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

inputs/disk/disk_axi.in

@@ -80,9 +80,8 @@ omega = 1.0
 type = alpha
 alpha = 1e-3
 
-<gravity>
-mass_tot = 1.0
 <gravity/point>
+mass = 1.0
 
 <problem>
 r0 = 1.0

inputs/disk/disk_cart.in

@@ -110,9 +110,8 @@ riemann = hlle
 dfloor = 1.0e-10
 pfloor = 1.0e-15
 
-<gravity>
-mass_tot = 1.0
 <gravity/point>
+mass = 1.0
 
 <problem>
 r0 = 1.0

inputs/disk/disk_collision.in

@@ -79,9 +79,8 @@ riemann = hllc
 dfloor = 1.0e-10
 siefloor = 1.0e-10
 
-<gravity>
-mass_tot = 1.0
 <gravity/nbody>
+mtot = 1.0
 
 <gas/damping>
 inner_x1 = 0.45

inputs/disk/disk_cyl.in

@@ -81,9 +81,8 @@ omega = 1.0
 type = alpha
 alpha = 1e-3
 
-<gravity>
-mass_tot = 1.0
 <gravity/point>
+mass = 1.0
 
 <problem>
 r0 = 1.0

inputs/disk/disk_nbody_cyl.in

@@ -78,8 +78,6 @@ siefloor = 1.0e-10
 type = alpha
 alpha = 1e-3
 
-<gravity>
-mass_tot = 1.0
 <gravity/nbody>
 
 <nbody>

inputs/disk/disk_sph.in

@@ -80,9 +80,8 @@ omega = 1.0
 type = alpha
 alpha = 1e-3
 
-<gravity>
-mass_tot = 1.0
 <gravity/point>
+mass = 1.0
 
 <problem>
 r0 = 1.0

inputs/ssheet/ssheet.in

@@ -76,9 +76,8 @@ refine_type = magnitude
 refine_thr = 3.0
 deref_thr = 0.8
 
-<gravity>
-mass_tot = 1.0e-5
 <gravity/point>
+mass = 1.0e-5
 soft = 0.03
 x = 0.0
 y = 0.0

src/CMakeLists.txt

@@ -146,8 +146,15 @@ if (CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
    message(STATUS "Standalone mode. Adding artemis executable")
    add_executable(artemis main.cpp)
    target_link_libraries(artemis PRIVATE artemislib)
-   add_custom_command(TARGET artemis POST_BUILD
-                      COMMAND ${CMAKE_COMMAND} -E copy
-                              ${CMAKE_BINARY_DIR}/rebound/librebound.so
-                              $<TARGET_FILE_DIR:artemis>)
+
+   # Bake in rpath to rebound on mac
+   if(${CMAKE_SYSTEM_NAME} STREQUAL "Darwin")
+    set_target_properties(artemis PROPERTIES
+      BUILD_RPATH "${CMAKE_BINARY_DIR}/rebound"
+    )
+    add_custom_command(TARGET artemis POST_BUILD
+      COMMAND install_name_tool -add_rpath @executable_path/../rebound $<TARGET_FILE:artemis>
+      COMMAND install_name_tool -change librebound.so @rpath/librebound.so $<TARGET_FILE:artemis>
+    )
+   endif()
 endif()

src/artemis.cpp

@@ -105,13 +105,13 @@ Packages_t ProcessPackages(std::unique_ptr<ParameterInput> &pin) {
   artemis->AddParam("coord_sys", sys);
 
   // Call package initializers here
-  if (do_gas) packages.Add(Gas::Initialize(pin.get(), units, constants));
-  if (do_dust) packages.Add(Dust::Initialize(pin.get()));
-  if (do_gravity) packages.Add(Gravity::Initialize(pin.get(), constants));
+  if (do_nbody) packages.Add(NBody::Initialize(pin.get(), constants));
+  if (do_gravity) packages.Add(Gravity::Initialize(pin.get(), constants, packages));
+  if (do_gas) packages.Add(Gas::Initialize(pin.get(), units, constants, packages));
+  if (do_dust) packages.Add(Dust::Initialize(pin.get(), units));
   if (do_rotating_frame) packages.Add(RotatingFrame::Initialize(pin.get()));
   if (do_cooling) packages.Add(Gas::Cooling::Initialize(pin.get()));
   if (do_drag) packages.Add(Drag::Initialize(pin.get()));
-  if (do_nbody) packages.Add(NBody::Initialize(pin.get(), constants));
   if (do_coagulation) {
     auto &dustPars = packages.Get("dust")->AllParams();
     packages.Add(Dust::Coagulation::Initialize(pin.get(), dustPars, units, constants));

src/artemis_params.yaml

@@ -23,37 +23,42 @@ artemis:
     _type: bool
     _default: "false"
     _description: "Add user-defined AMR criterion."
-  units:
-    _description: "Unit conversions between code and cgs."
   physical_units:
     _type: "string"
     _default: "scalefree"
     _description: "What unit system to use for physical units"
-    code:
+    scalefree:
       _type: opt
       _description: "Native code units; no conversions"
     cgs:
       _type: opt
       _description: "CGS unit system"
-  unit_conversion:
+  unit_specifier:
     _type: "string"
     _default: "base"
     _description: "How to provide unit conversions between code and physical units"
     base:
       _type: opt
-      _description: "Provide base unit conversions (length, time, mass)"
+      _description: "Provide base unit conversions (length, time, mass, temperature)"
     ppd:
       _type: opt
       _description: "AU, Year/(2 pi), solar mass units for protoplanetary disks"
   length:
     _type: "Real"
+    _default: "1.0"
     _description: "Physical units value of length equal to 1 code unit"
   time:
     _type: "Real"
+    _default: "1.0"
     _description: "Physical units value of time equal to 1 code unit"
   mass:
     _type: "Real"
+    _default: "1.0"
     _description: "Physical units value of mass equal to 1 code unit"
+  temperature:
+    _type: "Real"
+    _default: "1.0"
+    _description: "Physical units value of temperature equal to 1 code unit"
 
 
 physics:

src/drag/drag.cpp

@@ -110,8 +110,8 @@ TaskStatus DragSource(MeshData<Real> *md, const Real time, const Real dt) {
       auto &gas_pkg = pm->packages.Get("gas");
       const auto &dp = gas_pkg->template Param<Diffusion::DiffCoeffParams>("visc_params");
       const auto &eos_d = gas_pkg->template Param<EOS>("eos_d");
-      if (dp.type == Diffusion::DiffType::viscosity_const) {
-        return SelfDragSourceImpl<Diffusion::DiffType::viscosity_const, GEOM>(
+      if (dp.type == Diffusion::DiffType::viscosity_plaw) {
+        return SelfDragSourceImpl<Diffusion::DiffType::viscosity_plaw, GEOM>(
             md, time, dt, dp, eos_d, gas_self_par, dust_self_par);
       } else if (dp.type == Diffusion::DiffType::viscosity_alpha) {
         return SelfDragSourceImpl<Diffusion::DiffType::viscosity_alpha, GEOM>(
@@ -134,13 +134,13 @@ TaskStatus DragSource(MeshData<Real> *md, const Real time, const Real dt) {
         drag_pkg->template Param<StoppingTimeParams>("stopping_time_params");
     if (gas_self_par.damp_to_visc) {
       auto &dp = gas_pkg->template Param<Diffusion::DiffCoeffParams>("visc_params");
-      if (dp.type == Diffusion::DiffType::viscosity_const) {
+      if (dp.type == Diffusion::DiffType::viscosity_plaw) {
         if (stop_par.model == DragModel::constant) {
-          return SimpleDragSourceImpl<Diffusion::DiffType::viscosity_const,
+          return SimpleDragSourceImpl<Diffusion::DiffType::viscosity_plaw,
                                       DragModel::constant, GEOM>(
               md, time, dt, dp, eos_d, gas_self_par, dust_self_par, stop_par);
         } else if (stop_par.model == DragModel::stokes) {
-          return SimpleDragSourceImpl<Diffusion::DiffType::viscosity_const,
+          return SimpleDragSourceImpl<Diffusion::DiffType::viscosity_plaw,
                                       DragModel::stokes, GEOM>(
               md, time, dt, dp, eos_d, gas_self_par, dust_self_par, stop_par);
         }