Commit 26a11733 authored by Henderson, Shane's avatar Henderson, Shane
Browse files

Deprecates csv interface and implements JSON interface for input/output as... 

Deprecates csv interface and implements JSON interface for input/output as well as an hdf5 interface for input.
parent 48fe42c6

.gitlab-ci.yml

+25 −37
Original line number Diff line number Diff line
@@ -10,36 +10,25 @@ stages: 
  - build

  - deploy



#Primarily concerned with setting up micromamba for the appropriate platforms

#All the build requirements excepting some compiler magic is there

.bash_before: &bash_before

  - export MAMBA_ROOT_PREFIX="$CI_PROJECT_DIR/tools/micromamba"

  - source ./ci/setup_mamba.sh

  - micromamba activate saline_39

  - pip install build



.powershell_before: &powershell_before

  - $env:MAMBA_ROOT_PREFIX="$CI_PROJECT_DIR/tools/micromamba"

  - . $CI_PROJECT_DIR/ci/setup_mamba.ps1

  - micromamba activate saline_39

  - pip install build



build_macos:

  stage: build

  variables:

    GIT_SUBMODULE_STRATEGY: normal

  tags:

    - macOS

  before_script:

    - *bash_before

  script:

    - source $HOME/spack/share/spack/setup-env.sh

    - spack env activate saline

    - pip install delocate

    - echo $PATH

    - cmake -S $CI_PROJECT_DIR -B "$CI_PROJECT_DIR/build" -DCMAKE_BUILD_TYPE=RELEASE

      -Dsaline_ENABLE_Fortran=ON -DCMAKE_Fortran_FLAGS:STRING="-ffree-line-length-none"

      -Dsaline_ENABLE_Python=ON -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0

      -Dsaline_ENABLE_Python=ON -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0 -Dsaline_ENABLE_hdf5=ON

      -DPython_EXECUTABLE=`which python`

    - cmake --build "$CI_PROJECT_DIR/build"

    - cmake --build "$CI_PROJECT_DIR/build" --target SalinePy_wheel

    - ctest --test-dir "$CI_PROJECT_DIR/build"

    - cmake --install build --prefix install

    - delocate-wheel -w ${CI_PROJECT_DIR}/install/wheelhouse ${CI_PROJECT_DIR}/build/src/python/dist/SalinePy*.whl

    - delocate-wheel -w ${CI_PROJECT_DIR}/install/wheelhouse ${CI_PROJECT_DIR}/build/src/python/dist/salinepy*.whl

    - tar -czf darwin_arm.tar.gz install

  artifacts:

    name: darwin
@@ -49,15 +38,16 @@ build_macos: 


build_windows:

  stage: build

  variables:

    GIT_SUBMODULE_STRATEGY: normal

  tags:

    - windows

  before_script:

    - *powershell_before

  script:

    - pip install delvewheel

    - cmake

      -S $CI_PROJECT_DIR

      -B build

    - $env:MAMBA_ROOT_PREFIX="$CI_PROJECT_DIR/tools/micromamba"

    - . $CI_PROJECT_DIR/ci/setup_mamba.ps1

    - micromamba activate saline_39

    - pip install build delvewheel

    - cmake -S $CI_PROJECT_DIR -B build

      -Dsaline_ENABLE_Fortran=OFF

      -Dsaline_ENABLE_Python=ON

      -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE
@@ -75,22 +65,21 @@ build_windows: 


build_linux:

  stage: build

  variables:

    GIT_SUBMODULE_STRATEGY: normal

  rules:

    - when: always

  tags:

    - linux

  before_script:

    - *bash_before

    - docker

  script:

    - pip install auditwheel

    - pip install patchelf

    - cmake -S $CI_PROJECT_DIR -B build -DCMAKE_BUILD_TYPE=RELEASE

      -Dsaline_ENABLE_Fortran=ON -DCMAKE_Fortran_FLAGS:STRING="-ffree-line-length-none"

      -Dsaline_ENABLE_Python=ON

    - cmake --build build

      -Dsaline_ENABLE_Python=ON -Dsaline_ENABLE_hdf5=ON

    - cmake --build "$CI_PROJECT_DIR/build"

    - cmake --build "$CI_PROJECT_DIR/build" --target SalinePy_wheel

    - ctest --test-dir build --output-on-failure

    - cmake --install build --prefix install

    - auditwheel repair -w ${CI_PROJECT_DIR}/install/wheelhouse --plat manylinux_2_34_x86_64 ${CI_PROJECT_DIR}/build/src/python/dist/SalinePy*.whl

    - auditwheel repair -w ${CI_PROJECT_DIR}/install/wheelhouse --plat manylinux_2_28_x86_64 ${CI_PROJECT_DIR}/build/src/python/dist/salinepy*.whl

    - tar -czf linux_x86.tar.gz install

  artifacts:

    name: linux_x86
@@ -100,15 +89,14 @@ build_linux: 


deploy_code:

  stage: deploy

  image: saline_deploy:latest

  tags:

    - linux

    - docker

  rules:

    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH

      when: never

    - when: manual

  needs: [build_linux,build_windows,build_macos]

  before_script:

    - *bash_before

  script:

    # Code

    - CODE_SALINE_URL="https://code.ornl.gov/api/v4/projects/10738/packages"

.gitmodules

0 → 100644
+3 −0
Original line number Diff line number Diff line 
[submodule "thirdparty/nlohmann_json"]

	path = thirdparty/nlohmann_json

	url = https://github.com/nlohmann/json.git

CMakeLists.txt

+7 −3
Original line number Diff line number Diff line
@@ -13,9 +13,13 @@ project(saline 
)



# Supported standards

set(CMAKE_CXX_STANDARD 11)

set(CMAKE_CXX_STANDARD 17) #c++20 is not fully supported on likely compilers

set(CMAKE_CXX_STANDARD_REQUIRED ON)



#

option(${PROJECT_NAME}_USE_EXTERNAL_JSON "Use an external JSON library" OFF)

add_subdirectory(thirdparty)



# Configure the library

add_subdirectory(src)

ci/build_env.yml

+1 −0
Original line number Diff line number Diff line
@@ -7,3 +7,4 @@ dependencies: 
  - swig=4.2.1

  - setuptools

  - twine

  - hdf5

include/default_data_store.hh

+291 −272
Original line number Diff line number Diff line
@@ -8,19 +8,23 @@ 
 */

//---------------------------------------------------------------------------//



#include "data_store.hh"



#include <cmath>

#include <iostream>

#include <ostream>

#include <istream>

#include <limits>

#include <list>

#include <ostream>

#include <string>

#include <vector>

#include <list>



namespace saline

{

#include <nlohmann/json.hpp>

#ifdef SALINE_USE_HDF5

#include <hdf5.h>

#endif



#include "data_store.hh"



namespace saline {

//===========================================================================//

/*!

 * \class Default_Data_Store
@@ -28,22 +32,21 @@ namespace saline 
 *

 * The default data is transcribed from

 *

 * Jerden, James. Molten Salt Thermophysical Properties Database Development: 2019 Update.

 * United States: N. p., 2019. Web. doi:10.2172/1559846.

 * Jerden, James. Molten Salt Thermophysical Properties Database Development:

 * 2019 Update. United States: N. p., 2019. Web. doi:10.2172/1559846.

 *

 * Units:

 *   Conductivity  - Watts per Meter-Kelvin (W/m K)

 *   Pressure      - Kilopascal (kPa)

 *   Temperature   - Kelvin (K)

 *   Enthalpy      - Joule per mole (J/mole)

 *   Viscosity     - Centipoise (cP) or milli Newton-second per square Meter (mN.s/m^2)

 *   Specific Heat - Joules per Kelvin Mole (J/K mole)

 *   Density       - Grams per Cubic Centimeter (g/cc)

 *   Viscosity     - Centipoise (cP) or milli Newton-second per square Meter

 * (mN.s/m^2) Specific Heat - Joules per Kelvin Mole (J/K mole) Density       -

 * Grams per Cubic Centimeter (g/cc)

 */

//===========================================================================//



enum DataQualifier

{

enum DataQualifier {

  NONE, // Default assignment

  // /* Represent variations on melting and boiling data

  PRESSURIZED,
@@ -53,10 +56,8 @@ enum DataQualifier 
  NONSPECIFIC // This is targeted at uncharacterized data (uncertainty).

};



class Default_Data_Store : public Data_Store

{

class Default_Data_Store : public Data_Store {

public:



  //@{

  //! Types

  using Id = std::size_t;
@@ -78,32 +79,40 @@ class Default_Data_Store : public Data_Store 
  Vec_Name names(Id id) const { return compounds[id].names; }



  // specific heat

    double cp(Id id, Id data_id, double temperature, double pressure = 101.325) const;

    double cp_h(Id id, Id data_id, double enthalpy, double pressure = 101.325) const;

  double cp(Id id, Id data_id, double temperature,

            double pressure = 101.325) const;

  double cp_h(Id id, Id data_id, double enthalpy,

              double pressure = 101.325) const;

  virtual bool valid_cp(Id id, Id data_id) const;

  double cp_unc(Id id, Id data_id) const;

  std::pair<double, double> cp_rng(Id id, Id data_id) const;

  std::string cp_ref(Id id, Id data_id) const;



  // viscosity

    double mu(Id id, Id data_id, double temperature, double pressure = 101.325) const;

    double mu_h(Id id, Id data_id, double enthalpy, double pressure = 101.325) const;

  double mu(Id id, Id data_id, double temperature,

            double pressure = 101.325) const;

  double mu_h(Id id, Id data_id, double enthalpy,

              double pressure = 101.325) const;

  virtual bool valid_mu(Id id, Id data_id) const;

  double mu_unc(Id id, Id data_id) const;

  std::pair<double, double> mu_rng(Id id, Id data_id) const;

  std::string mu_ref(Id id, Id data_id) const;



  // conductivity

    double k(Id id, Id data_id, double temperature, double pressure = 101.325) const;

    double k_h(Id id, Id data_id, double enthalpy, double pressure = 101.325) const;

  double k(Id id, Id data_id, double temperature,

           double pressure = 101.325) const;

  double k_h(Id id, Id data_id, double enthalpy,

             double pressure = 101.325) const;

  virtual bool valid_k(Id id, Id data_id) const;

  double k_unc(Id id, Id data_id) const;

  std::pair<double, double> k_rng(Id id, Id data_id) const;

  std::string k_ref(Id id, Id data_id) const;



  // density

    double rho(Id id, Id data_id, double temperature, double pressure = 101.325) const;

    double rho_h(Id id, Id data_id, double enthalpy, double pressure = 101.325) const;

  double rho(Id id, Id data_id, double temperature,

             double pressure = 101.325) const;

  double rho_h(Id id, Id data_id, double enthalpy,

               double pressure = 101.325) const;

  virtual bool valid_rho(Id id, Id data_id) const;

  double rho_unc(Id id, Id data_id) const;

  std::pair<double, double> rho_rng(Id id, Id data_id) const;
@@ -135,7 +144,12 @@ class Default_Data_Store : public Data_Store 
  std::size_t constituent_count(Id id) const;



  void load(const std::string &fPath);

  [[deprecated("Use from_json(std::istream& inFile) instead.")]]

  void load(std::istream &inFile);

  void from_json(nlohmann::json);

#ifdef SALINE_USE_HDF5

  void from_h5(hid_t file);

#endif



  View setView(const Vec_Name &names, const Vec_Mole &mole_percents);
@@ -144,7 +158,8 @@ class Default_Data_Store : public Data_Store 
  bool valid(Vec_Name &names) const { return valid(names_to_id(names)); };

  bool valid(Name &name) const { return valid(name_to_id(name)); };



    // obtain data store id given a set of compound names (e.g., LiF-NaF-KF, LiF-BeF2-ZrF4-ThF4)

  // obtain data store id given a set of compound names (e.g., LiF-NaF-KF,

  // LiF-BeF2-ZrF4-ThF4)

  Id names_to_id(Vec_Name names) const;

  // obtain data store id given a compound name (e.g., BeF2, NaCl)

  Id name_to_id(Name &name) const;
@@ -155,14 +170,11 @@ class Default_Data_Store : public Data_Store 
  // The list accessible salt names

  Vec_Name getSaltKeys() const;

  std::vector<std::vector<double>> getSaltComps(Vec_Name names) const;

  void to_json(nlohmann::json &j) const;



private:



    class Data

    {

  class Data {

  public:



        void to_stream(std::ostream& s) const;

    Vec_Mole &mole_percents() { return m_mole_percents; };

    const Vec_Mole &mole_percents() const { return m_mole_percents; };
@@ -193,13 +205,17 @@ class Default_Data_Store : public Data_Store 
    double rho_b() const { return m_rho_b; }



    // viscosity

        double mu(double t) const {return std::isnan(m_mu_c) ?

                                  m_mu_a * std::exp(m_mu_b / t) :

                                  std::pow(10.0,m_mu_a + (m_mu_b/t) + (m_mu_c/(t*t)));}

    double mu(double t) const {

      return std::isnan(m_mu_c)

                 ? m_mu_a * std::exp(m_mu_b / t)

                 : std::pow(10.0, m_mu_a + (m_mu_b / t) + (m_mu_c / (t * t)));

    }

    double mu_h(double h) const { return mu(h_to_t(h)); }

        bool valid_mu() const {return std::isnan(m_mu_c) ?

                                  (mu_a() != 0.0 ) :

                                  ((mu_a() != 0.0) || (mu_b() != 0.0) || (m_mu_c != 0.0));}

    bool valid_mu() const {

      return std::isnan(m_mu_c)

                 ? (mu_a() != 0.0)

                 : ((mu_a() != 0.0) || (mu_b() != 0.0) || (m_mu_c != 0.0));

    }

    double mu_unc() const { return m_mu_unc; }

    std::string mu_ref() const { return m_mu_ref; }
@@ -220,10 +236,15 @@ class Default_Data_Store : public Data_Store 
    double k_b() const { return m_k_b; }



    // specific heat

        double cp(double t) const {double t2 = t * t;

                                  return m_cp_a + m_cp_b * t + m_cp_c * 1/(t2) + m_cp_d * t2;}

    double cp(double t) const {

      double t2 = t * t;

      return m_cp_a + m_cp_b * t + m_cp_c * 1 / (t2) + m_cp_d * t2;

    }

    double cp_h(double h) const { return cp(h_to_t(h)); }

        bool valid_cp() const {return ((cp_a() != 0.0) || (cp_b() != 0.0) || (cp_c() != 0.0) || (cp_d() != 0.0)); }

    bool valid_cp() const {

      return ((cp_a() != 0.0) || (cp_b() != 0.0) || (cp_c() != 0.0) ||

              (cp_d() != 0.0));

    }

    double cp_unc() const { return m_cp_unc; }

    std::string cp_ref() const { return m_cp_ref; }
@@ -248,9 +269,9 @@ class Default_Data_Store : public Data_Store 
    Vec_Mole m_mole_percents;



    // Melting Temperature

        double m_melt;

    double m_melt = 0.0;

    DataQualifier m_melt_qualifier;

        double m_melt_unc;

    double m_melt_unc = 0.0;

    DataQualifier m_melt_unc_qualifier;

    std::string m_melt_ref;
@@ -258,43 +279,43 @@ class Default_Data_Store : public Data_Store 
    double m_mole_weight;



    // Boiling Temperature

        double m_boil;

    double m_boil = 0.0;

    DataQualifier m_boil_qualifier;

        double m_boil_unc;

    double m_boil_unc = 0.0;

    DataQualifier m_boil_unc_qualifier;

    std::string m_boil_ref;



    // density

        double m_rho_a;

        double m_rho_b;

        double m_rho_unc;

    double m_rho_a = 0.0;

    double m_rho_b = 0.0;

    double m_rho_unc = 0.0;

    DataQualifier m_rho_unc_qualifier;

    std::pair<double, double> m_rho_rng;

    std::string m_rho_ref;



    // viscosity

        double m_mu_a;

        double m_mu_b;

        double m_mu_c;

        double m_mu_unc;

    double m_mu_a = 0.0;

    double m_mu_b = 0.0;

    double m_mu_c = std::numeric_limits<double>::quiet_NaN();

    double m_mu_unc = 0.0;

    DataQualifier m_mu_unc_qualifier;

    std::pair<double, double> m_mu_rng;

    std::string m_mu_ref;



    // conductivity

        double m_k_a;

        double m_k_b;

        double m_k_unc;

    double m_k_a = 0.0;

    double m_k_b = 0.0;

    double m_k_unc = 0.0;

    DataQualifier m_k_unc_qualifier;

    std::pair<double, double> m_k_rng;

    std::string m_k_ref;



    // specific heat

        double m_cp_a;

        double m_cp_b;

        double m_cp_c;

        double m_cp_d;

        double m_cp_unc;

    double m_cp_a = 0.0;

    double m_cp_b = 0.0;

    double m_cp_c = 0.0;

    double m_cp_d = 0.0;

    double m_cp_unc = 0.0;

    DataQualifier m_cp_unc_qualifier;

    std::pair<double, double> m_cp_rng;

    std::string m_cp_ref;
@@ -307,17 +328,16 @@ class Default_Data_Store : public Data_Store 


    // h(t)'s E simplification (a * melt + b * melt^2  + d * melt^3 - c / melt)

    double m_e;



  };



  void to_json(nlohmann::json &j, Data &d) const;

  using Vec_Data = std::vector<Data>;

    struct Compound

    {

  struct Compound {

    Vec_Name names;

    Vec_Data data;

  };

  private:



private:

  // >>> DATA

  void parse_data_qualifier(std::string &, DataQualifier &);

  void parse_data_token(std::string &, double &);
@@ -332,7 +352,6 @@ class Default_Data_Store : public Data_Store 
  void setup_enthalpy_tables();



  Default_Data_Store::Data &getDataReference(std::string, std::string);



};



} // namespace saline