FLASH User's Guide Version 2.2 November 2002 ASCI FLASH Center University of Chicago i Acknowledgments The FLASH Code Group is supported by the ASCI FLASH Center at the University of Chicago under U. S. Department of Energy contract B341495. Some of the test calculations described here were performed using the Origin 2000 computer at Argonne National Laboratory and the ASCI Nirvana computer at Los Alamos National Laboratory. Contents I Getting Started 1 1 Introduction 3 1.1 What's new in FLASH 2.2 . 3 1.2 About the user's guide . 4 2 Quick start 5 2.1 System requirements . 5 2.2 Unpacking and con¯guring FLASH for quick start . 6 2.3 Running FLASH . 8 3 The FLASH con¯guration script (setup) 11 4 Creating new problems 15 4.1 Creating a Config ¯le . 15 4.2 Creating an init block.F90 . 16 4.3 The runtime parameter ¯le (flash.par) . 22 II Structure and Modules 25 5 Overview of FLASH architecture 27 5.1 Structure of a FLASH module . 27 5.1.1 Con¯guration layer . 27 5.1.2 Interface layer and database module . 29 5.1.3 Algorithms . 41 5.2 The FLASH source tree . 41 5.2.1 Code infrastructure . 42 5.3 Modules included with FLASH: a brief overview . 44 6 Driver modules 47 6.1 Delta-formulation and Strang-state driver modules . 49 6.1.1 The euler1 module . 50 6.1.2 The rk3 module . 51 6.1.3 strang state and strang delta modules . 51 6.1.4 New formulation modules . 52 6.2 Simulation services . 54 6.2.1 Runtime parameters . 54 6.2.2 Physical constants . 56 6.2.3 Monitoring performance . 57 6.2.4 Pro¯ling with Jumpshot or Vampir . 58 6.2.5 Log ¯le maintenance . 58 iii iv CONTENTS 7 FLASH I/O modules and output formats 61 7.1 General parameters . 62 7.1.1 Output ¯le names . 64 7.2 Restarting a simulation . 64 7.3 Output formats . 65 7.3.1 HDF . 65 7.3.2 HDF5 . 69 7.4 Working with output ¯les . 73 7.5 User-de¯ned variables . 73 8 Mesh module 75 8.1 Adaptive mesh re¯nement (AMR) . 76 8.1.1 Algorithm . 76 8.1.2 Usage . 76 8.1.3 Choice of grid geometry . 80 8.1.4 Using a uniform grid in PARAMESH . 83 8.1.5 Boundary conditions . 84 8.1.6 Modifying the re¯nement criteria with MarkRefLib . 84 8.2 Uniform grid . 85 8.2.1 Algorithm . 85 8.2.2 Usage . 85 9 Hydrodynamics modules 87 9.1 The piecewise-parabolic method (PPM) . 89 9.1.1 Algorithm . 89 9.1.2 Usage . 90 9.1.3 Di®usion . 90 9.2 The Kurganov hydrodynamics module . 92 9.2.1 Algorithm . 92 9.2.2 Usage . 93 9.3 The magnetohydrodynamics module . 95 9.3.1 Description . 95 9.3.2 Algorithm . 95 9.3.3 New features . 97 10 Material properties modules 99 10.1 The multifluid database . 99 10.2 Equations of state . 102 10.2.1 Algorithm . 102 10.2.2 Usage . 104 10.3 Compositions . 106 10.3.1 Fuel plus ash mixture (fuel+ash) . 107 10.3.2 Minimal seven-isotope alpha-chain model (iso7) . 107 10.3.3 Thirteen-isotope alpha-chain model (aprox13) . 108 10.3.4 Nineteen-isotope alpha-chain model (aprox19) . 108 10.3.5 Proton-proton/CNO network model (ppcno) . 109 10.3.6 Proton-electron plasma composition (prot+elec) . 109 10.3.7 Multi-ion plasma composition (ioniz) . 110 10.4 Thermal conductivity . 110 10.4.1 Stellar thermal conductivity . 110 10.4.2 Spitzer thermal conductivity . 111 10.5 Viscosity . 111 10.5.1 Spitzer viscosity . 111 10.6 Magnetic resistivity and viscosity . 111 CONTENTS v 10.6.1 Constant resistivity . 111 10.6.2 Spitzer resistivity . 112 11 Local source terms 113 11.1 The nuclear burning module . 113 11.1.1 Detecting shocks . 114 11.1.2 Algorithms . 114 11.1.3 Energy generation rates and reaction rates . 119 11.2 Ionization . 120 11.2.1 Algorithms . 120 11.2.2 Usage . 121 11.3 Stirring . 121.