Changes between Version 22 and Version 23 of AccretionDiskTutorial

Timestamp:

08/29/12 14:26:09 (12 years ago)

Author:

idilernia

Comment:

—

AccretionDiskTutorial

@@ -21 +21 @@
 == Getting familiar with the module ==
 
-After checking that the disk module compiles and runs without any issues, you can examine the chombo files created by the first run of this module.[[BR]][[BR]]
-If you have no experience on visualization tools, the page [https://clover.pas.rochester.edu/trac/astrobear/wiki/VisItBasics VisIt Basics] is a good resource to learn the fundamentals of it.[[BR]][[BR]]
+After checking that the disk module compiles and runs without any issues, you can examine the chombo files created by this first run.[[BR]][[BR]]
+If you have no experience in visualization tools, the page [https://clover.pas.rochester.edu/trac/astrobear/wiki/VisItBasics VisIt Basics] is a good resource to learn the fundamentals of it.[[BR]][[BR]]
 The following image is a density plot of the disk at time ''t=0'', a log scale has been applied to these perpendicular and parallel slices.
 
@@ -38 +38 @@
 == Initial Conditions ==
 
-Now you can proceed to examine ''problem.data'' contained in the ''!BasicDisk'' folder.
+Now you can proceed to examine ''problem.data'' contained in the ''!BasicDisk'' folder.[[BR]]
 The default problem.data file contains a list of initial conditions that can be changed depending on the user's needs, let's analyze some of them
 
@@ -51 +51 @@
 '''Note:''' for this specific module, all the values reported in ''problem.data'' are in physical units.
 
-Sometimes it can be useful to change the size of the physical boundaries of the simulation, this can be done by modifying the section below contained in ''global.data''
+Sometimes it can be useful to change the size of the physical boundaries of the simulation, this can be done by changing the section below contained in ''global.data'' :
 {{{
 GxBounds          = -10.d0,         ! Problem boundaries in computational units.
@@ -117 +117 @@
 
 Softening is a numerical trick commonly used in simulations to prevent divergences when a particle comes close to another and the force of gravity goes to infinity.[[BR]]
-In our case, as the disk radius gets smaller, the force of gravity is approximated to a well defined value.[[BR]]
+In our case, softening approximates the force of gravity to a well defined value as the disk radius gets smaller.[[BR]]
 
 Problem.data provides a field in which the user can set the preferred softening parameter:
@@ -157 +157 @@
 In this specific module refining is accomplished by defining a region around the disk that will always be marked for refinement. For more information on how this is done please visit [https://clover.pas.rochester.edu/trac/astrobear/wiki/ControllingRefinement Controlling Refinement in AstroBEAR 2.0].[[BR]]
 
-Below is an image of what the mesh looks like in the default module:
+Below is an image of our mesh in the default module:
 
 [[Image(visit0040.png, 400px)]]
 
-A subroutine named ''!ProblemSetErrFlag'' in ''problem.f90'' is responsible for marking the regions for refinement and giving the mesh the pattern seen above. [[BR]][[BR]]
-Depending on the initial conditions of a specific run it may be the case that a disk undergoes gravitational collapse and its boundaries can expand within reasonable limits. This event can cause a significant part of the disk to outflow the refined area.
+A subroutine named ''!ProblemSetErrFlag'' in ''problem.f90'' is responsible for marking the regions for refinement and giving the pattern seen above. [[BR]][[BR]]
+Depending on the initial conditions of a specific run it may be the case that a disk undergoes gravitational collapse and its boundaries can expand within reasonable limits. This event can cause part of the disk to outflow the refined area.
 
 ''!ProblemSetErrFlag'' can be altered to address this issue. By changing the following line
@@ -178 +178 @@
 we can increase the radius in which additional refinement in enabled.
 
-Here is a comparison of our mesh before and after the change above.[[BR]]
+Here is a comparison of our mesh before and after this change.[[BR]]
 [[Image(refinement.png, 800px)]]
 
-'''Note:''' You need to recompile AstroBEAR after making any changes to problem.f90
+'''Notes:''' 
+- You need to recompile AstroBEAR after making any changes to problem.f90
+- Keep in mind that increasing the refined region also increases computational time
 
 [[BR]]
@@ -189 +191 @@
 When setting up a new simulation it is good practice to check that the Mach values are below a certain threshold, in most of numerical simulations this value is ~60. [[BR]]Values above this threshold may create difficulties in evolving a model and therefore create computational errors.
 [[BR]][[BR]]
-To plot the Mach numbers in Visit you can check [https://clover.pas.rochester.edu/trac/astrobear/wiki/VisIt Chombo expressions] and locate Mach in the list. [[BR]][[BR]]
+To plot the Mach numbers in Visit you can check [https://clover.pas.rochester.edu/trac/astrobear/wiki/VisIt Chombo expressions] and locate ''Mach'' in the expression list. [[BR]][[BR]]
 The plot below represents a disk simulation that respects the limits stated above:[[BR]]
 [[Image(mach.png, 500px)]]
@@ -195 +197 @@
 == Additional parameters  ==
 
-Now that you have acquired the essential knowledge to set up your disk module, you should be capable to change other aspects of a simulation such as:[[BR]]
+Now that you have acquired the essential knowledge to set up your disk module, you should be capable to make other changes such as:[[BR]]
 - Equation of state
 - Solvers