{"action":"created","comment":{"url":"https://api.github.com/repos/cb-geo/mpm/pulls/comments/207722237","pull_request_review_id":143396657,"id":207722237,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwNzcyMjIzNw==","diff_hunk":"@@ -0,0 +1,565 @@\n+#include <iostream>\n+#include <limits>\n+#include <vector>\n+\n+#include \"Eigen/Dense\"\n+#include \"catch.hpp\"\n+#include \"json.hpp\"\n+\n+#include \"factory.h\"\n+#include \"hex_shapefn.h\"\n+#include \"material/material.h\"\n+#include \"mesh.h\"\n+#include \"node.h\"\n+#include \"shapefn.h\"\n+\n+//! \\brief Check Bingham class\n+TEST_CASE(\"Bingham is checked in 2D\", \"[material][bingham][2D]\") {\n+  // Tolerance\n+  const double Tolerance = 1.E-7;\n+\n+  const unsigned Dim = 2;\n+\n+  //! Check for id = 0\n+  SECTION(\"Bingham id is zero\") {\n+    unsigned id = 0;\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham2D\", std::move(id));\n+    REQUIRE(material->id() == 0);\n+  }\n+\n+  SECTION(\"Bingham id is positive\") {\n+    //! Check for id is a positive value\n+    unsigned id = std::numeric_limits<unsigned>::max();\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham2D\", std::move(id));\n+    REQUIRE(material->id() == std::numeric_limits<unsigned>::max());\n+  }\n+\n+  //! Read material properties\n+  SECTION(\"Bingham check properties\") {\n+    unsigned id = 0;\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham2D\", std::move(id));\n+    REQUIRE(material->id() == 0);\n+\n+    // Initialise material\n+    Json jmaterial;\n+    jmaterial[\"density\"] = 1000.;\n+    jmaterial[\"youngs_modulus\"] = 1.0E+7;\n+    jmaterial[\"poisson_ratio\"] = 0.3;\n+    jmaterial[\"tau0\"] = 771.8;\n+    jmaterial[\"mu\"] = 0.0451;\n+    jmaterial[\"critical_shear_rate\"] = 0.2;\n+\n+    // Check material status before assigning material property\n+    REQUIRE(material->status() == false);\n+\n+    // Get material properties\n+    REQUIRE(material->property(\"density\") ==\n+            Approx(std::numeric_limits<double>::max()).epsilon(Tolerance));\n+\n+    // Check for property that does not exist\n+    REQUIRE(material->property(\"noproperty\") ==\n+            Approx(std::numeric_limits<double>::max()).epsilon(Tolerance));\n+\n+    material->properties(jmaterial);\n+\n+    // Check material status after assigning material property\n+    REQUIRE(material->status() == true);\n+\n+    // Get material properties\n+    REQUIRE(material->property(\"density\") ==\n+            Approx(jmaterial[\"density\"]).epsilon(Tolerance));\n+  }\n+\n+  SECTION(\"Bingham check stresses with no strain rate\") {\n+    unsigned id = 0;\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham2D\", std::move(id));\n+    REQUIRE(material->id() == 0);\n+\n+    // Initialise material\n+    Json jmaterial;\n+    jmaterial[\"density\"] = 1000.;\n+    jmaterial[\"youngs_modulus\"] = 1.0E+7;\n+    jmaterial[\"poisson_ratio\"] = 0.3;\n+    jmaterial[\"tau0\"] = 771.8;\n+    jmaterial[\"mu\"] = 0.0451;\n+    jmaterial[\"critical_shear_rate\"] = 0.2;\n+\n+    material->properties(jmaterial);\n+\n+    // Check material status after assigning material property\n+    REQUIRE(material->property_handle() == true);\n+\n+    // Initialise stress\n+    mpm::Material<Dim>::Vector6d stress;\n+    stress.setZero();\n+    REQUIRE(stress(0) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(1) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(2) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(3) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(4) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(5) == Approx(0.).epsilon(Tolerance));\n+\n+    // Initialise dstrain\n+    mpm::Material<Dim>::Vector6d dstrain;\n+    dstrain.setZero();\n+    dstrain(0) = 0.0010000;\n+    dstrain(1) = 0.0005000;\n+    dstrain(2) = 0.0000000;\n+    dstrain(3) = 0.0000000;\n+    dstrain(4) = 0.0000000;\n+    dstrain(5) = 0.0000000;\n+\n+    // Add particle\n+    mpm::Index pid = 0;\n+    Eigen::Matrix<double, Dim, 1> coords;\n+    coords << 0.5, 0.5;\n+    auto particle = std::make_shared<mpm::Particle<Dim, 1>>(pid, coords);\n+\n+    // Coordinates of nodes for the cell\n+    mpm::Index cell_id = 0;\n+    const unsigned Dim = 2;\n+    const unsigned Dof = 2;\n+    const unsigned Nphases = 1;\n+    const unsigned Nnodes = 4;\n+    const unsigned phase = 0;\n+    const double dt = 1;\n+\n+    coords << -2, -2;\n+    std::shared_ptr<mpm::NodeBase<Dim>> node0 =\n+        std::make_shared<mpm::Node<Dim, Dof, Nphases>>(0, coords);\n+    coords << 2, -2;\n+    std::shared_ptr<mpm::NodeBase<Dim>> node1 =\n+        std::make_shared<mpm::Node<Dim, Dof, Nphases>>(1, coords);\n+    coords << 2, 2;\n+    std::shared_ptr<mpm::NodeBase<Dim>> node2 =\n+        std::make_shared<mpm::Node<Dim, Dof, Nphases>>(2, coords);\n+    coords << -2, 2;\n+    std::shared_ptr<mpm::NodeBase<Dim>> node3 =\n+        std::make_shared<mpm::Node<Dim, Dof, Nphases>>(3, coords);\n+\n+    std::shared_ptr<mpm::ShapeFn<Dim>> shapefn =\n+        Factory<mpm::ShapeFn<Dim>>::instance()->create(\"SFQ4\");\n+\n+    auto cell = std::make_shared<mpm::Cell<Dim>>(cell_id, Nnodes, shapefn);\n+\n+    cell->add_node(0, node0);\n+    cell->add_node(1, node1);\n+    cell->add_node(2, node2);\n+    cell->add_node(3, node3);\n+\n+    particle->assign_cell(cell);\n+    particle->compute_shapefn();\n+    particle->compute_strain(phase, dt);\n+\n+    // Reset stress\n+    stress.setZero();\n+\n+    // Compute updated stress\n+    stress = material->compute_stress(stress, dstrain, particle.get());\n+\n+    // Check stressees\n+    REQUIRE(stress(0) == Approx(12500.00000000).epsilon(Tolerance));\n+    REQUIRE(stress(1) == Approx(12500.00000000).epsilon(Tolerance));\n+    REQUIRE(stress(2) == Approx(0.000000e+00).epsilon(Tolerance));\n+    REQUIRE(stress(3) == Approx(0.000000e+00).epsilon(Tolerance));\n+    REQUIRE(stress(4) == Approx(0.000000e+00).epsilon(Tolerance));\n+    REQUIRE(stress(5) == Approx(0.000000e+00).epsilon(Tolerance));\n+  }\n+\n+  SECTION(\"Bingham check stresses with strain rate\") {\n+    unsigned id = 0;\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham2D\", std::move(id));\n+    REQUIRE(material->id() == 0);\n+\n+    // Initialise material\n+    Json jmaterial;\n+    jmaterial[\"density\"] = 1000.;\n+    jmaterial[\"youngs_modulus\"] = 1.0E+7;\n+    jmaterial[\"poisson_ratio\"] = 0.3;\n+    jmaterial[\"tau0\"] = 771.8;\n+    jmaterial[\"mu\"] = 0.0451;\n+    jmaterial[\"critical_shear_rate\"] = 0.2;\n+\n+    material->properties(jmaterial);\n+\n+    // Check material status after assigning material property\n+    REQUIRE(material->property_handle() == true);\n+\n+    // Initialise stress\n+    mpm::Material<Dim>::Vector6d stress;\n+    stress.setZero();\n+    REQUIRE(stress(0) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(1) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(2) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(3) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(4) == Approx(0.).epsilon(Tolerance));\n+    REQUIRE(stress(5) == Approx(0.).epsilon(Tolerance));\n+\n+    // Initialise dstrain\n+    mpm::Material<Dim>::Vector6d dstrain;\n+    dstrain.setZero();\n+    dstrain(0) = 0.0010000;\n+    dstrain(1) = 0.0005000;\n+    dstrain(2) = 0.0000000;\n+    dstrain(3) = 0.0000000;\n+    dstrain(4) = 0.0000000;\n+    dstrain(5) = 0.0000000;\n+\n+    // Add particle\n+    mpm::Index pid = 0;\n+    Eigen::Matrix<double, Dim, 1> coords;\n+    coords << 0.5, 0.5;\n+    auto particle = std::make_shared<mpm::Particle<Dim, 1>>(pid, coords);\n+\n+    // Coordinates of nodes for the cell\n+    mpm::Index cell_id = 0;\n+    mpm::Index mesh_id = 0;\n+    const unsigned Dim = 2;\n+    const unsigned Dof = 2;\n+    const unsigned Nphases = 1;\n+    const unsigned Nnodes = 4;\n+    const unsigned phase = 0;\n+    const double dt = 1;\n+\n+    coords << -2, -2;\n+    std::shared_ptr<mpm::NodeBase<Dim>> node0 =\n+        std::make_shared<mpm::Node<Dim, Dof, Nphases>>(0, coords);\n+    coords << 2, -2;\n+    std::shared_ptr<mpm::NodeBase<Dim>> node1 =\n+        std::make_shared<mpm::Node<Dim, Dof, Nphases>>(1, coords);\n+    coords << 2, 2;\n+    std::shared_ptr<mpm::NodeBase<Dim>> node2 =\n+        std::make_shared<mpm::Node<Dim, Dof, Nphases>>(2, coords);\n+    coords << -2, 2;\n+    std::shared_ptr<mpm::NodeBase<Dim>> node3 =\n+        std::make_shared<mpm::Node<Dim, Dof, Nphases>>(3, coords);\n+\n+    std::shared_ptr<mpm::ShapeFn<Dim>> shapefn =\n+        Factory<mpm::ShapeFn<Dim>>::instance()->create(\"SFQ4\");\n+\n+    node0->assign_velocity_constraint(0, 2);\n+    node0->assign_velocity_constraint(1, 3);\n+    node0->apply_velocity_constraints();\n+\n+    auto cell = std::make_shared<mpm::Cell<Dim>>(cell_id, Nnodes, shapefn);\n+\n+    cell->add_node(0, node0);\n+    cell->add_node(1, node1);\n+    cell->add_node(2, node2);\n+    cell->add_node(3, node3);\n+\n+    particle->assign_cell(cell);\n+    particle->compute_shapefn();\n+    particle->compute_strain(phase, dt);\n+\n+    // Reset stress\n+    stress.setZero();\n+\n+    // Compute updated stress\n+    stress = material->compute_stress(stress, dstrain, particle.get());\n+\n+    // Check stressees\n+    REQUIRE(stress(0) == Approx(12145.8400481974).epsilon(Tolerance));\n+    REQUIRE(stress(1) == Approx(11968.7600722961).epsilon(Tolerance));\n+    REQUIRE(stress(2) == Approx(0.000000e+00).epsilon(Tolerance));\n+    REQUIRE(stress(3) == Approx(-885.3998795065).epsilon(Tolerance));\n+    REQUIRE(stress(4) == Approx(0.000000e+00).epsilon(Tolerance));\n+    REQUIRE(stress(5) == Approx(0.000000e+00).epsilon(Tolerance));\n+  }\n+}\n+\n+TEST_CASE(\"Bingham is checked in 3D\", \"[material][bingham][3D]\") {\n+  // Tolerance\n+  const double Tolerance = 1.E-7;\n+\n+  const unsigned Dim = 3;\n+\n+  //! Check for id = 0\n+  SECTION(\"Bingham id is zero\") {\n+    unsigned id = 0;\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham3D\", std::move(id));\n+    REQUIRE(material->id() == 0);\n+  }\n+\n+  SECTION(\"Bingham id is positive\") {\n+    //! Check for id is a positive value\n+    unsigned id = std::numeric_limits<unsigned>::max();\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham3D\", std::move(id));\n+    REQUIRE(material->id() == std::numeric_limits<unsigned>::max());\n+  }\n+\n+  //! Read material properties\n+  SECTION(\"Bingham check properties\") {\n+    unsigned id = 0;\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham3D\", std::move(id));\n+    REQUIRE(material->id() == 0);\n+\n+    // Initialise material\n+    Json jmaterial;\n+    jmaterial[\"density\"] = 1000.;\n+    jmaterial[\"youngs_modulus\"] = 1.0E+7;\n+    jmaterial[\"poisson_ratio\"] = 0.3;\n+    jmaterial[\"tau0\"] = 771.8;\n+    jmaterial[\"mu\"] = 0.0451;\n+    jmaterial[\"critical_shear_rate\"] = 0.2;\n+\n+    // Check material status before assigning material property\n+    REQUIRE(material->status() == false);\n+\n+    // Get material properties\n+    REQUIRE(material->property(\"density\") ==\n+            Approx(std::numeric_limits<double>::max()).epsilon(Tolerance));\n+\n+    // Check for property that does not exist\n+    REQUIRE(material->property(\"noproperty\") ==\n+            Approx(std::numeric_limits<double>::max()).epsilon(Tolerance));\n+\n+    material->properties(jmaterial);\n+\n+    // Check material status after assigning material property\n+    REQUIRE(material->status() == true);\n+\n+    // Get material properties\n+    REQUIRE(material->property(\"density\") ==\n+            Approx(jmaterial[\"density\"]).epsilon(Tolerance));\n+  }\n+\n+  SECTION(\"Bingham check stresses with no strain rate\") {\n+    unsigned id = 0;\n+    auto material = Factory<mpm::Material<Dim>, unsigned>::instance()->create(\n+        \"Bingham3D\", std::move(id));\n+    REQUIRE(material->id() == 0);\n+\n+    // Initialise material\n+    Json jmaterial;\n+    jmaterial[\"density\"] = 1000.;\n+    jmaterial[\"youngs_modulus\"] = 1.0E+7;\n+    jmaterial[\"poisson_ratio\"] = 0.3;\n+    jmaterial[\"tau0\"] = 771.8;\n+    jmaterial[\"mu\"] = 0.0451;\n+    jmaterial[\"critical_shear_rate\"] = 0.2;\n+\n+    material->properties(jmaterial);\n+\n+    // Check material status after assigning material property\n+    REQUIRE(material->property_handle() == true);\n+\n+    // Initialise stress\n+    mpm::Material<Dim>::Vector6d stress;\n+    stress.setZero();\n+    REQUIRE(stress(0) == Approx(0.).epsilon(Tolerance));","path":"tests/material/bingham_test.cc","position":99,"original_position":358,"commit_id":"a5b62c88a73230397dbdad7727af9d95dc44c429","original_commit_id":"a5b62c88a73230397dbdad7727af9d95dc44c429","user":{"login":"ezrayst","id":22064721,"node_id":"MDQ6VXNlcjIyMDY0NzIx","avatar_url":"https://avatars3.githubusercontent.com/u/22064721?v=4","gravatar_id":"","url":"https://api.github.com/users/ezrayst","html_url":"https://github.com/ezrayst","followers_url":"https://api.github.com/users/ezrayst/followers","following_url":"https://api.github.com/users/ezrayst/following{/other_user}","gists_url":"https://api.github.com/users/ezrayst/gists{/gist_id}","starred_url":"https://api.github.com/users/ezrayst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ezrayst/subscriptions","organizations_url":"https://api.github.com/users/ezrayst/orgs","repos_url":"https://api.github.com/users/ezrayst/repos","events_url":"https://api.github.com/users/ezrayst/events{/privacy}","received_events_url":"https://api.github.com/users/ezrayst/received_events","type":"User","site_admin":false},"body":"Is it always zero when you initialize it? I thought we need to set zero to make it zero according to this: https://eigen.tuxfamily.org/dox/group__TutorialAdvancedInitialization.html","created_at":"2018-08-04T23:57:47Z","updated_at":"2018-08-04T23:57:47Z","html_url":"https://github.com/cb-geo/mpm/pull/166#discussion_r207722237","pull_request_url":"https://api.github.com/repos/cb-geo/mpm/pulls/166","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/cb-geo/mpm/pulls/comments/207722237"},"html":{"href":"https://github.com/cb-geo/mpm/pull/166#discussion_r207722237"},"pull_request":{"href":"https://api.github.com/repos/cb-geo/mpm/pulls/166"}},"in_reply_to_id":207702448},"pull_request":{"url":"https://api.github.com/repos/cb-geo/mpm/pulls/166","id":204524567,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA0NTI0NTY3","html_url":"https://github.com/cb-geo/mpm/pull/166","diff_url":"https://github.com/cb-geo/mpm/pull/166.diff","patch_url":"https://github.com/cb-geo/mpm/pull/166.patch","issue_url":"https://api.github.com/repos/cb-geo/mpm/issues/166","number":166,"state":"open","locked":false,"title":":computer: Implementation of 3D Bingham model fixes #23","user":{"login":"ezrayst","id":22064721,"node_id":"MDQ6VXNlcjIyMDY0NzIx","avatar_url":"https://avatars3.githubusercontent.com/u/22064721?v=4","gravatar_id":"","url":"https://api.github.com/users/ezrayst","html_url":"https://github.com/ezrayst","followers_url":"https://api.github.com/users/ezrayst/followers","following_url":"https://api.github.com/users/ezrayst/following{/other_user}","gists_url":"https://api.github.com/users/ezrayst/gists{/gist_id}","starred_url":"https://api.github.com/users/ezrayst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ezrayst/subscriptions","organizations_url":"https://api.github.com/users/ezrayst/orgs","repos_url":"https://api.github.com/users/ezrayst/repos","events_url":"https://api.github.com/users/ezrayst/events{/privacy}","received_events_url":"https://api.github.com/users/ezrayst/received_events","type":"User","site_admin":false},"body":"- [x] Make `Bingham` material\r\n- [x] Make unit test and make sure it passes\r\n- [x] Make necessary functions from node to output strain 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