Merge branch 'develop' of github.com:lanl/artemis into sli/dust

Author: shengtai

.github/workflows/ci.yml

@@ -40,11 +40,11 @@ jobs:
           python-version: '3.x'  # Specify the Python version you need
       - name: Install dependencies
         run: |
+          pip install clang-format==12.0.1.2
           pip install black
       - name: Run format check
         run: |
-          source env/bash
-          VERBOSE=1 ./style/format.sh
+          VERBOSE=1 CFM=clang-format ./style/format.sh
           git diff --exit-code --ignore-submodules
 
   cpu:

CMakeLists.txt

@@ -119,6 +119,11 @@ if(ARTEMIS_ENABLE_ASAN)
   add_link_options(-fsanitize=address -fsanitize=undefined)
 endif()
 
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Darwin")
+  # silence sprintf warnings on mac
+  add_compile_options(-Wno-deprecated-declarations)
+endif()
+
 # NOTE(@jonahm): For some reason, order still matters for including
 # parthenon and singularity. Likely has to do with project
 # includes other than Kokkos. MPI and OpenMP likely culprits.
@@ -186,7 +191,8 @@ set(ARTEMIS_SINGULARITY_INCLUDE_PATHS
     ${CMAKE_CURRENT_SOURCE_DIR}/external/singularity-eos/utils/variant/include
     ${CMAKE_CURRENT_SOURCE_DIR}/external/singularity-opac/utils
     ${CMAKE_CURRENT_SOURCE_DIR}/src
-    ${CMAKE_CURRENT_SOURCE_DIR})
+    ${CMAKE_CURRENT_SOURCE_DIR}
+    $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/generated>)
 
 # Set Jaybenne config options and paths
 # NOTE(@pdmullen): For the life of us, we are still not sure why we can't treat

doc/src/physics.rst

@@ -673,10 +673,7 @@ Specifically, |code|, adds the body force,
 .. math::
    \rho \frac{D \mathbf{v}}{D t} = \rho \mathbf{g}
 
-To activate external gravity, there must be a ``<gravity>`` node and ``gravity = true`` under the ``<physics>`` node.
-The ``<gravity>`` requires setting the parameter ``gm``, typically this is set to ``gm = 1.0``.
-In addition to ``gm``, the ``tstart`` and ``tstop`` parameters control when gravity is active.
-
+To activate external gravity, there must be a subnode of ``<gravity>`` (e.g., ``<gravity/point>``) and ``gravity = true`` under the ``<physics>`` node.
 The specific model for the gravitational acceleration, :math:`\mathbf{g}`, is controlled by adding the appropriate subnode.
 Available options are:
 
@@ -687,8 +684,6 @@ Available options are:
 
   ::
 
-   <gravity>
-   gm = 1.0
    <gravity/constant>
    gx1 = 0.0
    gx2 = 0.0
@@ -703,9 +698,8 @@ Available options are:
 
   ::
 
-   <gravity>
-   gm = 1.0
    <gravity/point>
+   mass = 1.0
    x = 0.0
    y = 0.0
    z = 0.0
@@ -721,9 +715,8 @@ Available options are:
 
   ::
 
-   <gravity>
-   gm = 1.0            # Binary total GM
    <gravity/binary>
+   mass = 1.0          # Total binary mass
    x = 0.0             # Binary x center of mass
    y = 0.0             # Binary y center of mass
    z = 0.0             # Binary z center of mass
@@ -745,14 +738,11 @@ Available options are:
 * ``<gravity/nbody>``
 
   This indicates that the gravitational force will be calculated by the N-body system defined in the ``<nbody>`` input block.
-  The only parameter required is the ``gm`` parameter.
-  Note that the total mass of the system defined in the ``<nbody>`` block will be rescaled to ``gm``.
-  An example input block would thus read:
+  Unlike the other gravity nodes, ``<gravity/nbody>`` has no parameters. Instead, all parameters live under the ``<nbody>`` node.
+  To activate nbody gravity, simply add:
 
   ::
 
-   <gravity>
-   gm = 1.0
    <gravity/nbody>
 
 See `N-Body Dynamics`_ for a description of how to set up the N-body system.

inputs/diffusion/alpha_disk.in

@@ -83,9 +83,8 @@ beta0 = 0.0
 tcyl = .0025
 cyl_plaw = -1.0
 
-<gravity>
-mass_tot = 1.0
 <gravity/point>
+mass = 1.0
 
 <problem>
 r0 = 1.0

inputs/diffusion/conduction.in

@@ -71,7 +71,7 @@ dfloor = 1.0e-10
 siefloor = 1.0e-15
 
 <gas/conductivity>
-type = constant 
+type = conductivity 
 cond = 1.0e-1
 
 <gravity/uniform>

inputs/diffusion/gaussian_bump.in

@@ -80,7 +80,7 @@ type = constant
 nu = 5.0e-3
 
 <gas/conductivity>
-type = constant
+type = conductivity 
 cond = 5.0e-3
 
 <problem>

inputs/disk/binary_cyl.in

@@ -86,9 +86,8 @@ omega = 1.0
 type = alpha
 alpha = 1e-3
 
-<gravity>
-mass_tot = 1.0
 <gravity/binary>
+mass = 1.0
 q = 1.0e-5
 a = 1.0
 e = 0.0

inputs/disk/binary_nbody_cyl.in

@@ -92,9 +92,8 @@ omega = 1.0
 type = alpha
 alpha = 1e-3
 
-<gravity>
-mass_tot = 1.0
 <gravity/nbody>
+mtot = 1.0
 
 <nbody>
 dt_reb = 0.01

inputs/disk/cb_disk.in

@@ -81,9 +81,8 @@ siefloor = 1.0e-6
 type = constant
 nu = 1e-3
 
-<gravity>
-mass_tot = 1.0
 <gravity/nbody>
+mtot = 1.0
 
 <nbody>
 integrator = ias15

inputs/disk/disk_alpha.in

@@ -74,9 +74,8 @@ siefloor = 1.0e-10
 type = alpha
 alpha = 1e-2
 
-<gravity>
-mass_tot = 1.0
 <gravity/point>
+mass = 1.0
 
 <cooling>
 type = beta