Merge branch 'main' into new_convection_bcs

.github/workflows/pytest.yml

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/regtest.yml

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

.zenodo.json

@@ -12,20 +12,30 @@
             "name": "Chen, Zhi",
             "orcid": "0000-0002-2839-107X"
         },
+	{
+	    "affiliation": "McGill University",
+	    "name": "Guichandut, Simon",
+	    "orcid": "0000-0002-5211-2122"
+	},
         {
             "affiliation": "University of Southampton",
             "name": "Hawke, Ian",
             "orcid": "0000-0003-4805-0309"
         },
         {
-            "affiliation": "Department of Physics and Astronomy, Stony Brook University",
             "name": "Harpole, Alice",
             "orcid": "0000-0002-1530-781X"
         },
-        {   "affiliation": "Department of Physics and Astronomy, Stony Brook University",
+        {
+	    "affiliation": "Department of Physics and Astronomy, Stony Brook University",
             "name": "Johnson, Eric",
             "orcid": "0000-0003-3603-6868"
         },
+	{
+	    "affiliation": "Department of Physics and Astronomy, Stony Brook University",
+	    "name": "Smith Clark, Alexander",
+	    "orcid": "0000-0001-5961-1680"
+	},
         {
             "affiliation": "Department of Physics and Astronomy, Stony Brook University",
             "name": "Zingale, Michael",

CITATION.md

@@ -0,0 +1,46 @@
+If you use pyro, please cite the pyro JOSS paper *and* the latest Zenodo DOI.
+
+## JOSS
+
+The pyro JOSS paper is at: https://joss.theoj.org/papers/10.21105/joss.01265
+
+You can cite it as:
+
+```bibtex
+@article{pyro_joss,
+         doi = {10.21105/joss.01265},
+         url = {https://doi.org/10.21105/joss.01265},
+         year = {2019},
+         publisher = {The Open Journal},
+         volume = {4},
+         number = {34},
+         pages = {1265},
+         author = {Alice Harpole and Michael Zingale and Ian Hawke and Taher Chegini},
+         title = {pyro: a framework for hydrodynamics explorations and prototyping},
+         journal = {Journal of Open Source Software}
+}
+```
+
+## Astronomy and Computing
+
+You can also additionally cite the paper from *Astronomy and Computing*:
+
+```bibtex
+@article{pyro_ac,
+         author = {{Zingale}, M.},
+         title = "{pyro: A teaching code for computational astrophysical hydrodynamics}",
+         journal = {Astronomy and Computing},
+         year = 2014,
+         month = {oct},
+         volume = 6,
+         pages = {52-62},
+         doi = {10.1016/j.ascom.2014.07.003}
+}
+```
+
+## Zenodo
+
+The latest pyro Zenodo record is at https://doi.org/10.5281/zenodo.2575564
+
+
+

docs/Makefile

@@ -18,4 +18,5 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	./document_problems.py
+	curl -L -H 'Accept: application/x-bibtex' https://zenodo.org/api/records/2575564 > source/zenodo.bibtex.txt
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/ack.rst

@@ -1,44 +1,5 @@
 Acknowledgments
 ===============
 
-The current pyro developers are listed in the `.zenodo.json` file that
-is used for releases.
-
-You are free to use this code and the accompanying notes in your
-classes. Please credit "pyro development team" for the code, and
-*please send a note to the pyro-help e-mail list describing how you
-use it, so we can keep track of it (and help justify the development
-effort).*
-
-If you use pyro in a publication, please cite it using this bibtex
-citation::
-
-    @article{pyro,
-      doi = {10.21105/joss.01265},
-      url = {https://doi.org/10.21105/joss.01265},
-      year = {2019},
-      publisher = {The Open Journal},
-      volume = {4},
-      number = {34},
-      pages = {1265},
-      author = {Alice Harpole and Michael Zingale and Ian Hawke and Taher Chegini},
-      title = {pyro: a framework for hydrodynamics explorations and prototyping},
-      journal = {Journal of Open Source Software}
-    }
-
 pyro benefited from numerous useful discussions with Ann Almgren, John
 Bell, and Andy Nonaka.
-
-
-History
-=======
-
-The original pyro code was written in 2003-4 to help developer
-Zingale understand these methods for himself. It was originally written
-using the Numeric array package and handwritten C extensions for the
-compute-intensive kernels.  It was ported to numarray when that
-replaced Numeric, and continued to use C extensions.  This version
-"pyro2" was resurrected beginning in 2012 and rewritten for numpy
-using f2py, and brought up to date.  Most recently we've dropped
-f2py and are using numba for the compute-intensive kernels.
-

docs/source/citing.rst

@@ -0,0 +1,17 @@
+Citing pyro
+===========
+
+You are free to use this code and the accompanying notes in your
+classes. Please credit "pyro development team" for the code, and
+*please make a post to the pyro github discussions describing how you
+use it, so we can keep track of it (and help justify the development
+effort).*
+
+.. mdinclude:: ../../CITATION.md
+
+The bibtex for the latest version is included below (updated automatically):
+
+.. literalinclude:: ./zenodo.bibtex.txt
+   :language: bibtex
+
+

docs/source/conf.py

@@ -47,6 +47,7 @@
     'sphinx_copybutton',
     'sphinx_math_dollar',
     'sphinx-prompt',
+    'sphinx_mdinclude',
     'IPython.sphinxext.ipython_console_highlighting',
     'sphinx.ext.githubpages']
 
@@ -182,6 +183,9 @@
                     r"https://doi.org/10.1061/(ASCE)0733-9429(1999)125:11(1210)",
                     r"https://pubs.aip.org/physicstoday/article/11/8/28/927415/Water-Waves"]
 
+linkcheck_retries = 3
+linkcheck_timeout = 100
+linkcheck_allow_unauthorized = True
 
 # -- Options for HTMLHelp output ------------------------------------------
 

docs/source/history.rst

@@ -0,0 +1,12 @@
+History
+=======
+
+The original pyro code was written in 2003-4 to help developer
+Zingale understand these methods for himself. It was originally written
+using the Numeric array package and handwritten C extensions for the
+compute-intensive kernels.  It was ported to numarray when that
+replaced Numeric, and continued to use C extensions.  This version
+"pyro2" was resurrected beginning in 2012 and rewritten for numpy
+using f2py, and brought up to date.  Most recently we've dropped
+f2py and are using numba for the compute-intensive kernels.
+

docs/source/index.rst

@@ -90,7 +90,9 @@ new ideas.
    :hidden:
 
    help
+   history
    ack
+   citing
 
 .. toctree::
    :maxdepth: 1

pyro/compressible/_defaults

@@ -21,6 +21,8 @@ grav = 0.0                ; gravitational acceleration (in y-direction)
 
 riemann = HLLC            ; HLLC or CGF
 
+small_dens = -1.e200      ; minimum allowed density
+small_eint = -1.e200      ; minimum allowed specific internal energy
 
 [sponge]
 do_sponge = 0             ; do we include a sponge source term

pyro/compressible/derives.py

@@ -57,6 +57,9 @@ def derive_primitives(myd, varnames):
         elif var == "soundspeed":
             derived_vars.append(np.sqrt(gamma*p/dens))
 
+        elif var == "machnumber":
+            derived_vars.append(np.sqrt(u**2 + v**2) / np.sqrt(gamma*p/dens))
+
         elif var == "vorticity":
             derived_vars.append(vort)
 

pyro/compressible/simulation.py

@@ -65,8 +65,10 @@ def cons_to_prim(U, gamma, ivars, myg):
                   out=np.zeros_like(U[:, :, ivars.iener]),
                   where=(U[:, :, ivars.idens] != 0.0))
 
-    assert e.v().min() > 0.0
-    assert q.v(n=ivars.irho).min() > 0.0
+    e_min = e.v().min()
+    rho_min = q.v(n=ivars.irho).min()
+
+    assert e_min > 0.0 and rho_min > 0.0, f"invalid state, min(rho) = {rho_min}, min(e) = {e_min}"
 
     q[:, :, ivars.ip] = eos.pres(gamma, q[:, :, ivars.irho], e)
 
@@ -291,6 +293,8 @@ def evolve(self):
         timestep dt.
         """
 
+        self.clean_state(self.cc_data.data)
+
         tm_evolve = self.tc.timer("evolve")
         tm_evolve.begin()
 
@@ -435,6 +439,12 @@ def evolve(self):
 
         tm_evolve.end()
 
+    def clean_state(self, U):
+        """enforce minimum density and eint on the conserved state U"""
+
+        U.v(n=self.ivars.idens)[:, :] = np.maximum(U.v(n=self.ivars.idens),
+                                                   self.rp.get_param("compressible.small_dens"))
+
     def dovis(self):
         """
         Do runtime visualization.

pyro/compressible_fv4/_defaults

@@ -23,6 +23,7 @@ grav = 0.0                ; gravitational acceleration (in y-direction)
 
 riemann = CGF
 
+small_dens = -1.e200      ; minimum allowed density
 
 [sponge]
 do_sponge = 0             ; do we include a sponge source term

pyro/compressible_fv4/simulation.py

@@ -1,7 +1,7 @@
 import pyro.compressible_fv4.fluxes as flx
 from pyro import compressible_rk
 from pyro.compressible import get_external_sources, get_sponge_factor
-from pyro.mesh import fv, integration
+from pyro.mesh import fv
 
 
 class Simulation(compressible_rk.Simulation):
@@ -19,6 +19,8 @@ def substep(self, myd):
         compute the advective source term for the given state
         """
 
+        self.clean_state(myd.data)
+
         myg = myd.grid
 
         # compute the source terms -- we need to do this first
@@ -66,37 +68,3 @@ def preevolve(self):
         # we just initialized cell-centers, but we need to store averages
         for var in self.cc_data.names:
             self.cc_data.from_centers(var)
-
-    def evolve(self):
-
-        """
-        Evolve the equations of compressible hydrodynamics through a
-        timestep dt.
-        """
-
-        tm_evolve = self.tc.timer("evolve")
-        tm_evolve.begin()
-
-        myd = self.cc_data
-
-        method = self.rp.get_param("compressible.temporal_method")
-
-        rk = integration.RKIntegrator(myd.t, self.dt, method=method)
-        rk.set_start(myd)
-
-        for s in range(rk.nstages()):
-            ytmp = rk.get_stage_start(s)
-            ytmp.fill_BC_all()
-            k = self.substep(ytmp)
-            rk.store_increment(s, k)
-
-        rk.compute_final_update()
-
-        if self.particles is not None:
-            self.particles.update_particles(self.dt)
-
-        # increment the time
-        myd.t += self.dt
-        self.n += 1
-
-        tm_evolve.end()

pyro/compressible_rk/_defaults

@@ -25,6 +25,7 @@ riemann = HLLC            ; HLLC or CGF
 
 well_balanced = 0         ; use a well-balanced scheme to keep the model in hydrostatic equilibrium
 
+small_dens = -1.e200      ; minimum allowed density
 
 [sponge]
 do_sponge = 0             ; do we include a sponge source term

pyro/compressible_rk/simulation.py

@@ -15,6 +15,8 @@ def substep(self, myd):
         conservative state defined as part of myd
         """
 
+        self.clean_state(myd.data)
+
         myg = myd.grid
 
         # source terms -- note: this dt is the entire dt, not the

pyro/compressible_sdc/_defaults

@@ -15,14 +15,11 @@ delta = 0.33              ; flattening delta parameter
 
 cvisc = 0.1               ; artificial viscosity coefficient
 
-limiter = 2               ; limiter (0 = none, 1 = 2nd order, 2 = 4th order)
-
-temporal_method = RK4     ; integration method (see mesh/integration.py)
-
 grav = 0.0                ; gravitational acceleration (in y-direction)
 
 riemann = CGF
 
+small_dens = -1.e200      ; minimum allowed density
 
 [sponge]
 do_sponge = 0             ; do we include a sponge source term