StateInit.cpp

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#include <polyfem/State.hpp>
 
#include <polyfem/problem/ProblemFactory.hpp>
#include <polyfem/assembler/GenericProblem.hpp>
#include <polyfem/assembler/Mass.hpp>
 
#include <polyfem/autogen/auto_p_bases.hpp>
#include <polyfem/autogen/auto_q_bases.hpp>
 
#include <polyfem/utils/Logger.hpp>
#include <polyfem/utils/GeogramUtils.hpp>
#include <polyfem/problem/KernelProblem.hpp>
#include <polyfem/utils/par_for.hpp>
 
#include <polyfem/utils/JSONUtils.hpp>
 
#include <jse/jse.h>
 
#include <spdlog/sinks/stdout_color_sinks.h>
#include <spdlog/sinks/basic_file_sink.h>
#include <spdlog/sinks/ostream_sink.h>
 
#include <ipc/utils/logger.hpp>
#include <wmtk/utils/Logger.hpp>
 
#include <polyfem/mesh/mesh2D/Mesh2D.hpp>
#include <polyfem/mesh/mesh3D/Mesh3D.hpp>
 
#include <sstream>
 
namespace spdlog::level
{
    NLOHMANN_JSON_SERIALIZE_ENUM(
        spdlog::level::level_enum,
        {{spdlog::level::level_enum::trace, "trace"},
         {spdlog::level::level_enum::debug, "debug"},
         {spdlog::level::level_enum::info, "info"},
         {spdlog::level::level_enum::warn, "warning"},
         {spdlog::level::level_enum::err, "error"},
         {spdlog::level::level_enum::critical, "critical"},
         {spdlog::level::level_enum::off, "off"},
         {spdlog::level::level_enum::trace, 0},
         {spdlog::level::level_enum::debug, 1},
         {spdlog::level::level_enum::info, 2},
         {spdlog::level::level_enum::warn, 3},
         {spdlog::level::level_enum::err, 3},
         {spdlog::level::level_enum::critical, 4},
         {spdlog::level::level_enum::off, 5}})
}
 
namespace polyfem
{
    using namespace problem;
    using namespace utils;
 
    State::State()
    {
        using namespace polysolve;
 
        GeogramUtils::instance().initialize();
 
        problem = ProblemFactory::factory().get_problem("Linear");
    }
    State::State() {…}
 
    void State::init_logger(
        const std::string &log_file,
        const spdlog::level::level_enum log_level,
        const spdlog::level::level_enum file_log_level,
        const bool is_quiet)
    {
        std::vector<spdlog::sink_ptr> sinks;
 
        if (!is_quiet)
        {
            console_sink_ = std::make_shared<spdlog::sinks::stdout_color_sink_mt>();
            sinks.emplace_back(console_sink_);
        }
 
        if (!log_file.empty())
        {
            file_sink_ = std::make_shared<spdlog::sinks::basic_file_sink_mt>(log_file, /*truncate=*/true);
            // Set the file sink separately from the console so it can save all messages
            file_sink_->set_level(file_log_level);
            sinks.push_back(file_sink_);
        }
 
        init_logger(sinks, log_level);
        spdlog::flush_every(std::chrono::seconds(3));
    }
    void State::init_logger( {…}
 
    void State::init_logger(std::ostream &os, const spdlog::level::level_enum log_level)
    {
        std::vector<spdlog::sink_ptr> sinks;
        sinks.emplace_back(std::make_shared<spdlog::sinks::ostream_sink_mt>(os, false));
        init_logger(sinks, log_level);
    }
    void State::init_logger(std::ostream &os, const spdlog::level::level_enum log_level) {…}
 
    void State::init_logger(
        const std::vector<spdlog::sink_ptr> &sinks,
        const spdlog::level::level_enum log_level)
    {
        set_logger(std::make_shared<spdlog::logger>("polyfem", sinks.begin(), sinks.end()));
        GeogramUtils::instance().set_logger(logger());
 
        ipc::set_logger(std::make_shared<spdlog::logger>("ipctk", sinks.begin(), sinks.end()));
 
        wmtk::set_logger(std::make_shared<spdlog::logger>("wmtk", sinks.begin(), sinks.end()));
 
        // Set the logger at the lowest level, so all messages are passed to the sinks
        logger().set_level(spdlog::level::trace);
        ipc::logger().set_level(spdlog::level::trace);
        wmtk::logger().set_level(spdlog::level::trace);
 
        set_log_level(log_level);
    }
    void State::init_logger( {…}
 
    void State::set_log_level(const spdlog::level::level_enum log_level)
    {
        spdlog::set_level(log_level);
        if (console_sink_)
        {
            // Set only the level of the console
            console_sink_->set_level(log_level); // Shared by all loggers
        }
        else
        {
            // Set the level of all sinks
            logger().set_level(log_level);
            ipc::logger().set_level(log_level);
        }
    }
    void State::set_log_level(const spdlog::level::level_enum log_level) {…}
 
    void State::init(const json &p_args_in, const bool strict_validation)
    {
        json args_in = p_args_in; // mutable copy
 
        apply_common_params(args_in);
 
        // CHECK validity json
        json rules;
        jse::JSE jse;
        {
            jse.strict = strict_validation;
            const std::string polyfem_input_spec = POLYFEM_INPUT_SPEC;
            std::ifstream file(polyfem_input_spec);
 
            if (file.is_open())
                file >> rules;
            else
            {
                logger().error("unable to open {} rules", polyfem_input_spec);
                throw std::runtime_error("Invald spec file");
            }
 
            jse.include_directories.push_back(POLYFEM_JSON_SPEC_DIR);
            jse.include_directories.push_back(POLYSOLVE_JSON_SPEC_DIR);
            rules = jse.inject_include(rules);
 
            polysolve::linear::Solver::apply_default_solver(rules, "/solver/linear");
            polysolve::linear::Solver::apply_default_solver(rules, "/solver/adjoint_linear");
        }
 
        polysolve::linear::Solver::select_valid_solver(args_in["solver"]["linear"], logger());
        if (args_in["solver"]["adjoint_linear"].is_null())
            args_in["solver"]["adjoint_linear"] = args_in["solver"]["linear"];
        else
            polysolve::linear::Solver::select_valid_solver(args_in["solver"]["adjoint_linear"], logger());
 
        // Use the /solver/nonlinear settings as the default for /solver/augmented_lagrangian/nonlinear
        if (args_in.contains("/solver/nonlinear"_json_pointer))
        {
            if (args_in.contains("/solver/augmented_lagrangian/nonlinear"_json_pointer))
            {
                assert(args_in["solver"]["augmented_lagrangian"]["nonlinear"].is_object());
                // Merge the augmented lagrangian settings into the nonlinear settings,
                // and then replace the augmented lagrangian settings with the merged settings.
                json nonlinear = args_in["solver"]["nonlinear"]; // copy
                nonlinear.merge_patch(args_in["solver"]["augmented_lagrangian"]["nonlinear"]);
                args_in["solver"]["augmented_lagrangian"]["nonlinear"] = nonlinear;
            }
            else
            {
                // Copy the nonlinear settings to the augmented_lagrangian settings
                args_in["solver"]["augmented_lagrangian"]["nonlinear"] = args_in["solver"]["nonlinear"];
            }
        }
        const bool valid_input = jse.verify_json(args_in, rules);
 
        if (!valid_input)
        {
            logger().error("invalid input json:\n{}", jse.log2str());
            throw std::runtime_error("Invald input json file");
        }
        // end of check
 
        this->args = jse.inject_defaults(args_in, rules);
        units.init(this->args["units"]);
 
        if (!args_in.contains("/space/advanced/bc_method"_json_pointer) && this->args["space"]["basis_type"] != "Lagrange")
        {
            logger().warn("Setting bc method to lsq for non-Lagrange basis");
            this->args["space"]["advanced"]["bc_method"] = "lsq";
        }
 
        // Save output directory and resolve output paths dynamically
        const std::string output_dir = resolve_input_path(this->args["output"]["directory"]);
        if (!output_dir.empty())
        {
            std::filesystem::create_directories(output_dir);
        }
        this->output_dir = output_dir;
 
        std::string out_path_log = this->args["output"]["log"]["path"];
        if (!out_path_log.empty())
        {
            out_path_log = resolve_output_path(out_path_log);
        }
 
        init_logger(
            out_path_log,
            this->args["output"]["log"]["level"],
            this->args["output"]["log"]["file_level"],
            this->args["output"]["log"]["quiet"]);
 
        logger().info("Saving output to {}", output_dir);
 
        const unsigned int thread_in = this->args["solver"]["max_threads"];
        set_max_threads(thread_in);
 
        has_dhat = args_in["contact"].contains("dhat");
 
        init_time();
 
        if (is_contact_enabled())
        {
            if (args["solver"]["contact"]["friction_iterations"] == 0)
            {
                logger().info("specified friction_iterations is 0; disabling friction");
                args["contact"]["friction_coefficient"] = 0.0;
            }
            else if (args["solver"]["contact"]["friction_iterations"] < 0)
            {
                args["solver"]["contact"]["friction_iterations"] = std::numeric_limits<int>::max();
            }
            if (args["contact"]["friction_coefficient"] == 0.0)
            {
                args["solver"]["contact"]["friction_iterations"] = 0;
            }
        }
        else
        {
            args["solver"]["contact"]["friction_iterations"] = 0;
            args["contact"]["friction_coefficient"] = 0;
            args["contact"]["periodic"] = false;
        }
 
        const std::string formulation = this->formulation();
        assembler = assembler::AssemblerUtils::make_assembler(formulation);
        assert(assembler->name() == formulation);
        mass_matrix_assembler = std::make_shared<assembler::Mass>();
        const auto other_name = assembler::AssemblerUtils::other_assembler_name(formulation);
 
        if (!other_name.empty())
        {
            mixed_assembler = assembler::AssemblerUtils::make_mixed_assembler(formulation);
            pressure_assembler = assembler::AssemblerUtils::make_assembler(other_name);
        }
 
        if (args["solver"]["advanced"]["check_inversion"] == "Conservative")
        {
            if (auto elastic_assembler = std::dynamic_pointer_cast<assembler::ElasticityAssembler>(assembler))
                elastic_assembler->set_use_robust_jacobian();
        }
 
        if (!args.contains("preset_problem"))
        {
            if (!assembler->is_tensor())
                problem = std::make_shared<assembler::GenericScalarProblem>("GenericScalar");
            else
                problem = std::make_shared<assembler::GenericTensorProblem>("GenericTensor");
 
            problem->clear();
            if (!args["time"].is_null())
            {
                const auto tmp = R"({"is_time_dependent": true})"_json;
                problem->set_parameters(tmp);
            }
            // important for the BC
 
            auto bc = args["boundary_conditions"];
            bc["root_path"] = root_path();
            problem->set_parameters(bc);
            problem->set_parameters(args["initial_conditions"]);
 
            problem->set_parameters(args["output"]);
        }
        else
        {
            if (args["preset_problem"]["type"] == "Kernel")
            {
                problem = std::make_shared<KernelProblem>("Kernel", *assembler);
                problem->clear();
                KernelProblem &kprob = *dynamic_cast<KernelProblem *>(problem.get());
            }
            else
            {
                problem = ProblemFactory::factory().get_problem(args["preset_problem"]["type"]);
                problem->clear();
            }
            // important for the BC
            problem->set_parameters(args["preset_problem"]);
        }
 
        problem->set_units(*assembler, units);
 
        if (optimization_enabled == solver::CacheLevel::Derivatives)
        {
            if (is_contact_enabled())
            {
                if (!args["contact"]["use_convergent_formulation"])
                {
                    args["contact"]["use_convergent_formulation"] = true;
                    logger().info("Use convergent formulation for differentiable contact...");
                }
                if (args["/solver/contact/barrier_stiffness"_json_pointer].is_string())
                {
                    logger().error("Only constant barrier stiffness is supported in differentiable contact!");
                }
            }
 
            if (args.contains("boundary_conditions") && args["boundary_conditions"].contains("rhs"))
            {
                json rhs = args["boundary_conditions"]["rhs"];
                if ((rhs.is_array() && rhs.size() > 0 && rhs[0].is_string()) || rhs.is_string())
                    logger().error("Only constant rhs over space is supported in differentiable code!");
            }
        }
    }
    void State::init(const json &p_args_in, const bool strict_validation) {…}
 
    void State::set_max_threads(const int max_threads)
    {
        NThread::get().set_num_threads(max_threads);
    }
    void State::set_max_threads(const int max_threads) {…}
 
    void State::init_time()
    {
        if (!is_param_valid(args, "time"))
            return;
 
        const double t0 = Units::convert(args["time"]["t0"], units.time());
        double tend, dt;
        int time_steps;
 
        // from "tend", "dt", "time_steps" only two can be used at a time
        const int num_valid = is_param_valid(args["time"], "tend")
                              + is_param_valid(args["time"], "dt")
                              + is_param_valid(args["time"], "time_steps");
        if (num_valid < 2)
        {
            log_and_throw_error("Exactly two of (tend, dt, time_steps) must be specified");
        }
        else if (num_valid == 2)
        {
            if (is_param_valid(args["time"], "tend"))
            {
                tend = Units::convert(args["time"]["tend"], units.time());
                assert(tend > t0);
                if (is_param_valid(args["time"], "dt"))
                {
                    dt = Units::convert(args["time"]["dt"], units.time());
                    assert(dt > 0);
                    time_steps = int(ceil((tend - t0) / dt));
                    assert(time_steps > 0);
                }
                else if (is_param_valid(args["time"], "time_steps"))
                {
                    time_steps = args["time"]["time_steps"];
                    assert(time_steps > 0);
                    dt = (tend - t0) / time_steps;
                    assert(dt > 0);
                }
                else
                {
                    throw std::runtime_error("This code should be unreachable!");
                }
            }
            else if (is_param_valid(args["time"], "dt"))
            {
                // tend is already confirmed to be invalid, so time_steps must be valid
                assert(is_param_valid(args["time"], "time_steps"));
 
                dt = Units::convert(args["time"]["dt"], units.time());
                assert(dt > 0);
 
                time_steps = args["time"]["time_steps"];
                assert(time_steps > 0);
 
                tend = t0 + time_steps * dt;
            }
            else
            {
                // tend and dt are already confirmed to be invalid
                throw std::runtime_error("This code should be unreachable!");
            }
        }
        else if (num_valid == 3)
        {
            tend = Units::convert(args["time"]["tend"], units.time());
            dt = Units::convert(args["time"]["dt"], units.time());
            time_steps = args["time"]["time_steps"];
 
            // Check that all parameters agree
            if (abs(t0 + dt * time_steps - tend) > 1e-12)
            {
                log_and_throw_error("Exactly two of (tend, dt, time_steps) must be specified");
            }
        }
 
        // Store these for use later
        args["time"]["tend"] = tend;
        args["time"]["dt"] = dt;
        args["time"]["time_steps"] = time_steps;
 
        units.characteristic_length() *= dt;
 
        logger().info("t0={}, dt={}, tend={}", t0, dt, tend);
    }
    void State::init_time() {…}
 
    void State::set_materials(std::vector<std::shared_ptr<assembler::Assembler>> &assemblers) const
    {
        const int size = (assembler->is_tensor() || assembler->is_fluid()) ? mesh->dimension() : 1;
        for (auto &a : assemblers)
            a->set_size(size);
 
        if (!utils::is_param_valid(args, "materials"))
            return;
 
        if (!args["materials"].is_array() && args["materials"]["type"] == "AMIPSAutodiff")
        {
            json transform_params = {};
            transform_params["canonical_transformation"] = json::array();
            if (!mesh->is_volume())
            {
                Eigen::MatrixXd regular_tri(3, 3);
                regular_tri << 0, 0, 1,
                    1, 0, 1,
                    1. / 2., std::sqrt(3) / 2., 1;
                regular_tri.transposeInPlace();
                Eigen::MatrixXd regular_tri_inv = regular_tri.inverse();
 
                const auto &mesh2d = *dynamic_cast<mesh::Mesh2D *>(mesh.get());
                for (int e = 0; e < mesh->n_elements(); e++)
                {
                    Eigen::MatrixXd transform;
                    mesh2d.compute_face_jacobian(e, regular_tri_inv, transform);
                    transform_params["canonical_transformation"].push_back(json({
                        {
                            transform(0, 0),
                            transform(0, 1),
                        },
                        {
                            transform(1, 0),
                            transform(1, 1),
                        },
                    }));
                }
            }
            else
            {
                Eigen::MatrixXd regular_tet(4, 4);
                regular_tet << 0, 0, 0, 1,
                    1, 0, 0, 1,
                    1. / 2., std::sqrt(3) / 2., 0, 1,
                    1. / 2., 1. / 2. / std::sqrt(3), std::sqrt(3) / 2., 1;
                regular_tet.transposeInPlace();
                Eigen::MatrixXd regular_tet_inv = regular_tet.inverse();
 
                const auto &mesh3d = *dynamic_cast<mesh::Mesh3D *>(mesh.get());
                for (int e = 0; e < mesh->n_elements(); e++)
                {
                    Eigen::MatrixXd transform;
                    mesh3d.compute_cell_jacobian(e, regular_tet_inv, transform);
                    transform_params["canonical_transformation"].push_back(json({
                        {
                            transform(0, 0),
                            transform(0, 1),
                            transform(0, 2),
                        },
                        {
                            transform(1, 0),
                            transform(1, 1),
                            transform(1, 2),
                        },
                        {
                            transform(2, 0),
                            transform(2, 1),
                            transform(2, 2),
                        },
                    }));
                }
            }
            transform_params["solve_displacement"] = true;
            assembler->set_materials({}, transform_params, units);
 
            return;
        }
 
        std::vector<int> body_ids(mesh->n_elements());
        for (int i = 0; i < mesh->n_elements(); ++i)
            body_ids[i] = mesh->get_body_id(i);
 
        for (auto &a : assemblers)
            a->set_materials(body_ids, args["materials"], units);
    }
    void State::set_materials(std::vector<std::shared_ptr<assembler::Assembler>> &assemblers) const {…}
 
    void State::set_materials(assembler::Assembler &assembler) const
    {
        const int size = (this->assembler->is_tensor() || this->assembler->is_fluid()) ? this->mesh->dimension() : 1;
        assembler.set_size(size);
 
        if (!utils::is_param_valid(args, "materials"))
            return;
 
        std::vector<int> body_ids(mesh->n_elements());
        for (int i = 0; i < mesh->n_elements(); ++i)
            body_ids[i] = mesh->get_body_id(i);
 
        assembler.set_materials(body_ids, args["materials"], units);
    }
    void State::set_materials(assembler::Assembler &assembler) const {…}
 
} // namespace polyfem