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Allow in memory manipulation of nalu yaml files (#51)
* Adjust nalu to construct with yaml * Add logfile naming option * Add test case that shows syntax * Style * Add comments and parallel check for file writing * Style * Fix logic error * Subtle fix for being careles with what I renamed in nalu
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,4 @@ | ||
| .DS_Store | ||
| spack* | ||
| compile_commands.json | ||
| .cache |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,97 @@ | ||
| #include "yaml-cpp/yaml.h" | ||
| #include <stdexcept> | ||
| #include <iostream> | ||
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| namespace YEDIT { | ||
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| /* Exception if the graph is not formatted correctly | ||
| * This exception is designed to reproduce the failing portion of the YAML graph | ||
| * when called recursively so it can be echo'd to the user | ||
| */ | ||
| class YamlNodeMatchException : public std::exception | ||
| { | ||
| public: | ||
| YamlNodeMatchException( | ||
| std::string currentNode, std::string accumulatedPath = "") | ||
| : std::exception() | ||
| { | ||
| std::string extra = | ||
| accumulatedPath.empty() ? "" : ":" + accumulatedPath; | ||
| graphPath_ = currentNode + extra; | ||
| } | ||
| const char* what() const noexcept override { return graphPath_.c_str(); } | ||
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| private: | ||
| std::string graphPath_; | ||
| }; | ||
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| namespace { | ||
| /* A function that will traverse the src node based on the key node | ||
| * The two nodes must be identical until the final leaf values and then the | ||
| * values of the key will override the src values. If the two graphs don't match | ||
| * at any point prior to the leaves then it will trigger a | ||
| * YamlNodeMatchException. | ||
| */ | ||
| inline void impl_find_and_replace(YAML::Node src, YAML::Node key) | ||
| { | ||
| switch (key.Type()) { | ||
| case YAML::NodeType::Map: | ||
| // case 1: it's a map | ||
| //- pass the contents of the map recursively | ||
| for (auto n : key) { | ||
| std::string k = static_cast<std::string>(n.first.Scalar()); | ||
| try { | ||
| impl_find_and_replace(src[k], key[k]); | ||
| } catch (YamlNodeMatchException& e) { | ||
| throw YamlNodeMatchException(k, std::string(e.what())); | ||
| } | ||
| } | ||
| break; | ||
| case YAML::NodeType::Sequence: | ||
| // case 2: it's a list | ||
| //- pass the contents of the list recursively (order matters when | ||
| // looking for a match) | ||
| for (int i = 0; i < key.size(); ++i) { | ||
| try { | ||
| impl_find_and_replace(src[i], key[i]); | ||
| } catch (YamlNodeMatchException& e) { | ||
| throw YamlNodeMatchException( | ||
| "[" + std::to_string(i) + "]", std::string(e.what())); | ||
| } | ||
| } | ||
| break; | ||
| case YAML::NodeType::Scalar: { | ||
| // case 3: it's a scalar | ||
| //- replace value | ||
| if (src.Type() != key.Type()) { | ||
| // we have a invalid path in the key | ||
| throw YamlNodeMatchException(key.as<std::string>()); | ||
| } | ||
| src = key; | ||
| break; | ||
| } | ||
| default: | ||
| break; | ||
| } | ||
| } | ||
| } // namespace | ||
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| /* The accessible version of impl_find_and_replace that collects the final | ||
| * error and makes it more readable | ||
| */ | ||
| inline void find_and_replace(YAML::Node src, YAML::Node key) | ||
| { | ||
| try { | ||
| impl_find_and_replace(src, key); | ||
| } catch (YamlNodeMatchException& e) { | ||
| auto failingPath = static_cast<std::string>(e.what()); | ||
| std::string message = | ||
| "\nFailure trying to replace YAML\nFailing Graph:\n\t"; | ||
| message += failingPath + "\n"; | ||
| message += | ||
| "Please double check and make sure this matches the source YAML"; | ||
| throw std::runtime_error(message); | ||
| } | ||
| } | ||
|
|
||
| } // namespace YEDIT |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| # | ||
| # SIMULATION STOP # | ||
| #.......................................# | ||
| time.stop_time = 22000.0 # Max (# | ||
| tim.max_step = -1 | ||
| time.fixed_dt = 0.15 | ||
| time.cfl = 1.0 | ||
| time.plot_interval = 10 | ||
| time.checkpoint_interval = -10 | ||
| io.plot_file = out/plt | ||
| io.check_file = out/chk | ||
| # PHYSICS # | ||
| #.......................................# | ||
| incflo.gravity = 0. 0. 0.0 # Gravitational force (3D) | ||
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| incflo.use_godunov = 1 | ||
| incflo.do_initial_proj = 0 | ||
| incflo.initial_iterations = 0 | ||
| transport.viscosity = 0.005 | ||
| turbulence.model = Laminar | ||
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| incflo.physics = FreeStream | ||
| incflo.velocity = 1.0 0.0 0.0 | ||
| incflo.density = 1.0 | ||
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| amr.n_cell = 160 56 4 # Grid cells at coarsest AMRlevel | ||
| amr.max_level = 0 # Max AMR level in hierarchy | ||
| amr.blocking_factor_z = 4 | ||
| amr.blocking_factor_x = 8 | ||
| amr.blocking_factor_y = 8 | ||
| amr.max_grid_size_z = 4 | ||
| amr.max_grid_size_x = 16 | ||
| amr.max_grid_size_y = 16 | ||
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| geometry.prob_lo = -15 -5.0 -0.375 # Lo corner coordinates | ||
| geometry.prob_hi = 7.5 5.0 0.375 # Hi corner coordinates | ||
| geometry.is_periodic = 0 0 1 # Periodicity x y z (0/1) | ||
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| # Boundary conditions | ||
| xlo.type = "mass_inflow" | ||
| xlo.velocity = 1.0 0.0 0.0 | ||
| xlo.density = 1.0 | ||
| xhi.type = "pressure_outflow" | ||
| xhi.pressure = 0.0 | ||
| ylo.type = "slip_wall" | ||
| yhi.type = "slip_wall" | ||
| #zlo.type = "slip_wall" | ||
| #zhi.type = "slip_wall" | ||
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| incflo.verbose = 0 # incflo_level | ||
| amrex.fpe_trap_invalid = 0 # Trap NaNs | ||
| amrex.throw_exception = 1 | ||
| amrex.signal_handling = 0 | ||
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| mac_proj.verbose = 0 | ||
| nodal_proj.verbose = 0 | ||
| nodal_proj.mg_rtol = 1.0e-6 | ||
| nodal_proj.mg_atol = 1.0e-10 | ||
| nodal_proj.num_pre_smooth = 10 | ||
| nodal_proj.num_post_smooth = 10 |
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