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Greg Bryan committed ca9895a

Removed entire doc/userguid directory as this is, I believe, all old documentation that has been subsumed into the new doc/manual. It is confusing to have this here (and it is out of date).

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doc/userguide/Index.txt

-= Enzo User's Guide =
-
-Note: This user guide for the public trunk of Enzo development. For a particular release, please the [http://lca.ucsd.edu/software/enzo/v1.0.1/ Enzo v1.0.1 docs], or the [wiki:Enzo1.5 Enzo v1.5 docs].
-
- 1. Introduction
- 1. Preparing and testing enzo
-   * Obtaining the code
-   * Requirements for Compilation
-   * Compiling the code
-   * Running the tests
-   * ENZO Test Suite (2D Hydro Tests)
- 1. Setting up and running a cosmological simulation
-   * Generating the initial conditions
-     * Running inits
-   * Preparing a cosmology simulation
-   * Running a cosmology simulation
-   * Analyzing the output
-      * Analyzing the output: projections
-      * Analyzing the output: extractions
-      * Analyzing the output: profiles
- 1. Reference information
-   * A complete list of Enzo parameters
-   * A complete list of Inits parameters
-   * Summary of all executables, their arguments and their outputs.
-   * Output format
-

doc/userguide/LICENSE

-
-Enzo Public License
-
----------------- University of Illinois/NCSA Open Source License -----------
-
-Copyright (c)  1993-2000 by Greg Bryan and the Laboratory for Computational 
-Astrophysics and the Board of Trustees of the University of Illinois in 
-Urbana-Champaign.  All rights reserved.
-
-Developed by:           Laboratory for Computational Astrophysics
-			National Center for Supercomputing Applications
-			University of Illinois in Urbana-Champaign
-			http://cosmos.ucsd.edu/
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal 
-with the Software without restriction, including without limitation the 
-rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
-sell copies of the Software, and to permit persons to whom the Software is 
-furnished to do so, subject to the following conditions:
-	1.  Redistributions of source code must retain the above copyright 
-	    notice, this list of conditions and the following disclaimers.
-	2.  Redistributions in binary form must reproduce the above copyright 
-	    notice, this list of conditions and the following disclaimers 
-	    in the documentation and/or other materials provided with the 
-            distribution.
-	3.  Neither the names of The Laboratory for Computational 
-            Astrophysics, The National Center for Supercomputing 
-            Applications, The University of Illinois in Urbana-Champaign, 
-            nor the names of its contributors may be used to endorse or 
-            promote products derived from this Software without specific 
-            prior written permission.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH 
-THE SOFTWARE.
-
-
---------------- University of California/BSD License -------------------
-
-Copyright (c) 2000-2004 by Greg Bryan and the Laboratory for Computational 
-Astrophysics and the Regents of the University of California.
-
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
-	1.  Redistributions of source code must retain the above copyright 
-            notice, this list of conditions and the following disclaimer.
-	2.  Redistributions in binary form must reproduce the above copyright
-            notice, this list of conditions and the following disclaimer in 
-            the documentation and/or other materials provided with the 
-            distribution.
-	3.  Neither the name of the Laboratory for Computational 
-	    Astrophysics, the University of California, nor the names of its 
-	    contributors may be used to endorse or promote products derived 
-	    from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF 
-THE POSSIBILITY OF SUCH DAMAGE.
-
-
-

doc/userguide/TO-DO

-To-do items:
-
-1.  add counter to enzo download page (mike's request)
-
-2.  instructions on how to interpret jbPerf/jbmem outputs - James?
-
-3.  troubleshooting help (common problems/common questions)
-
-add uncommented but worked parameter files
-
-add images to image gallery, movies to movie 
-	gallery (especially AMR level movies)
-
-add section on press releases - 
-	link to SDSC Pascal's page
-
-put counter on home page
-
-
-

doc/userguide/amr_guide/AMRShockPool2D

-#
-# AMR PROBLEM DEFINITION FILE: 2D Shock Propogation test (amr version)
-#
-#  define problem
-#
-ProblemType                = 3        // Shock Pool
-TopGridRank                = 2
-TopGridDimensions          = 75 75
-RightFaceBoundaryCondition = 1 1  // set right faces to outflow 
-HydroMethod                = 0
-#
-#  problem parameters
-#
-ShockPoolAngle          = 45.0    // angle relative to x-axis (in degrees)
-ShockPoolMachNumber     = 2.0 
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.2
-#dtDataDump             = 0.05
-#
-#  set Hydro parameters
-#
-Gamma                  = 1.4
-CourantSafetyNumber    = 0.5
-PPMDiffusionParameter  = 0       // diffusion off
-PPMFlatteningParameter = 0       // flattening on
-PPMSteepeningParameter = 0       // steepening on
-FluxCorrection         = 1
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // dynamic hierarchy
-MaximumRefinementLevel    = 1    // 2 levels total
-RefineBy                  = 3    // refinement factor
-CellFlaggingMethod        = 3    // use shock criteria for refinement 
-MinimumEfficiency         = 0.8  // good value for 2d
-#
-#  set some misc global parameters
-#
-tiny_number               = 1.0e-6  // fixes velocity slope problem
-

doc/userguide/amr_guide/AMRShockTube

-#
-# AMR PROBLEM DEFINITION FILE: ShockTube test (amr version)
-#
-#  define problem
-#
-ProblemType            = 1       // Shock Tube
-TopGridRank            = 1
-TopGridDimensions      = 100
-HydroMethod            = 0
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.251
-dtDataDump             = 0.4
-#
-#  set hydro parameters
-#
-Gamma                  = 1.4
-CourantSafetyNumber    = 0.8
-PPMDiffusionParameter  = 0       // diffusion off
-#
-#  set grid refinement parameters
-#
-CellFlaggingMethod        = 1
-StaticHierarchy           = 0    // dynamic hierarchy
-MaximumRefinementLevel    = 1    // use up to 2 levels
-RefineBy                  = 3    // refinement factor
-MinimumSlopeForRefinement = 0.1  // set this to <= 0.2 to refine CD
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-3  // fixes velocity slope problem
-MinimumEfficiency      = 0.8     // better value for 1d than 0.2

doc/userguide/amr_guide/AdiabaticExpansion

-#
-# AMR PROBLEM DEFINITION FILE: Adiabatic Expansion test
-#
-#  define problem
-#
-ProblemType                = 22      // Adiabatic Expansion
-TopGridRank                = 1
-TopGridDimensions          = 8
-SelfGravity                = 0       // gravity off
-TopGridGravityBoundary     = 0       // Periodic BC for gravity
-LeftFaceBoundaryCondition  = 3       // same for fluid
-RightFaceBoundaryCondition = 3
-#
-#  problem parameters
-#
-AdiabaticExpansionInitialTemperature = 1000   // K
-AdiabaticExpansionInitialVelocity    = 100   // km/s
-#
-#  define cosmology parameters
-#
-ComovingCoordinates        = 1       // Expansion ON
-CosmologyHubbleConstantNow = 0.5
-CosmologyComovingBoxSize   = 64.0    // 64 Mpc/h
-CosmologyMaxExpansionRate  = 0.01    //
-CosmologyInitialRedshift   = 20      // start at z=20
-GravitationalConstant      = 1       // this must be true for cosmology
-#
-#  set I/O and stop/start parameters
-#
-dtDataDump             = 80.0
-#
-#  set hydro parameters
-#
-Gamma                  = 1.6667
-CourantSafetyNumber    = 0.5
-PPMDiffusionParameter  = 0       // diffusion off
-DualEnergyFormalism    = 1       // use total & internal energy
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 1    // static hierarchy
-#
-#  set some global parameters
-#

doc/userguide/amr_guide/AnalyzeClusterParameterFile

-#
-# Sample parameter file for AnalyzeCluster
-#
-Rinner          = 0.01   ! in Mpc
-Router          = 10     ! in Mpc
-NumberOfPoints  = 16     ! default is 16
-VirialDensity   = 200    ! default is 200
-XrayLowerCutoffkeV = 0.5
-XrayUpperCutoffkeV = 2.0
-XrayTableFileName = lookup_metal0.3.data
-#CenterPosition = 0.5 0.5 0.5  ! default is maximum point

doc/userguide/amr_guide/CollapseTest

-#
-# AMR PROBLEM DEFINITION FILE: Collapse test
-#
-#  define problem
-#
-ProblemType                = 27      // Collapse test
-TopGridRank                = 3
-TopGridDimensions          = 16 16 16
-SelfGravity                = 1       // gravity on
-TopGridGravityBoundary     = 0       // periodic
-LeftFaceBoundaryCondition  = 3 3 3   // periodic
-RightFaceBoundaryCondition = 3 3 3
-PointSourceGravity         = 0
-PointSourceGravityPosition = 0.5 0.5 0.5
-PointSourceGravityConstant = 0.02
-ZEUSQuadraticArtificialViscosity = 2.0
-BaryonSelfGravityApproximation = 0
-#
-# problem parameters
-#
-CollapseTestRefineAtStart   = 1
-CollapseTestNumberOfSpheres = 1
-CollapseTestUseParticles    = 1
-#
-CollapseTestSphereRadius[0]     = 0.2
-CollapseTestSphereDensity[0]    = 5
-CollapseTestSphereType[0]       = 1       // NFW
-CollapseTestSphereCoreRadius[0] = 0.05
-CollapseTestSpherePosition[0]   = 0.25 0.25 0.25
-#CollapseTestSphereVelocity[0]   = 0.2 -0.2 -0.2
-CollapseTestUniformVelocity     = 0.6 0.6 0.6
-#
-#  define cosmology parameters
-#
-ComovingCoordinates        = 1       // Expansion ON
-CosmologyOmegaMatterNow    = 1.0
-CosmologyOmegaLambdaNow    = 0.0
-CosmologyHubbleConstantNow = 0.5     // in km/s/Mpc
-CosmologyComovingBoxSize   = 1.0     // in Mpc/h
-CosmologyMaxExpansionRate  = 0.015   // maximum allowed delta(a)/a
-CosmologyInitialRedshift   = 10      // 
-CosmologyFinalRedshift     = 0.3       //
-GravitationalConstant      = 1       // this must be true for cosmology
-#
-#  set I/O and stop/start parameters
-#
-#StopTime               = 0.0002
-dtDataDump             = 0.1
-DataDumpName           = moving7_
-#StopCycle              = 4
-#
-#  set hydro parameters
-#
-Gamma                       = 1.6667
-PPMDiffusionParameter       = 0       // diffusion off
-DualEnergyFormalism         = 0       // use total & internal energy
-InterpolationMethod         = 4       // FirstOrderA
-CourantSafetyNumber         = 0.5
-RadiativeCooling            = 1
-MultiSpecies                = 0
-FluxCorrection              = 1
-ConservativeInterpolation   = 0
-HydroMethod                 = 2
-Initialdt                   = 0.003
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // dynamic hierarchy
-MaximumRefinementLevel    = 9    // use up to 2 levels
-RefineBy                  = 2    // refinement factor
-CellFlaggingMethod        = 2    // use baryon mass for refinement 
-MinimumEfficiency         = 0.3  // fraction efficiency
-MinimumOverDensityForRefinement = 0.2 // times the initial density
-MinimumMassForRefinementLevelExponent = -0.1
-MinimumEnergyRatioForRefinement = 0.4 // min Egas/Etot for shock refinement
-RefineRegionLeftEdge            = 0.2 0.2 0.2
-RefineRegionRightEdge           = 0.9 0.9 0.9
-#
-#  set some global parameters
-#
-GreensFunctionMaxNumber   = 10   // # of greens function at any one time

doc/userguide/amr_guide/EnzoMultipleParameterFile

-#
-# AMR PROBLEM DEFINITION FILE: Cosmology Simulation (amr version)
-#
-#  define problem
-#
-ProblemType                = 30      // cosmology simulation
-TopGridRank                = 3
-TopGridDimensions          = 64 64 64
-SelfGravity                = 1       // gravity on
-TopGridGravityBoundary     = 0       // Periodic BC for gravity
-LeftFaceBoundaryCondition  = 3 3 3   // same for fluid
-RightFaceBoundaryCondition = 3 3 3
-#
-#  problem parameters
-#
-CosmologySimulationOmegaBaryonNow       = 0.1
-CosmologySimulationOmegaCDMNow          = 0.9
-CosmologySimulationDensityName          = GridDensity
-CosmologySimulationVelocity1Name        = GridVelocities
-CosmologySimulationVelocity2Name        = GridVelocities
-CosmologySimulationVelocity3Name        = GridVelocities
-CosmologySimulationParticlePositionName = ParticlePositions
-CosmologySimulationParticleVelocityName = ParticleVelocities
-CosmologySimulationNumberOfInitialGrids = 3
-CosmologySimulationGridDimension[1]     = 32 32 32
-CosmologySimulationGridLeftEdge[1]      = 0.593750 0.156250 0.156250 
-CosmologySimulationGridRightEdge[1]     = 0.843750 0.406250 0.406250
-CosmologySimulationGridLevel[1]         = 1
-CosmologySimulationGridDimension[2]     = 56 56 56
-CosmologySimulationGridLeftEdge[2]      = 0.609375 0.171875 0.171875
-CosmologySimulationGridRightEdge[2]     = 0.828125 0.390625 0.390625
-CosmologySimulationGridLevel[2]         = 2
-#
-#  define cosmology parameters
-#
-ComovingCoordinates        = 1       // Expansion ON
-CosmologyOmegaMatterNow    = 1.0
-CosmologyOmegaLambdaNow    = 0.0
-CosmologyHubbleConstantNow = 0.5     // in km/s/Mpc
-CosmologyComovingBoxSize   = 16.0    // in Mpc/h
-CosmologyMaxExpansionRate  = 0.015   // maximum allowed delta(a)/a
-CosmologyInitialRedshift   = 30      // 
-CosmologyFinalRedshift     = 0       //
-GravitationalConstant      = 1       // this must be true for cosmology
-#
-#  set I/O and stop/start parameters
-#
-#StopCycle              = 40          // stop after this many cycles
-dtDataDump             = 4.0         // dump at beginning and end
-#CycleSkipDataDump      = 20
-DataDumpName           = cosmo3d_amr_
-CosmologyOutputRedshift[0] = 10
-CosmologyOutputRedshift[1] = 8
-CosmologyOutputRedshift[2] = 6
-CosmologyOutputRedshift[3] = 5
-CosmologyOutputRedshift[4] = 4
-CosmologyOutputRedshift[5] = 3
-CosmologyOutputRedshift[6] = 2
-CosmologyOutputRedshift[7] = 1
-CosmologyOutputRedshift[8] = 0
-#
-#  set hydro parameters
-#
-HydroMethod            = 2       // ZEUS style hydro
-Gamma                  = 1.6667
-DualEnergyFormalism    = 0       // use total & internal energy
-InterpolationMethod    = 1     // SecondOrderA
-CourantSafetyNumber    = 0.4
-ParticleCourantSafetyNumber = 0.8
-RadiativeCooling            = 1
-MultiSpecies                = 0
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // dynamic hierarchy
-MaximumRefinementLevel    = 10    // use up to 2 levels
-RefineBy                  = 2    // refinement factor
-CellFlaggingMethod        = 2    // use baryon mass for refinement 
-MinimumEfficiency         = 0.4  // fraction efficiency
-MinimumOverDensityForRefinement = 0.062 // times the initial density
-MinimumMassForRefinementLevelExponent = -0.0
-RefineRegionLeftEdge            = 0.63 0.18 0.18
-RefineRegionRightEdge           = 0.79 0.37 0.36

doc/userguide/amr_guide/EnzoSingleParameterFile

-#
-# AMR PROBLEM DEFINITION FILE: Cosmology Simulation (amr version)
-#
-#  define problem
-#
-ProblemType                = 30      // cosmology simulation
-TopGridRank                = 3
-TopGridDimensions          = 16 16 16
-SelfGravity                = 1       // gravity on
-TopGridGravityBoundary     = 0       // Periodic BC for gravity
-LeftFaceBoundaryCondition  = 3 3 3   // same for fluid
-RightFaceBoundaryCondition = 3 3 3
-#
-#  problem parameters
-#
-CosmologySimulationOmegaBaryonNow       = 0.06
-CosmologySimulationOmegaCDMNow          = 0.94
-CosmologySimulationDensityName          = GridDensity
-CosmologySimulationVelocity1Name        = GridVelocities
-CosmologySimulationVelocity2Name        = GridVelocities
-CosmologySimulationVelocity3Name        = GridVelocities
-CosmologySimulationParticlePositionName = ParticlePositions
-CosmologySimulationParticleVelocityName = ParticleVelocities
-#
-#  define cosmology parameters
-#
-ComovingCoordinates        = 1       // Expansion ON
-CosmologyOmegaMatterNow    = 1.0
-CosmologyOmegaLambdaNow    = 0.0
-CosmologyHubbleConstantNow = 0.5     // in km/s/Mpc
-CosmologyComovingBoxSize   = 64.0    // in Mpc/h
-CosmologyMaxExpansionRate  = 0.015   // maximum allowed delta(a)/a
-CosmologyInitialRedshift   = 30      // 
-CosmologyFinalRedshift     = 0       //
-GravitationalConstant      = 1       // this must be true for cosmology
-#
-#  set I/O and stop/start parameters
-#
-#StopCycle              = 10          // stop after this many cycles
-dtDataDump             = 10.0         // dump at beginning and end
-#CycleSkipDataDump      = 20
-DataDumpName           = output_
-CosmologyOutputRedshift[0] = 10
-CosmologyOutputRedshift[1] = 8
-CosmologyOutputRedshift[2] = 6
-CosmologyOutputRedshift[3] = 4
-CosmologyOutputRedshift[4] = 3
-CosmologyOutputRedshift[5] = 2
-CosmologyOutputRedshift[6] = 1
-CosmologyOutputRedshift[7] = 0
-#
-#  set hydro parameters
-#
-Gamma                  = 1.6667
-PPMDiffusionParameter  = 0       // diffusion off
-DualEnergyFormalism    = 1       // use total & internal energy
-InterpolationMethod    = 1     // SecondOrderA
-CourantSafetyNumber    = 0.4
-ParticleCourantSafetyNumber = 0.8
-RadiativeCooling            = 0
-MultiSpecies                = 0
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // dynamic hierarchy
-MaximumRefinementLevel    = 0    // use up to 2 levels
-RefineBy                  = 2    // refinement factor
-CellFlaggingMethod        = 2    // use baryon mass for refinement 
-MinimumEfficiency         = 0.4  // fraction efficiency
-MinimumOverDensityForRefinement = 4.0 // times the initial density
-MinimumMassForRefinementLevelExponent = -0.0
-#RefineRegionLeftEdge            = 0.15 0.20 0.41
-#RefineRegionRightEdge           = 0.35 0.45 0.79
-

doc/userguide/amr_guide/InitsMultipleParameterFile.l0

-#
-#  Generates initial grid and particle fields for the top grid of a
-#    multiple-grid CDM simulation
-#
-#  Cosmology Parameters
-#
-CosmologyOmegaMatterNow      = 0.3
-CosmologyOmegaLambdaNow      = 0.7
-CosmologyOmegaBaryonNow      = 0.04
-CosmologyComovingBoxSize     = 64.0      // in Mpc/h
-CosmologyHubbleConstantNow   = 0.67      // in units of 100 km/s/Mpc
-CosmologyInitialRedshift     = 40.0
-#
-#  Power spectrum Parameters
-#
-PowerSpectrumType            = 11        // Eisenstein & Hu
-PowerSpectrumSigma8          = 0.9
-PowerSpectrumPrimordialIndex = 1.0
-PowerSpectrumRandomSeed      = -12345
-#
-#  Grid info
-#
-Rank                = 3
-GridDims            = 64 64 64
-InitializeGrids     = 1
-GridRefinement      = 2
-#
-#  Particle info
-#
-ParticleDims        = 64 64 64
-InitializeParticles = 1
-ParticleRefinement  = 2
-#
-#  Overall field parameters
-#
-MaxDims             = 128 128 128
-#
-#  Re-center the grid on the object
-#
-NewCenterFloat      = 0.67 0.44 0.59
-RootGridDims        = 64 64 64
-#
-#  Names
-#
-ParticlePositionName = ParticlePositions.0
-ParticleVelocityName = ParticleVelocities.0
-GridDensityName      = GridDensity.0
-GridVelocityName     = GridVelocities.0

doc/userguide/amr_guide/InitsMultipleParameterFile.l1

-#
-#  Generates initial grid and particle fields for the bottom grid of a
-#    multiple-grid CDM simulation
-#
-#  Cosmology Parameters
-#
-CosmologyOmegaMatterNow      = 0.3
-CosmologyOmegaLambdaNow      = 0.7
-CosmologyOmegaBaryonNow      = 0.04
-CosmologyComovingBoxSize     = 64.0      // in Mpc/h
-CosmologyHubbleConstantNow   = 0.67      // in units of 100 km/s/Mpc
-CosmologyInitialRedshift     = 40.0
-#
-#  Power spectrum Parameters
-#
-PowerSpectrumType            = 11        // Eisenstein & Hu
-PowerSpectrumSigma8          = 0.9
-PowerSpectrumPrimordialIndex = 1.0
-PowerSpectrumRandomSeed      = -12345
-#
-#  Grid info
-#
-Rank                = 3
-GridDims            = 64 64 64
-InitializeGrids     = 1
-GridRefinement      = 1
-#
-#  Particle info
-#
-ParticleDims        = 64 64 64
-InitializeParticles = 1
-ParticleRefinement  = 1
-#
-#  Overall field parameters
-#
-MaxDims             = 128 128 128
-#
-#  Re-center the grid on the object
-#
-NewCenterFloat      = 0.67 0.44 0.59
-StartIndexInNewCenterTopGridSystem = 16 16 16
-EndIndexInNewCenterTopGridSystem   = 47 47 47
-RootGridDims        = 64 64 64
-#
-#  Names
-#
-ParticlePositionName = ParticlePositions.1
-ParticleVelocityName = ParticleVelocities.1
-GridDensityName      = GridDensity.1
-GridVelocityName     = GridVelocities.1

doc/userguide/amr_guide/InitsSingleParameterFile

-#
-#  Generates initial grid and particle fields for a single-grid
-#    CDM simulation
-#
-#  Cosmology Parameters
-#
-CosmologyOmegaMatterNow      = 1
-CosmologyOmegaLambdaNow      = 0
-CosmologyOmegaBaryonNow      = 0.06
-CosmologyComovingBoxSize     = 64       // in Mpc/h
-CosmologyHubbleConstantNow   = 0.5      // in units of 100 km/s/Mpc
-CosmologyInitialRedshift     = 30
-#
-#  Power spectrum Parameters
-#
-PowerSpectrumType            = 1             // BBKS
-PowerSpectrumSigma8          = 0.7
-PowerSpectrumPrimordialIndex = 1.0
-PowerSpectrumRandomSeed      = -123456789
-#
-#  Grid info
-#
-Rank                = 3
-GridDims            = 16 16 16
-InitializeGrids     = 1
-GridRefinement      = 1
-#
-#  Particle info
-#
-ParticleDims        = 16 16 16
-InitializeParticles = 1
-ParticleRefinement  = 1
-#
-#  Overall field parameters
-#
-MaxDims             = 16 16 16
-#
-#  Names
-#
-ParticlePositionName = ParticlePositions
-ParticleVelocityName = ParticleVelocities
-GridDensityName      = GridDensity
-GridVelocityName     = GridVelocities

doc/userguide/amr_guide/PressurelessCollapse

-#
-# AMR PROBLEM DEFINITION FILE: Pressureless collapse
-#
-#  define problem
-#
-ProblemType            = 21      // Pressureless collapse
-TopGridRank            = 1
-TopGridDimensions      = 100
-SelfGravity            = 1       // gravity on
-TopGridGravityBoundary = 1       // Isolated BCs
-LeftFaceBoundaryCondition  = 1    // outflow ?
-RightFaceBoundaryCondition = 1    // outflow ?
-PressureFree           = 1       // turn off pressure
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.37
-dtDataDump             = 0.4
-#
-#  set hydro parameters
-#
-Gamma                  = 1.4
-CourantSafetyNumber    = 0.05    // needs to be lower for pressurefree
-PPMDiffusionParameter  = 0       // diffusion off
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 1    // dynamic hierarchy
-MaximumRefinementLevel    = 1    // use up to 2 levels
-RefineBy                  = 4    // refinement factor
-MinimumSlopeForRefinement = 0.2  // set this to <= 0.2 to refine CD
-#
-#  set some global parameters
-#
-SubcycleSafetyFactor   = 2       // 
-tiny_number            = 1.0e-10 // fixes velocity slope problem
-MinimumEfficiency      = 0.4     // better value for 1d than 0.2

doc/userguide/amr_guide/ShockPool2D

-#
-# AMR PROBLEM DEFINITION FILE: 2D Shock Propogation test
-#
-#  define problem
-#
-ProblemType            = 3        // Shock Pool
-TopGridRank            = 2
-TopGridDimensions      = 50 50
-RightFaceBoundaryCondition = 1 1  // set right faces to outflow
-HydroMethod            = 0
-#
-ShockPoolAngle          = 30.0    // angle relative to x-axis (in degrees)
-ShockPoolMachNumber     = 2.0 
-#ShockPoolSubgridLeft    = 0.38   // start of subgrid
-#ShockPoolSubgridRight   = 0.62   // end of subgrid
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.4
-#dtDataDump             = 0.05
-#
-#  set Hydro parameters
-#
-Gamma                  = 1.4
-CourantSafetyNumber    = 0.5
-PPMDiffusionParameter  = 0       // diffusion off
-PPMFlatteningParameter = 0       // flattening on
-PPMSteepeningParameter = 0       // steepening on
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // static hierarchy
-RefineBy                  = 4    // refinement factor
-MaximumRefinementLevel    = 1
-CellFlaggingMethod        = 1
-MinimumEfficiency         = 0.4
-#
-#  set some misc global parameters
-#
-tiny_number            = 1.0e-6  // fixes velocity slope problem

doc/userguide/amr_guide/ShockPool3D

-#
-# AMR PROBLEM DEFINITION FILE: 3D Shock Propogation test
-#
-#  define problem
-#
-ProblemType            = 3        // Shock Pool
-TopGridRank            = 3
-TopGridDimensions      = 50 50 50
-RightFaceBoundaryCondition = 1 1 1  // set right faces to outflow
-HydroMethod            = 0
-#
-ShockPoolAngle          = 30.0    // angle relative to x-axis (in degrees)
-ShockPoolMachNumber     = 2.0 
-#ShockPoolSubgridLeft    = 0.38   // start of subgrid
-#ShockPoolSubgridRight   = 0.62   // end of subgrid
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.4
-#dtDataDump             = 0.05
-#
-#  set Hydro parameters
-#
-Gamma                  = 1.4
-CourantSafetyNumber    = 0.5
-PPMDiffusionParameter  = 0       // diffusion off
-PPMFlatteningParameter = 0       // flattening on
-PPMSteepeningParameter = 0       // steepening on
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // static hierarchy
-RefineBy                  = 4    // refinement factor
-MaximumRefinementLevel    = 1
-CellFlaggingMethod        = 1
-MinimumEfficiency         = 0.5
-#
-#  set some misc global parameters
-#
-tiny_number            = 1.0e-6  // fixes velocity slope problem

doc/userguide/amr_guide/ShockTube

-#
-# AMR PROBLEM DEFINITION FILE: ShockTube test (1 grid version)
-#
-#  define problem
-#
-ProblemType            = 1       // Shock Tube
-TopGridRank            = 1
-TopGridDimensions      = 100
-HydroMethod            = 0
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.251
-dtDataDump             = 0.4
-#
-#  set hydro parameters
-#
-Gamma                  = 1.4
-PPMDiffusionParameter  = 0       // diffusion off
-CourantSafetyNumber    = 0.8
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 1    // static hierarchy
-MaximumRefinementLevel    = 1    // use up to 2 levels
-RefineBy                  = 4    // refinement factor
-MinimumSlopeForRefinement = 0.2  // set this to <= 0.2 to refine CD
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-6  // fixes velocity slope problem
-MinimumEfficiency      = 0.4     // better value for 1d than 0.2

doc/userguide/amr_guide/ShockTube1

-#
-# PROBLEM DEFINITION FILE: ShockTube test1 (unigrid version)
-#
-#  Sod Problem (uses default initial conditions). A mild test.
-#
-#  define problem
-#
-ProblemType            = 1       // Shock Tube
-TopGridRank            = 1
-TopGridDimensions      = 100
-HydroMethod            = 0
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.25
-dtDataDump             = 0.25
-#
-#  set hydro parameters
-#
-Gamma                  = 1.4
-PPMDiffusionParameter  = 0       // diffusion off
-CourantSafetyNumber    = 0.8     // ppm
-#CourantSafetyNumber    = 0.5     // Zeus
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // dynamic hierarchy
-MaximumRefinementLevel    = 0    // use up to 0 levels
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-6  // fixes velocity slope problem
-MinimumEfficiency      = 0.4     // better value for 1d than 0.2

doc/userguide/amr_guide/ShockTube2

-#
-# PROBLEM DEFINITION FILE: ShockTube test2 (unigrid version)
-#
-# "123-problem" Two strong rarefactions and a trivial stationary
-# 		contact discontinuity. The pressure p_* is very
-#		small (close to vacuum). Also useful as a test
-#		of RS performance in low density flows. 
-#
-#  define problem
-#
-ProblemType            = 1       // Shock Tube
-TopGridRank            = 1
-TopGridDimensions      = 1000
-HydroMethod            = 0
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.15
-dtDataDump             = 0.15
-#
-#  set hydro parameters
-#
-Gamma                  = 1.4
-PPMDiffusionParameter  = 0       // diffusion off
-#PPMFlatteningParameter = 1
-CourantSafetyNumber    = 0.8     // PPM
-#CourantSafetyNumber    = 0.5     // Zeus
-#
-#  set initial conditions (TR-case)
-#
-ShockTubeLeftDensity   = 1.0
-ShockTubeLeftVelocity  = -2.0
-ShockTubeLeftPressure  = 0.4
-ShockTubeRightDensity  = 1.0
-ShockTubeRightVelocity = 2.0
-ShockTubeRightPressure = 0.4
-#
-#  set outflow boundary conditions
-#
-LeftFaceBoundaryCondition  = 1
-RightFaceBoundaryCondition = 1
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // no static hierarchy
-MaximumRefinementLevel    = 0    // use up to 0 levels
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-6  // 
-MinimumEfficiency      = 0.4     // better value for 1d than 0.2
-
-
-
-

doc/userguide/amr_guide/ShockTube3

-#
-# PROBLEM DEFINITION FILE: ShockTube test3 (unigrid version)
-#
-# The left half of the blast wave problem from Woodward & Colella
-# A Left rarefaction, a contact and a Right shock. 
-# A very severe test.
-#
-#
-#  define problem
-#
-ProblemType            = 1       // Shock Tube
-TopGridRank            = 1
-TopGridDimensions      = 100
-HydroMethod            = 0       // ppm_de
-#HydroMethod            = 2       // Zeus
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.012
-dtDataDump             = 0.012
-#
-#  set hydro parameters
-#
-Gamma                  = 1.4
-PPMDiffusionParameter  = 0       // diffusion off
-CourantSafetyNumber    = 0.8     // ppm
-#CourantSafetyNumber    = 0.8     // Zeus
-#
-#  set initial conditions
-#
-ShockTubeLeftDensity   = 1.0
-ShockTubeLeftVelocity  = 0.0
-ShockTubeLeftPressure  = 1000.0
-ShockTubeRightDensity  = 1.0
-ShockTubeRightVelocity = 0.0
-ShockTubeRightPressure = 0.01
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // no static hierarchy
-MaximumRefinementLevel    = 0    // use up to 0 levels
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-6  // fixes velocity slope problem
-MinimumEfficiency      = 0.4     // better value for 1d than 0.2

doc/userguide/amr_guide/ShockTube4

-#
-# PROBLEM DEFINITION FILE: ShockTube test4 (unigrid version)
-#
-# Right half of Woodward & Collella problem: Left shock, a contact,
-# and a Right rarefaction.
-#
-#  define problem
-#
-ProblemType            = 1       // Shock Tube
-TopGridRank            = 1
-TopGridDimensions      = 100
-HydroMethod            = 0
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.035
-dtDataDump             = 0.035
-#
-#  set hydro parameters
-#
-Gamma                  = 1.4
-PPMDiffusionParameter  = 0       // diffusion off
-CourantSafetyNumber    = 0.8     // ppm
-#CourantSafetyNumber    = 0.5     // Zeus
-#
-#  set initial conditions
-#
-ShockTubeLeftDensity   = 1.0
-ShockTubeLeftVelocity  = 0.0
-ShockTubeLeftPressure  = 0.01
-ShockTubeRightDensity  = 1.0
-ShockTubeRightVelocity = 0.0
-ShockTubeRightPressure = 100.0
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // no static hierarchy
-MaximumRefinementLevel    = 0    // use up to 0 levels
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-6  // fixes velocity slope problem
-MinimumEfficiency      = 0.4     // better value for 1d than 0.2

doc/userguide/amr_guide/ShockTube5

-#
-# PROBLEM DEFINITION FILE: ShockTube test5 (unigrid version)
-#
-# A combination of left and right shocks from tests 3 and 4, resp.
-# Collision of two strong shocks produces a left facing shock
-# (travelling very slowly to the right), a right travelling contact
-# discontinuity, and a right travelling shock wave.
-#
-#  define problem
-#
-ProblemType            = 1       // Shock Tube
-TopGridRank            = 1
-TopGridDimensions      = 100
-HydroMethod            = 0       // 0 - ppm_de, 2 - Zeus
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.035
-dtDataDump             = 0.035
-#
-#  set hydro parameters
-#
-Gamma                  = 1.4
-PPMDiffusionParameter  = 0       // diffusion off
-PPMSteepeningParameter = 1
-CourantSafetyNumber    = 0.8     // ppm
-#CourantSafetyNumber    = 0.5     // Zeus
-#
-#  set initial conditions
-#
-ShockTubeLeftDensity   = 5.99924
-ShockTubeLeftVelocity  = 19.5975
-ShockTubeLeftPressure  = 460.894
-ShockTubeRightDensity  = 5.99242
-ShockTubeRightVelocity = -6.19633
-ShockTubeRightPressure = 46.0950
-#
-#  set "outflow" boundary conditions
-#
-LeftFaceBoundaryCondition  = 1
-RightFaceBoundaryCondition = 1
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // no static hierarchy
-MaximumRefinementLevel    = 0    // use up to 0 levels
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-6  // fixes velocity slope problem
-MinimumEfficiency      = 0.4     // better value for 1d than 0.2

doc/userguide/amr_guide/TestGravity

-#
-# AMR PROBLEM DEFINITION FILE: Gravity Test Problem
-#
-#  define problem
-#
-ProblemType            = 23      // Gravity test
-TopGridRank            = 3
-TopGridDimensions      = 32 32 32
-SelfGravity            = 1       // gravity on
-TopGridGravityBoundary = 0       // Periodic BCs
-PressureFree           = 1       // turn off pressure
-S2ParticleSize         = 3.4
-GravityResolution      = 1.0
-#
-TestGravityNumberOfParticles = 5000
-#TestGravityUseBaryons        = 1
-TestGravitySubgridLeft       = 0.4375   // start of subgrid
-TestGravitySubgridRight      = 0.5625   // end of subgrid
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.001
-dtDataDump             = 0.0
-#
-#  set hydro parameters
-#
-CourantSafetyNumber    = 0.5     // 
-PPMDiffusionParameter  = 0       // diffusion off
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // dynamic hierarchy
-MaximumRefinementLevel    = 1    // use up to 2 levels
-RefineBy                  = 2    // refinement factor
-CellFlaggingMethod        = 0
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-10 // fixes velocity slope problem

doc/userguide/amr_guide/TestGravitySphere

-#
-# AMR PROBLEM DEFINITION FILE: Gravity Test (Sphere) Problem
-#
-#  define problem
-#
-ProblemType            = 25      // Gravity test (Sphere)
-TopGridRank            = 3
-TopGridDimensions      = 32 32 32
-SelfGravity            = 1       // gravity on
-TopGridGravityBoundary = 0       // Periodic BCs
-#NumberOfParticles      = 5000
-#
-TestGravitySphereInteriorDensity   = 100000.0
-TestGravitySphereExteriorDensity   = 0.01
-TestGravitySphereRadius            = 0.01
-TestGravitySphereUseBaryons        = 1
-#TestGravitySphereSubgridLeft       = 0.4375   // start of subgrid
-#TestGravitySphereSubgridRight      = 0.5625   // end of subgrid
-TestGravitySphereType              = 0
-TestGravitySphereRefineAtStart     = 1
-TestGravitySphereCenter            = 0.49 0.5 0.5
-#TestGravitySphereCenter            = 0.484375 0.484375 0.484375
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 0.00001
-dtDataDump             = 0.01
-#
-#  set hydro parameters
-#
-CourantSafetyNumber    = 0.5     // 
-PPMDiffusionParameter  = 0       // diffusion off
-HydroMethod            = 2
-#
-#  set grid refinement parameters
-#
-StaticHierarchy                 = 0    // dynamic hierarchy
-MaximumRefinementLevel          = 6    // use up to 3 levels
-MaximumGravityRefinementLevel   = 6
-RefineBy                        = 2    // refinement factor
-MinimumOverDensityForRefinement = 0.1
-CellFlaggingMethod              = 2
-FluxCorrection                  = 0
-ConservativeInterpolation       = 0
-#
-#  set some global parameters
-#
-tiny_number            = 1.0e-10 // fixes velocity slope problem

doc/userguide/amr_guide/WavePool

-#
-# AMR PROBLEM DEFINITION FILE: Wave Propogation test
-#
-#  define problem
-#
-ProblemType            = 2       // Wave Pool
-TopGridRank            = 1
-TopGridDimensions      = 100
-HydroMethod            = 0
-#
-WavePoolAmplitude      = 0.01    // linear amplitude in density
-WavePoolWavelength     = 0.1     // 1/10 of the box
-WavePoolNumberOfWaves  = 1
-WavePoolSubgridLeft    = 0.5     // start of subgrid
-WavePoolSubgridRight   = 0.75    // end of subgrid
-#
-#  set I/O and stop/start parameters
-#
-StopTime               = 1.0
-dtDataDump             = 0.1
-#
-#  set Hydro parameters
-#
-Gamma                  = 1.4
-PPMDiffusionParameter  = 0       // diffusion off
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 1    // static hierarchy
-RefineBy                  = 4    // refinement factor
-#
-#  set some misc global parameters
-#
-tiny_number            = 1.0e-6  // fixes velocity slope problem

doc/userguide/amr_guide/ZeldovichPancake

-#
-# AMR PROBLEM DEFINITION FILE: Zeldovich Pancake (one grid version)
-#
-#  define problem
-#
-ProblemType                = 20      // Zeldovich pancake
-TopGridRank                = 1
-TopGridDimensions          = 256
-SelfGravity                = 1       // gravity on
-TopGridGravityBoundary     = 0       // Periodic BC for gravity
-LeftFaceBoundaryCondition  = 3       // same for fluid
-RightFaceBoundaryCondition = 3
-#
-#  problem parameters
-#
-ZeldovichPancakeCentralOffset    = 0
-ZeldovichPancakeCollapseRedshift = 1
-#
-#  define cosmology parameters
-#
-ComovingCoordinates        = 1       // Expansion ON
-CosmologyHubbleConstantNow = 0.5
-CosmologyComovingBoxSize   = 64.0    // 64 Mpc/h
-CosmologyMaxExpansionRate  = 0.01    //
-CosmologyInitialRedshift   = 20      // start at z=20
-GravitationalConstant      = 1       // this must be true for cosmology
-#
-#  set I/O and stop/start parameters
-#
-dtDataDump             = 10.0    // dump at beginning and end
-#
-#  set hydro parameters
-#
-Gamma                  = 1.6667
-CourantSafetyNumber    = 0.5
-PPMDiffusionParameter  = 0       // diffusion off
-DualEnergyFormalism    = 1       // use total & internal energy
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 1    // static hierarchy
-RefineBy                  = 2
-#
-#  set some global parameters
-#

doc/userguide/amr_guide/analyze.html

-<html>
-  <head>
-    <link href="../enzo.css" rel="stylesheet" type="text/css">
-    <title>Enzo user's guide: analyzing the output</title>
-  </head>
-<body>
-<h1>Analyzing Enzo output</h1>
-Analyzing the output from an Enzo AMR simulation is more difficult because of
-the complicated grid structures.  However a number of tools have been developed
-to help. First, as pointed out in the section on the output format, since
-each grid is it's own self-contained HDF file, each grid can be analyzed
-by itself with any tool that reads HDF (IDL, Transform, etc.). Unfortunately,
-for simulations with hundreds or thousands of grids this is of little assistance.
-More practically, here are some other analysis methods, most of which assume
-that you are doing a 3D simulation (and often that it is a cosmological
-simulation).
-<ol>
-<li>
-<b><a href="#2D projections">2D projections</a> </b>- The code has the
-built-in ability to make two-dimensional projections, at a specified resolution,
-of a number of quantities (tailored for cosmology) along any axis of a
-given three-dimensional region. The resulting 2D HDF SDS's can then be
-imaged with a number of tools, including IDL.</li>
-
-<li>
-<b><a href="#Extractions">Extractions</a> </b>- A region (generally 3D,
-but this option also works for 1 and 2-dimensions) can be extracted with
-a uniform resolution and saved as a single grid. This is useful for other
-packages developed for single-grid codes. This option is built into
-the Enzo code.</li>
-
-<li>
-<a href="#Peakfinder"><b>Peakfinder</b> </a>- In the analysis package (amr_mpi/anyl),
-there is a routine which can find peaks in the baryon or dark-matter distribution,
-subject to a number of qualifications (such as minimum separation).&nbsp;
-[Note: enzohop is recommended for most peak finding].</li>
-
-<li>
-<b><a href="#halofinder">Hop halo finder</a> </b>- Also in the analysis
-package is a version of Eisenstein &amp; Hut's hop halo finder, as applied
-to the dark matter.</li>
-
-<li>
-<b><a href="#Profiler">Profiles</a></b> - Radial profile of density and
-many other quantities can be generated with another analysis routine, given
-an object's position.</li>
-
-<li>
-<b><a href="#Particle Representation">Particle representation</a></b> -
-The code also has the ability to convert the grid into a set of particle
-positions and densities, temperatures, etc. This can then be read into
-a particle-analysis code.</li>
-</ol>
-
-<hr WIDTH="100%">
-<br>(Note: in this section we drop the "mpirun -np 1" that is required
-to run MPIprograms.&nbsp; Note also that all analysis programs only function
-with one processor -- they are not parallelized.&nbsp; Finally, the square
-brackets [] used below imply an optional argument and are not meant to
-be typed.)
-<h3>
-<a NAME="2D projections"></a>2D projections</h3>
-The projection is done with the Enzo code itself and is of the following
-format:
-<p><tt>enzo -p <i>dim</i> [-l <i>level</i>] [-m] [-b <i>point1</i>] [-f
-<i>point2</i>]
-<i>enzo_filename</i></tt>
-<p>an example might be:
-<p><tt>enzo -p 1 -l 6 -b 0.4 0.4 0.4 -f 0.6 0.6 0.6 data0015</tt>
-<p>The -p option, which specifies the dimension along which the projection
-is to occur, and the Enzo output_filename are the only arguments required.
-The projection dimension (<i>dim</i>) is an integer from 0 to 2, and indicates
-along which dimension the projection occurs. For example, a projection
-along axis-0 produces an image with y-z axis.
-<p>The -l option specifies the resolution of the image, by indicating a
-level at which the projection will occur. The integer value <i>level </i>is
-zero-based so <tt>-l 0</tt>&nbsp; produces an image with the same resolution
-as the root grid. Levels larger than the maximum in the output_filename
-may be used. The default value is 0.
-<p>The -m option smooths the image by doing a linear interpolation between
-coarse-grid points. If this option is not invoked, the result will be pixelated
-in regions in which the pixels are smaller than the grid cells (although
-this may be useful information). This option takes somewhat longer. The
-default is no smoothing.
-<p>Finally, there are two ways to specify the three-dimensional region
-in which the projection is to occur, one of which is shown in the commend-line
-above. This uses the -b and -f (begin and finish) flags. These flags each
-take a triplet (in 3D) of floats which specify the the two corners of the
-projection volume. The units are those of the problem (set by DomainLeftEdge
-and DomainRightEdge). For cosmology problems, this means numbers that range
-from 0 to 1. The default is the entire domain.
-<p>The other mechanism for specifying the projection volume is to specify
-coordinate indexes. This is done with the -s and -e flags, each of which
-take a triplet of integers. The integers refer to index positions (zero-based)
-within that level. This means the numbers should range between 0 and n*r^l-1
-where n is the size of the top grid, r is the refinement factor and l is
-the level. The advantage of this method is that the size of the region
-can be precisely set, the disadvantage is the calculation is a bit more
-difficult. Although these two methods can be mixed (by specifying one corner
-with one method and the other corner with the other method), it is undefined
-to specify one corner twice. Finally, the error checking on these values
-is not great, and specifying a region with negative volume or one that
-goes off the edge may result in a core dump rather than an error message.
-<p>The result is placed in the file amr.project and consists of 2D scientific
-data sets (HDF format) of the following quantities (subject to change):
-
-    <ul>
-      <li>baryon density (M(solar)/Mpc^3)</li>
-      <li>a field proportional to the bolometric free-free emission (but see below)</li>
-      <li>dark matter density (M(solar)/Mpc^3)</li>
-      <li>temperature (K, weighted by free-free emission)</li>
-      <li>maximum level along projection</li>
-      <li>the y-parameter of thermal SZ effect</li>
-      <li>the DT/T value of the kinematic SZ effect</li>
-      <li>The mean density-weighted fractional metallicity of the gas along the line
-	of sight</li>
-      <li>The star particle density (M(solar)/Mpc^3)</li>
-    </ul>
-
-If there is a file called "ProjectionParameters" in the same directory,
-then this file is opened and searched for parameters relating to the generation
-of the X-ray emission field.&nbsp; The following parameters (specified
-with the usual conventions: Parameter = ...) are recognized: <tt>XrayLowerCutoffkeV</tt>,
-<tt>XrayUpperCutoffkeV</tt>
-and <tt>XrayTableFileName</tt>.&nbsp; The first two specify the X-ray band
-(observed at z=0) to be used, and the last gives the name of an ascii file
-that contains the X-ray spectral information.&nbsp; A gzipped version of
-this file good for bands within the 0.1 - 20 keV range is available in
-amr_mpi/exe/lookup_metal0.3.data.gz.&nbsp; If these parameters are specified,
-then the second field is replaced with integrated emissivity along the
-long of sight in units of 10^-23 erg/cm^2/s.&nbsp; Also, see below in the
-profiling section.
-<p>
-<hr WIDTH="100%">
-
-<h3><a NAME="Extractions"></a>Extractions</h3>
-The command-line for an extraction is very similar to a projection:
-<p><tt>enzo -x&nbsp;</tt> <tt>[-l <i>level</i>] [-b <i>point1</i>] [-f
-<i>point2</i>]
-<i>enzo_filename</i></tt>
-<p>The&nbsp; meaning of the level (-l) and region (-b, -f) flags are the
-same as for the projection (see above).
-<p>The output is a standard grid file and so consists of an HDF file with
-a number of scientific data sets.&nbsp; The scientific data sets are named
-and have dimensional axis.&nbsp; The units are code units with the exception
-of temperature, with is in degrees K.&nbsp; See the file CosmologyGetUnits.C
-for a definition of code units, or look in the ascii output file (search
-for lines which start DataCGSConversionFactor = ...).
-<p>
-<hr WIDTH="100%">
-
-<h3><a NAME="Peakfinder"></a>Peakfinder</h3>
-The peakfinder is part of the <tt>amr_mpi/anyl</tt> package and is
-the executable <tt>bin/findpeaks</tt>.
-
-It is run with the command-line:
-<p><tt>findpeaks [-n <i>number</i>] [-m <i>min_density</i>] [-s <i>separation</i>]
-<i>enzo_filename peak_filename</i></tt>
-<p>The algorithm reads in the Enzo output file <i>enzo_filename</i> and looks
-for peaks (a density larger than it's 26 neighbours) in the baryon density
-distribution.&nbsp; The result is output as a series of locations (float
-triplets between 0 and 1) to the file <i>peak_filename, </i>sorted by the
-peak density.
-<p>The -n option takes an integer argument and returns the <i>number</i>
-largest peaks.&nbsp; Default: 1
-<p>The flag -m tells the algorithm to only check peaks with densities
-larger than the float value <i>min_density</i> which, for cosmology, is
-in units of the mean density of non-relativistic mass (at the redshift
-at which the output occurred).&nbsp; This option is mostly useful for speeding
-up the algorithm, since a large value for the minimum density can drastically
-cut down the number of cells that need to be checked.&nbsp; Default: 1
-<p>The last option, -s,&nbsp; specified the minimum separation between
-peaks (the lower density peak is discarded), and the float value <i>separation</i>
-should be in terms of comoving Mpc/h.&nbsp; Default: 0
-<p>This peakfinder really does just find local peaks -- a halo finder (see
-below) is probably what you're looking for.
-<p>
-<hr WIDTH="100%">
-
-<h3><a NAME="halofinder"></a>Halofinder</h3>
-The halo finder is part of the analysis package.&nbsp; It
-uses the hop algorithm (and source code) developed by Daniel Eisenstein
-and Wayne Hu (<a href="http://arXiv.org/abs/astro-ph/?9712200">astro-ph/9712200</a>)
--- thanks to them for making the code available.&nbsp; The compilation
-is currently a bit convoluted because hop assumes 4 byte floats.&nbsp;
-This means that you must compile everything in single precision; change
-the PRECISION = r8 macro to PRECISION = r4 (in both amr_mpi/src/Makefile
-and amr_mpi/anyl/Makefile).&nbsp; Then compile enzo (make clean first if
-previously compiled with PRECISION = r8), and then compile enzohop: "cd
-amr_mpi/anyl; make enzohop".&nbsp; Run with:
-<p><tt>enzohop [-b #] [-f #] [-t #] [-g] [-d] </tt><i>enzo_filename</i>
-<p>The only required argument, <i>enzo_filename,</i> is the name of an Enzo
-output file.
-<p>The optional flags that specify a region to work on (-b for begin and
--f for finish) are as described in the projection section.&nbsp; Default:
-the whole region
-<p>The next flag (-t) takes a float and specifies the most important threshold
-used in hop (the outer density definition).&nbsp; Default: 160
-<p>The -g flag indicates that baryon grid points should be converted to
-particles and passed into hop (along with the dark matter).&nbsp; This
-is not recommended.&nbsp; Finally, the -d flag is the usual debugging flag.
-<p>The output is placed into a number of files, only one of which is described
-here (see hop for the others).&nbsp; HopAnalysis.out contains a list of
-the results groups, their particle number, mass and the location of the
-densest particle.
-<p>
-<hr WIDTH="100%">
-
-<h3><a NAME="Profiler"></a>Profiler</h3>
-It is often useful to compute azimuthally-averaged radial profiles.&nbsp;
-The utility <tt>bin/enzo_anyl </tt>can be used for this.&nbsp;
-It runs
-with the command-line:
-<p><tt>enzo_anyl&nbsp;</tt> <i>enzo_filename&nbsp;&nbsp; anyl_parameter_file</i>
-<p>The first argument, <i>enzo_filename</i>, is the name of an Enzo output
-file, and the second argument is the name of an ascii file which contains
-some parameters for the analysis routine.&nbsp; An <a href="AnalyzeClusterParameterFile">example
-</a>of
-this file should be in <tt>amr_mpi/anyl/AnalyzeClusterParameterFile</tt>.&nbsp;
-The format of the parameters is the same as for the enzo code itself.&nbsp;
-The parameters are:
-<ul>
-<li>
-<b>Rinner </b>- The inner edge of the profile in comoving Mpc.&nbsp; Default:
-0.0001 of the ComovingBoxSize</li>
-
-<li>
-<b>Router</b> - The outer edge of the profile in comoving Mpc.&nbsp; This
-should be well outside the expected virial radius of the object.&nbsp;
-Default: 0.1 of the ComovingBoxSize</li>
-
-<li>
-<b>CenterPosition</b> - A triplet of floats from 0 to 1 specifying the
-location of the center.&nbsp; This parameter is ignored if CenterListName
-is set.&nbsp; Default: if left unspecified, the location of the maximum
-density in the volume is used.</li>
-
-<li>
-<b>NumberOfPoints</b> - An integer: the number of points in the profile.&nbsp;
-The radial shells are spaced in equal logarithmic intervals in radius (except
-for the first point)&nbsp;&nbsp; Default: 16</li>
-
-<li>
-<b>VirialDensity</b> - This float indicates the overdensity, relative to
-the critical (not mean) density, that is to be used to define the virial
-radius.&nbsp; Default: 200</li>
-
-<li>
-<b>CenterListName </b>- The name of a file containing a list of center
-positions (each line should contain a triplet of floats, between 0 and
-1).&nbsp; Up to 1000 positions may be specified.&nbsp; If not set, then
-the parameter CenterPosition is used to define a single center.&nbsp; Default:
-NULL</li>
-
-<li>
-<b>MeanVelocityVirialFraction</b> - This is the fraction of the virial
-radius which is used to determine the mass-weighted mean velocity of the
-object.&nbsp; It can be useful to set this significantly less than the
-1.0 (i.e. the virial radius) if the center of the object is moving relative
-to the center-of-motion of the entire object.&nbsp; Default: 1.0</li>
-
-<li>
-<b>XrayLowerCutoffkeV</b> - If this and the next three parameters are specified,
-then an accurate calculation of the X-ray emissivity is made.&nbsp; This
-parameter and the next indicate the X-ray band (in keV at z=0) that is
-to be used in the calculation. Default: none</li>
-
-<li>
-<b>XrayUpperCutoffkeV</b> - The high energy end of the X-ray band in keV.&nbsp;
-Default: none</li>
-
-<li>
-<b>XrayTableFileName</b> - The name of the ascii file which contains the
-spectral lookup table.&nbsp; There is a version computed with a Raymond-Smith
-code for a low density hot gas with a metallicity of 0.3 relative to solar
-in the file amr_mpi/exe/lookup_metal0.3.data.gz.</li>
-
-<li>
-<b>ComputeDiskInformation</b> - This toggle flag (1 is on, 0 off) controls
-whether a disk profile and image is generated.&nbsp; If yes, then the angular
-momentum vector of the dense gas (see below) is used to define a disk.&nbsp;
-Default: 0</li>
-
-<li>
-<b>DiskImageSize</b> - The number of pixels on a side in the three disk
-images (face, and two sides) which are computed if the above flag is turned
-on.&nbsp; Default: 100</li>
-
-<li>
-<b>DiskRadius</b> - This is the fraction of the virial radius which the
-disk image comprises (i.e. each pixel is of size r_virial*DiskRadius/DiskImageSize).&nbsp;
-Default: 0.2</li>
-
-<li>
-<b>LowerDensityCutoff </b>- This is lower density cutoff (in Msolar/Mpc^3)
-for material to be counted as dense for the calculation of the "dense"
-angular momentum gas, the cold fraction and the dense fraction.&nbsp; Default:
-1e14</li>
-
-<li>
-<b>UpperDensityCutoff </b>- The maximum density (in Msolar/Mpc^3) for gas
-to be counted in the "dense" angular momentum.&nbsp; Default: 1e35</li>
-
-<li>
-<b>ColdTemperatureCutoff </b>- The highest temperature (in K) for gas to
-be considered cold.&nbsp; Used in the calculation of the "dense" angular
-momentum gas and in the cold fraction.&nbsp; Can be over-written by the
-following parameter.&nbsp; Default: 15000</li>
-
-<li>
-<b>ColdTemperatureCutoffVirialFraction </b>- If set, this parameter sets
-ColdTemperatureCutoff (for each cluster) to this value times the predicted
-virial temperature (see below).&nbsp; Default: none</li>
-
-<li>
-<b>VirialTemperatureNormalize</b> - The normalization of the predicted
-virial temperature relation (mass - temperature - redshift relation), relative
-to that in Bryan &amp; Norman (1998).&nbsp; If the virial mass is > 1e8
-solar masses then mu (the mean mass per particle) is set to 0.6, otherwise
-mu=1.22.</li>
-</ul>
-The output is a set of files starting with <tt>AnalyzeCluster</tt>.&nbsp;
-If the CenterListName was set, then they are numbered with a three digit
-identifier (<tt>AnalyzeCluster000</tt>, etc.).&nbsp; Each profile produces
-for (or more) files, the first contains general information as well as
-the baryon profile and has no suffix.&nbsp; Then there are three more which
-have the suffixes <tt>.DarkMatter, .Species</tt> and <tt>.Inertial</tt>,
-which contain profile relating to the particles, the multiple species (if
-used) and the inertial tensors of the gas and particles.&nbsp; Finally,
-two other disk profiles may be generated if requested (see parameters above).
-<p>Each file consists of description information with the pound symbol
-(i.e. a comment) at the start of the line, and then the profile itself.&nbsp;
-The first column is the center of the bin, while the second column is the
-right edge of the bin, in terms of Mpc (note: not comoving Mpc/h).
-<p>Virial information is also included in <tt>AnalyzeCluster,</tt> (mass,
-radius, mean velocity within, etc.), and each file contains a line which
-gives the mean of the profile quantities within the virial radius.
-<p>
-<hr WIDTH="100%">
-
-<h3><a NAME="Particle Representation"></a>Particle Representation</h3>
-To turn the grid points into particles, use the command-line:
-<p><tt>enzo -o&nbsp;</tt>&nbsp; <i>enzo_filename</i>
-<p>This will create two HDF files, one called amr.particles.gas and the
-other amr.particles.dm which contain one-dimension scientific data sets
-of the "particle" positions, velocities, radii, density, temperature, etc.
-<p>This description will be lengthened if interest is expressed in this
-format.&nbsp; Note that there is a version which outputs ascii files called
-dumpgrids (in amr_mpi/anyl).&nbsp; Again, this is under development and
-is intended for conversion to other analysis/visualization programs.
-<br>
-
-<p>&nbsp;</p>
-<p><a href="../index.html">Go to the Enzo home page</a></p>
-
-<hr WIDTH="100%">
-<center>&copy; 2004 &nbsp; <a href="http://cosmos.ucsd.edu">Laboratory for Computational Astrophysics</a><br></center>
-<center>last modified February 2004<br>
-by <a href="mailto:bwoshea (AT) lanl.gov">B.W. O'Shea</a></center>
-
-</body>
-</html>

doc/userguide/amr_guide/binaries.html

-<html>
-  <head>
-    <link href="../enzo.css" rel="stylesheet" type="text/css">
-    <title>Executable Arguments and Outputs</title>
-  </head>
-<body>
-
-    <p><h1>Executable Arguments and Outputs</h1></p>
-    <p>This page is a summary of all of the binaries that are created after 
-      <tt>'make; make install'</tt> is run in the 
-      enzo code bundle.  They should be located in the <tt>bin/</tt> directory.  Links to the various 
-      pages of the manual that describe a particular binary are also included.</p>
-
-
-    <p><b><font size=+1>enzo</font></b></p>
-    <p>This is the main simulation code executable.  See <a href="cosmo_run.html">this page</a>
-      for more detailed information.  In addition to performing the actual simulations, the enzo
-      binary performs projections and various kinds of extractions.  Enzo projections are described
-      on <a href="analyze.html#2D%20projections">here</a> and extractions are described on
-      <a href="analyze.html#Extractions">here</a>.  The projection output file is called 
-      <tt>amr.project</tt> and the extraction file is called <tt>amr.grid</tt>.</p>
-      
-    <p>When an Enzo simulation is run, at every datastep several files are output.  There is
-      an ascii file which has no extension (ie, if your output dumps are named
-      RedshiftOutput then the first parameter file output will be RedshiftOutput0000).  This
-      file contains all of the parameters that Enzo needs to be able to restart the simulation,
-      such as cosmology information, redshift, information on box volume, and which physics modules
-      are turned on.  Another file, which has the same root and the extension '.hierarchy', contains
-      ascii information on all of the Enzo AMR grids, such as their positions, sizes, number of particles
-      per grid, etc.  There are two files with extensions '.boundary' and '.boundary.hdf' which contain
-      information on boundary conditions.  And then there will be at least one file with the extension
-      '.gridNNNN', where NNNN is a number between 0 and 9999. For simulations with more than 10,000
-      files, the numbering will have 5 digits and start from 10000.  These files are where all of the 
-      simulation data is actually contained.</p>
-
-<pre>
-usage: enzo [options] &lt;param_file&gt;
-
-   general options:
-      -d                            display debug information
-      -r                            restart
-      -x                            extract
-      -l &lt;level&gt;                    level of extract
-      -p &lt;dimension&gt;                project to plane
-      -m                            smooth projection
-      -o                            output as particle data
-      -h                            help
-      -i                            information output
-      -s &lt;dim0&gt; [&lt;dim1&gt; [&lt;dim2&gt;]]   start index region
-      -e &lt;dim0&gt; [&lt;dim1&gt; [&lt;dim2&gt;]]   end index region
-      -b &lt;dim0&gt; [&lt;dim1&gt; [&lt;dim2&gt;]]   begin coordinates
-      -f &lt;dim0&gt; [&lt;dim1&gt; [&lt;dim2&gt;]]   finish coordinate region
-
-   performance options:
-      -P mode &lt;modeval&gt;             set jbPerf mode
-      -P event &lt;eventname&gt;          set jbPerf event
-      -P dir &lt;directory&gt;            set jbPerf directory
-</pre>
-
-
-    <p>&nbsp;</p>
-    <p><b><font size=+1>inits</font></b></p>
-    <p>This is the initial conditions generator.  See <a href="index-inits.html">this page</a>
-      for more detailed information.  Initial conditions with a single initial grid or multiple
-      nested grids can be created with this executable.  Output file names are user-specified, but
-      in a standard cosmology simulation with a single initial grid
-      there should be a file containing baryon density information, another containing baryon velocity
-      information, and two more files containing particle position and velocity information.  Simulations
-      with multiple grids will have a set of these files for each level, appended with numbers to make them
-      unique.</p>
-    
-<pre>
-usage: inits [options] param_file
-   options are:
-      -d(ebug)
-      -s(ubgrid) param_file
-</pre>
-    
-    <p>&nbsp;</p>
-    <p><b><font size=+1>ring</font></b></p>
-    <p><tt>ring</tt> must be run on the simulation particle position and velocity information
-      before a simulation is executed when the parameter <tt>ParallelParticleIO</tt> is set to 1.
-      Running ring generates files called PPos.nnnn PVel.nnnn  where nnnn goes from 0001 to the 
-      total number of processors that are used for the simulation.  These files contain the particle
-      position and velocity information for particles that belong to each processor individually,
-      and will be read into the code instead of the monolithic particle position and velocity files.
-      Note that if <tt>ParallelParticleIO</tt> is on and ring is NOT run, the simulation will crash.</p>
-
-
-<pre>
-usage:  ring &lt;particle position file&gt; &lt;particle velocity file&gt;
-</pre>
-
-
-    
-    <p>&nbsp;</p>
-    <p><b><font size=+1>differ</font></b></p>
-    <p>This piece of code compares two different HDF5 files/datasets (which are supposedly the same) and
-      tells how many values are different, and outputs this to stdout.  No files are output.</p>
-
-<pre>
-usage:  differ &lt;file 1&gt; &lt;file 2&gt; &lt;dataname 1&gt; &lt;dataname 2&gt;    
-</pre>
-
-
-    <p>&nbsp;</p>
-    <p><b><font size=+1>glue</font></b></p>
-    <p>Glue takes single-grid or fractured unigrid enzo hierarchies (ie, ones that have been created using 
-      a simulation with <tt>ParallelRootGridIO</tt> on) and extracts individual fields into monolithic
-      files, which is useful for user-written data analysis.  The files that are output have the same
-      name as the field name.</p>
-
-<pre>
-usage:  glue &lt;GridName&gt; &lt;FieldName&gt; &lt;gridsize&gt; &lt;ngrids&gt;
-</pre>
-
-
-    <p>&nbsp;</p>
-    <p><b><font size=+1>dumpgrids</font></b></p>
-    <p>This executable takes an enzo hierarchy (amr or unigrid) and outputs all non-overlapping
-      cells into a file called DumpGridData.grid in four column format, corresponding to:
-      temperature, density, (junk), grid size, all of which are in code units.</p>
-
-<pre>
-usage: dumpgrids [-d] [-g] [-p] [-s] amr_saved_filename [dump_filename]
-  -d)ebug
-  -g)rid data output
-  -p)article data output
-  -s)tar data output
-</pre>
-
-    <p>&nbsp;</p>
-    <p><b><font size=+1>enzo_anyl</font></b></p>
-    <p>This executable generates sperhically-averaged radial profiles of halos.  
-      See <a href="analyze.html#profiler">this page</a> for more information. <tt>enzo_anyl</tt>
-      dumps information into files that start with the string 'AnalyzeCluster'.  See the previously
-      mentioned page for more details.</a>
-
-<pre>
-usage: enzo_anyl amr_file anyl_parameter_file
-</pre>
-
-
-    <p>&nbsp;</p>
-    <p><b><font size=+1>enzostats</font></b></p>
-    <p>This code generates some globally averaged information about a given simulation.  No files
-      are output, only information to stdout.</p>
-<pre>
-    enzostats [-b #] [-f #] [-d] amr_file
-  -b)egin region
-  -f)inish region
-  -d)ebug
-</pre>
-
-
-
-    <p>&nbsp;</p>
-    <p><b><font size=+1>findinit</font></b></p>
-    <p>This binary finds the extent of the initial positions of all particles in a given halo.  It
-      is used for generating multi-grid initial conditions, and more information about it can be
-      found <a href="index-inits.html#multigrid">here</a>.  No files are input, only text to
-      stdout.</p>
-
-<pre>
-    usage: findinit amr_final_output amr_initial_output cluster_file
-    or: findinit amr_output cluster_file
-    (cluster_file format: x y z r   in box units)
-</pre>
-    <p>&nbsp;</p>
-    <p><b><font size=+1>findpeaks</font></b></p>
-    <p>One of the two methods for finding density peaks (ie, halos) in an Enzo simulation.  
-      More information can be found <a href="analyze.html#Peakfinder">here</a>.  The output
-      is an ascii file with a user-specified filename (cluster_file) where there are halo
-      positions sorted by peak density.</p>
-
-<pre>    
-usage: findpeaks [options] amr_file cluster_file
-  options: -n # (number of peaks)
-           -m # (minimum density)
-           -s # (min peak separation, comoving Mpc)
-           -b   (use baryon density in peak seach, default)
-           -d   (use dark matter density in peak seach)
-           -p   (use potential in peak search)
-           -x   (use bolometric x-ray in peak seach)
-</pre>
-
-
-    <p>&nbsp;</p>
-    <p><b><font size=+1>enzohop</font></b></p>
-    <p>The second (and generally favored) method used for finding density peaks in an Enzo simulation.
-      More information can be found <a href="analyze.html#halofinder">here</a>.  A file called
-      HopAnalysis.out is output which contains halo position and mass information.</p>
-
-<pre>
-enzohop [-b #] [-f #] [-t #] [-g] [-d] amr_file
-  -b)egin region
-  -f)inish region
-  -t)hreshold for hop (default 160)
-  -g)as particles also used (normally just dm)
-  -d)ebug
-</pre>
-
-
-
-<p>&nbsp;</p>
-<p>&nbsp;</p>
-<p>
-<a href="../index.html">Go to the Enzo home page</a>
-</p>
-
-    <hr WIDTH="100%">
-<center>&copy; 2004 &nbsp; <a href="http://cosmos.ucsd.edu">Laboratory for Computational Astrophysics</a><br></center>
-    <center>last modified February 2004<br>
-      by <a href="mailto:bwoshea (AT) lanl.gov">B.W. O'Shea</a></center>
-    
-    
-  </body>
-</html>

doc/userguide/amr_guide/compile.html

-<html>
-<head>
-<link href="../enzo.css" rel="stylesheet" type="text/css">
-   <title>Enzo user's guide: compilation</title>
-</head>
-<body>
-<h1>Enzo user's guide: compilation</h1>
-
-    <h2>Compiling</h2>
-
-<p>For instructions on the basic make options, go to the top-level enzo directory and type:</p>
-
-<p>&nbsp;&nbsp;&nbsp;&nbsp;<tt>make help</tt></p>
-
-<p>
-On systems you may have to use <tt>gmake</tt> instead of <tt>make</tt>.  If you get
-errors complaining about the makefiles, try using the command <tt>gmake</tt>.
-The compilation process is fairly straightforward.  Enzo is already pre-configured to
-compile on most NCSA, SDSC and PSC machines.  While in the top-level directory, type:
-</p>
-
-<p>&nbsp;&nbsp;&nbsp;&nbsp;<tt>./configure</tt></p>
-<p>&nbsp;&nbsp;&nbsp;&nbsp;<tt>make</tt></p>
-<p>&nbsp;&nbsp;&nbsp;&nbsp;<tt>make install</tt></p>
-
-<p>
-All portions of the code should automatically compile and executables should
-be placed in the enzo-code/bin directory.  If you are compiling on non-NCSA machine you may have
-to add extra makefiles in the config directory to get the code to compile correctly.
-See the README in enzo-code/config for more information.  Instructions for
-adding makefiles to get enzo to compile on a machine
-type/architecture that isn't explicitly supported will be added at a later date.</p>
-
-<p>The general philosophy of enzo is that all options are specified in the
-parameter file at run-time, so that once the code is compiled it does not need
-to be recompiled to run another problem or change a parameter.  There are some
-compiler-time parameters, which can be seen by typing:</p>
-
-<p>&nbsp;&nbsp;&nbsp;&nbsp;<tt>make help-config</tt></p>
-
-<p>This allows the user to specify the specific machine, the
-desired precision of the code, the version of HDF, and various timing 
-and optimization settings.  The code is parallelized using MPI, so 
-compiler-based parallelization is NOT recommended.</p>
-
-
-<p>&nbsp;</p>
-<p><a href="../index.html">Go to the Enzo home page</a></p>
-
-<hr WIDTH="100%">
-<center>&copy; 2004 &nbsp; <a href="http://cosmos.ucsd.edu">Laboratory for Computational Astrophysics</a><br></center>
-<center>last modified February 2004<br>
-by <a href="mailto:bwoshea (AT) lanl.gov">B.W. O'Shea</a></center>
-
-</body>
-</html>

doc/userguide/amr_guide/cosmo.html

-Initializing and Running a Cosmology Simulation
-
-The initial conditions for a cosmology simulation can be conveniently generated with the inits package, described below.  The resulting files can then be read by the Enzo code using the CosmologySimulation problem type.
-
-<ul>
-<item><aref=inits_compile.html>Compiling the inits package</a>
-<item><aref=inits_parameters.html>Setting the inits parameter file</a>
-<item><aref=inits_running.html>Running inits</a>
-<item><aref=cosmo_sim.html>Setting up a cosmology simulation</a>
-<item><aref=cosmo_run.html>Runing a cosmology simulation</a>
-<item><aref=project.html>Analyzing the output: projections</a>
-<item><aref=extract.html>Analyzing the o