Replace Castro microphysics with starkiller-astro Microphysics (#760)

This implements the Microphysics part of #651. We replace the local Castro Microphysics directory with a dependence on the main starkiller-astro Microphysics directory. This means that obtaining Microphysics is now a requirement for using Castro. If the user sets MICROPHYSICS_HOME as before, then their workflow does not change. A new path is that Microphysics is a git submodule of Castro, so if the user does git submodule update --init --recursive then they will obtain the version of Microphysics that we specify in the repo, and if they do not have MICROPHYSICS_HOME set then this submodule will be used. The repo is now updated with git pull --recurse-submodules, so that updates to Microphysics come along when you pull.

A minor associated change is that we've standardized on NETWORK_INPUTS in all of the makefiles, instead of using GENERAL_NET_INPUTS with the hardcoded path.

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "Microphysics"]
+	path = Microphysics
+	url = https://github.com/starkiller-astro/Microphysics.git

CHANGES.md

@@ -1,5 +1,26 @@
 # 20.03
 
+   * We have updated our workflow when it comes to Castro's microphysics.
+     Previously Castro shipped with it a minimal set of microphysics that
+     allowed basic problem setups like Sedov to compile, and more advanced
+     setups (like ones that include nuclear burning) required downloading
+     the starkiller-astro Microphysics repository as an additional step.
+     Now, that Microphysics repository is a requirement for using Castro.
+     If you are a current user of the Microphysics repository and prefer
+     the current workflow where you maintain Microphysics as a separate
+     installation from Castro, no change in your workflow is necessary:
+     if MICROPHYSICS_HOME is set as an environment variable, Castro will
+     use the Microphysics installation in that directory. However we have
+     also added Microphysics as a git submodule to Castro, which is now
+     the required path if you previously were not using the more advanced
+     microphysics (but is also a possibility for those previously using a
+     standalone Microphysics installation). To obtain this, you can use
+     git submodule update --init --recursive from the top-level directory
+     of Castro. The developer team ensures that the version of Microphysics
+     that you obtain this way is consistent with the current version of Castro.
+     Then, you can keep up to date with the code mostly as normal, except now
+     using git pull --recurse-submodules instead of git pull. (#760)
+
    * The names of the conserved state variables in C++ (Density, Xmom, etc.)
      have been changed to match the names in Fortran (URHO, UMX, etc.).
      For user code, this will only affect problem-specific setup code

Exec/Make.Castro

@@ -9,11 +9,20 @@ BLAS_LIBRARY ?= -lopenblas
 
 TOP := $(CASTRO_HOME)
 
+MICROPHYSICS_HOME ?= $(TOP)/Microphysics
+
+# Check to make sure that Microphysics actually exists,
+# using an arbitrary file that must exist to check.
+# Throw an error if we don't have Microphysics.
+ifeq ("$(wildcard $(MICROPHYSICS_HOME)/Make.Microphysics)","")
+  $(error Microphysics has not been downloaded. Please run "git submodule update --init" from the top level of the code)
+endif
+
 # the Castro microphysics locations
-EOS_HOME ?= $(TOP)/Microphysics/EOS
-NETWORK_HOME ?= $(TOP)/Microphysics/networks
-COND_HOME ?= $(TOP)/Microphysics/conductivity
-VISC_HOME ?= $(TOP)/Microphysics/viscosity
+EOS_HOME ?= $(MICROPHYSICS_HOME)/EOS
+NETWORK_HOME ?= $(MICROPHYSICS_HOME)/networks
+COND_HOME ?= $(MICROPHYSICS_HOME)/conductivity
+VISC_HOME ?= $(MICROPHYSICS_HOME)/viscosity
 
 # default integrator
 INTEGRATOR_DIR ?= VODE90
@@ -163,6 +172,8 @@ ifeq ($(USE_DIFFUSION), TRUE)
   Bdirs += Source/diffusion
   DEFINES += -DDIFFUSION
   USE_MLMG = TRUE
+  USE_CONDUCTIVITY = TRUE
+  USE_VISCOSITY = TRUE
 endif
 
 ifeq ($(USE_HYBRID_MOMENTUM), TRUE)
@@ -257,29 +268,10 @@ Bpack	+= $(foreach dir, $(Pdirs), $(AMREX_HOME)/Src/$(dir)/Make.package)
 # microphysics 
 #------------------------------------------------------------------------------
 
-ifdef MICROPHYSICS_HOME
-   EOS_PATH := $(MICROPHYSICS_HOME)/EOS/$(strip $(EOS_DIR))
-   NETWORK_PATH := $(MICROPHYSICS_HOME)/networks/$(strip $(NETWORK_DIR))
+EOS_PATH := $(MICROPHYSICS_HOME)/EOS/$(strip $(EOS_DIR))
+NETWORK_PATH := $(MICROPHYSICS_HOME)/networks/$(strip $(NETWORK_DIR))
 ifeq ($(USE_DIFFUSION), TRUE)
    COND_PATH := $(MICROPHYSICS_HOME)/conductivity/$(strip $(CONDUCTIVITY_DIR))
-endif
-endif
-
-# if the EOS / network / conductivity name exists in
-# Castro/Microphysics, then use that version
-
-ifneq "$(wildcard $(EOS_HOME)/$(strip $(EOS_DIR)) )" ""
-   EOS_PATH := $(EOS_HOME)/$(strip $(EOS_DIR))
-endif
-
-ifneq "$(wildcard $(NETWORK_HOME)/$(strip $(NETWORK_DIR)) )" ""
-   NETWORK_PATH := $(NETWORK_HOME)/$(strip $(NETWORK_DIR))
-endif
-
-ifeq ($(USE_DIFFUSION), TRUE)
-ifneq "$(wildcard $(COND_HOME)/$(strip $(CONDUCTIVITY_DIR)) )" ""
-   COND_PATH := $(COND_HOME)/$(strip $(CONDUCTIVITY_DIR))
-endif
    VISC_PATH := $(VISC_HOME)/constant
 endif
 
@@ -290,7 +282,7 @@ ifndef GENERAL_NET_INPUTS
    ifneq "$(wildcard $(NETWORK_INPUTS))" ""
       GENERAL_NET_INPUTS := $(NETWORK_INPUTS)
    else
-      GENERAL_NET_INPUTS := $(CASTRO_HOME)/Microphysics/networks/general_null/$(NETWORK_INPUTS)
+      GENERAL_NET_INPUTS := $(MICROPHYSICS_HOME)/networks/general_null/$(NETWORK_INPUTS)
    endif
 endif
 
@@ -313,23 +305,24 @@ EXTERN_CORE += $(NETWORK_PATH)
 # Network includes since it has actions that depend on variables set
 # there.
 
-ifdef MICROPHYSICS_HOME
-  EXTERN_CORE += $(MICROPHYSICS_HOME)/EOS
-  EXTERN_CORE += $(MICROPHYSICS_HOME)/networks
-endif
+EXTERN_CORE += $(MICROPHYSICS_HOME)/EOS
+EXTERN_CORE += $(MICROPHYSICS_HOME)/networks
+EXTERN_CORE += $(MICROPHYSICS_HOME)/interfaces
 
-ifeq ($(USE_DIFFUSION), TRUE)
-   EXTERN_CORE += $(TOP)/Microphysics/conductivity
+ifeq ($(USE_CONDUCTIVITY), TRUE)
    EXTERN_CORE += $(COND_HOME)
    EXTERN_CORE += $(COND_PATH)
+endif
+
+ifeq ($(USE_VISCOSITY), TRUE)
    EXTERN_CORE += $(VISC_PATH)
 endif
 
 ifeq ($(USE_RAD), TRUE)
    ifeq ($(Opacity_dir), null)
      $(error The null opacity directory has been removed, please update to rad_power_law)
    endif
-   OPAC_PATH := $(TOP)/Microphysics/opacity/$(Opacity_dir)
+   OPAC_PATH := $(MICROPHYSICS_HOME)/opacity/$(Opacity_dir)
    EXTERN_CORE += $(OPAC_PATH)
 endif
 
@@ -408,9 +401,7 @@ EXTERN_TEMPLATE := $(TOP)/Source/driver/extern_probin.template
 
 # these are for finding runtime parameters
 EXTERN_SEARCH += $(EXTERN_CORE) $(TOP)/constants $(TOP)/Util/model_parser $(TOP)/Util/conservative_interpolate
-ifdef MICROPHYSICS_HOME
-   EXTERN_SEARCH += $(MICROPHYSICS_HOME)/networks/
-endif
+EXTERN_SEARCH += $(MICROPHYSICS_HOME)/networks/
 
 EXTERN_PARAMETERS := $(shell $(AMREX_HOME)/Tools/F_scripts/findparams.py $(EXTERN_SEARCH))
 

Exec/gravity_tests/DustCollapse/GNUmakefile

@@ -20,12 +20,12 @@ GPU_COMPATIBLE_PROBLEM = TRUE
 # define the location of the CASTRO top directory
 CASTRO_HOME  := ../../..
 
-# This sets the EOS directory in $(CASTRO_HOME)/EOS
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the EOS directory in $(CASTRO_HOME)/Networks
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/Networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/ignition.net
+NETWORK_INPUTS = ignition.net
 
 Bpack	:= ./Make.package
 Blocs	:= .

Exec/gravity_tests/StarGrav/GNUmakefile

@@ -16,20 +16,12 @@ USE_REACT  = FALSE
 
 USE_PROB_PARAMS = TRUE
 
-ifdef MICROPHYSICS_HOME
-
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(MICROPHYSICS_HOME)/networks/$(NETWORK_DIR)/ignition_wdconvect.net
-
-else
-
-$(error Error: This problem requires the Microphysics repository. Please ensure that you have downloaded it and set $$MICROPHYSICS_HOME appropriately)
-
-endif
+NETWORK_INPUTS = ignition_wdconvect.net
 
 Bpack   := ./Make.package
 Blocs   := .

Exec/gravity_tests/code_comp/GNUmakefile

@@ -18,20 +18,12 @@ GPU_COMPATIBLE_PROBLEM = TRUE
 
 USE_PROB_PARAMS = TRUE
 
-ifdef MICROPHYSICS_HOME
-
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
 EOS_DIR     := gamma_law_general
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = simple.net
-
-else
-
-$(error Error: This problem requires the Microphysics repository. Please ensure that you have downloaded it and set $$MICROPHYSICS_HOME appropriately)
-
-endif
+NETWORK_INPUTS = simple.net
 
 Bpack   := ./Make.package
 Blocs   := .

Exec/gravity_tests/evrard_collapse/GNUmakefile

@@ -26,16 +26,12 @@ USE_PROB_PARAMS = TRUE
 
 GPU_COMPATIBLE_PROBLEM = TRUE
 
-ifdef MICROPHYSICS_HOME
-  # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
-  EOS_DIR     := gamma_law_general
-else
-  $(error Error: This problem requires the Microphysics repository. Please ensure that you have downloaded it and set $$MICROPHYSICS_HOME appropriately)
-endif
-
-# This sets the network directory in Castro/Networks
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+EOS_DIR     := gamma_law_general
+
+# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/gammalaw.net
+NETWORK_INPUTS = gammalaw.net
 
 Bpack   += $(TEST_DIR)/Make.package
 Blocs   += $(TEST_DIR)

Exec/gravity_tests/hydrostatic_adjust/GNUmakefile

@@ -15,20 +15,12 @@ USE_PROB_PARAMS = TRUE
 
 CASTRO_HOME = ../../..
 
-ifdef MICROPHYSICS_HOME
-
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
 EOS_DIR     := helmholtz
 
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(MICROPHYSICS_HOME)/networks/$(NETWORK_DIR)/ignition.net
-
-else
-
-$(error Error: This problem requires the Microphysics repository. Please ensure that you have downloaded it and set $$MICROPHYSICS_HOME appropriately)
-
-endif
+NETWORK_INPUTS = ignition.net
 
 Bpack	:= ./Make.package
 Blocs	:= .

Exec/gravity_tests/uniform_cube_sphere/GNUmakefile

@@ -26,12 +26,12 @@ GPU_COMPATIBLE_PROBLEM = TRUE
 
 USE_PROB_PARAMS = TRUE
 
-# This sets the EOS directory in $(CASTRO_HOME)/EOS
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in Castro/Networks
+# This sets the network directory in $(MICROPHSICS_HOME)/Networks
 NETWORK_DIR ?= general_null
-GENERAL_NET_INPUTS = $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/gammalaw.net
+NETWORK_INPUTS = gammalaw.net
 
 Bpack   += $(TEST_DIR)/Make.package
 Blocs   += $(TEST_DIR)

Exec/hydro_tests/HCBubble/GNUmakefile

@@ -15,19 +15,12 @@ USE_PROB_PARAMS = TRUE
 # define the location of the CASTRO top directory
 CASTRO_HOME  := ../../..
 
-ifdef MICROPHYSICS_HOME
-  # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
-  EOS_DIR     := gamma_law_general
-else
-  $(error Error: This problem requires the Microphysics repository. Please ensure that you have downloaded it and set $$MICROPHYSICS_HOME appropriately)
-endif
-
-# This sets the EOS directory in Castro/EOS
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
 EOS_DIR     := gamma_law_general
 
-# This sets the network directory in Castro/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/gammalaw.net
+NETWORK_INPUTS = gammalaw.net
 
 Bpack   := ./Make.package
 Blocs   := .

Exec/hydro_tests/KH/GNUmakefile

@@ -24,12 +24,12 @@ USE_PROB_PARAMS = TRUE
 
 NUMADV := 1
 
-# This sets the EOS directory in Castro/EOS
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     ?= gamma_law
 
-# This sets the network directory in Castro/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
 NETWORK_DIR ?= general_null
-GENERAL_NET_INPUTS ?= $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/gammalaw.net
+NETWORK_INPUTS ?= gammalaw.net
 
 Bpack   += $(TEST_DIR)/Make.package
 Blocs   += $(TEST_DIR)/.

Exec/hydro_tests/Noh/GNUmakefile

@@ -20,11 +20,12 @@ COMP	   = gnu
 USE_MPI    = TRUE
 USE_OMP    = FALSE
 
+# This sets the network directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR   := gamma_law
 
-# This sets the network directory in Castro/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/gammalaw.net
+NETWORK_INPUTS = gammalaw.net
 
 Bpack   += $(TEST_DIR)/Make.package
 Blocs   += $(TEST_DIR)

Exec/hydro_tests/RT/GNUmakefile

@@ -17,12 +17,12 @@ USE_PROB_PARAMS = TRUE
 # define the location of the CASTRO top directory
 CASTRO_HOME  := ../../..
 
-# This sets the EOS directory in $(CASTRO_HOME)/EOS
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(CASTRO_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/gammalaw.net
+NETWORK_INPUTS = gammalaw.net
 
 Bpack   := ./Make.package
 Blocs   := .

Exec/hydro_tests/Sedov/GNUmakefile

@@ -16,12 +16,12 @@ USE_PROB_PARAMS = TRUE
 # define the location of the CASTRO top directory
 CASTRO_HOME  := ../../..
 
-# This sets the EOS directory in Castro/EOS
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in Castro/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/gammalaw.net
+NETWORK_INPUTS = gammalaw.net
 
 Bpack   := ./Make.package
 Blocs   := .

Exec/hydro_tests/Sod/GNUmakefile

@@ -18,12 +18,12 @@ USE_PROB_PARAMS = TRUE
 # define the location of the CASTRO top directory
 CASTRO_HOME  := ../../..
 
-# This sets the EOS directory in Castro/EOS
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in Castro/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(CASTRO_HOME)/Microphysics/networks/$(NETWORK_DIR)/gammalaw.net
+NETWORK_INPUTS = gammalaw.net
 
 Bpack   := ./Make.package
 Blocs   := .

Exec/hydro_tests/Sod_stellar/GNUmakefile

@@ -17,23 +17,12 @@ USE_PROB_PARAMS = TRUE
 # define the location of the CASTRO top directory
 CASTRO_HOME := ../../..
 
-ifdef MICROPHYSICS_HOME
-
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
 EOS_DIR     := helmholtz
 
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
-GENERAL_NET_INPUTS = $(MICROPHYSICS_HOME)/networks/$(NETWORK_DIR)/ignition.net
-
-else
-
-$(error Error: This problem requires the Microphysics repository. Please ensure that you have downloaded it and set $$MICROPHYSICS_HOME appropriately)
-
-endif
-
-# This sets the network directory in Castro/Networks
-
+NETWORK_INPUTS = ignition.net
 
 Bpack   := ./Make.package 
 #$(CASTRO_HOME)/Util/exact_riemann/Make.package