add implementation and test for MOSAIC function mean_molecular_speed (#110)

* add implementation of mean_molecular_speed

* add verification data

* testing logic

Author: zdaq12

src/core/impl/TChem_Impl_MOSAIC.hpp

@@ -2566,6 +2566,14 @@ struct MOSAIC{
                 b_mtem(5,jA,jE) ))));
   } // fnlog_gamZ
 
+  KOKKOS_INLINE_FUNCTION static
+  void mean_molecular_speed(const real_type& T_K,
+                            const real_type& MW,
+                            real_type& mean_molec_speed) {
+
+    mean_molec_speed = 1.455e4 * ats<real_type>::sqrt(T_K/MW);
+  } // mean_molecular_speed
+
   KOKKOS_INLINE_FUNCTION static
   void fn_Keq(const real_type& Keq_298,
               const real_type& a,

src/verification/data_sets/mosaic/mean_molecular_speed_input_ts_0.yaml

@@ -0,0 +1,7 @@
+
+TChem-atm:
+  function: mean_molecular_speed
+input:
+  fixed:
+    T_K: [  0.29142360000000002E+003]
+    MW: [  0.98000000000000000E+002]

src/verification/data_sets/mosaic/mean_molecular_speed_output_ts_0.py

@@ -0,0 +1,17 @@
+
+# This file was generated by PartMC-mosaic.
+
+from math import nan as nan, inf as inf
+
+# Object is just a dynamic container that stores input/output data.
+class Object(object):
+    pass
+# Settings are stored here.
+settings = Object()
+# Input is stored here.
+input = Object()
+input.T_K=[[  0.29142360000000002E+003],]
+input.MW=[[  0.98000000000000000E+002],]
+# Output data is stored here.
+output = Object()
+output.mean_molecular_speed=[[  0.25090673256801860E+005],]

src/verification/mosaic/CMakeLists.txt

@@ -9,6 +9,7 @@ add_executable(${DRIVER_NAME}.x
                do_full_deliquescence.cpp
                calculate_XT.cpp
                fnlog_gamZ.cpp
+               mean_molecular_speed.cpp
                fn_Keq.cpp
                drh_mutual.cpp
                fn_Po.cpp
@@ -31,6 +32,7 @@ SET(TEST_LIST
      do_full_deliquescence_input_ts_0
      calculate_XT_input_ts_0
      fnlog_gamZ_input_ts_0
+     mean_molecular_speed_input_ts_0
      fn_Keq_input_ts_0
      drh_mutual_input_ts_0
      fn_Po_input_ts_0
@@ -48,6 +50,7 @@ SET(TEST_BASELINE
     do_full_deliquescence_output_ts_0
     calculate_XT_output_ts_0
     fnlog_gamZ_output_ts_0
+    mean_molecular_speed_output_ts_0
     fn_Keq_output_ts_0
     drh_mutual_output_ts_0
     fn_Po_output_ts_0
@@ -66,6 +69,7 @@ set(ERROR_THRESHOLDS
     ${DEFAULT_TOL} # do_full_deliquescence_output_ts_0
     ${DEFAULT_TOL} # calculate_XT_output_ts_0
     1e-6           # fnlog_gamZ_output_ts_0
+    ${DEFAULT_TOL} # mean_molecular_speed_output_ts_0
     1e-6           # fn_Keq_output_ts_0
     1e-6           # drh_mutual_output_ts_0
     1e-8           # fn_Po_output_ts_0

src/verification/mosaic/mean_molecular_speed.cpp

@@ -0,0 +1,56 @@
+#include "TChem.hpp"
+#include "TChem_Impl_MOSAIC.hpp"
+#include <verification.hpp>
+#include "skywalker.hpp"
+
+using device_type = typename Tines::UseThisDevice<TChem::exec_space>::type;
+using real_type_1d_view = TChem::real_type_1d_view;
+using oridinal_type_1d_view = TChem::ordinal_type_1d_view;
+using ordinal_type = TChem::ordinal_type;
+using namespace skywalker;
+using namespace TChem;
+
+void mean_molecular_speed(Ensemble *ensemble) {
+  ensemble->process([=](const Input &input, Output &output) {
+
+    const auto T_K_arr = input.get_array("T_K");
+    const auto MW_arr = input.get_array("MW");
+
+    real_type_1d_view T_K("T_K", 1);
+    verification::convert_1d_vector_to_1d_view_device(T_K_arr, T_K);
+
+    real_type_1d_view MW("MW", 1);
+    verification::convert_1d_vector_to_1d_view_device(MW_arr, MW);
+
+    // Reals or int that are defined outside of the parallel_for region are passed as const.
+    real_type_1d_view outputs_mean_molecular_speed("outputs_mean_molecular_speed", 1);
+
+    std::string profile_name ="Verification_test_mean_molecular_speed";
+    using policy_type =
+          typename TChem::UseThisTeamPolicy<TChem::exec_space>::type;
+    const auto exec_space_instance = TChem::exec_space();
+    const auto host_exec_space = TChem::host_exec_space();
+    policy_type policy(exec_space_instance, 1, Kokkos::AUTO());
+
+    Kokkos::parallel_for(
+    profile_name,
+    policy,
+    KOKKOS_LAMBDA(const typename policy_type::member_type& member) {
+
+      Real& mean_molecular_speed = outputs_mean_molecular_speed(0);
+
+    // Perform the adjustment calculation
+    TChem::Impl::MOSAIC<real_type, device_type>::mean_molecular_speed(
+      T_K(0),
+      MW(0),
+      mean_molecular_speed);
+    });
+
+    const auto outputs_mean_molecular_speed_h = Kokkos::create_mirror_view_and_copy(host_exec_space, outputs_mean_molecular_speed);
+
+    Real mean_molecular_speed = outputs_mean_molecular_speed_h(0);
+
+    output.set("mean_molecular_speed", mean_molecular_speed);
+
+  });
+}

src/verification/mosaic/mosaic_driver.cpp

@@ -27,6 +27,8 @@ void calculate_XT(Ensemble *ensemble);
 
 void fnlog_gamZ(Ensemble *ensemble);
 
+void mean_molecular_speed(Ensemble *ensemble);
+
 void fn_Keq(Ensemble *ensemble);
 
 void drh_mutual(Ensemble *ensemble);
@@ -78,6 +80,8 @@ int main(int argc, char **argv) {
       calculate_XT(ensemble);
     } else if (func_name == "fnlog_gamZ") {
       fnlog_gamZ(ensemble);
+    } else if (func_name == "mean_molecular_speed") {
+      mean_molecular_speed(ensemble);
     } else if (func_name == "fn_Keq") {
       fn_Keq(ensemble);
     } else if (func_name == "drh_mutual") {