New version of paper2_examples

paper2_examples/README.md

@@ -1,10 +1,18 @@
-The code in this repository supplements a paper that is currently in production.
 
+# Computational Experiments to accompany the paper
 
-## Computational Experiments for the paper Analysis and Performance Evaluation of Adjoint-Guided Adaptive Mesh Refinement Using Clawpack
+###  "Analysis and Performance Evaluation of Adjoint-Guided Adaptive Mesh Refinement Using Clawpack" 
 
-The code in this repository supplements the paper (currently in production): "Analysis and Performance Evaluation of Adjoint-Guided Adaptive Mesh Refinement Using Clawpack."
+by Brisa N. Davis and Randall J. LeVeque
 
+This version goes with version 2 of the paper, currently submitted for publication.
+
+Check out the `paper2v1` branch for the version of the code that accompanies the original preprint https://arxiv.org/abs/1810.00927. 
+
+This version is updated in the following ways:
+ - It uses Clawpack v5.6.1, which has the adjoint flagging now built in.
+ - Example 1 from the original paper has been dropped from v2 of the paper, so the subdirectories have been renamed.
+
 The code is designed to work with the Clawpack 5 software. For more information visit 
 [the Clawpack webpage](http://www.clawpack.org/ ). 
 The Clawpack software is open source, and the code is openly available at 
@@ -18,10 +26,10 @@ the use of the adjoint method for guiding adaptive mesh refinement in Clawpack i
 
 * gfortran 5.0.0
 * python 2.7.10
-* clawpack 5.3.0 : [Clawpack](http://www.clawpack.org/ )
+* clawpack 5.6.1 : [Clawpack](http://www.clawpack.org/ )
 * git: to clone this repository
 
-Note: Clawpack 5.0 or higher is required, other versions of gfortran and python might work as well.
+Note: Later versions of Clawpack should work, other versions of gfortran and python might work as well.
 
 **Operating system.**
 
@@ -30,24 +38,24 @@ Note: Clawpack 5.0 or higher is required, other versions of gfortran and python
 
 ### Examples Included and Folder Organization
 
-* **acoustics_1d_ex1:** contains the code to run the first one-dimensional variable coefficients 
-linear acoustics equations example. 
+* **acoustics_1d_ex1_old:** contains the code to run the first one-dimensional variable coefficients 
+linear acoustics example from v1 of the paper, not used in v2 of the paper.
 The internal folder: **adjoint**, contains the code for the adjoint problem. 
 
-* **acoustics_1d_ex2:** contains the code to run the second one-dimensional variable coefficients 
-linear acoustics equations example. 
+* **acoustics_1d_example1:** contains the code to run the one-dimensional variable coefficients 
+linear acoustics example that is Example 1 in v2 of the paper. 
 The internal folder: **adjoint**, contains the code for the adjoint problem. 
 
-* **acoustics_2d_ex1:** contains the code to run the first two-dimensional variable coefficients 
-linear acoustics equations example. 
+* **acoustics_2d_example2:** contains the code to run the first two-dimensional variable coefficients 
+linear acoustics problem that is Example 2 in v2 of the paper.
 The internal folder: **adjoint**, contains the code for the adjoint problem. 
 
-* **acoustics_2d_ex2:** contains the code to run the second two-dimensional variable coefficients 
-linear acoustics equations example. 
+* **acoustics_2d_example3:** contains the code to run the second two-dimensional variable coefficients 
+linear acoustics problem that is Example 3 in v2 of the paper.
 The internal folder: **adjoint**, contains the code for the adjoint problem. 
 
 ### Running the Code
-* **Install Clawpack 5.3.0:**
+* **Install Clawpack 5.6.1:**
 - Go to: http://www.clawpack.org/installing.html#installation-instructions
 - Follow the download and installation intructions in the section: Install all Clawpack packages 
 - Follow the setup instructions in the section: Set environment variables.
@@ -60,9 +68,11 @@ The internal folder: **adjoint**, contains the code for the adjoint problem.
 - Create a copy of the adjoint repository by running the code:
 
 ```
-git://github.com/BrisaDavis/adjoint.git
+    git clone https://github.com/clawpack/adjoint.git
+    cd adjoint
+    git checkout paper2v2
 ```
 
 * **Run the code**
 
-* Go any of the folders and follow the instructions in the README.md in that folder.
+* Go any of the folders in `paper2_examples` and follow the instructions in the README.md in that folder.

paper2_examples/acoustics_1d_ex2/Makefile → paper2_examples/acoustics_1d_ex1_old/Makefile

@@ -31,8 +31,8 @@ FFLAGS ?=
 # package sources for this program:
 # ---------------------------------
 
-AMRLIB = $(CLAW)/amrclaw/src/1d_adjoint
-include $(AMRLIB)/Makefile.adjoint_amr_1d
+AMRLIB = $(CLAW)/amrclaw/src/1d
+include $(AMRLIB)/Makefile.amr_1d
 
 # ---------------------------------------
 # package sources specifically to exclude

paper2_examples/acoustics_1d_ex1/README.md → paper2_examples/acoustics_1d_ex1_old/README.md

@@ -1,4 +1,6 @@
-This code produces Example 1, the first one-dimensional variable coefficient acoustics example, presented in ''Analysis and Performance Evaluation of Adjoint-Guided Adaptive Mesh Refinement Using Clawpack''.
+This code was for the original Example 1, the first one-dimensional variable
+coefficient acoustics example, presented in the preprint version of
+''Analysis and Performance Evaluation of Adjoint-Guided Adaptive Mesh Refinement Using Clawpack''.
 
 ### Folder Organization
 * **adjoint:**

paper2_examples/acoustics_1d_ex2/setaux.f → paper2_examples/acoustics_1d_ex1_old/setaux.f

@@ -22,10 +22,15 @@ subroutine setaux(mbc,mx,xlower,dx,maux,aux)
       common /comaux/ Zl, cl, Zr, cr
       double precision Zl, cl, Zr, cr
 
-      integer i,ii
+      integer i
       double precision xcell
 
       do i=1-mbc,mx+mbc
+
+         if (aux(1,i) .eq. NEEDS_TO_BE_SET) then
+            aux(innerprod_index,i) = 0.d0
+         endif
+
          xcell = xlower + (i-0.5d0)*dx
          if (xcell .lt. 0.0d0) then
             aux(1,i) = Zl
@@ -36,10 +41,5 @@ subroutine setaux(mbc,mx,xlower,dx,maux,aux)
          endif
       enddo
 
-      ! Initialize innerproduct to zero.
-      do ii=1-mbc,mx+mbc
-          aux(innerprod_index,ii) = 0.d0
-      enddo
-
       return
       end