Merge branch 'development'

CHANGES

@@ -1,10 +1,18 @@
+changes since last release:
+
+  * Minor changes
+
+   -- simplified conductivity interface to match the eos interface by
+      storing the conductivity in the eos type.
+
 18.08
 
   * Major changes
 
    -- We fixed a corner coupling bug when advecting conservative
       scalars (predicting rho, rhoh, or rhoX)
 
+
 18.07
 
   * Major changes

Microphysics/EOS/eos_type.f90

@@ -145,6 +145,8 @@ module eos_type_module
     real(dp_t) :: dedA
     real(dp_t) :: dedZ
 
+    real(dp_t) :: conductivity
+
   end type eos_t
 
 contains

Microphysics/conductivity/conductivity.f90

@@ -26,7 +26,7 @@ end subroutine conductivity_init
 
   ! a generic wrapper that calls the EOS and then the conductivity
 
-  subroutine conducteos(input, state, cond)
+  subroutine conducteos(input, state)
 
     use actual_conductivity_module
     use eos_type_module, only : eos_t
@@ -36,12 +36,11 @@ subroutine conducteos(input, state, cond)
 
     integer         , intent(in   ) :: input
     type (eos_t)    , intent(inout) :: state
-    real (kind=dp_t), intent(inout) :: cond
 
     ! call the EOS, passing through the arguments we called conducteos with
     call eos(input, state)
 
-    call actual_conductivity(state, cond)
+    call actual_conductivity(state)
 
   end subroutine conducteos
 

Microphysics/conductivity/constant/conducteos.f90

@@ -9,16 +9,15 @@ subroutine actual_conductivity_init()
     implicit none
   end subroutine actual_conductivity_init
 
-  subroutine actual_conductivity(eos_state, conductivity)
+  subroutine actual_conductivity(eos_state)
 
     use eos_type_module
     use extern_probin_module, only: conductivity_constant
 
     type (eos_t)    , intent(inout) :: eos_state
-    real (kind=dp_t), intent(inout) :: conductivity
 
     ! fill the conductivity
-    conductivity = conductivity_constant
+    eos_state % conductivity = conductivity_constant
 
   end subroutine actual_conductivity
 

Source/make_explicit_thermal.f90

@@ -307,7 +307,6 @@ subroutine make_thermal_coeffs_1d(lo,hi,s,ng_s,Tcoeff,ng_T,hcoeff,ng_h, &
     ! local
     integer :: i,comp    
     type (eos_t) :: eos_state
-    real (kind=dp_t) :: conductivity
 
 
     do i=lo(1)-1,hi(1)+1
@@ -328,17 +327,17 @@ subroutine make_thermal_coeffs_1d(lo,hi,s,ng_s,Tcoeff,ng_T,hcoeff,ng_h, &
           eos_state%xn(:) = s(i,spec_comp:spec_comp+nspec-1)/eos_state%rho
 
           ! dens, temp, and xmass are inputs
-          call conducteos(eos_input_rt, eos_state, conductivity)
+          call conducteos(eos_input_rt, eos_state)
 
-          Tcoeff(i) = -conductivity
-          hcoeff(i) = -conductivity/eos_state%cp
-          pcoeff(i) = (conductivity/eos_state%cp)* &
+          Tcoeff(i) = -eos_state % conductivity
+          hcoeff(i) = -eos_state % conductivity/eos_state%cp
+          pcoeff(i) = (eos_state % conductivity/eos_state%cp)* &
                ((1.0d0/eos_state%rho)* &
                (1.0d0-eos_state%p/(eos_state%rho*eos_state%dpdr))+ &
                eos_state%dedr/eos_state%dpdr)
 
           do comp=1,nspec
-             Xkcoeff(i,comp) = (conductivity/eos_state%cp)*eos_state%dhdX(comp)
+             Xkcoeff(i,comp) = (eos_state % conductivity/eos_state%cp)*eos_state%dhdX(comp)
           enddo
 
        endif
@@ -374,7 +373,6 @@ subroutine make_thermal_coeffs_2d(lo,hi,s,ng_s,Tcoeff,ng_T,hcoeff,ng_h, &
     ! local
     integer :: i,j,comp    
     type (eos_t) :: eos_state
-    real (kind=dp_t) :: conductivity
 
     do j=lo(2)-1,hi(2)+1
        do i=lo(1)-1,hi(1)+1
@@ -395,17 +393,17 @@ subroutine make_thermal_coeffs_2d(lo,hi,s,ng_s,Tcoeff,ng_T,hcoeff,ng_h, &
              eos_state%xn(:) = s(i,j,spec_comp:spec_comp+nspec-1)/eos_state%rho
 
              ! dens, temp, and xmass are inputs
-             call conducteos(eos_input_rt, eos_state, conductivity)
+             call conducteos(eos_input_rt, eos_state)
 
-             Tcoeff(i,j) = -conductivity
-             hcoeff(i,j) = -conductivity/eos_state%cp
-             pcoeff(i,j) = (conductivity/eos_state%cp)* &
+             Tcoeff(i,j) = -eos_state % conductivity
+             hcoeff(i,j) = -eos_state % conductivity/eos_state%cp
+             pcoeff(i,j) = (eos_state % conductivity/eos_state%cp)* &
                   ((1.0d0/eos_state%rho)* &
                   (1.0d0-eos_state%p/(eos_state%rho*eos_state%dpdr))+ &
                   eos_state%dedr/eos_state%dpdr)
 
              do comp=1,nspec
-                Xkcoeff(i,j,comp) = (conductivity/eos_state%cp)*eos_state%dhdX(comp)
+                Xkcoeff(i,j,comp) = (eos_state % conductivity/eos_state%cp)*eos_state%dhdX(comp)
              enddo
 
           endif
@@ -442,9 +440,8 @@ subroutine make_thermal_coeffs_3d(lo,hi,s,ng_s,Tcoeff,ng_T,hcoeff,ng_h, &
     ! local
     integer :: i,j,k,comp
     type (eos_t) :: eos_state
-    real (kind=dp_t) :: conductivity
 
-    !$OMP PARALLEL DO PRIVATE(i,j,k,comp,eos_state,conductivity)
+    !$OMP PARALLEL DO PRIVATE(i,j,k,comp,eos_state)
     do k=lo(3)-1,hi(3)+1
        do j=lo(2)-1,hi(2)+1
           do i=lo(1)-1,hi(1)+1
@@ -466,17 +463,17 @@ subroutine make_thermal_coeffs_3d(lo,hi,s,ng_s,Tcoeff,ng_T,hcoeff,ng_h, &
                 eos_state%xn(:) = s(i,j,k,spec_comp:spec_comp+nspec-1)/eos_state%rho
 
                 ! dens, temp, and xmass are inputs
-                call conducteos(eos_input_rt, eos_state, conductivity)
+                call conducteos(eos_input_rt, eos_state)
 
-                Tcoeff(i,j,k) = -conductivity
-                hcoeff(i,j,k) = -conductivity/eos_state%cp
-                pcoeff(i,j,k) = (conductivity/eos_state%cp)* &
+                Tcoeff(i,j,k) = -eos_state % conductivity
+                hcoeff(i,j,k) = -eos_state % conductivity/eos_state%cp
+                pcoeff(i,j,k) = (eos_state % conductivity/eos_state%cp)* &
                      ((1.0d0/eos_state%rho)* &
                      (1.0d0-eos_state%p/(eos_state%rho*eos_state%dpdr))+ &
                      eos_state%dedr/eos_state%dpdr)
 
                 do comp=1,nspec
-                   Xkcoeff(i,j,k,comp) = (conductivity/eos_state%cp)*eos_state%dhdX(comp)
+                   Xkcoeff(i,j,k,comp) = (eos_state % conductivity/eos_state%cp)*eos_state%dhdX(comp)
                 enddo
 
              endif

Source/make_plot_variables.f90

@@ -482,17 +482,16 @@ subroutine make_conductivity_1d(cond,ng_c,state,ng_s,lo,hi)
     integer :: i
 
     type (eos_t) :: eos_state
-    real (kind=dp_t) :: conductivity
 
     do i = lo(1), hi(1)
 
        eos_state%rho   = state(i,rho_comp)
        eos_state%T     = state(i,temp_comp)
        eos_state%xn(:) = state(i,spec_comp:spec_comp+nspec-1) / eos_state%rho
 
-       call conducteos(eos_input_rt, eos_state, conductivity)
+       call conducteos(eos_input_rt, eos_state)
 
-       cond(i) = conductivity
+       cond(i) = eos_state % conductivity
 
     enddo
 
@@ -514,7 +513,6 @@ subroutine make_conductivity_2d(cond,ng_c,state,ng_s,lo,hi)
     integer :: i, j
 
     type (eos_t) :: eos_state
-    real (kind=dp_t) :: conductivity
 
     do j = lo(2), hi(2)
        do i = lo(1), hi(1)
@@ -523,9 +521,9 @@ subroutine make_conductivity_2d(cond,ng_c,state,ng_s,lo,hi)
           eos_state%T     = state(i,j,temp_comp)
           eos_state%xn(:) = state(i,j,spec_comp:spec_comp+nspec-1) / eos_state%rho
 
-          call conducteos(eos_input_rt, eos_state, conductivity)
+          call conducteos(eos_input_rt, eos_state)
 
-          cond(i,j) = conductivity
+          cond(i,j) = eos_state % conductivity
 
        enddo
     enddo
@@ -548,9 +546,8 @@ subroutine make_conductivity_3d(cond,ng_c,state,ng_s,lo,hi)
     integer :: i, j, k
 
     type (eos_t) :: eos_state
-    real (kind=dp_t) :: conductivity
 
-    !$OMP PARALLEL DO PRIVATE(i,j,k,eos_state,conductivity)
+    !$OMP PARALLEL DO PRIVATE(i,j,k,eos_state)
     do k = lo(3), hi(3)
        do j = lo(2), hi(2)
           do i = lo(1), hi(1)
@@ -560,9 +557,9 @@ subroutine make_conductivity_3d(cond,ng_c,state,ng_s,lo,hi)
              eos_state%xn(:) = state(i,j,k,spec_comp:spec_comp+nspec-1) / &
                            eos_state%rho
 
-             call conducteos(eos_input_rt, eos_state, conductivity)
+             call conducteos(eos_input_rt, eos_state)
 
-             cond(i,j,k) = conductivity
+             cond(i,j,k) = eos_state % conductivity
 
           enddo
        enddo

Util/postprocessing/urca-tools/plot_fconv_slopes.py

@@ -62,8 +62,8 @@ def plot(self, fmt=None, rup=None, outname=None, show=False):
         ax.plot(self.r[:idxup], dledoux, color='red', linestyle='-.', label='ledoux $\mathrm{\\nabla_{conv}}$')
         mx = max(np.amax(dadiabatic), np.amax(dledoux))
         mn = min(np.amin(dadiabatic), np.amin(dledoux))
-        mx = max(abs(mx), abs(mn))
-        plt.yscale('symlog', linthreshy=0.1*mx)
+        mlin = min(abs(mx), abs(mn))
+        plt.yscale('symlog', linthreshy=0.5*mlin)
         ax.set_ylabel('$\mathrm{\\nabla_{actual} - \\nabla_{conv}}$')
         plt.legend()
         if fmt=='png':