 +762,43 @@ bool mpm::MPMBase<Tdim>::initialise_math_functions(const Json& math_functions) {
const std::string function_type =
function_props["type"].template get<std::string>();

// Initiate another function_prop to be passed
auto function_props_update = function_props;
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Why do we need this?


// Create a file reader
const std::string io_type =
io_->json_object("mesh")["io_type"].template get<std::string>();
auto reader = Factory<mpm::IOMesh<Tdim>>::instance()->create(io_type);

// Math function is specified in a file, replace function_props_update
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Read files in io class not in mpm_base. Create a separate class in io or use the read_mesh_ascii to read these files. I'd prefer for now if you use read_mesh_ascii to read the input file.

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That's what I have tried to use in the beginning, and you requested CSV. Can we agree on which one to use now before I make more changes?

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I'm not asking you to revert back, this is an io operation and reading the CSV should be in the io class as an additional function and not in the mpm_base

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I see, so still CSV but within read_mesh_ascii. But doesn't it refer to ascii not csv?

if (function_props.find("file") != function_props.end()) {
std::string math_file =
function_props.at("file").template get<std::string>();
auto math_function_values =
reader->read_math_function(io_->file_name(math_file));

// Make separate arrays
std::vector<double> xvalues;
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Having separate vectors makes it decoupled between x and y values, use a vector of arrays instead.

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OK

std::vector<double> fxvalues;
for (const auto& math_function_value : math_function_values) {
xvalues.emplace_back(std::get<0>(math_function_value));
fxvalues.emplace_back(std::get<1>(math_function_value));
}

function_props_update["xvalues"] = xvalues;
function_props_update["fxvalues"] = fxvalues;
}

// Create a new function from JSON object
auto function =
Factory<mpm::FunctionBase, unsigned, const Json&>::instance()->create(
function_type, std::move(function_id), function_props);

// Add material to list
// Add math function to list
auto insert_status =
math_functions_.insert(std::make_pair(function->id(), function));

// If insert material failed
// If insert math function failed
if (!insert_status.second) {
status = false;
throw std::runtime_error(
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53 changes: 52 additions & 1 deletion tests/io/io_mesh_ascii_test.cc
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Expand Up @@ -337,7 +337,7 @@ TEST_CASE("IOMeshAscii is checked for 2D", "[IOMesh][IOMeshAscii][2D]") {
// Create a read_mesh object
auto read_mesh = std::make_unique<mpm::IOMeshAscii<dim>>();

// Try to read constrtaints from a non-existant file
// Try to read forces from a non-existant file
auto forces = read_mesh->read_forces("forces-missing.txt");
// Check number of forces
REQUIRE(forces.size() == 0);
Expand Down Expand Up @@ -482,6 +482,57 @@ TEST_CASE("IOMeshAscii is checked for 2D", "[IOMesh][IOMeshAscii][2D]") {
}
}
}

SECTION("Check math function file") {
// Vector of math function
std::vector<std::tuple<double, double>> math_function_values;

// Constraint
math_function_values.emplace_back(std::make_tuple(0.0, 1.75));
math_function_values.emplace_back(std::make_tuple(0.2, -1.25));
math_function_values.emplace_back(std::make_tuple(0.4, -3.99));
math_function_values.emplace_back(std::make_tuple(0.6, 4.55));

// Dump constraints as an input file to be read
std::ofstream file;
file.open("math-functions.txt");
// Write particle coordinates
for (const auto& math_function_value : math_function_values) {
file << std::get<0>(math_function_value) << "\t";
file << std::get<1>(math_function_value) << "\t";

file << "\n";
}

file.close();

// Check read math function
SECTION("Check math functions") {
// Create a read_mesh object
auto read_mesh = std::make_unique<mpm::IOMeshAscii<dim>>();

// Try to read function from a non-existant file
auto math_functions =
read_mesh->read_math_function("math-functions-missing.txt");
// Check number of function
REQUIRE(math_functions.size() == 0);

// Check math function
math_functions = read_mesh->read_math_function("math-functions.txt");
// Check number of values
REQUIRE(math_functions.size() == math_function_values.size());

// Check math function
for (unsigned i = 0; i < math_function_values.size(); ++i) {
REQUIRE(
std::get<0>(math_functions.at(i)) ==
Approx(std::get<0>(math_function_values.at(i))).epsilon(Tolerance));
REQUIRE(
std::get<1>(math_functions.at(i)) ==
Approx(std::get<1>(math_function_values.at(i))).epsilon(Tolerance));
}
}
}
}

// Check IOMeshAscii
Expand Down