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Pull in smoke tests for build_ext (#8)
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* Update to main (#7)

* Remove testing output files

* Fix license text formatting for github to recognize it

* Adding smoke test CXX file, header, and pybind files
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@dbhart
dbhart authored Sep 1, 2024
1 parent 59d6e32 commit 5789690
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11 changes: 10 additions & 1 deletion setup.py
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# with open(path.join(here, 'README.md'), encoding='utf-8') as f:
# long_description = f.read()

smoke_tests_only = True

if smoke_tests_only:
sources = [
"src/ext_modules/libsansmic/smoke.cxx",
"src/ext_modules/libsansmic/libsansmic.cpp",
]
else:
sources = sorted(glob("src/ext_modules/libsansmic/*.cpp"))

ext_modules = [
Pybind11Extension(
"sansmic.libsansmic",
sources=sorted(glob("src/ext_modules/libsansmic/*.cpp")),
sources=sources,
cxx_std=17,
# Example: passing in the version to the compiled code
define_macros=[
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275 changes: 275 additions & 0 deletions src/ext_modules/libsansmic/libsansmic.cpp
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// © 2024 National Technology & Engineering Solutions of Sandia, LLC
// (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S.
// Government retains certain rights in this software.

// SPDX-License-Identifier: BSD-3-Clause

/**
* @file libsansmic.cpp
* @author See AUTHORS.md file
* @brief Python bindings for SANSMIC
* @version 1.0.0
*/

#include <pybind11/iostream.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>

#include "sansmic.hpp"

namespace py = pybind11;

PYBIND11_MODULE (libsansmic, m)
{
m.doc () = "SANSMIC model plugin";

py::enum_<sansmic::Mode> (m, "CRunMode",
"See :py:class:`sansmic.model.SimulationMode`.")
.value ("ORDINARY", sansmic::Mode::Ordinary,
"ordinary leaching (water in, brine out)")
.value ("WITHDRAWAL", sansmic::Mode::Withdrawal,
"oil withdrawal (water in, oil out)")
.value ("LEACH_FILL", sansmic::Mode::LeachFill,
"leach and fill (water and oil in, brine out)")
.value ("OIL_FILL", sansmic::Mode::OilFill,
"oil fill (oil in, brine out)")
.export_values ();

py::enum_<sansmic::IData> (m, "CGeometryFormat",
"See :py:class:`sansmic.model.GeometryFormat`.")
.value ("RADIUS_LIST", sansmic::IData::RadiusList, "radius list")
.value ("VOLUME_LIST", sansmic::IData::VolumeList,
"volumes follow depths")
.value ("VOLUME_TABLE", sansmic::IData::VolumeTable,
"volume-depth pairs")
.value ("RADIUS_TABLE", sansmic::IData::RadiusTable,
"radius-depth pairs")
.export_values ();

py::class_<sansmic::Stage> (m, "CStage",
"See :py:class:`sansmic.model.StageDefinition`")
.def (py::init<> ())
.def_readwrite ("title", &sansmic::Stage::title, "str : stage title")
.def_readwrite ("mode", &sansmic::Stage::leach_mode,
":class:`RunMode` : leaching mode")
.def_readwrite ("print_interval", &sansmic::Stage::print_freq,
"int : steps between report output")
.def_readwrite ("subsequent", &sansmic::Stage::is_subsequent,
"int : is this a subsequent stage?")
.def_readwrite (
"rest_duration", &sansmic::Stage::t_rest,
"double : time cavern sits static before next stage (in hours)")
.def_readwrite ("num_coallescing", &sansmic::Stage::coalesce_num_wells,
"int : number of coallescing wells (typically 1)")
.def_readwrite ("geometry_format", &sansmic::Stage::data_format,
"int : cavern geometry format")
.def_readwrite (
"stop_value", &sansmic::Stage::stop_cond_val,
"double : stop criteria; >0 = volume; <0 = OBI; 0 = time")
.def_readwrite ("injection_depth", &sansmic::Stage::h_inj,
"double : injection height above floor (in feet)")
.def_readwrite ("production_depth", &sansmic::Stage::h_prod,
"double : production height above floor (in feet)")
.def_readwrite (
"interface_depth", &sansmic::Stage::h_obi,
"double : oil-brine interface height above floor (in feet)")
.def_readwrite ("ullage_standoff", &sansmic::Stage::h_ullSO,
"double : ullage reference height above floor (in feet)")
.def_readwrite ("injection_rate", &sansmic::Stage::Q_raw,
"double : water input rate (in bbl/d)")
.def_readwrite ("inn_tbg_inside_radius", &sansmic::Stage::r_tbgID,
"double : inner radius of inner tubing (in inches)")
.def_readwrite ("inn_tbg_outside_radius", &sansmic::Stage::r_tbgOD,
"double : outer radius of inner tubing (in inches)")
.def_readwrite ("out_csg_inside_radius", &sansmic::Stage::r_csgID,
"double : inner radius of outer tubing (in inches)")
.def_readwrite ("out_csg_outside_radius", &sansmic::Stage::r_csgOD,
"double : outer radius of outer tubing (in inches)")
.def_readwrite ("injection_fluid_sg", &sansmic::Stage::sg_raw,
"double : injected water specific gravity")
.def_readwrite ("cavern_sg", &sansmic::Stage::sg_init,
"double : cavern brine specific gravity")
.def_readwrite ("timestep", &sansmic::Stage::dt,
"double : simulation timestep size (in hours)")
.def_readwrite ("injection_duration", &sansmic::Stage::t_stage,
"double : injection duration (in hours)")
.def_readwrite ("fill_rate", &sansmic::Stage::Q_oil,
"double : oil input rate (in bbl/d)")
.def_readwrite ("coallescing_well_separation",
&sansmic::Stage::coalesce_well_sep,
"double : coallescing wells separation (in feet)")
.def_readwrite ("radius_vector", &sansmic::Stage::radii,
"list[num_cells+1] : radius at each node "
"(num_cells+1)")
.def_readwrite ("depth_vector", &sansmic::Stage::depths,
"list[num_cells+1] : depth at each node (num_cells+1)")
.def_readwrite ("volume_vector", &sansmic::Stage::volumes,
"list[num_cells+1] : volume at each node (num_cells+1)");

py::class_<sansmic::Salt> (m, "CSalt",
"A model for salt density and saturation.")
.def (py::init<> ())
.def ("set_saturated_sg", &sansmic::Salt::set_sg_max, py::arg ("sg"),
"Set the maximum sg of saturated brine")
.def ("get_saturated_sg", &sansmic::Salt::get_sg_max,
"Get the maximum sg of saturated brine")
.def ("set_solid_density", &sansmic::Salt::set_solid_density,
py::arg ("rho"), "Set the density (g/cc) of the rock salt")
.def ("get_solid_density", &sansmic::Salt::get_solid_density,
"Get the density (g/cc) of the rock salt")
.def ("get_recession_rate_coeff",
&sansmic::Salt::get_recession_rate_coeff,
"**a** for the recession rate equation")
.def (
"get_wt_pct_sg_coeff", &sansmic::Salt::get_sg_wt_pct_convert_coeff,
"Get coefficients **c** for the wt-pct vs specific gravity equation")
.def ("set_recession_rate_coeff",
&sansmic::Salt::set_recession_rate_coeff, py::arg ("a"),
"Set coefficients **a**[n=6] for the recession rate equation")
.def ("set_wt_pct_sg_coeff",
&sansmic::Salt::set_density_conversion_coeff, py::arg ("c"),
"Set coefficients **c**[n=3] for the wt-pct vs specific gravity "
"equation")
.def ("wt_pct_to_sg", &sansmic::Salt::get_sg, py::arg ("wt"),
py::arg ("T") = 75.0,
"Convert weight-percent NaCl to specific gravity")
.def ("recession_rate", &sansmic::Salt::get_recession_rate,
py::arg ("sg"),
"Calculate the recession rate in ft/s for wall dissolution")
.def ("sg_to_wt_pct", &sansmic::Salt::get_wt_pct, py::arg ("sg"),
py::arg ("T") = 75.0,
"Convert specific gravity to weight-percent NaCl");

py::class_<sansmic::Model> (m, "CModel",
"See :py:class:`sansmic.model.Scenario`.")
.def (py::init<std::string> ())
.def ("add_stage", &sansmic::Model::add_stage, py::arg ("stage"),
"int : Add `stage` to the model and return new number of stages.")
.def ("open_outfiles", &sansmic::Model::open_outfiles,
py::arg ("append"),
"Open output files, optionally in `append` mode, by default "
"append=false.")
.def ("initialize", &sansmic::Model::init_model,
"Initialize the model object.")
.def ("run_sim", &sansmic::Model::run_sim,
py::call_guard<py::scoped_ostream_redirect,
py::scoped_estream_redirect> (),
"Run complete sansmic simulation.")
// .def ("run_next_stage", &sansmic::Model::run_stage,
// py::call_guard<py::scoped_ostream_redirect,
// py::scoped_estream_redirect> (),
// "Run the stage `istage` of the model.")
.def ("run_next_step", &sansmic::Model::run_step,
py::call_guard<py::scoped_ostream_redirect,
py::scoped_estream_redirect> (),
"Run the next step in stage `istage` of the model.")
.def ("num_stages", &sansmic::Model::num_stages,
"Get the number of model stages.")
.def ("is_running", &sansmic::Model::get_running_status,
"int: Is the model in the middle of a stage.")
.def ("close_outfiles", &sansmic::Model::close_outfiles,
"Close the C-library model output files.")
.def ("_get_results", &sansmic::Model::get_results)
.def ("_get_current_stage", &sansmic::Model::get_current_stage)
.def ("_get_current_time", &sansmic::Model::get_current_time)
.def ("_get_current_volume", &sansmic::Model::get_current_volume)
.def ("_get_current_state", &sansmic::Model::get_current_state)
.def ("_set_jet_model_version", &sansmic::Model::set_jet_model_version,
py::arg ("ver"), "Set the jet model version to `ver`.")
.def ("_set_plume_model_version",
&sansmic::Model::set_plume_model_version, py::arg ("ver"),
"Set the plume model version to `ver`.")
.def ("_set_temperature_model_version",
&sansmic::Model::set_temperature_model_version, py::arg ("ver"),
"Set the temperature model version to `ver`.")
.def ("_set_num_cells", &sansmic::Model::set_num_cells,
py::arg ("n_cells"))
.def ("_set_cavern_height", &sansmic::Model::set_cavern_height,
py::arg ("height"))
.def ("_set_floor_depth", &sansmic::Model::set_initial_floor_depth,
py::arg ("measured_depth"))
.def ("_set_entrainment_alpha", &sansmic::Model::set_entrainment_coeff,
py::arg ("alpha"))
.def ("_set_diffusion_beta", &sansmic::Model::set_diffusion_beta_coeff,
py::arg ("beta"))
.def ("_set_diffusion_D_mol",
&sansmic::Model::set_molecular_diffusion_coeff, py::arg ("D_mol"))
.def ("_set_diffusion_D_0", &sansmic::Model::set_eddy_coeff,
py::arg ("D_0"))
.def ("_set_fraction_insol", &sansmic::Model::set_fraction_insolubles,
py::arg ("f_insol"))
.def ("_set_dissolution_factor", &sansmic::Model::set_dissolution_factor,
py::arg ("f_diss"))
.def ("_set_solver_abserr",
&sansmic::Model::set_ODESolver_absolute_tolerance, py::arg ("tol"))
.def ("_set_solver_relerr",
&sansmic::Model::set_ODESolver_relative_tolerance, py::arg ("tol"))
// .def_readonly ("_salt", &sansmic::Model::salt, "CSalt : salt
// properties")
.def_readwrite ("_geometry_format", &sansmic::Model::geom_data_format,
"int : cavern geometry format")
.def_readwrite ("_radius_vector", &sansmic::Model::geom_radii,
"list[num_cells+1] : radius at each node "
"(num_cells+1)")
.def_readwrite ("_depth_vector", &sansmic::Model::geom_depths,
"list[num_cells+1] : depth at each node (num_cells+1)")
.def_readwrite ("_volume_vector", &sansmic::Model::geom_volumes,
"list[num_cells+1] : volume at each node (num_cells+1)")
.def ("_get_stages", &sansmic::Model::get_stages);

m.def ("get_error_text", &sansmic::error::get_error_text,
"Convert error code to text", py::arg ("code"));

py::class_<sansmic::Results> (m, "CResults",
"See :class:`sansmic.model.Results`.")
.def (py::init<> ())
.def_readwrite ("r_0", &sansmic::Results::r_0)
.def_readwrite ("z_0", &sansmic::Results::z_0)
.def_readwrite ("h_0", &sansmic::Results::h_0)
.def_readwrite ("step", &sansmic::Results::step)
.def_readwrite ("stage", &sansmic::Results::stage)
.def_readwrite ("phase", &sansmic::Results::phase)
.def_readwrite ("injCell", &sansmic::Results::injCell)
.def_readwrite ("prodCell", &sansmic::Results::prodCell)
.def_readwrite ("obiCell", &sansmic::Results::obiCell)
.def_readwrite ("plumCell", &sansmic::Results::plmCell)
.def_readwrite ("t", &sansmic::Results::t)
.def_readwrite ("err", &sansmic::Results::err)
.def_readwrite ("z_obi", &sansmic::Results::z_obi)
.def_readwrite ("z_inj", &sansmic::Results::z_inj)
.def_readwrite ("z_prod", &sansmic::Results::z_prod)
.def_readwrite ("z_plm", &sansmic::Results::z_plm)
.def_readwrite ("z_insol", &sansmic::Results::z_insol)
.def_readwrite ("h_insol", &sansmic::Results::h_insol)
.def_readwrite ("l_jet", &sansmic::Results::l_jet)
.def_readwrite ("r_jet", &sansmic::Results::r_jet)
.def_readwrite ("u_jet", &sansmic::Results::u_jet)
.def_readwrite ("V_injTot", &sansmic::Results::V_injTot)
.def_readwrite ("V_fillTot", &sansmic::Results::V_fillTot)
.def_readwrite ("V_cavTot", &sansmic::Results::V_cavTot)
.def_readwrite ("V_insolTot", &sansmic::Results::V_insolTot)
.def_readwrite ("V_insolVent", &sansmic::Results::V_insolVent)
.def_readwrite ("Q_out", &sansmic::Results::Q_out)
.def_readwrite ("sg_out", &sansmic::Results::sg_out)
.def_readwrite ("sg_cavAve", &sansmic::Results::sg_cavAve)
.def_readwrite ("dt", &sansmic::Results::dt)
.def_readwrite ("r", &sansmic::Results::r_cav)
.def_readwrite ("dr_0", &sansmic::Results::dr_cav)
.def_readwrite ("sg", &sansmic::Results::sg)
.def_readwrite ("theta", &sansmic::Results::theta)
.def_readwrite ("Q_inj", &sansmic::Results::Q_inj)
.def_readwrite ("V", &sansmic::Results::V)
.def_readwrite ("f_dis", &sansmic::Results::f_dis)
.def_readwrite ("f_flag", &sansmic::Results::f_flag)
.def_readwrite ("xincl", &sansmic::Results::xincl)
.def_readwrite ("amd", &sansmic::Results::amd)
.def_readwrite ("D_coeff", &sansmic::Results::D_coeff)
.def_readwrite ("dC_dz", &sansmic::Results::dC_dz)
.def_readwrite ("C_old", &sansmic::Results::C_old)
.def_readwrite ("C_new", &sansmic::Results::C_new)
.def_readwrite ("dC", &sansmic::Results::dC_dt)
.def_readwrite ("dr", &sansmic::Results::dr_dt)
.def_readwrite ("C_plm", &sansmic::Results::C_plm)
.def_readwrite ("u_plm", &sansmic::Results::u_plm)
.def_readwrite ("r_plm", &sansmic::Results::r_plm);
}
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