Updated ppml

config/linux_gcc.cmake

@@ -11,7 +11,13 @@ if(NOT __processedUserDefaults)
   set(CMAKE_Fortran_COMPILER gfortran CACHE STRING "")
   # Note (12/2021): passing -march=native to gfortran seems to slow down the
   # PPM solver
-  set(CMAKE_Fortran_FLAGS "-ffixed-line-length-132" CACHE STRING "Default Fortran flags")
+  set(CMAKE_Fortran_FLAGS "-ffixed-line-length-132 -std=legacy " CACHE STRING "Default Fortran flags")
+
+  set(__ARCH_C_OPT_FLAGS "-O3 -g -funroll-loops")
+  set(CMAKE_C_FLAGS_RELEASE "${__ARCH_C_OPT_FLAGS}")
+  set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g ${__ARCH_C_OPT_FLAGS}")
+  set(CMAKE_CXX_FLAGS_RELEASE "${__ARCH_C_OPT_FLAGS}")
+  set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g ${__ARCH_C_OPT_FLAGS}")
 
   # these flag(s) are currently only used when using openmp-simd optimizations
   # (to specify available/prefered instruction sets).

config/linux_gcc_9.py

@@ -0,0 +1,78 @@
+
+import os
+from _common_search_paths import charm_path_search, grackle_path_search
+
+is_arch_valid = 1
+
+#
+#flags_arch = '-g -fprofile-arcs -ftest-coverage' # gcov
+#flags_arch = '-O3 -fopenmp -Wall -g -ffast-math -funroll-loops -fPIC'
+flags_arch = '-O3 -fopenmp -Wall -g -ffast-math -funroll-loops -fPIC'
+#flags_arch = '-Wall -O1 -g -fPIC -pedantic'
+#flags_arch = '-Wall -O0 -g'
+#flags_arch = '-O3 -pg -g'
+#flags_arch = '-Wall -g -fsanitize=address -fno-omit-frame-pointer'
+
+# rdynamic required for backtraces
+#flags_link_charm = '-rdynamic' 
+#flags_link_charm = '-memory paranoid'
+#flags_link_charm = '-fprofile-arcs' # gcov
+
+#optional fortran flag
+flags_arch_fortran = '-ffixed-line-length-132 -std=legacy '
+
+cc  = 'gcc '
+f90 = 'gfortran'
+
+flags_prec_single = ''
+flags_prec_double = '-fdefault-real-8 -fdefault-double-8'
+
+libpath_fortran = '/usr/lib/gcc/x86_64-linux-gnu/9'
+libs_fortran    = ['gfortran']
+
+home = os.getenv('HOME')
+
+# use Charm++ with randomized message queues for debugging and stress-testing
+# charm_path = home + '/Charm/charm.random'
+
+charm_path = charm_path_search(home)
+
+# use_papi = 1
+# papi_inc = os.getenv('PAPI_INC', '/usr/include')
+# papi_lib = os.getenv('PAPI_LIB', '/usr/lib')
+
+hdf5_inc = os.getenv('HDF5_INC')
+if hdf5_inc is None:
+	if os.path.exists('/usr/include/hdf5.h'):
+	        hdf5_inc    = '/usr/include'
+	elif os.path.exists('/usr/include/hdf5/serial/hdf5.h'):
+		hdf5_inc    = '/usr/include/hdf5/serial'
+	else:
+		raise Exception('HDF5 include file was not found.  Try setting the HDF5_INC environment variable such that $HDF5_INC/hdf5.h exists.')
+
+hdf5_lib = os.getenv('HDF5_LIB')
+if hdf5_lib is None:
+	if os.path.exists('/usr/lib/libhdf5.a'):
+		hdf5_lib    = '/usr/lib'
+	elif os.path.exists('/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.a'):
+		hdf5_lib    = '/usr/lib/x86_64-linux-gnu/hdf5/serial'
+	else:
+		raise Exception('HDF5 lib file was not found.  Try setting the HDF5_LIB environment variable such that $HDF5_LIB/libhdf5.a exists.')
+
+png_path = os.getenv('LIBPNG_HOME', '/lib/x86_64-linux-gnu')
+
+boost_inc = os.getenv('BOOST_INC', '/usr/include/boost')
+boost_lib = os.getenv('BOOST_LIB', '/usr/lib/x86_64-linux-gnu')
+
+grackle_path = grackle_path_search(home)
+
+cello_var = os.environ.get('CELLO_VAR',"net")
+
+if (cello_var == "net"):
+    parallel_run = charm_path + "/bin/charmrun +p4 "
+    parallel_arg = " "
+    smp = 0
+elif (cello_var == "net-smp"):
+    parallel_run = charm_path + "/bin/charmrun +p4 "
+    parallel_arg = " ++ppn 4 "
+    smp = 1

config/linux_gnu.py

@@ -0,0 +1,69 @@
+
+import os
+from _common_search_paths import charm_path_search, grackle_path_search
+
+is_arch_valid = 1
+
+#
+#flags_arch = '-g -fprofile-arcs -ftest-coverage' # gcov
+flags_arch = '-O3 -g -ffast-math -funroll-loops -fPIC'
+#flags_arch = '-Wall -O3 -g'
+#flags_arch = '-Wall -O0 -g'
+
+#flags_arch = '-O3 -pg -g'
+#flags_arch = '-fprofile-arcs -ftest-coverage'
+#flags_arch = '-Wall -g -fsanitize=address -fno-omit-frame-pointer'
+#flags_arch = '-Wall -O3 -pg'
+
+# rdynamic required for backtraces
+#flags_link_charm = '-rdynamic'
+#flags_link_charm = '-memory paranoid'
+#flags_link_charm = '-fprofile-arcs' # gcov
+
+#optional fortran flag
+flags_arch_fortran = '-ffixed-line-length-132'
+
+cc  = 'gcc '
+f90 = 'gfortran'
+
+flags_prec_single = ''
+flags_prec_double = '-fdefault-real-8 -fdefault-double-8'
+
+libpath_fortran = '/usr/lib/x86_64-linux-gnu'
+libs_fortran    = ['gfortran']
+
+home = os.getenv('HOME')
+
+# use Charm++ with randomized message queues for debugging and stress-testing
+# charm_path = home + '/Charm/charm.random'
+
+charm_path = charm_path_search(home)
+
+# use_papi = 1
+# papi_inc = os.getenv('PAPI_INC', '/usr/include')
+# papi_lib = os.getenv('PAPI_LIB', '/usr/lib')
+
+hdf5_inc = os.getenv('HDF5_INC')
+if hdf5_inc is None:
+	if os.path.exists('/usr/include/hdf5.h'):
+	        hdf5_inc    = '/usr/include'
+	elif os.path.exists('/usr/include/hdf5/serial/hdf5.h'):
+		hdf5_inc    = '/usr/include/hdf5/serial'
+	else:
+		raise Exception('HDF5 include file was not found.  Try setting the HDF5_INC environment variable such that $HDF5_INC/hdf5.h exists.')
+
+hdf5_lib = os.getenv('HDF5_LIB')
+if hdf5_lib is None:
+	if os.path.exists('/usr/lib/libhdf5.a'):
+		hdf5_lib    = '/usr/lib'
+	elif os.path.exists('/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.a'):
+		hdf5_lib    = '/usr/lib/x86_64-linux-gnu/hdf5/serial'
+	else:
+		raise Exception('HDF5 lib file was not found.  Try setting the HDF5_LIB environment variable such that $HDF5_LIB/libhdf5.a exists.')
+
+png_path = os.getenv('LIBPNG_HOME', '/lib/x86_64-linux-gnu')
+
+boost_inc = os.getenv('BOOST_INC', '/usr/include/boost')
+boost_lib = os.getenv('BOOST_LIB', '/usr/lib/x86_64-linux-gnu')
+
+grackle_path = grackle_path_search(home)

doc/source/param/index.rst

@@ -1,9 +1,15 @@
 .. include:: ../roles.incl
-	     
+
 *************************
 Enzo-E / Cello Parameters
 *************************
 
+.. toctree::
+   :maxdepth: 1
+   :glob:
+   :titlesonly:
+   :numbered:
+
 This page documents all current parameters implemented in Enzo-E /
 Cello.  Each parameter is summarized, its type or types are listed,
 and the default value (if any) is provided.  The scope of the
@@ -152,7 +158,6 @@ Mesh
 
 .. include:: mesh.incl
 
-
 ------
 Method
 ------

doc/source/param/method.incl

@@ -31,13 +31,17 @@
      * :t:`"ppml"` :e:`for the PPML ideal MHD solver.`  *This may be phased
        out in favor of using a more general "mhd" method instead, with a
        specific mhd solver specified.*
+     * :t:`"ppml_it"` :e:`alternate name for "ppml".`
+     * :t:`"ppml_ig"` :e:`for the adiabatic version of PPML.`   *This may be phased
+       out in favor of using a more general "mhd" method instead, with a
+       specific mhd solver specified.*
      * :t:`"mhd_vlct"` :e:`for the VL + CT (van Leer + Constrained Transport) MHD
        solver.`
      * :t:`"trace"` :e:`for moving tracer particles.`  **This will be phased
        out in favor of a more general "move_particles" method.**
      * :t:`"turbulence"` :e:`computes random forcing for turbulence
        simulations.`
-
+     * :t:`"turbulence_ou"` :e:`implements Ornstein-Uhlenbeck driven turbulence.`
 
    :e:`Parameters specific to individual methods are specified in subgroups, e.g.`::
 
@@ -461,6 +465,12 @@ ppm
 .. include:: method_ppm.incl
 
 
+ppml
+----
+
+.. include:: method_ppml.incl
+
+
 sink_maker
 ----------
 
@@ -569,6 +579,8 @@ turbulence
    :Scope:     :z:`Enzo`
    :Todo: :o:`write`
 
+   :e:`Prescribes kinetic energy injection rate for a forcing method based on random but constant-in-time external x-, y-, z-acceleration fields. The code would normalize the accelerations so that the resulting actual injection rate is constant during the simulation and equal to edot. For details of the method see` `Mac Low (1999) <https://ui.adsabs.harvard.edu/abs/1999ApJ...524..169M/abstract>`_  :e:`The default setting edot=-1 turns this forcing off.`
+
 ----
 
 .. par:parameter:: Method:turbulence:mach_number
@@ -578,3 +590,10 @@ turbulence
    :Default: :d:`0.0`
    :Scope:     :z:`Enzo`
    :Todo: :o:`write`
+
+   :e:`Specifies the target sonic Mach number for a forced turbulence simulation. If` :p:`mach_number` :e:`is not zero, the energy injection rate will be calculated based on the Mach number.`
+
+turbulence_ou
+-------------
+
+.. include:: method_turbulence_ou.incl

doc/source/param/method_ppml.incl

@@ -0,0 +1,15 @@
+
+:p:`Method:ppml` parameters are used to initialize parameters for
+Enzo-E's PPML MHD methods. These include "ppml" (or "ppml_it") for the
+idealized solver, and "ppml_ig" for the adiabatic version.
+
+----
+
+.. par:parameter:: Method:ppml:dt_weight
+
+   :Summary: :s:`Timestep adjust for Strang splitting`
+   :Type:   :par:typefmt:`float`
+   :Default: :d:`1.0`
+   :Scope:     :z:`Enzo`
+
+   :e:`This parameter is used to implement Strang splitting to preserve the 2nd order of accurace of time integration of PPML when forcing and cooling/heating source terms are present. In that case dt_weight should be set to 0.5 and PPML called twice in the` :par:paramfmt:`Method:list` :e:` parameter list with methods implementing forcing terms between them. The default is not to use Strang splitting so dt_weight = 1.0`