Fix #628: Fetch Pyro from upstream (#633)

Author: henryleberre

src/common/m_thermochem.fpp

@@ -3,8 +3,16 @@
 module m_thermochem
 
     #:if chemistry
-        use m_pyrometheus
-    #:else
+        use m_pyrometheus, only: &
+            num_species, species_names, gas_constant, mol_weights, &
+            get_temperature, get_net_production_rates, get_pressure, &
+            get_mixture_molecular_weight, get_mixture_energy_mass, &
+            get_temperature
+    #:endif
+
+    implicit none
+
+    #:if not chemistry
         integer, parameter :: num_species = 0
         character(len=:), allocatable, dimension(:) :: species_names
     #:endif

src/post_process/m_global_parameters.fpp

@@ -126,7 +126,7 @@ module m_global_parameters
     integer :: pi_inf_idx                          !< Index of liquid stiffness func. eqn.
     type(int_bounds_info) :: stress_idx            !< Indices of elastic stresses
     integer :: c_idx                               !< Index of color function
-    type(int_bounds_info) :: chemistry_idx           !< Indexes of first & last concentration eqns.
+    type(int_bounds_info) :: species_idx           !< Indexes of first & last concentration eqns.
     type(int_bounds_info) :: temperature_idx       !< Indexes of first & last temperature eqns.
     !> @}
 
@@ -611,13 +611,18 @@ contains
         end if
 
         if (chemistry) then
-            chemistry_idx%beg = sys_size + 1
-            chemistry_idx%end = sys_size + num_species
-            sys_size = chemistry_idx%end
+            species_idx%beg = sys_size + 1
+            species_idx%end = sys_size + num_species
+            sys_size = species_idx%end
 
             temperature_idx%beg = sys_size + 1
             temperature_idx%end = sys_size + 1
             sys_size = temperature_idx%end
+        else
+            species_idx%beg = 1
+            species_idx%end = 1
+            temperature_idx%beg = 1
+            temperature_idx%end = 1
         end if
 
         momxb = mom_idx%beg
@@ -632,8 +637,8 @@ contains
         strxe = stress_idx%end
         intxb = internalEnergies_idx%beg
         intxe = internalEnergies_idx%end
-        chemxb = chemistry_idx%beg
-        chemxe = chemistry_idx%end
+        chemxb = species_idx%beg
+        chemxe = species_idx%end
         tempxb = temperature_idx%beg
         tempxe = temperature_idx%end
 

src/pre_process/m_global_parameters.fpp

@@ -105,7 +105,7 @@ module m_global_parameters
     integer :: pi_inf_idx                          !< Index of liquid stiffness func. eqn.
     type(int_bounds_info) :: stress_idx            !< Indexes of elastic shear stress eqns.
     integer :: c_idx                               !< Index of the color function
-    type(int_bounds_info) :: chemistry_idx     !< Indexes of first & last concentration eqns.
+    type(int_bounds_info) :: species_idx           !< Indexes of first & last concentration eqns.
     type(int_bounds_info) :: temperature_idx       !< Indexes of first & last temperature eqns.
 
     type(int_bounds_info) :: bc_x, bc_y, bc_z !<
@@ -696,9 +696,9 @@ contains
         end if
 
         if (chemistry) then
-            chemistry_idx%beg = sys_size + 1
-            chemistry_idx%end = sys_size + num_species
-            sys_size = chemistry_idx%end
+            species_idx%beg = sys_size + 1
+            species_idx%end = sys_size + num_species
+            sys_size = species_idx%end
 
             temperature_idx%beg = sys_size + 1
             temperature_idx%end = sys_size + 1
@@ -717,8 +717,8 @@ contains
         strxe = stress_idx%end
         intxb = internalEnergies_idx%beg
         intxe = internalEnergies_idx%end
-        chemxb = chemistry_idx%beg
-        chemxe = chemistry_idx%end
+        chemxb = species_idx%beg
+        chemxe = species_idx%end
         tempxb = temperature_idx%beg
         tempxe = temperature_idx%end
 

src/simulation/m_global_parameters.fpp

@@ -232,7 +232,7 @@ module m_global_parameters
     integer :: pi_inf_idx                !< Index of liquid stiffness func. eqn.
     type(int_bounds_info) :: stress_idx                !< Indexes of first and last shear stress eqns.
     integer :: c_idx         ! Index of the color function
-    type(int_bounds_info) :: chemistry_idx          !< Indexes of first & last concentration eqns.
+    type(int_bounds_info) :: species_idx           !< Indexes of first & last concentration eqns.
     type(int_bounds_info) :: temperature_idx       !< Indexes of first & last temperature eqns.
     !> @}
 
@@ -286,7 +286,7 @@ module m_global_parameters
 
     integer :: startx, starty, startz
 
-    !$acc declare create(sys_size, buff_size, startx, starty, startz, E_idx, gamma_idx, pi_inf_idx, alf_idx, n_idx, stress_idx, chemistry_idx)
+    !$acc declare create(sys_size, buff_size, startx, starty, startz, E_idx, gamma_idx, pi_inf_idx, alf_idx, n_idx, stress_idx, species_idx)
 
     ! END: Simulation Algorithm Parameters =====================================
 
@@ -1068,9 +1068,9 @@ contains
         end if
 
         if (chemistry) then
-            chemistry_idx%beg = sys_size + 1
-            chemistry_idx%end = sys_size + num_species
-            sys_size = chemistry_idx%end
+            species_idx%beg = sys_size + 1
+            species_idx%end = sys_size + num_species
+            sys_size = species_idx%end
 
             temperature_idx%beg = sys_size + 1
             temperature_idx%end = sys_size + 1
@@ -1089,13 +1089,13 @@ contains
         strxe = stress_idx%end
         intxb = internalEnergies_idx%beg
         intxe = internalEnergies_idx%end
-        chemxb = chemistry_idx%beg
-        chemxe = chemistry_idx%end
+        chemxb = species_idx%beg
+        chemxe = species_idx%end
         tempxb = temperature_idx%beg
         tempxe = temperature_idx%end
 
         !$acc update device(momxb, momxe, advxb, advxe, contxb, contxe, bubxb, bubxe, intxb, intxe, sys_size, buff_size, E_idx, alf_idx, n_idx, adv_n, adap_dt, pi_fac, strxb, strxe, chemxb, chemxe, tempxb, tempxe)
-        !$acc update device(chemistry_idx)
+        !$acc update device(species_idx)
         !$acc update device(cfl_target, m, n, p)
 
         !$acc update device(alt_soundspeed, acoustic_source, num_source)

toolchain/requirements.txt

@@ -25,4 +25,4 @@ pandas
 
 # Chemistry
 cantera
-pyrometheus @ git+https://github.com/henryleberre/pyrometheus.git@multi-lang-part-2
+pyrometheus @ git+https://github.com/pyrometheus/pyrometheus.git@mfc