Upstream non-Phase Change additions from #179 (#223)

Co-authored-by: JRChreim <jrchreim@outlook.com>

.gitattributes

@@ -0,0 +1 @@
+/tests/**/* linguist-generated=true

mfc.sh

@@ -146,13 +146,15 @@ if [ "$1" == 'load' ]; then
 
     return
 elif [ "$1" == "format" ]; then
+    shift
+
     if ! command -v fprettify > /dev/null 2>&1; then
         pip3 install --upgrade fprettify
     fi
 
-    fprettify src --exclude "src/*/autogen" --recursive \
+    fprettify ${@:-src} --exclude "src/*/autogen" --recursive --silent \
         --indent 4 --c-relations --enable-replacements --enable-decl \
-        --whitespace-comma 1 --whitespace-multdiv 0 --whitespace-plusminus 1 \
+        --whitespace-comma 1 --whitespace-multdiv 1 --whitespace-plusminus 1 \
         --case 1 1 1 1 --strict-indent
     ret="$?"
 

src/common/m_variables_conversion.fpp

@@ -1002,6 +1002,11 @@ contains
                         q_cons_vf(i)%sf(j, k, l) = q_prim_vf(i)%sf(j, k, l)
                     end do
 
+                    ! Transferring the advection equation(s) variable(s)
+                    do i = adv_idx%beg, adv_idx%end
+                        q_cons_vf(i)%sf(j, k, l) = q_prim_vf(i)%sf(j, k, l)
+                    end do
+
                     ! Zeroing out the dynamic pressure since it is computed
                     ! iteratively by cycling through the velocity equations
                     dyn_pres = 0d0
@@ -1030,19 +1035,15 @@ contains
 
                     ! Computing the internal energies from the pressure and continuities
                     if (model_eqns == 3) then
-                        do i = internalEnergies_idx%beg, internalEnergies_idx%end
-                            q_cons_vf(i)%sf(j, k, l) = q_cons_vf(i - adv_idx%end)%sf(j, k, l)* &
-                                                       fluid_pp(i - adv_idx%end)%gamma* &
-                                                       q_prim_vf(E_idx)%sf(j, k, l) + &
-                                                       fluid_pp(i - adv_idx%end)%pi_inf
+                        do i = 1, num_fluids
+                            ! internal energy calculation for each of the fluids
+                            q_cons_vf(i + internalEnergies_idx%beg - 1)%sf(j, k, l) = &
+                                q_cons_vf(i + adv_idx%beg - 1)%sf(j, k, l)* &
+                                (fluid_pp(i)%gamma*q_prim_vf(E_idx)%sf(j, k, l) + &
+                                 fluid_pp(i)%pi_inf)
                         end do
                     end if
 
-                    ! Transferring the advection equation(s) variable(s)
-                    do i = adv_idx%beg, adv_idx%end
-                        q_cons_vf(i)%sf(j, k, l) = q_prim_vf(i)%sf(j, k, l)
-                    end do
-
                     if (bubbles) then
                         ! From prim: Compute nbub = (3/4pi) * \alpha / \bar{R^3}
                         do i = 1, nb
@@ -1061,8 +1062,7 @@ contains
                             !Initialize nb 
                             nbub = 3d0 * q_prim_vf(alf_idx)%sf(j, k, l) / (4d0 * pi * R3tmp)
                         end if
-
-
+
                         if (j == 0 .and. k == 0 .and. l == 0) print *, 'In convert, nbub:', nbub
                         do i = bub_idx%beg, bub_idx%end
                             q_cons_vf(i)%sf(j, k, l) = q_prim_vf(i)%sf(j, k, l)*nbub

src/pre_process/m_assign_variables.f90

@@ -480,6 +480,13 @@ subroutine s_assign_patch_species_primitive_variables(patch_id, j, k, l, &
                  + (1d0 - eta)*orig_prim_vf(1 + cont_idx%end))
          end if
 
+        ! Set partial pressures to mixture pressure for the 6-eqn model
+        if (model_eqns == 3) then
+            do i = internalEnergies_idx%beg, internalEnergies_idx%end
+                q_prim_vf(i)%sf(j, k, l) = q_prim_vf(E_idx)%sf(j, k, l)
+            end do
+        end if
+
         ! Smoothed bubble variables
         if (bubbles) then
             do i = 1, nb

toolchain/mfc/args.py

@@ -93,6 +93,7 @@ def add_common_arguments(p, mask = None):
     test_meg = test.add_mutually_exclusive_group()
     test_meg.add_argument("--generate",          action="store_true", default=False, help="(Test Generation) Generate golden files.")
     test_meg.add_argument("--add-new-variables", action="store_true", default=False, help="(Test Generation) If new variables are found in D/ when running tests, add them to the golden files.")
+    test_meg.add_argument("--remove-old-tests",  action="store_true", default=False, help="(Test Generation) Delete tests directories that are no longer.")
 
     # === RUN ===
     engines = [ e.slug for e in ENGINES ]

toolchain/mfc/test/test.py

@@ -64,14 +64,17 @@ def __filter():
 
 def test():
     global CASES, nFAIL
-    
+
     # Delete UUIDs that are not in the list of CASES from tests/
-    if ARG("generate"):
-        dir_uuids = set([name for name in os.listdir(".") if os.path.isdir(name)])
+    if ARG("remove_old_tests"):
+        dir_uuids = set(os.listdir(common.MFC_TESTDIR))
         new_uuids = set([case.get_uuid() for case in CASES])
 
         for old_uuid in dir_uuids - new_uuids:
+            cons.print(f"[bold red]Deleting:[/bold red] {old_uuid}")
             common.delete_directory(f"{common.MFC_TESTDIR}/{old_uuid}")
+
+        return
 
     __filter()