Committing to the Enzo-P -> Enzo-E name change

Author: aemerick

.gitignore

@@ -12,7 +12,6 @@ test/START
 test/STOP
 include
 build
-bin/enzo-p
 charmrun
 config.log
 errors.org
@@ -27,5 +26,5 @@ build-*/External/*
 build-*/SConscript
 
 # ignore the binaries
-bin/enzo-p
-bin/enzo-p.prev
+bin/enzo-e
+bin/enzo-e.prev

BRANCHES

@@ -4,4 +4,4 @@ charm-pupping:    For adding pup() and migration constructors
 lcaperf:          For incorporating lcaperf into the Performance component
 remove-mpi        For converting to Charm++ only to simplify code
 simplify          For simplify Cello, including moving some of Cello into 
-                  Enzo-P, but excluding removing MPI
+                  Enzo-E, but excluding removing MPI

LICENSE_CELLO

@@ -1,4 +1,4 @@
-= Enzo-P / Cello Software Public License =
+= Enzo-E / Cello Software Public License =
 
 Copyright (c) 2011-2016, James Bordner and the Regents of the University of California
 All rights reserved.

Makefile

@@ -1,15 +1,15 @@
 #----------------------------------------------------------------------
-.PHONY: bin/enzo-p
-bin/enzo-p:
-	./build.sh bin/enzo-p
+.PHONY: bin/enzo-e
+bin/enzo-e:
+	./build.sh bin/enzo-e
 #----------------------------------------------------------------------
 .PHONY: help
 help:
 	@echo 
-	@echo "make [compile]  Compile Enzo-P as ./bin/enzo-p"
+	@echo "make [compile]  Compile Enzo-E as ./bin/enzo-e"
 	@echo "make cccc       Compute code quality metrics in src/.cccc/cccc.html"
 	@echo "make clean      Remove object and test files"
-	@echo "make coverity   Compile enzo-p using the coverity static analysis tool"
+	@echo "make coverity   Compile enzo-e using the coverity static analysis tool"
 	@echo "make diff       Generate org-mode 'diff.org' file from 'git diff' output"
 	@echo "make gdb        Generate org-mode 'gdb.org' from gdb 'where' output in gdb.out"
 	@echo "make doc        Generate html documentation from Sphinx in doc/build/html"

SConstruct

@@ -659,7 +659,7 @@ Clean('.','src-html')
 Clean('.','src-latex')
 Clean('.','src-xml')
 
-# files left behind by enzo-p
+# files left behind by enzo-e
 Clean('.','Checkpoint')
 Clean('.','parameters.out')
 Clean('.','parameters.libconfig')
@@ -669,7 +669,7 @@ Clean('.','parameters.libconfig')
 #======================================================================
 
 # env = Environment(tools=['default', 'packaging'])
-# title = 'Enzo-P / Cello Extreme AMR Astrophysics and Cosmology'
+# title = 'Enzo-E / Cello Extreme AMR Astrophysics and Cosmology'
 # env.Package( NAME           = 'cello',
 #              VERSION        = '0.5.0',
 #              PACKAGEVERSION = 0,

build.sh

@@ -74,7 +74,7 @@ if [ "$#" -ge 1 ]; then
       echo
       echo "Usage: $0 [clean|compile|test]"
       echo
-      echo "       $0 bin/enzo-p"
+      echo "       $0 bin/enzo-e"
       echo
       echo "       $0 bin/test_Foo"
       echo
@@ -87,15 +87,15 @@ if [ "$#" -ge 1 ]; then
 	echo "Remove $target"
    fi
 else
-   # assume enzo-p
+   # assume enzo-e
    k_switch=""
-   target="bin/enzo-p"
+   target="bin/enzo-e"
 fi
 
-if [ $target == "bin/enzo-p" ]; then
+if [ $target == "bin/enzo-e" ]; then
    if [ -e $target ]; then
-       echo "Saving existing bin/enzo-p to bin/enzo-p.prev"
-       mv bin/enzo-p bin/enzo-p.prev
+       echo "Saving existing bin/enzo-e to bin/enzo-e.prev"
+       mv bin/enzo-e bin/enzo-e.prev
    fi
 fi
 
@@ -106,7 +106,7 @@ date=`date +"%Y-%m-%d"`
 start=`date +"%H:%M:%S"`
 echo "$date $start BEGIN"
 
-echo "BEGIN Enzo-P/Cello ${0}"
+echo "BEGIN enzo-e/Cello ${0}"
 echo "arch=$arch"
 echo "prec=$prec"
 echo "target=$target"
@@ -202,9 +202,9 @@ fi
 if [ x$CELLO_ARCH == "xncsa-bw" ]; then
     echo "Relinking with static libpng15.a..."
     build_dir="build"
-   /u/sciteam/bordner/Charm/charm/bin/charmc -language charm++ -tracemode projections -o $build_dir/charm/Enzo/enzo-p -g -g $build_dir/charm/Enzo/enzo-p.o $build_dir/charm/Cello/main_enzo.o -Llib/charm -L/opt/cray/hdf5/default/cray/74/lib -lcharm -lenzo -lsimulation -lproblem -lcomm -lmesh -lfield -lio -ldisk -lmemory -lparameters -lerror -lmonitor -lparallel -lperformance -ltest -lcello -lexternal -lhdf5 -lz /u/sciteam/bordner/lib/libpng15.a -lgfortran
+   /u/sciteam/bordner/Charm/charm/bin/charmc -language charm++ -tracemode projections -o $build_dir/charm/Enzo/enzo-e -g -g $build_dir/charm/Enzo/enzo-e.o $build_dir/charm/Cello/main_enzo.o -Llib/charm -L/opt/cray/hdf5/default/cray/74/lib -lcharm -lenzo -lsimulation -lproblem -lcomm -lmesh -lfield -lio -ldisk -lmemory -lparameters -lerror -lmonitor -lparallel -lperformance -ltest -lcello -lexternal -lhdf5 -lz /u/sciteam/bordner/lib/libpng15.a -lgfortran
 
-   mv $build_dir/charm/Enzo/enzo-p bin/charm
+   mv $build_dir/charm/Enzo/enzo-e bin/charm
 
 fi
 
@@ -216,7 +216,7 @@ S1=`date +"%S"`
 
 t=`echo "scale=2; (( $S1 - $S0 ) + 60 * ( ( $M1 - $M0 ) + 60 * ( $H1 - $H0) ))/60.0" | bc`
 
-echo "END   Enzo-P/Cello ${0}: arch = $arch  prec = $prec  target = $target time = ${t} min"
+echo "END   enzo-e/Cello ${0}: arch = $arch  prec = $prec  target = $target time = ${t} min"
 
 d=`date "+%H:%M:%S"`
 

config/README.ncsa_bw

@@ -1,4 +1,4 @@
-The following are steps for preparing to run Enzo-P / Cello on NCSA
+The following are steps for preparing to run Enzo-E / Cello on NCSA
 Blue Waters.     
 
 1. Run the following commands, and also put them in your shell startup
@@ -25,25 +25,25 @@ Blue Waters.
    cd charm
    ./build charm++ gni-crayxe   smp  -j16  --with-production
 
-3. Download and install Enzo-P in your home directory
+3. Download and install Enzo-E in your home directory
 
    mkdir ~/Cello
    cd ~/Cello
    hg clone ssh://[email protected]/cello-project/cello-src
    cd cello-src
    hg update solver
 
-4. Compile Enzo-P (bin/enzo-p)
+4. Compile Enzo-E (bin/enzo-e)
 
    cd ~/Cello
    make
 
-5. Run Enzo-P
+5. Run Enzo-E
 
    Below is a sample batch script for running on 4 nodes, with 15 (out
    of 16) floating-point cores per node.  (This is recommended when
    using Charm++ compiled with the SMP mode).  It is assumed the
-   executable is ./enzo-p, and the input parameter file is
+   executable is ./enzo-e, and the input parameter file is
    test-problem.in.  If you have multiple accounts, you may also need
    a "#PBS -A <project>" header line.
 
@@ -67,6 +67,6 @@ Blue Waters.
    charmrun="aprun -n 4 -N 1"
    charmarg="+ppn15 +pemap 2-30:2"
 
-   $charmrun ./enzo-p $charmarg $input >& $output
+   $charmrun ./enzo-e $charmarg $input >& $output
    ==================================================
 

config/ncsa_bw.py

@@ -1,5 +1,5 @@
 #
-# Enzo-P/Cello Configuration file for NCSA Blue Waters
+# Enzo-E/Cello Configuration file for NCSA Blue Waters
 #
 # See README.ncsa_bw for additional information
 

doc/source/conf.py

@@ -214,7 +214,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'enzo-pcello', u'Enzo-E / Cello Documentation',
+    ('index', 'enzo-ecello', u'Enzo-E / Cello Documentation',
      [u'James Bordner'], 1)
 ]
 

doc/source/faq.rst.old

@@ -5,7 +5,7 @@
 Frequently Asked Questions
 **************************
 
-**This document is currently incomplete; for a PDF version of this page, please visit the** `State of Enzo-P / Cello <http://cello-project.org/faq.pdf>`_ **talk presented (in part) at the Enzo Days 2014 meeting.  It is organized as a FAQ, and contains the source material being used for this page.  It is best viewed using acroread or other PDF reader that supports hyperlinks.  Click on the
+**This document is currently incomplete; for a PDF version of this page, please visit the** `State of Enzo-E / Cello <http://cello-project.org/faq.pdf>`_ **talk presented (in part) at the Enzo Days 2014 meeting.  It is organized as a FAQ, and contains the source material being used for this page.  It is best viewed using acroread or other PDF reader that supports hyperlinks.  Click on the
 "Home" button at the bottom right to go to the Table of Contents page.**
 
 What is the current state of Enzo-P/Cello?

doc/source/index.org

@@ -9,10 +9,10 @@
            Parameter File Example
         Developer Guide (index_develop)
            Developing with Cello
-           Enzo-P / Cello Guiding Principles
+           Enzo-E / Cello Guiding Principles
            Design
         Reference (index_reference)
-           Enzo-P / Cello parameter reference
+           Enzo-E / Cello parameter reference
 
 ** TODO Files
    - [ ] [[file:index.rst][index.rst]]

doc/source/index.rst

@@ -110,16 +110,16 @@ presentation, and some sections are somewhat outdated.  This document,
 while currently still useful, is being phased out in favor of the
 above online content.
 
-   :download:`Using and Developing Enzo-P/Cello <http://client65-90.sdsc.edu/cello-doc/_downloads/4e523174654f2009e024ac3aa718a5d1/enzo-p-cello.pdf>`
+   :download:`Using and Developing Enzo-E/Cello <http://client65-90.sdsc.edu/cello-doc/_downloads/4e523174654f2009e024ac3aa718a5d1/enzo-p-cello.pdf>`
 
 Presentations given at the 2018 Enzo Days Workshop are also available
 below.  They are more up-to-date, but are also still rather large.
 
-   :download:`Enzo-P / Cello Status and What's New? <http://client65-90.sdsc.edu/cello-doc/_downloads/11ba173e00a03e5688c2d351f2476881/1805-1-status.pdf>`
+   :download:`Enzo-E / Cello Status and What's New? <http://client65-90.sdsc.edu/cello-doc/_downloads/11ba173e00a03e5688c2d351f2476881/1805-1-status.pdf>`
 
-   :download:`Introduction to Enzo-P <http://client65-90.sdsc.edu/cello-doc/_downloads/014af2086ca3c5899855903ea7d79d78/1805-2-intro.pdf>`
+   :download:`Introduction to Enzo-E <http://client65-90.sdsc.edu/cello-doc/_downloads/014af2086ca3c5899855903ea7d79d78/1805-2-intro.pdf>`
 
-   :download:`First Steps with Enzo-P <http://client65-90.sdsc.edu/cello-doc/_downloads/0bb42a270c3e64905ffce6517df0e971/1805-3-using.pdf>`
+   :download:`First Steps with Enzo-E <http://client65-90.sdsc.edu/cello-doc/_downloads/0bb42a270c3e64905ffce6517df0e971/1805-3-using.pdf>`
 
 James Bordner
 [email protected]

doc/source/output.rst.old

@@ -1,4 +1,4 @@
-Enzo-P Output
+Enzo-E Output
 -------------
 
 The output log is useful for monitoring different aspects of the
@@ -23,11 +23,11 @@ configuration settings:
     0 00000.02  
     0 00000.02  [*] CONFIG_USE_PAPI
 
-Here this shows that Enzo-P was compiled using single precision
+Here this shows that Enzo-E was compiled using single precision
 floating point data, MPI was used, and the optional PAPI performance
 API was used.
 
-Next, Enzo-P displays all parameters as they are accessed in the code:
+Next, Enzo-E displays all parameters as they are accessed in the code:
 
   :: 
 
@@ -78,7 +78,7 @@ a line including the type of output and the file name:
     0 00000.04  Output      writing image file E-010.png
 
 When the simulation concludes, various components may output status
-information.  For example, if Enzo-P was compiled using the optional
+information.  For example, if Enzo-E was compiled using the optional
 PAPI library, a brief performance summary is displayed:
 
   ::

doc/source/param/boundary.incl

@@ -30,7 +30,7 @@
 :Default: :d:`"undefined"`
 :Scope:     :c:`Cello`
 
-:e:`Boundary conditions in Enzo-P include` :t:`"reflecting"` :e:`,` :t:`"outflow"` :e:`,` :t:`"inflow"` :e:`, and` :t:`"periodic"`.  :e:`Other boundary condition types can be implemented by either a) modifying the existing` :p:`EnzoBoundary` :e:`class or b) creating a new class inherited from the` :p:`Boundary` :e:`base class.`  :t:`"inflow"` :e:`boundary conditions additionally require` :p:`value` :e:`and` :p:`field_list` :e:`parameters.`
+:e:`Boundary conditions in Enzo-E include` :t:`"reflecting"` :e:`,` :t:`"outflow"` :e:`,` :t:`"inflow"` :e:`, and` :t:`"periodic"`.  :e:`Other boundary condition types can be implemented by either a) modifying the existing` :p:`EnzoBoundary` :e:`class or b) creating a new class inherited from the` :p:`Boundary` :e:`base class.`  :t:`"inflow"` :e:`boundary conditions additionally require` :p:`value` :e:`and` :p:`field_list` :e:`parameters.`
 
 ----
 

doc/source/param/field.incl

@@ -50,7 +50,7 @@
 :Default: :d:`[ ]`
 :Scope:     :c:`Cello`
 
-:e:`Different Fields may belong to any number of different "groups".  For example, Enzo uses "color fields", which Enzo-P implements as defining color fields to belong to the group "color".`
+:e:`Different Fields may belong to any number of different "groups".  For example, Enzo uses "color fields", which Enzo-E implements as defining color fields to belong to the group "color".`
 
 ----
 

doc/source/param/method.incl

@@ -17,13 +17,13 @@ list is applied in the order specified.  Possible methods include:`
     and particle density fields.`
   * :t:`"heat"` :e:`for the forward-Euler heat-equation solver, which
     is used primarily for demonstrating how new Methods are
-    implemented in Enzo-P`
+    implemented in Enzo-E`
   * :t:`"pm_deposit"` :e:`deposits "dark" particle density into
     "density_particle" field using CIC for "gravity" method.`
   * :t:`"pm_update"` :e:`moves cosmological "dark" particles based on
     positions, velocities, and accelerations.`  **This will be phased out
     in favor of a more general "move_particles" method.**
-  * :t:`"ppm"` :e:`for Enzo-P's PPM hydrodynamics method.`  *This may be
+  * :t:`"ppm"` :e:`for Enzo-E's PPM hydrodynamics method.`  *This may be
     phased out in favor of using a more general "hydro" method
     instead, with a specific hydro solver specified.*
   * :t:`"ppml"` :e:`for the PPML ideal MHD solver.`  *This may be phased

doc/source/param/method_ppm.incl

@@ -1,6 +1,6 @@
 
 :p:`Method:ppm` parameters are used to initialize parameters for
-Enzo-P's PPM hydrodynamics method.
+Enzo-E's PPM hydrodynamics method.
 
 ----
 

doc/source/param/testing.incl

@@ -1,20 +1,20 @@
 :Parameter:  :p:`Testing` : :p:`cycle_final`
-:Summary: :s:`Enzo-P unit test parameter for expected final cycle number`
+:Summary: :s:`Enzo-E unit test parameter for expected final cycle number`
 :Type:    :t:`integer`
 :Default: :d:`0`
 :Scope:     :c:`Cello`
 
-:e:`Enzo-P unit test parameter for expected final cycle number.`
+:e:`Enzo-E unit test parameter for expected final cycle number.`
 
 ----
 
 :Parameter:  :p:`Testing` : :p:`time_final`
-:Summary: :s:`Enzo-P unit test parameter for expected final time`
+:Summary: :s:`Enzo-E unit test parameter for expected final time`
 :Type:    :t:`float`
 :Default: :d:`0.0`
 :Scope:     :c:`Cello`
 
-:e:`Enzo-P unit test parameter for expected final time.`
+:e:`Enzo-E unit test parameter for expected final time.`
 
 ----
 
@@ -24,5 +24,5 @@
 :Default: :d:`1.0e-6`
 :Scope:     :c:`Cello`
 
-:e:`Enzo-P unit test parameter for tolerance on the expected final time.`
+:e:`Enzo-E unit test parameter for tolerance on the expected final time.`
 

doc/source/parameters-list-method-ppm.incl

@@ -1,6 +1,6 @@
 
 :p:`Method:ppm` parameters are used to initialize parameters for
-Enzo-P's PPM hydrodynamics method.
+Enzo-E's PPM hydrodynamics method.
 
 ----
 

doc/source/tutorial/getting_started.rst

@@ -201,7 +201,7 @@ regression tests, and running code analysis tools.
 
         ==================  ===============================================================
         ==================  ===============================================================
-	``make``            *Compile Enzo-E as* ``./bin/enzo-p``
+	``make``            *Compile Enzo-E as* ``./bin/enzo-e``
 	``make clean``      *Remove object and test files*
 	``make reset``      *Clear any settings from an incomplete build*
 	``make doc``        *Generate doxygen documentation from source in* ``src-html`` *(requires* ``doxygen`` *)*
@@ -225,12 +225,12 @@ and take a look at Enzo-E's output.
 An included "Hello World" problem can be run using the following
 from the ``$CELLO_HOME`` directory:
 
-     ``charmrun +p4 bin/enzo-p input/Hi.in``
+     ``charmrun +p4 bin/enzo-e input/Hi.in``
 
 This assumes that the ``charmrun`` command is in your path.  If it
 is not, then you will need to include the path name as well, e.g.:
 
-     ``~/Charm/bin/charmrun +p4 bin/enzo-p input/Hi.in``
+     ``~/Charm/bin/charmrun +p4 bin/enzo-e input/Hi.in``
 
 If all goes well, Enzo-E will run the Hello World problem.  Below are
 some of the generated images from the longer-running "HelloWorld.in"

doc/source/tutorial/getting_started_comet.rst

@@ -111,7 +111,7 @@ parameter file (``input/method_ppm-8.in``) accordingly.
 
 ..  code-block:: bash
 		 
-    $ ./charmrun ++runscript ./run-enzoe.sh +p8 bin/enzo-p input/method_ppm-8.in
+    $ ./charmrun ++runscript ./run-enzoe.sh +p8 bin/enzo-e input/method_ppm-8.in
 
 
 This assumes that the charmrun command is in your path--if it is not,

doc/source/what_is_cello.RST

@@ -10,5 +10,5 @@ The development of Cello is driven by Enzo, a parallel astrophysics
 and cosmology application.  The primary goal is to efficiently map
 Enzo's multi-resolution multi-physics capabilities onto large parallel
 computers with millions of computational units. We refer to this next
-generation "petascale" branch of Enzo built using the Cello framework
-as "Enzo-P".
+generation "exascale" branch of Enzo built using the Cello framework
+as "Enzo-E", previously known as a "petascale" version, or "Enzo-P".

input/Sedov/gordon.2/plot.py

@@ -82,7 +82,7 @@ def max_per_cycle(p,metric):
 top = [sum(pair) for pair in zip(top,time_refresh)]
 plot_prepare   = plt.bar(x,time_prepare,color='y',bottom=top)
 
-plt.title("Enzo-P Scaling")
+plt.title("Enzo-E Scaling")
 plt.legend( (plot_wallclock[0], 
              plot_cycle[0],
              plot_compute[0],