Clawpack git diffs...

===========
classic
===========
/Users/mandli/src/clawpack/classic

diff --git a/examples/acoustics_1d_example1/qinit.f90 b/examples/acoustics_1d_example1/qinit.f90
index 945d91f..b7b0fbf 100644
--- a/examples/acoustics_1d_example1/qinit.f90
+++ b/examples/acoustics_1d_example1/qinit.f90
@@ -16,6 +16,7 @@ subroutine qinit(meqn,mbc,mx,xlower,dx,q,maux,aux)
     real(kind=8) :: beta, xcell
     common /cqinit/ beta
  
+     print *, "stuff"
  
       do i=1,mx
          xcell = xlower + (i-0.5d0)*dx


===========
amrclaw
===========
/Users/mandli/src/clawpack/amrclaw

diff --git a/examples/acoustics_1d_heterogeneous/setrun.py b/examples/acoustics_1d_heterogeneous/setrun.py
index 7296715..71d84dc 100644
--- a/examples/acoustics_1d_heterogeneous/setrun.py
+++ b/examples/acoustics_1d_heterogeneous/setrun.py
@@ -127,7 +127,7 @@ def setrun(claw_pkg='amrclaw'):
         clawdata.output_t0 = True  # output at initial (or restart) time?
         
 
-    clawdata.output_format = 'ascii'      # 'ascii', 'binary', 'netcdf'
+    clawdata.output_format = 'binary'      # 'ascii', 'binary', 'netcdf'
 
     clawdata.output_q_components = 'all'   # could be list such as [True,True]
     clawdata.output_aux_components = 'none'  # could be list
diff --git a/examples/advection_2d_swirl/Makefile b/examples/advection_2d_swirl/Makefile
index d42491c..87ee3cb 100644
--- a/examples/advection_2d_swirl/Makefile
+++ b/examples/advection_2d_swirl/Makefile
@@ -24,7 +24,8 @@ OVERWRITE ?= True                   # False ==> make a copy of OUTDIR first
 # Environment variable FC should be set to fortran compiler, e.g. gfortran
 
 # Compiler flags can be specified here or set as an environment variable
-FFLAGS ?=  
+FFLAGS += -DHDF5 -I$(HDF5_DIR)/include
+LFLAGS += -lhdf5
 
 # ---------------------------------
 # package sources for this program:
diff --git a/examples/advection_2d_swirl/setplot.py b/examples/advection_2d_swirl/setplot.py
index e8ddce6..91ac681 100644
--- a/examples/advection_2d_swirl/setplot.py
+++ b/examples/advection_2d_swirl/setplot.py
@@ -27,7 +27,7 @@ def setplot(plotdata=None):
         plotdata = ClawPlotData()
 
     plotdata.clearfigures()  # clear any old figures,axes,items data
-    
+    plotdata.format = 'binary'
 
     # Figure for pcolor plot
     plotfigure = plotdata.new_plotfigure(name='q[0]', figno=0)
diff --git a/examples/advection_2d_swirl/setrun.py b/examples/advection_2d_swirl/setrun.py
index 1091600..5aaae6f 100644
--- a/examples/advection_2d_swirl/setrun.py
+++ b/examples/advection_2d_swirl/setrun.py
@@ -127,7 +127,7 @@ def setrun(claw_pkg='amrclaw'):
         clawdata.output_t0 = True  # output at initial (or restart) time?
 
 
-    clawdata.output_format = 'ascii'       # 'ascii', 'binary', 'netcdf'
+    clawdata.output_format = 'binary'       # 'ascii', 'binary', 'netcdf'
 
     clawdata.output_q_components = 'all'    # only 'all'
     clawdata.output_aux_components = 'all'  # 'all' or 'none'


===========
clawutil
===========
/Users/mandli/src/clawpack/clawutil

diff --git a/src/python/clawutil/data.py b/src/python/clawutil/data.py
index d03aab6..a1ee6eb 100644
--- a/src/python/clawutil/data.py
+++ b/src/python/clawutil/data.py
@@ -21,6 +21,7 @@ except ImportError:
     from urllib2 import urlopen
 
 import tarfile
+import zipfile
 import string
 
 import numpy as np
diff --git a/src/python/clawutil/data.py b/src/python/clawutil/data.py
index 248d239..d03aab6 100644
--- a/src/python/clawutil/data.py
+++ b/src/python/clawutil/data.py
@@ -92,28 +92,40 @@ def get_remote_file(url, output_dir=None, file_name=None, force=False,
                 if verbose:
                     print("*** Aborting download.")
                 return None
-            
-        if not os.path.exists(output_path):
-            # Fetch remote file, will raise a variety of exceptions depending on
-            # the retrieval problem if it happens
-            if verbose:
-                print("Downloading %s to %s..." % (url, output_path))
-            with open(output_path, "wb") as output_file:
-                remote_file = urlopen(url)
-                output_file.write(remote_file.read())
-            if verbose:
-                print("Done downloading.")
-        elif verbose:
-            print("File already exists, not downloading")
+
+        # if not os.path.exists(output_path):
+        # Fetch remote file, will raise a variety of exceptions depending on
+        # the retrieval problem if it happens
+        if verbose:
+            print("Downloading %s to %s..." % (url, output_path))
+        with open(output_path, "wb") as output_file:
+            remote_file = urlopen(url)
+            output_file.write(remote_file.read())
+        if verbose:
+            print("Done downloading.")
 
         if tarfile.is_tarfile(output_path) and unpack:
             if verbose:
-                print("Un-archiving %s to %s..." % (output_path, 
+                print("Un-archiving %s to %s..." % (output_path,
                                                     unarchived_output_path))
             with tarfile.open(output_path, mode="r:*") as tar_file:
                 tar_file.extractall(path=output_dir)
             if verbose:
                 print("Done un-archiving.")
+
+        elif zipfile.is_zipfile(output_path) and unpack:
+            if verbose:
+                print("Un-archiving %s to %s..." % (output_path,
+                                                    unarchived_output_path))
+            with zipfile.ZipFile(output_path, mode="r") as zip_file:
+                zip_file.extractall(path=output_dir)
+                # Add file suffix
+                extension = os.path.splitext(zip_file.namelist()[0])[-1]
+                unarchived_output_path = "".join((unarchived_output_path,
+                                                  extension))
+            if verbose:
+                print("Done un-archiving.")
+
     else:
         if verbose:
             print("Skipping %s " % url)


===========
pyclaw
===========
/Users/mandli/src/clawpack/pyclaw



===========
visclaw
===========
/Users/mandli/src/clawpack/visclaw



===========
riemann
===========
/Users/mandli/src/clawpack/riemann



===========
geoclaw
===========
/Users/mandli/src/clawpack/geoclaw

diff --git a/tests/multilayer/qinit_module.f90 b/tests/multilayer/qinit_module.f90
index b7182fb..8a637f8 100644
--- a/tests/multilayer/qinit_module.f90
+++ b/tests/multilayer/qinit_module.f90
@@ -35,10 +35,75 @@ module qinit_module
 
 contains
 
+    subroutine set_qinit(fname)
+    
+        use geoclaw_module, only: GEO_PARM_UNIT
+    
+        implicit none
+        
+        ! Subroutine arguments
+        character(len=*), optional, intent(in) :: fname
+        
+        ! File handling
+        character(len=150) :: qinit_fname
+        integer, parameter :: unit = 7
+        character(len=150) :: x
+        
+        if (.not.module_setup) then
+
+            write(GEO_PARM_UNIT,*) ' '
+            write(GEO_PARM_UNIT,*) '--------------------------------------------'
+            write(GEO_PARM_UNIT,*) 'SETQINIT:'
+            write(GEO_PARM_UNIT,*) '-------------'
+            
+            ! Open the data file
+            if (present(fname)) then
+                call opendatafile(unit,fname)
+            else
+                call opendatafile(unit,"qinit.data")
+            endif
+            
+            read(unit,"(i1)") qinit_type
+            if (qinit_type == 0) then
+                ! No perturbation specified
+                write(GEO_PARM_UNIT,*)  '  qinit_type = 0, no perturbation'
+                print *,'  qinit_type = 0, no perturbation'
+                return
+            else if (qinit_type > 0 .and. qinit_type < 5) then
+                read(unit,*) qinit_fname
+                read(unit,"(2i2)") min_level_qinit, max_level_qinit
+
+                write(GEO_PARM_UNIT,*) '   min_level, max_level, qinit_fname:'
+                write(GEO_PARM_UNIT,*)  min_level_qinit, max_level_qinit, qinit_fname
+                
+                call read_qinit(qinit_fname)
+            else if (qinit_type >= 5) then
+                read(unit,*) epsilon
+                read(unit,*) init_location
+                read(unit,*) wave_family
+                read(unit,*) angle
+                read(unit,*) sigma
+
+                write(GEO_PARM_UNIT,*) " epsilon = ",  epsilon
+                write(GEO_PARM_UNIT,*) " init_location = ",  init_location
+                write(GEO_PARM_UNIT,*) " wave_family = ",  wave_family
+                write(GEO_PARM_UNIT,*) " angle = ",  angle
+                write(GEO_PARM_UNIT,*) " sigma = ",  sigma
+            endif
+
+            close(unit)
+
+            module_setup = .true.
+        end if
+
+    end subroutine set_qinit
+
+
+
     subroutine add_perturbation(meqn,mbc,mx,my,xlower,ylower,dx,dy,q,maux,aux)
     
         use geoclaw_module, only: sea_level, pi, g => grav, rho
-        use multilayer_module, only: aux_layer_index, r
+        use multilayer_module, only: aux_layer_index, r, eta_init
     
         implicit none
     
@@ -52,181 +117,113 @@ contains
         integer :: i,j
         real(kind=8) :: ximc,xim,x,xc,xip,xipc,yjmc,yjm,y,yc,yjp,yjpc,dq
 
-        real(kind=8) :: xmid,m,x_c,y_c
+        real(kind=8) :: xmid,m,x_c,y_c, effective_b
         real(kind=8) :: eigen_vector(6),gamma,lambda,alpha,h_1,h_2,deta
         
         ! Topography integral function
         real(kind=8) :: topointegral
-        
-        if (.not.module_setup) then
-            if (qinit_type > 0 .and. qinit_type < 5) then
-                do i=1-mbc,mx+mbc
-                    x = xlower + (i-0.5d0)*dx
-                    xim = x - 0.5d0*dx
-                    xip = x + 0.5d0*dx
-                    do j=1-mbc,my+mbc
-                        y = ylower + (j-0.5d0)*dy
-                        yjm = y - 0.5d0*dy
-                        yjp = y + 0.5d0*dy
 
-                        ! Check to see if we are in the qinit region at this grid point
-                        if ((xip > x_low_qinit).and.(xim < x_hi_qinit).and.  &
-                            (yjp > y_low_qinit).and.(yjm < y_hi_qinit)) then
+        if (qinit_type == 4) then
+            do i = 1-mbc, mx+mbc
+                x = xlower + (i - 0.5d0)*dx
+                xim = x - 0.5d0 * dx
+                xip = x + 0.5d0 * dx
+                do j = 1-mbc, my+mbc
+                    y = ylower + (j - 0.5d0) * dy
+                    yjm = y - 0.5d0 * dy
+                    yjp = y + 0.5d0 * dy
 
-                            xipc=min(xip,x_hi_qinit)
-                            ximc=max(xim,x_low_qinit)
-                            xc=0.5d0*(xipc+ximc)
+                    ! Check to see if we are in the qinit region at this grid point
+                    if ((xip > x_low_qinit).and.(xim < x_hi_qinit).and.  &
+                        (yjp > y_low_qinit).and.(yjm < y_hi_qinit)) then
 
-                            yjpc=min(yjp,y_hi_qinit)
-                            yjmc=max(yjm,y_low_qinit)
-                            yc=0.5d0*(yjmc+yjpc)
+                        xipc = min(xip, x_hi_qinit)
+                        ximc = max(xim, x_low_qinit)
 
-                            dq = topointegral(ximc,xc,xipc,yjmc,yc,yjpc,x_low_qinit, &
-                                              y_low_qinit,dx_qinit,dy_qinit,mx_qinit, &
-                                              my_qinit,qinit,1)
-                            dq = dq / ((xipc-ximc)*(yjpc-yjmc)*aux(2,i,j))
+                        yjpc=min(yjp,y_hi_qinit)
+                        yjmc=max(yjm,y_low_qinit)
 
-                            if (qinit_type < 4) then 
-                                if (aux(1,i,j) <= sea_level) then
-                                    q(qinit_type,i,j) = q(qinit_type,i,j) + dq
-                                endif
-                            else if (qinit_type == 4) then
-                                q(1,i,j) = max(dq-aux(1,i,j),0.d0)
-                            endif
-                        endif
-                    enddo
+                        dq = topointegral(ximc,xipc,yjmc,yjpc,x_low_qinit, &
+                                          y_low_qinit,dx_qinit,dy_qinit,mx_qinit, &
+                                          my_qinit,qinit,1)
+                        dq = dq / ((xipc-ximc)*(yjpc-yjmc))
+
+                        effective_b = max(aux(1,i,j), eta_init(2))
+                        q(1,i,j) = max((dq-effective_b) * rho(1),0.d0)
+                    endif
                 enddo
-            else if (qinit_type > 4) then
-                do i=1,mx
-                    x = xlower + (i - 0.5d0) * dx
-                    do j=1,my
-                        y = ylower + (j - 0.5d0) * dy
-                        
-                        ! Test perturbations - these only work in the x-direction
-                        if (qinit_type == 5 .or. qinit_type == 6) then
-                            ! Calculate wave family for perturbation
-                            gamma = aux(aux_layer_index+1,i,j) / aux(aux_layer_index,i,j)
-                            select case(wave_family)
-                                case(1) ! Shallow water, left-going
-                                    alpha = 0.5d0 * (gamma - 1.d0 + sqrt((gamma-1.d0)**2+4.d0*r*gamma))
-                                    lambda = -sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
-                                case(2) ! Internal wave, left-going
-                                    alpha = 0.5d0 * (gamma - 1.d0 - sqrt((gamma-1.d0)**2+4.d0*r*gamma))
-                                    lambda = -sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
-                                case(3) ! Internal wave, right-going
-                                    alpha = 0.5d0 * (gamma - 1.d0 - sqrt((gamma-1.d0)**2+4.d0*r*gamma))
-                                    lambda = sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
-                                case(4) ! Shallow water, right-going
-                                    alpha = 0.5d0 * (gamma - 1.d0 + sqrt((gamma-1.d0)**2+4.d0*r*gamma))
-                                    lambda = sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
-                            end select
-                            eigen_vector = [1.d0,lambda,0.d0,alpha,lambda*alpha,0.d0]
+            enddo
 
-                            if (qinit_type == 5) then
-                                ! Add perturbation
-                                if ((x < init_location(1)).and.(wave_family >= 3)) then
-                                    q(1:3,i,j) = q(1:3,i,j) + rho(1) * epsilon * eigen_vector(1:3)
-                                    q(4:6,i,j) = q(4:6,i,j) + rho(2) * epsilon * eigen_vector(4:6)
-                                else if ((x > init_location(1)).and.(wave_family < 3)) then
-                                    q(1:2,i,j) = q(1:2,i,j) + rho(1) * epsilon * eigen_vector(1:2)
-                                    q(4:5,i,j) = q(4:5,i,j) + rho(2) * epsilon * eigen_vector(4:5)
-                                endif
-                            ! Gaussian wave along a direction on requested wave family
-                            else if (qinit_type == 6) then
-                                ! Transform back to computational coordinates
-                                x_c = x * cos(angle) + y * sin(angle) - init_location(1)
-                                deta = epsilon * exp(-(x_c/sigma)**2)
-                                q(1,i,j) = q(1,i,j) + rho(1) * deta
-                                q(4,i,j) = q(4,i,j) + rho(2) * alpha * deta
-                            endif
-                        ! Symmetric gaussian hump
-                        else if (qinit_type == 7) then
-                            deta = epsilon * exp(-((x-init_location(1))/sigma)**2)  &
-                                           * exp(-((y-init_location(2))/sigma)**2)
-                            q(1,i,j) = q(1,i,j) + rho(1) * deta
-                        ! Shelf conditions from AN paper
-                        else if (qinit_type == 8) then
-                            alpha = 0.d0
-                            xmid = 0.5d0*(-180.e3 - 80.e3)
-                            if ((x > -130.e3).and.(x < -80.e3)) then
-                                deta = epsilon * sin((x-xmid)*pi/(-80.e3-xmid))
-                                q(4,i,j) = q(4,i,j) + rho(2) * alpha * deta
-                                q(1,i,j) = q(1,i,j) + rho(1) * deta * (1.d0 - alpha)
+        else if (qinit_type > 4) then
+            do i=1,mx
+                x = xlower + (i - 0.5d0) * dx
+                do j=1,my
+                    y = ylower + (j - 0.5d0) * dy
+                    
+                    ! Test perturbations - these only work in the x-direction
+                    if (qinit_type == 5 .or. qinit_type == 6) then
+                        ! Calculate wave family for perturbation
+                        gamma = aux(aux_layer_index+1,i,j) / aux(aux_layer_index,i,j)
+                        select case(wave_family)
+                            case(1) ! Shallow water, left-going
+                                alpha = 0.5d0 * (gamma - 1.d0 + sqrt((gamma-1.d0)**2+4.d0*r*gamma))
+                                lambda = -sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
+                            case(2) ! Internal wave, left-going
+                                alpha = 0.5d0 * (gamma - 1.d0 - sqrt((gamma-1.d0)**2+4.d0*r*gamma))
+                                lambda = -sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
+                            case(3) ! Internal wave, right-going
+                                alpha = 0.5d0 * (gamma - 1.d0 - sqrt((gamma-1.d0)**2+4.d0*r*gamma))
+                                lambda = sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
+                            case(4) ! Shallow water, right-going
+                                alpha = 0.5d0 * (gamma - 1.d0 + sqrt((gamma-1.d0)**2+4.d0*r*gamma))
+                                lambda = sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
+                        end select
+                        eigen_vector = [1.d0,lambda,0.d0,alpha,lambda*alpha,0.d0]
+
+                        if (qinit_type == 5) then
+                            ! Add perturbation
+                            if ((x < init_location(1)).and.(wave_family >= 3)) then
+                                q(1:3,i,j) = q(1:3,i,j) + rho(1) * epsilon * eigen_vector(1:3)
+                                q(4:6,i,j) = q(4:6,i,j) + rho(2) * epsilon * eigen_vector(4:6)
+                            else if ((x > init_location(1)).and.(wave_family < 3)) then
+                                q(1:2,i,j) = q(1:2,i,j) + rho(1) * epsilon * eigen_vector(1:2)
+                                q(4:5,i,j) = q(4:5,i,j) + rho(2) * epsilon * eigen_vector(4:5)
                             endif
-                        ! Inundation test
-                        else if (qinit_type == 9) then
-                            x_c = (x - init_location(1)) * cos(angle) &
-                                + (y - init_location(2)) * sin(angle)
+                        ! Gaussian wave along a direction on requested wave family
+                        else if (qinit_type == 6) then
+                            ! Transform back to computational coordinates
+                            x_c = x * cos(angle) + y * sin(angle) - init_location(1)
                             deta = epsilon * exp(-(x_c/sigma)**2)
                             q(1,i,j) = q(1,i,j) + rho(1) * deta
+                            q(4,i,j) = q(4,i,j) + rho(2) * alpha * deta
                         endif
-                    enddo
+                    ! Symmetric gaussian hump
+                    else if (qinit_type == 7) then
+                        deta = epsilon * exp(-((x-init_location(1))/sigma)**2)  &
+                                       * exp(-((y-init_location(2))/sigma)**2)
+                        q(1,i,j) = q(1,i,j) + rho(1) * deta
+                    ! Shelf conditions from AN paper
+                    else if (qinit_type == 8) then
+                        alpha = 0.d0
+                        xmid = 0.5d0*(-180.e3 - 80.e3)
+                        if ((x > -130.e3).and.(x < -80.e3)) then
+                            deta = epsilon * sin((x-xmid)*pi/(-80.e3-xmid))
+                            q(4,i,j) = q(4,i,j) + rho(2) * alpha * deta
+                            q(1,i,j) = q(1,i,j) + rho(1) * deta * (1.d0 - alpha)
+                        endif
+                    ! Inundation test
+                    else if (qinit_type == 9) then
+                        x_c = (x - init_location(1)) * cos(angle) &
+                            + (y - init_location(2)) * sin(angle)
+                        deta = epsilon * exp(-(x_c/sigma)**2)
+                        q(1,i,j) = q(1,i,j) + rho(1) * deta
+                    endif
                 enddo
+            enddo
 
-            endif
-
-            module_setup = .true.
-        end if
-        
-    end subroutine add_perturbation
-
-
-    subroutine set_qinit(fname)
-    
-        use geoclaw_module, only: GEO_PARM_UNIT
-    
-        implicit none
-        
-        ! Subroutine arguments
-        character(len=*), optional, intent(in) :: fname
-        
-        ! File handling
-        integer, parameter :: unit = 7
-        character(len=150) :: qinit_fname
-        
-        write(GEO_PARM_UNIT,*) ' '
-        write(GEO_PARM_UNIT,*) '--------------------------------------------'
-        write(GEO_PARM_UNIT,*) 'SETQINIT:'
-        write(GEO_PARM_UNIT,*) '-------------'
-        
-        ! Open the data file
-        if (present(fname)) then
-            call opendatafile(unit,fname)
-        else
-            call opendatafile(unit,"qinit.data")
         endif
         
-        read(unit,"(i1)") qinit_type
-        if (qinit_type == 0) then
-            ! No perturbation specified
-            write(GEO_PARM_UNIT,*)  '  qinit_type = 0, no perturbation'
-            print *,'  qinit_type = 0, no perturbation'
-            return
-        else if (qinit_type > 0 .and. qinit_type < 5) then
-            read(unit,*) qinit_fname
-            read(unit,"(2i2)") min_level_qinit, max_level_qinit
-
-            write(GEO_PARM_UNIT,*) '   min_level, max_level, qinit_fname:'
-            write(GEO_PARM_UNIT,*)  min_level_qinit, max_level_qinit, qinit_fname
-            
-            call read_qinit(qinit_fname)
-        else if (qinit_type >= 5) then
-            read(unit,*) epsilon
-            read(unit,*) init_location
-            read(unit,*) wave_family
-            read(unit,*) angle
-            read(unit,*) sigma
-
-            write(GEO_PARM_UNIT,*) " epsilon = ",  epsilon
-            write(GEO_PARM_UNIT,*) " init_location = ",  init_location
-            write(GEO_PARM_UNIT,*) " wave_family = ",  wave_family
-            write(GEO_PARM_UNIT,*) " angle = ",  angle
-            write(GEO_PARM_UNIT,*) " sigma = ",  sigma
-        endif
-
-        close(unit)
-
-    end subroutine set_qinit
+    end subroutine add_perturbation
 
         
     ! currently only supports one file type:
diff --git a/tests/multilayer/regression_data/claw_git_status.txt b/tests/multilayer/regression_data/claw_git_status.txt
index 1bf670d..51f0eb4 100644
--- a/tests/multilayer/regression_data/claw_git_status.txt
+++ b/tests/multilayer/regression_data/claw_git_status.txt
@@ -1,93 +1,118 @@
 Clawpack Git Status 
-Diffs can be found in /Users/rjl/git/clawpack/geoclaw/tests/multilayer/regression_data/claw_git_diffs.txt
+Diffs can be found in /Users/mandli/src/clawpack/geoclaw/tests/multilayer/regression_data/claw_git_diffs.txt
 
-Tue, 20 Dec 2016 22:06:32 PST
-$CLAW = /Users/rjl/git/clawpack
+Sun, 08 Apr 2018 20:47:31 EDT
+$CLAW = /Users/mandli/src/clawpack
 $FC = gfortran
 
 
 ===========
 classic
 ===========
-/Users/rjl/git/clawpack/classic
+/Users/mandli/src/clawpack/classic
 
 --- last commit ---
-8e6d0c2 make plotdata an optional argument in setplot
+8c4ef32 Merge pull request #79 from rjleveque/restart_None
 
 --- branch and status ---
-## setplot_fixes
+## master...clawpack/master
+ M examples/acoustics_1d_example1/qinit.f90
 
 
 ===========
 amrclaw
 ===========
-/Users/rjl/git/clawpack/amrclaw
+/Users/mandli/src/clawpack/amrclaw
 
 --- last commit ---
-5c81870 set xlimits and ylimits in quadrants example
+469833f Type bug fixed
 
 --- branch and status ---
-## setplot_fixes
+## bad-pt-moment-fix...mandli/bad-pt-moment-fix
+ M examples/acoustics_1d_heterogeneous/setrun.py
+ M examples/advection_2d_swirl/Makefile
+ M examples/advection_2d_swirl/setplot.py
+ M examples/advection_2d_swirl/setrun.py
 
 
 ===========
 clawutil
 ===========
-/Users/rjl/git/clawpack/clawutil
+/Users/mandli/src/clawpack/clawutil
 
 --- last commit ---
-c3950d1 Fix call to StringIO to match new way it is imported
+5c6bd99 Merge pull request #122 from rjleveque/convert_readme_string
 
 --- branch and status ---
-## claw_git_status_StringIO
+## master...clawpack/master
+MM src/python/clawutil/data.py
 
 
 ===========
 pyclaw
 ===========
-/Users/rjl/git/clawpack/pyclaw
+/Users/mandli/src/clawpack/pyclaw
 
 --- last commit ---
-695af06 Merge pull request #550 from clawpack/python3
+3fd86fad Remove pdb break poitn
 
 --- branch and status ---
-## master...origin/master
+## fix-gauges-funcs...clawpack/master [ahead 3]
 
 
 ===========
 visclaw
 ===========
-/Users/rjl/git/clawpack/visclaw
+/Users/mandli/src/clawpack/visclaw
 
 --- last commit ---
-6833be6 Merge pull request #190 from clawpack/python3
+33713bb Change to new structure for current pobj
 
 --- branch and status ---
-## master...origin/master
+## set-pobj...clawpack/master [ahead 1]
 
 
 ===========
 riemann
 ===========
-/Users/rjl/git/clawpack/riemann
+/Users/mandli/src/clawpack/riemann
 
 --- last commit ---
-b68d73d Merge pull request #111 from rjleveque/geoclaw_riemann_utils_update
+dcee832 Merge pull request #131 from chaulio/patch-1
 
 --- branch and status ---
-## master...origin/master
+## master...clawpack/master
 
 
 ===========
 geoclaw
 ===========
-/Users/rjl/git/clawpack/geoclaw
+/Users/mandli/src/clawpack/geoclaw
 
 --- last commit ---
-e29ead0 updated regression data for new Riemann solver from clawpack/riemann#111
+b1daad5 Turn off debugging info
 
 --- branch and status ---
-## regression_data_update_riemann
- M examples/tsunami/bowl-radial/setplot.py
- M tests/multilayer/regression_data/claw_git_diffs.txt
+## new-storm-module...mandli/new-storm-module [ahead 1]
+ M tests/multilayer/qinit_module.f90
  M tests/multilayer/regression_data/claw_git_status.txt
+ M tests/multilayer/regression_data/gauge00000.txt
+ M tests/multilayer/regression_data/gauge00001.txt
+ M tests/multilayer/regression_data/gauge00002.txt
+ M tests/multilayer/regression_data/gauge00003.txt
+ M tests/multilayer/regression_data/gauge00004.txt
+ M tests/multilayer/setplot.py
+ M tests/multilayer/setrun.py
+D  tests/multilayer_amr/Makefile
+D  tests/multilayer_amr/__init__.py
+D  tests/multilayer_amr/qinit.f90
+D  tests/multilayer_amr/qinit_module.f90
+D  tests/multilayer_amr/regression_data/claw_git_status.txt
+D  tests/multilayer_amr/regression_data/gauge00000.txt
+D  tests/multilayer_amr/regression_data/gauge00001.txt
+D  tests/multilayer_amr/regression_data/gauge00002.txt
+D  tests/multilayer_amr/regression_data/gauge00003.txt
+D  tests/multilayer_amr/regression_data/gauge00004.txt
+D  tests/multilayer_amr/regression_tests.py
+D  tests/multilayer_amr/setplot.py
+D  tests/multilayer_amr/setrun.py
diff --git a/tests/multilayer/regression_data/gauge00000.txt b/tests/multilayer/regression_data/gauge00000.txt
index d3cab05..7bdf46a 100644
--- a/tests/multilayer/regression_data/gauge00000.txt
+++ b/tests/multilayer/regression_data/gauge00000.txt
@@ -1,107 +1,107 @@
 # gauge_id=     0 location=(  -0.1000000E+00  -0.0000000E+00 ) num_var=  8
  # level, time, q[  1  2  3  4  5  6], eta[  1  2], aux[]
    01  0.0000000E+00  0.6057245E+00  0.0000000E+00  0.0000000E+00  0.4035816E+00  0.0000000E+00  0.0000000E+00  0.9306084E-02 -0.5964184E+00
-   01  0.2250000E-02  0.6057090E+00  0.3312530E-02  0.3312530E-02  0.4035721E+00  0.2082980E-02  0.2082980E-02  0.9281188E-02 -0.5964279E+00
-   01  0.1184747E-01  0.6047823E+00  0.9989230E-02  0.9989230E-02  0.4029792E+00  0.6581997E-02  0.6581997E-02  0.7761531E-02 -0.5970208E+00
-   01  0.2146018E-01  0.6027031E+00  0.6313314E-02  0.6313314E-02  0.4014171E+00  0.4471635E-02  0.4471635E-02  0.4120197E-02 -0.5985829E+00
-   01  0.3111379E-01  0.6008087E+00  0.1103156E-02  0.1103156E-02  0.4001245E+00  0.1150395E-02  0.1150395E-02  0.9331964E-03 -0.5998755E+00
-   01  0.4077456E-01  0.6000807E+00 -0.8059725E-03 -0.8059725E-03  0.3996143E+00 -0.2805526E-03 -0.2805526E-03 -0.3049986E-03 -0.6003857E+00
-   01  0.5043786E-01  0.6001737E+00 -0.4754867E-03 -0.4754867E-03  0.3996020E+00 -0.2157002E-03 -0.2157002E-03 -0.2242744E-03 -0.6003980E+00
-   01  0.6010236E-01  0.6003664E+00  0.1295783E-04  0.1295612E-04  0.3996822E+00  0.3287733E-04  0.3287996E-04  0.4859067E-04 -0.6003178E+00
-   01  0.6976776E-01  0.6004100E+00  0.1503814E-03  0.1503886E-03  0.3996667E+00  0.8492174E-04  0.8492872E-04  0.7670576E-04 -0.6003333E+00
-   01  0.7943390E-01  0.6003873E+00  0.6001150E-04  0.6001202E-04  0.3996388E+00 -0.1242847E-04 -0.1242807E-04  0.2611912E-04 -0.6003612E+00
-   01  0.8910079E-01  0.6003572E+00  0.4300001E-04  0.4076214E-04  0.3996269E+00 -0.6663596E-04 -0.6771539E-04 -0.1595260E-04 -0.6003731E+00
-   01  0.9876774E-01  0.6003478E+00  0.7459956E-04  0.5703397E-04  0.3996350E+00 -0.7813319E-04 -0.8889199E-04 -0.1718432E-04 -0.6003650E+00
-   01  0.1084360E+00  0.6003477E+00  0.8753773E-04  0.9133253E-04  0.3996556E+00 -0.8739722E-04 -0.8755178E-04  0.3307615E-05 -0.6003444E+00
-   01  0.1181047E+00  0.6003638E+00 -0.6944720E-05  0.9745967E-04  0.3996989E+00 -0.1525719E-03 -0.9493073E-04  0.6270423E-04 -0.6003011E+00
-   01  0.1277734E+00  0.6004367E+00 -0.3139651E-03  0.1038343E-03  0.3997844E+00 -0.3398763E-03 -0.9707813E-04  0.2210949E-03 -0.6002156E+00
-   01  0.1374422E+00  0.6006312E+00 -0.1033583E-02  0.1092554E-03  0.3999600E+00 -0.7750256E-03 -0.9414404E-04  0.5912257E-03 -0.6000400E+00
-   01  0.1471121E+00  0.6009293E+00 -0.2056110E-02  0.1381519E-03  0.4001935E+00 -0.1407954E-02 -0.7288141E-04  0.1122833E-02 -0.5998065E+00
-   01  0.1567832E+00  0.6012117E+00 -0.3048958E-02  0.1809087E-03  0.4004270E+00 -0.2038904E-02 -0.3686247E-04  0.1638608E-02 -0.5995730E+00
-   01  0.1664548E+00  0.6012716E+00 -0.3273793E-02  0.1613695E-03  0.4004832E+00 -0.2189101E-02 -0.3423420E-04  0.1754828E-02 -0.5995168E+00
-   01  0.1761270E+00  0.6012026E+00 -0.3187894E-02  0.9736005E-04  0.4004698E+00 -0.2135076E-02 -0.6019450E-04  0.1672407E-02 -0.5995302E+00
-   01  0.1857997E+00  0.6009891E+00 -0.2817037E-02  0.2020898E-04  0.4003878E+00 -0.1898267E-02 -0.9536296E-04  0.1376979E-02 -0.5996122E+00
-   01  0.1954728E+00  0.6006310E+00 -0.2217119E-02  0.4179169E-05  0.4002091E+00 -0.1515233E-02 -0.9476038E-04  0.8400379E-03 -0.5997909E+00
-   01  0.2051462E+00  0.6002078E+00 -0.1653398E-02  0.9643900E-04  0.3999853E+00 -0.1138165E-02 -0.2640846E-04  0.1930705E-03 -0.6000147E+00
-   01  0.2148201E+00  0.5997948E+00 -0.1144635E-02  0.2386283E-03  0.3997533E+00 -0.7990530E-03  0.7573398E-04 -0.4518428E-03 -0.6002467E+00
-   01  0.2244945E+00  0.5994480E+00 -0.6158590E-03  0.2997295E-03  0.3995538E+00 -0.4502469E-03  0.1317694E-03 -0.9982082E-03 -0.6004462E+00
-   01  0.2341693E+00  0.5991976E+00 -0.3233943E-04  0.2220891E-03  0.3994100E+00 -0.6839614E-04  0.1020595E-03 -0.1392405E-02 -0.6005900E+00
-   01  0.2438447E+00  0.5990569E+00  0.5442174E-03 -0.2185072E-04  0.3993349E+00  0.3098811E-03 -0.3206709E-04 -0.1608166E-02 -0.6006651E+00
-   01  0.2535204E+00  0.5990034E+00  0.1026924E-02 -0.3586756E-03  0.3993162E+00  0.6289575E-03 -0.2284934E-03 -0.1680347E-02 -0.6006838E+00
-   01  0.2631963E+00  0.5990166E+00  0.1275978E-02 -0.6578447E-03  0.3993421E+00  0.8016857E-03 -0.4074164E-03 -0.1641339E-02 -0.6006579E+00
-   01  0.2728723E+00  0.5990599E+00  0.1347245E-02 -0.8857767E-03  0.3993903E+00  0.8559395E-03 -0.5435475E-03 -0.1549821E-02 -0.6006097E+00
-   01  0.2825483E+00  0.5991206E+00  0.1311015E-02 -0.1031518E-02  0.3994414E+00  0.8401820E-03 -0.6306534E-03 -0.1438039E-02 -0.6005586E+00
-   01  0.2922245E+00  0.5991800E+00  0.1233249E-02 -0.1052192E-02  0.3994883E+00  0.7973909E-03 -0.6427007E-03 -0.1331715E-02 -0.6005117E+00
-   01  0.3019008E+00  0.5992296E+00  0.1153597E-02 -0.9431991E-03  0.3995291E+00  0.7519189E-03 -0.5745973E-03 -0.1241319E-02 -0.6004709E+00
-   01  0.3115768E+00  0.5992737E+00  0.1072229E-02 -0.7089971E-03  0.3995636E+00  0.7041538E-03 -0.4287999E-03 -0.1162776E-02 -0.6004364E+00
-   01  0.3212525E+00  0.5993096E+00  0.9830644E-03 -0.3749707E-03  0.3995888E+00  0.6497162E-03 -0.2198769E-03 -0.1101549E-02 -0.6004112E+00
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-   01  0.3406031E+00  0.5993823E+00  0.7307102E-03  0.2892966E-03  0.3996462E+00  0.4880312E-03  0.2020158E-03 -0.9714664E-03 -0.6003538E+00
-   01  0.3502781E+00  0.5994431E+00  0.5764200E-03  0.4552517E-03  0.3997085E+00  0.3813983E-03  0.3076120E-03 -0.8484456E-03 -0.6002915E+00
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-   01  0.3793027E+00  0.5996364E+00  0.1575220E-03  0.4515764E-03  0.3999883E+00  0.3845421E-04  0.2903763E-03 -0.3753648E-03 -0.6000117E+00
-   01  0.3889776E+00  0.5996671E+00  0.4788485E-04  0.4050576E-03  0.4000949E+00 -0.7568403E-04  0.2483759E-03 -0.2379744E-03 -0.5999051E+00
-   01  0.3986525E+00  0.5996630E+00 -0.4025801E-04  0.3945405E-03  0.4001971E+00 -0.1857728E-03  0.2254267E-03 -0.1398590E-03 -0.5998029E+00
-   01  0.4083275E+00  0.5996276E+00 -0.1043722E-03  0.4069840E-03  0.4002967E+00 -0.2891239E-03  0.2147323E-03 -0.7571368E-04 -0.5997033E+00
-   01  0.4180019E+00  0.5995712E+00 -0.1419992E-03  0.4163944E-03  0.4003967E+00 -0.3822528E-03  0.2006286E-03 -0.3213863E-04 -0.5996033E+00
-   01  0.4276743E+00  0.5995011E+00 -0.1569229E-03  0.4124546E-03  0.4004971E+00 -0.4648415E-03  0.1764138E-03 -0.1721569E-05 -0.5995029E+00
-   01  0.4373462E+00  0.5994211E+00 -0.1531915E-03  0.3916753E-03  0.4005985E+00 -0.5383549E-03  0.1397143E-03  0.1961533E-04 -0.5994015E+00
-   01  0.4470183E+00  0.5993337E+00 -0.1375421E-03  0.3504285E-03  0.4007030E+00 -0.6069404E-03  0.8840164E-04  0.3669455E-04 -0.5992970E+00
-   01  0.4566948E+00  0.5992424E+00 -0.1163022E-03  0.2964763E-03  0.4008099E+00 -0.6732962E-03  0.2730125E-04  0.5228137E-04 -0.5991901E+00
-   01  0.4663809E+00  0.5991485E+00 -0.8199239E-04  0.2428814E-03  0.4009116E+00 -0.7294037E-03 -0.3480192E-04  0.6007169E-04 -0.5990884E+00
-   01  0.4760724E+00  0.5990522E+00 -0.3574610E-04  0.1989185E-03  0.4010039E+00 -0.7734170E-03 -0.9102630E-04  0.5605244E-04 -0.5989961E+00
-   01  0.4857646E+00  0.5989574E+00  0.1869307E-04  0.1641941E-03  0.4010851E+00 -0.8053848E-03 -0.1405473E-03  0.4243231E-04 -0.5989149E+00
-   01  0.4954585E+00  0.5988665E+00  0.8844337E-04  0.1309428E-03  0.4011511E+00 -0.8189461E-03 -0.1874559E-03  0.1767474E-04 -0.5988489E+00
-   01  0.5051535E+00  0.5987812E+00  0.1650320E-03  0.9349486E-04  0.4012040E+00 -0.8187479E-03 -0.2347779E-03 -0.1474528E-04 -0.5987960E+00
-   01  0.5148484E+00  0.5987068E+00  0.2411693E-03  0.5267652E-04  0.4012441E+00 -0.8083642E-03 -0.2818710E-03 -0.4915599E-04 -0.5987559E+00
-   01  0.5245434E+00  0.5986445E+00  0.3107676E-03  0.1378777E-04  0.4012723E+00 -0.7914663E-03 -0.3257800E-03 -0.8316736E-04 -0.5987277E+00
-   01  0.5342383E+00  0.5985952E+00  0.3712184E-03 -0.1560635E-04  0.4012884E+00 -0.7695680E-03 -0.3619825E-03 -0.1163610E-03 -0.5987116E+00
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-   01  0.5633238E+00  0.5984935E+00  0.5201837E-03 -0.1519605E-04  0.4012977E+00 -0.6917268E-03 -0.4044890E-03 -0.2088204E-03 -0.5987023E+00
-   01  0.5730194E+00  0.5984709E+00  0.5631177E-03  0.5777698E-05  0.4012919E+00 -0.6644685E-03 -0.4009163E-03 -0.2371302E-03 -0.5987081E+00
-   01  0.5827151E+00  0.5984603E+00  0.5986493E-03  0.2735064E-04  0.4012769E+00 -0.6344347E-03 -0.3938535E-03 -0.2628886E-03 -0.5987231E+00
-   01  0.5924110E+00  0.5984620E+00  0.6278413E-03  0.4429902E-04  0.4012529E+00 -0.6007934E-03 -0.3860561E-03 -0.2851337E-03 -0.5987471E+00
-   01  0.6021072E+00  0.5984819E+00  0.6475187E-03  0.5589455E-04  0.4012161E+00 -0.5619917E-03 -0.3777886E-03 -0.3019959E-03 -0.5987839E+00
-   01  0.6118037E+00  0.5985249E+00  0.6553551E-03  0.6287523E-04  0.4011615E+00 -0.5162254E-03 -0.3669485E-03 -0.3135117E-03 -0.5988385E+00
-   01  0.6215001E+00  0.5985933E+00  0.6488911E-03  0.6566273E-04  0.4010868E+00 -0.4642140E-03 -0.3514922E-03 -0.3199010E-03 -0.5989132E+00
-   01  0.6311966E+00  0.5986865E+00  0.6271762E-03  0.6491540E-04  0.4009918E+00 -0.4062414E-03 -0.3309574E-03 -0.3217620E-03 -0.5990082E+00
-   01  0.6408930E+00  0.5988059E+00  0.5887568E-03  0.6057491E-04  0.4008749E+00 -0.3419352E-03 -0.3050573E-03 -0.3192093E-03 -0.5991251E+00
-   01  0.6505895E+00  0.5989494E+00  0.5337330E-03  0.5091678E-04  0.4007381E+00 -0.2736350E-03 -0.2739641E-03 -0.3125001E-03 -0.5992619E+00
-   01  0.6602863E+00  0.5991112E+00  0.4658798E-03  0.3684246E-04  0.4005867E+00 -0.2031628E-03 -0.2376413E-03 -0.3021368E-03 -0.5994133E+00
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+   01  0.5825525E+00  0.5986544E+00  0.5814066E-03  0.4133667E-03  0.4014967E+00 -0.6866750E-03 -0.1744662E-03  0.1511587E-03 -0.5985033E+00
+   01  0.5922469E+00  0.5986422E+00  0.6242324E-03  0.3917784E-03  0.4014743E+00 -0.6499562E-03 -0.1934577E-03  0.1164739E-03 -0.5985257E+00
+   01  0.6019413E+00  0.5986413E+00  0.6647890E-03  0.3545440E-03  0.4014390E+00 -0.6054180E-03 -0.2195643E-03  0.8027311E-04 -0.5985610E+00
+   01  0.6116357E+00  0.5986539E+00  0.6987878E-03  0.3135798E-03  0.4013892E+00 -0.5541482E-03 -0.2444788E-03  0.4310456E-04 -0.5986108E+00
+   01  0.6213300E+00  0.5986831E+00  0.7192367E-03  0.2766406E-03  0.4013235E+00 -0.4989547E-03 -0.2619187E-03  0.6624969E-05 -0.5986765E+00
+   01  0.6310243E+00  0.5987314E+00  0.7242559E-03  0.2465290E-03  0.4012408E+00 -0.4415612E-03 -0.2680882E-03 -0.2779815E-04 -0.5987592E+00
+   01  0.6407187E+00  0.5987998E+00  0.7109307E-03  0.2252482E-03  0.4011414E+00 -0.3832088E-03 -0.2627844E-03 -0.5880307E-04 -0.5988586E+00
+   01  0.6504132E+00  0.5988895E+00  0.6787363E-03  0.2075667E-03  0.4010269E+00 -0.3245939E-03 -0.2490643E-03 -0.8361380E-04 -0.5989731E+00
+   01  0.6601078E+00  0.5989977E+00  0.6335362E-03  0.1869609E-03  0.4009032E+00 -0.2661287E-03 -0.2306893E-03 -0.9914918E-04 -0.5990968E+00
+   01  0.6698026E+00  0.5991257E+00  0.5785527E-03  0.1625740E-03  0.4007711E+00 -0.2055680E-03 -0.2084583E-03 -0.1031734E-03 -0.5992289E+00
+   01  0.6794975E+00  0.5992673E+00  0.5186799E-03  0.1342681E-03  0.4006350E+00 -0.1444186E-03 -0.1834126E-03 -0.9761041E-04 -0.5993650E+00
+   01  0.6891926E+00  0.5994164E+00  0.4559191E-03  0.1017454E-03  0.4004980E+00 -0.8447794E-04 -0.1569137E-03 -0.8559874E-04 -0.5995020E+00
+   01  0.6988875E+00  0.5995689E+00  0.3903504E-03  0.6777863E-04  0.4003630E+00 -0.2780515E-04 -0.1289636E-03 -0.6809183E-04 -0.5996370E+00
+   01  0.7085823E+00  0.5997175E+00  0.3222234E-03  0.3559996E-04  0.4002350E+00  0.2264750E-04 -0.9962343E-04 -0.4749630E-04 -0.5997650E+00
+   01  0.7182770E+00  0.5998585E+00  0.2521052E-03  0.6695613E-05  0.4001167E+00  0.6496469E-04 -0.6852562E-04 -0.2480665E-04 -0.5998833E+00
+   01  0.7279717E+00  0.5999896E+00  0.1817074E-03 -0.1690214E-04  0.4000085E+00  0.9929274E-04 -0.3578129E-04 -0.1870866E-05 -0.5999915E+00
+   01  0.7376666E+00  0.6001073E+00  0.1121384E-03 -0.3501025E-04  0.3999128E+00  0.1249250E-03 -0.2771716E-05  0.2013750E-04 -0.6000872E+00
+   01  0.7473618E+00  0.6002071E+00  0.5000178E-04 -0.5010763E-04  0.3998329E+00  0.1431790E-03  0.2795528E-04  0.4005993E-04 -0.6001671E+00
+   01  0.7570572E+00  0.6002902E+00 -0.3386077E-05 -0.6269804E-04  0.3997683E+00  0.1558987E-03  0.5503074E-04  0.5848802E-04 -0.6002317E+00
+   01  0.7667526E+00  0.6003572E+00 -0.4798955E-04 -0.7249473E-04  0.3997177E+00  0.1635896E-03  0.7879541E-04  0.7490977E-04 -0.6002823E+00
+   01  0.7764481E+00  0.6004093E+00 -0.8234383E-04 -0.7815306E-04  0.3996801E+00  0.1667806E-03  0.1004930E-03  0.8937345E-04 -0.6003199E+00
+   01  0.7861435E+00  0.6004499E+00 -0.1082226E-03 -0.7912420E-04  0.3996528E+00  0.1677193E-03  0.1208477E-03  0.1026347E-03 -0.6003472E+00
+   01  0.7958388E+00  0.6004820E+00 -0.1254717E-03 -0.7561933E-04  0.3996341E+00  0.1684766E-03  0.1399931E-03  0.1160887E-03 -0.6003659E+00
+   01  0.8055344E+00  0.6005063E+00 -0.1328096E-03 -0.6711188E-04  0.3996247E+00  0.1702311E-03  0.1583481E-03  0.1310311E-03 -0.6003753E+00
+   01  0.8152304E+00  0.6005247E+00 -0.1273790E-03 -0.5317049E-04  0.3996249E+00  0.1746542E-03  0.1772152E-03  0.1496354E-03 -0.6003751E+00
+   01  0.8249269E+00  0.6005393E+00 -0.1113420E-03 -0.3380963E-04  0.3996328E+00  0.1820955E-03  0.1970841E-03  0.1721197E-03 -0.6003672E+00
+   01  0.8346234E+00  0.6005487E+00 -0.8810787E-04 -0.1109433E-04  0.3996473E+00  0.1906565E-03  0.2167186E-03  0.1959448E-03 -0.6003527E+00
+   01  0.8443201E+00  0.6005469E+00 -0.6567281E-04  0.8041526E-05  0.3996679E+00  0.1956897E-03  0.2300386E-03  0.2148137E-03 -0.6003321E+00
+   01  0.8540169E+00  0.6005274E+00 -0.5323386E-04  0.1626156E-04  0.3996947E+00  0.1903562E-03  0.2312305E-03  0.2221069E-03 -0.6003053E+00
+   01  0.8637137E+00  0.6004892E+00 -0.5075122E-04  0.1280865E-04  0.3997258E+00  0.1739143E-03  0.2195415E-03  0.2149809E-03 -0.6002742E+00
+   01  0.8734108E+00  0.6004321E+00 -0.6093227E-04 -0.5071602E-05  0.3997596E+00  0.1442244E-03  0.1945802E-03  0.1917176E-03 -0.6002404E+00
+   01  0.8831079E+00  0.6003584E+00 -0.7867763E-04 -0.3401243E-04  0.3997966E+00  0.1038892E-03  0.1585071E-03  0.1550439E-03 -0.6002034E+00
+   01  0.8928051E+00  0.6002738E+00 -0.9468342E-04 -0.6354956E-04  0.3998392E+00  0.5928025E-04  0.1179793E-03  0.1130145E-03 -0.6001608E+00
+   01  0.9025023E+00  0.6001875E+00 -0.9816283E-04 -0.8110500E-04  0.3998890E+00  0.1845417E-04  0.8160080E-04  0.7641156E-04 -0.6001110E+00
+   01  0.9121994E+00  0.6001055E+00 -0.7828316E-04 -0.7859782E-04  0.3999472E+00 -0.1053798E-04  0.5546937E-04  0.5264263E-04 -0.6000528E+00
+   01  0.9218967E+00  0.6000297E+00 -0.4121184E-04 -0.5795769E-04  0.4000132E+00 -0.2984664E-04  0.3900928E-04  0.4285389E-04 -0.5999868E+00
+   01  0.9315940E+00  0.5999593E+00  0.5229804E-05 -0.2653942E-04  0.4000830E+00 -0.4219488E-04  0.2803694E-04  0.4229421E-04 -0.5999170E+00
+   01  0.9412913E+00  0.5998926E+00  0.5013846E-04  0.5710375E-05  0.4001516E+00 -0.5306410E-04  0.1728830E-04  0.4422090E-04 -0.5998484E+00
+   01  0.9509886E+00  0.5998293E+00  0.8585639E-04  0.3121959E-04  0.4002156E+00 -0.6670664E-04  0.3653023E-05  0.4488164E-04 -0.5997844E+00
+   01  0.9606858E+00  0.5997723E+00  0.1082805E-03  0.4751879E-04  0.4002710E+00 -0.8447345E-04 -0.1306294E-04  0.4337271E-04 -0.5997290E+00
+   01  0.9703831E+00  0.5997246E+00  0.1183911E-03  0.5678278E-04  0.4003176E+00 -0.1046389E-03 -0.3127455E-04  0.4217913E-04 -0.5996824E+00
+   01  0.9800803E+00  0.5996866E+00  0.1204859E-03  0.6198792E-04  0.4003567E+00 -0.1247406E-03 -0.4914881E-04  0.4332956E-04 -0.5996433E+00
+   01  0.9897776E+00  0.5996584E+00  0.1198120E-03  0.6544310E-04  0.4003893E+00 -0.1415041E-03 -0.6518493E-04  0.4767430E-04 -0.5996107E+00
+   01  0.9994750E+00  0.5996386E+00  0.1201527E-03  0.6846393E-04  0.4004156E+00 -0.1527789E-03 -0.7850239E-04  0.5424753E-04 -0.5995844E+00
diff --git a/tests/multilayer/regression_data/gauge00001.txt b/tests/multilayer/regression_data/gauge00001.txt
index 02a27fa..ea2333e 100644
--- a/tests/multilayer/regression_data/gauge00001.txt
+++ b/tests/multilayer/regression_data/gauge00001.txt
@@ -2,106 +2,106 @@
  # level, time, q[  1  2  3  4  5  6], eta[  1  2], aux[]
    01  0.0000000E+00  0.6000000E+00  0.0000000E+00  0.0000000E+00  0.4000000E+00  0.0000000E+00  0.0000000E+00  0.2117894E-07 -0.6000000E+00
    01  0.2250000E-02  0.6000167E+00  0.2598827E-04  0.2598827E-04  0.4000104E+00  0.1486537E-04  0.1486537E-04  0.2705976E-04 -0.5999896E+00
-   01  0.1184747E-01  0.6006796E+00  0.1235182E-02  0.1235182E-02  0.4004090E+00  0.7052776E-03  0.7052776E-03  0.1088574E-02 -0.5995910E+00
-   01  0.2146018E-01  0.6022845E+00  0.5284226E-02  0.5284226E-02  0.4015693E+00  0.3176801E-02  0.3176801E-02  0.3853847E-02 -0.5984307E+00
-   01  0.3111379E-01  0.6035482E+00  0.8382404E-02  0.8382404E-02  0.4024596E+00  0.5199940E-02  0.5199940E-02  0.6007725E-02 -0.5975404E+00
-   01  0.4077456E-01  0.6031430E+00  0.7213926E-02  0.7213917E-02  0.4021699E+00  0.4632632E-02  0.4632634E-02  0.5312904E-02 -0.5978301E+00
-   01  0.5043786E-01  0.6015093E+00  0.3430861E-02  0.3430703E-02  0.4011265E+00  0.2346336E-02  0.2346355E-02  0.2635765E-02 -0.5988735E+00
-   01  0.6010236E-01  0.6000954E+00  0.4061976E-03  0.4027878E-03  0.4003221E+00  0.4166809E-03  0.4165515E-03  0.4174381E-03 -0.5996779E+00
-   01  0.6976776E-01  0.5995545E+00 -0.4952744E-03 -0.5163509E-03  0.4000822E+00 -0.2073216E-03 -0.2145460E-03 -0.3632795E-03 -0.5999178E+00
-   01  0.7943390E-01  0.5995981E+00 -0.3605841E-03 -0.3312916E-03  0.4001837E+00 -0.1287808E-03 -0.1077244E-03 -0.2181893E-03 -0.5998163E+00
-   01  0.8910079E-01  0.5998065E+00 -0.3024412E-03 -0.4874994E-04  0.4003115E+00 -0.6834555E-04  0.8510605E-04  0.1179946E-03 -0.5996885E+00
-   01  0.9876774E-01  0.5999961E+00 -0.7079479E-03 -0.4747169E-05  0.4004061E+00 -0.3011143E-03  0.1234268E-03  0.4022058E-03 -0.5995939E+00
-   01  0.1084360E+00  0.6002416E+00 -0.1568801E-02 -0.6181398E-04  0.4005341E+00 -0.8247250E-03  0.8725376E-04  0.7757114E-03 -0.5994659E+00
-   01  0.1181047E+00  0.6005716E+00 -0.2613054E-02 -0.6605056E-04  0.4007045E+00 -0.1478713E-02  0.7556948E-04  0.1276084E-02 -0.5992955E+00
-   01  0.1277734E+00  0.6008368E+00 -0.3380739E-02  0.2582116E-04  0.4008289E+00 -0.1975508E-02  0.1202552E-03  0.1665750E-02 -0.5991711E+00
-   01  0.1374422E+00  0.6009272E+00 -0.3553218E-02  0.1185900E-03  0.4008367E+00 -0.2117563E-02  0.1652651E-03  0.1763903E-02 -0.5991633E+00
-   01  0.1471121E+00  0.6008376E+00 -0.3139578E-02  0.1085895E-03  0.4007245E+00 -0.1894752E-02  0.1464227E-03  0.1562084E-02 -0.5992755E+00
-   01  0.1567832E+00  0.6006535E+00 -0.2442157E-02 -0.7959126E-05  0.4005712E+00 -0.1493418E-02  0.5789961E-04  0.1224662E-02 -0.5994288E+00
-   01  0.1664548E+00  0.6004312E+00 -0.1600841E-02 -0.1986057E-03  0.4003976E+00 -0.1001479E-02 -0.8052512E-04  0.8287289E-03 -0.5996024E+00
-   01  0.1761270E+00  0.6002252E+00 -0.8346940E-03 -0.3878441E-03  0.4002425E+00 -0.5532450E-03 -0.2209599E-03  0.4677116E-03 -0.5997575E+00
-   01  0.1857997E+00  0.6000333E+00 -0.1828671E-03 -0.5213688E-03  0.4001079E+00 -0.1832061E-03 -0.3293846E-03  0.1412523E-03 -0.5998921E+00
-   01  0.1954728E+00  0.5998296E+00  0.3529959E-03 -0.6041883E-03  0.3999865E+00  0.1044891E-03 -0.4070005E-03 -0.1838870E-03 -0.6000135E+00
-   01  0.2051462E+00  0.5996020E+00  0.7585643E-03 -0.6721536E-03  0.3998728E+00  0.3040011E-03 -0.4743117E-03 -0.5251393E-03 -0.6001272E+00
-   01  0.2148201E+00  0.5993445E+00  0.1001131E-02 -0.7193651E-03  0.3997612E+00  0.3956559E-03 -0.5302196E-03 -0.8943944E-03 -0.6002388E+00
-   01  0.2244945E+00  0.5990593E+00  0.1054696E-02 -0.6995775E-03  0.3996562E+00  0.3628718E-03 -0.5465269E-03 -0.1284467E-02 -0.6003438E+00
-   01  0.2341693E+00  0.5987660E+00  0.9654897E-03 -0.5957783E-03  0.3995763E+00  0.2289343E-03 -0.5110612E-03 -0.1657694E-02 -0.6004237E+00
-   01  0.2438447E+00  0.5985242E+00  0.8513953E-03 -0.4764924E-03  0.3995469E+00  0.7287714E-04 -0.4626780E-03 -0.1928893E-02 -0.6004531E+00
-   01  0.2535204E+00  0.5983831E+00  0.8350227E-03 -0.4413661E-03  0.3995934E+00 -0.2580220E-04 -0.4628752E-03 -0.2023510E-02 -0.6004066E+00
-   01  0.2631963E+00  0.5983426E+00  0.9333409E-03 -0.5032823E-03  0.3997121E+00 -0.5291239E-04 -0.5219767E-03 -0.1945353E-02 -0.6002879E+00
-   01  0.2728723E+00  0.5983652E+00  0.1102828E-02 -0.6211453E-03  0.3998886E+00 -0.3393307E-04 -0.6163891E-03 -0.1746179E-02 -0.6001114E+00
-   01  0.2825483E+00  0.5984141E+00  0.1275855E-02 -0.6979589E-03  0.4000913E+00 -0.1024108E-04 -0.6869842E-03 -0.1494655E-02 -0.5999087E+00
-   01  0.2922245E+00  0.5984453E+00  0.1369876E-02 -0.6206423E-03  0.4002838E+00 -0.2914761E-04 -0.6618748E-03 -0.1270867E-02 -0.5997162E+00
-   01  0.3019008E+00  0.5984384E+00  0.1370209E-02 -0.3834173E-03  0.4004507E+00 -0.9928555E-04 -0.5335725E-03 -0.1110970E-02 -0.5995493E+00
-   01  0.3115768E+00  0.5984061E+00  0.1304659E-02 -0.6423782E-04  0.4005912E+00 -0.2021997E-03 -0.3488558E-03 -0.1002712E-02 -0.5994088E+00
-   01  0.3212525E+00  0.5983591E+00  0.1202497E-02  0.2856694E-03  0.4007097E+00 -0.3188020E-03 -0.1405653E-03 -0.9312234E-03 -0.5992903E+00
-   01  0.3309279E+00  0.5983187E+00  0.1083088E-02  0.5888581E-03  0.4008192E+00 -0.4368410E-03  0.4248258E-04 -0.8621326E-03 -0.5991808E+00
-   01  0.3406031E+00  0.5983041E+00  0.9565312E-03  0.7899773E-03  0.4009313E+00 -0.5498960E-03  0.1633763E-03 -0.7645678E-03 -0.5990687E+00
-   01  0.3502781E+00  0.5983137E+00  0.8282242E-03  0.8898377E-03  0.4010477E+00 -0.6565712E-03  0.2198909E-03 -0.6385524E-03 -0.5989523E+00
-   01  0.3599530E+00  0.5983421E+00  0.7031882E-03  0.9169433E-03  0.4011576E+00 -0.7527124E-03  0.2308611E-03 -0.5003172E-03 -0.5988424E+00
-   01  0.3696279E+00  0.5983909E+00  0.5818629E-03  0.8818172E-03  0.4012537E+00 -0.8332888E-03  0.2029124E-03 -0.3554171E-03 -0.5987463E+00
-   01  0.3793027E+00  0.5984560E+00  0.4717813E-03  0.8064082E-03  0.4013242E+00 -0.8902384E-03  0.1515795E-03 -0.2198117E-03 -0.5986758E+00
-   01  0.3889776E+00  0.5985284E+00  0.3776725E-03  0.7273994E-03  0.4013586E+00 -0.9185199E-03  0.1005109E-03 -0.1130402E-03 -0.5986414E+00
-   01  0.3986525E+00  0.5985991E+00  0.2967983E-03  0.6613214E-03  0.4013588E+00 -0.9220224E-03  0.6133854E-04 -0.4205727E-04 -0.5986412E+00
-   01  0.4083275E+00  0.5986708E+00  0.2194555E-03  0.6088569E-03  0.4013279E+00 -0.9077844E-03  0.3415634E-04 -0.1339500E-05 -0.5986721E+00
-   01  0.4180019E+00  0.5987478E+00  0.1414645E-03  0.5580177E-03  0.4012715E+00 -0.8809262E-03  0.1158137E-04  0.1931799E-04 -0.5987285E+00
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diff --git a/tests/multilayer/regression_data/gauge00002.txt b/tests/multilayer/regression_data/gauge00002.txt
index d3af838..c417244 100644
--- a/tests/multilayer/regression_data/gauge00002.txt
+++ b/tests/multilayer/regression_data/gauge00002.txt
@@ -3,105 +3,105 @@
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diff --git a/tests/multilayer/regression_data/gauge00003.txt b/tests/multilayer/regression_data/gauge00003.txt
index 5111772..825c15c 100644
--- a/tests/multilayer/regression_data/gauge00003.txt
+++ b/tests/multilayer/regression_data/gauge00003.txt
@@ -3,105 +3,105 @@
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+   01  0.9703831E+00  0.2498296E+00 -0.6374331E-04  0.1010667E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4982965E-01 -0.2000000E+00
+   01  0.9800803E+00  0.2497885E+00 -0.1128889E-03  0.7117428E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4978848E-01 -0.2000000E+00
+   01  0.9897776E+00  0.2497645E+00 -0.1393397E-03  0.5293550E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4976446E-01 -0.2000000E+00
+   01  0.9994750E+00  0.2497573E+00 -0.1412392E-03  0.4432879E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4975729E-01 -0.2000000E+00
diff --git a/tests/multilayer/regression_data/gauge00004.txt b/tests/multilayer/regression_data/gauge00004.txt
index d199f9b..e1169e3 100644
--- a/tests/multilayer/regression_data/gauge00004.txt
+++ b/tests/multilayer/regression_data/gauge00004.txt
@@ -2,106 +2,106 @@
  # level, time, q[  1  2  3  4  5  6], eta[  1  2], aux[]
    01  0.0000000E+00  0.2000000E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
    01  0.2250000E-02  0.2000000E+00 -0.1413392E-32  0.2318458E-18  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.1184747E-01  0.2000000E+00  0.2105641E-18  0.1220633E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.2146018E-01  0.2000000E+00  0.1053980E-17  0.2243129E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.3111379E-01  0.2000000E+00  0.2088980E-17  0.3332608E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.4077456E-01  0.2000000E+00  0.3067980E-17  0.4767877E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.5043786E-01  0.2000000E+00 -0.1713582E-08 -0.2943220E-09  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1433486E-08 -0.2000000E+00
-   01  0.6010236E-01  0.2000000E+00  0.9584407E-08  0.1333371E-08  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.8279565E-08 -0.2000000E+00
-   01  0.6976776E-01  0.2000005E+00  0.5451817E-06  0.1292645E-06  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4766950E-06 -0.2000000E+00
-   01  0.7943390E-01  0.2000067E+00  0.7608832E-05  0.2186934E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.6732648E-05 -0.2000000E+00
-   01  0.8910079E-01  0.2000441E+00  0.5015655E-04  0.1676051E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4410153E-04 -0.2000000E+00
-   01  0.9876774E-01  0.2003502E+00  0.4164443E-03  0.1120603E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3502237E-03 -0.2000000E+00
-   01  0.1084360E+00  0.2015903E+00  0.1776356E-02  0.7737864E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1590274E-02 -0.2000000E+00
-   01  0.1181047E+00  0.2034677E+00  0.3891791E-02  0.2143545E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3467678E-02 -0.2000000E+00
-   01  0.1277734E+00  0.2050730E+00  0.5865392E-02  0.3465072E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5073042E-02 -0.2000000E+00
-   01  0.1374422E+00  0.2055998E+00  0.6606992E-02  0.4181895E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5599757E-02 -0.2000000E+00
-   01  0.1471121E+00  0.2050604E+00  0.6063648E-02  0.4096387E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5060375E-02 -0.2000000E+00
-   01  0.1567832E+00  0.2040276E+00  0.4907302E-02  0.3459602E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4027613E-02 -0.2000000E+00
-   01  0.1664548E+00  0.2025211E+00  0.3167447E-02  0.2476467E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.2521120E-02 -0.2000000E+00
-   01  0.1761270E+00  0.2009801E+00  0.1362214E-02  0.1350655E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.9800899E-03 -0.2000000E+00
-   01  0.1857997E+00  0.1998880E+00 -0.3915432E-05  0.4577812E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1120305E-03 -0.2000000E+00
-   01  0.1954728E+00  0.1993049E+00 -0.7494018E-03 -0.1540990E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.6951019E-03 -0.2000000E+00
-   01  0.2051462E+00  0.1990501E+00 -0.1018994E-02 -0.5234363E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9498904E-03 -0.2000000E+00
-   01  0.2148201E+00  0.1989393E+00 -0.1082129E-02 -0.7912310E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1060692E-02 -0.2000000E+00
-   01  0.2244945E+00  0.1988664E+00 -0.1084472E-02 -0.1018700E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1133576E-02 -0.2000000E+00
-   01  0.2341693E+00  0.1987908E+00 -0.1081939E-02 -0.1224261E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1209158E-02 -0.2000000E+00
-   01  0.2438447E+00  0.1987226E+00 -0.1069847E-02 -0.1391017E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1277413E-02 -0.2000000E+00
-   01  0.2535204E+00  0.1986683E+00 -0.1053770E-02 -0.1508454E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1331678E-02 -0.2000000E+00
-   01  0.2631963E+00  0.1986462E+00 -0.1028201E-02 -0.1576116E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1353796E-02 -0.2000000E+00
-   01  0.2728723E+00  0.1986651E+00 -0.9828556E-03 -0.1591331E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1334922E-02 -0.2000000E+00
-   01  0.2825483E+00  0.1987395E+00 -0.9055101E-03 -0.1540268E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1260469E-02 -0.2000000E+00
-   01  0.2922245E+00  0.1988539E+00 -0.7813755E-03 -0.1436346E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1146073E-02 -0.2000000E+00
-   01  0.3019008E+00  0.1990109E+00 -0.6249701E-03 -0.1274944E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9890523E-03 -0.2000000E+00
-   01  0.3115768E+00  0.1991698E+00 -0.4996976E-03 -0.1055939E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8302390E-03 -0.2000000E+00
-   01  0.3212525E+00  0.1993070E+00 -0.4201732E-03 -0.7940009E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.6930408E-03 -0.2000000E+00
-   01  0.3309279E+00  0.1994095E+00 -0.3777818E-03 -0.5277546E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.5904701E-03 -0.2000000E+00
-   01  0.3406031E+00  0.1994792E+00 -0.3728403E-03 -0.2697313E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.5208444E-03 -0.2000000E+00
-   01  0.3502781E+00  0.1995132E+00 -0.4080511E-03 -0.3999362E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.4867592E-03 -0.2000000E+00
-   01  0.3599530E+00  0.1995428E+00 -0.4386549E-03  0.1475179E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.4571531E-03 -0.2000000E+00
-   01  0.3696279E+00  0.1995707E+00 -0.4594801E-03  0.2876719E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.4293310E-03 -0.2000000E+00
-   01  0.3793027E+00  0.1996104E+00 -0.4538652E-03  0.3817105E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.3895546E-03 -0.2000000E+00
-   01  0.3889776E+00  0.1996649E+00 -0.4161303E-03  0.4441694E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.3350973E-03 -0.2000000E+00
-   01  0.3986525E+00  0.1997326E+00 -0.3480008E-03  0.4744444E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2674071E-03 -0.2000000E+00
-   01  0.4083275E+00  0.1998078E+00 -0.2624639E-03  0.4813621E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1921934E-03 -0.2000000E+00
-   01  0.4180019E+00  0.1998895E+00 -0.1687815E-03  0.4725778E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1104788E-03 -0.2000000E+00
-   01  0.4276743E+00  0.1999466E+00 -0.9443845E-04  0.4500204E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.5337098E-04 -0.2000000E+00
-   01  0.4373462E+00  0.1999777E+00 -0.5247978E-04  0.4196221E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2234712E-04 -0.2000000E+00
-   01  0.4470183E+00  0.1999881E+00 -0.3628911E-04  0.3819554E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1187588E-04 -0.2000000E+00
-   01  0.4566948E+00  0.1999829E+00 -0.3609191E-04  0.3362687E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1705760E-04 -0.2000000E+00
-   01  0.4663809E+00  0.1999705E+00 -0.4101487E-04  0.2842490E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2947204E-04 -0.2000000E+00
-   01  0.4760724E+00  0.1999567E+00 -0.4693529E-04  0.2322293E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.4333201E-04 -0.2000000E+00
-   01  0.4857646E+00  0.1999430E+00 -0.5150629E-04  0.1814479E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.5699907E-04 -0.2000000E+00
-   01  0.4954585E+00  0.1999284E+00 -0.5563558E-04  0.1324893E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.7157524E-04 -0.2000000E+00
-   01  0.5051535E+00  0.1999112E+00 -0.6266724E-04  0.8505548E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8882989E-04 -0.2000000E+00
-   01  0.5148484E+00  0.1998908E+00 -0.7355423E-04  0.3778980E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1091783E-03 -0.2000000E+00
-   01  0.5245434E+00  0.1998667E+00 -0.8899922E-04 -0.9347811E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1333113E-03 -0.2000000E+00
-   01  0.5342383E+00  0.1998374E+00 -0.1106450E-03 -0.5420464E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1626306E-03 -0.2000000E+00
-   01  0.5439334E+00  0.1998042E+00 -0.1377060E-03 -0.9456006E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1957787E-03 -0.2000000E+00
-   01  0.5536285E+00  0.1997706E+00 -0.1661729E-03 -0.1293995E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2293675E-03 -0.2000000E+00
-   01  0.5633238E+00  0.1997467E+00 -0.1861274E-03 -0.1580193E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2533481E-03 -0.2000000E+00
-   01  0.5730194E+00  0.1997328E+00 -0.1972503E-03 -0.1786245E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2671635E-03 -0.2000000E+00
-   01  0.5827151E+00  0.1997275E+00 -0.2004969E-03 -0.1914839E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2725125E-03 -0.2000000E+00
-   01  0.5924110E+00  0.1997282E+00 -0.1964258E-03 -0.1988591E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2718070E-03 -0.2000000E+00
-   01  0.6021072E+00  0.1997307E+00 -0.1910485E-03 -0.2043198E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2693083E-03 -0.2000000E+00
-   01  0.6118037E+00  0.1997337E+00 -0.1878939E-03 -0.2064314E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2662511E-03 -0.2000000E+00
-   01  0.6215001E+00  0.1997353E+00 -0.1871709E-03 -0.2041363E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2646624E-03 -0.2000000E+00
-   01  0.6311966E+00  0.1997371E+00 -0.1863083E-03 -0.1975781E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2628880E-03 -0.2000000E+00
-   01  0.6408930E+00  0.1997396E+00 -0.1866393E-03 -0.1866176E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2603717E-03 -0.2000000E+00
-   01  0.6505895E+00  0.1997429E+00 -0.1874733E-03 -0.1712270E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2570912E-03 -0.2000000E+00
-   01  0.6602863E+00  0.1997463E+00 -0.1889223E-03 -0.1528741E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2537047E-03 -0.2000000E+00
-   01  0.6699832E+00  0.1997497E+00 -0.1908479E-03 -0.1335893E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2502734E-03 -0.2000000E+00
-   01  0.6796804E+00  0.1997527E+00 -0.1932454E-03 -0.1131882E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2473088E-03 -0.2000000E+00
-   01  0.6893774E+00  0.1997564E+00 -0.1944528E-03 -0.9214563E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2436449E-03 -0.2000000E+00
-   01  0.6990743E+00  0.1997606E+00 -0.1939272E-03 -0.7086692E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2393769E-03 -0.2000000E+00
-   01  0.7087712E+00  0.1997655E+00 -0.1914389E-03 -0.4969743E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2345142E-03 -0.2000000E+00
-   01  0.7184681E+00  0.1997713E+00 -0.1869250E-03 -0.2925491E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2287209E-03 -0.2000000E+00
-   01  0.7281649E+00  0.1997792E+00 -0.1791101E-03 -0.1054748E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2208240E-03 -0.2000000E+00
-   01  0.7378617E+00  0.1997909E+00 -0.1662613E-03  0.4710179E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2091493E-03 -0.2000000E+00
-   01  0.7475585E+00  0.1998073E+00 -0.1484693E-03  0.1538773E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1927481E-03 -0.2000000E+00
-   01  0.7572553E+00  0.1998262E+00 -0.1269014E-03  0.2169394E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1738054E-03 -0.2000000E+00
-   01  0.7669521E+00  0.1998460E+00 -0.1039177E-03  0.2468821E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1539986E-03 -0.2000000E+00
-   01  0.7766490E+00  0.1998651E+00 -0.8209807E-04  0.2578622E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1348889E-03 -0.2000000E+00
-   01  0.7863460E+00  0.1998820E+00 -0.6288916E-04  0.2584520E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1179685E-03 -0.2000000E+00
-   01  0.7960431E+00  0.1998954E+00 -0.4681863E-04  0.2522237E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1045646E-03 -0.2000000E+00
-   01  0.8057402E+00  0.1999051E+00 -0.3471517E-04  0.2399544E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9491463E-04 -0.2000000E+00
-   01  0.8154374E+00  0.1999120E+00 -0.2615152E-04  0.2188888E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8799566E-04 -0.2000000E+00
-   01  0.8251347E+00  0.1999164E+00 -0.2079564E-04  0.1865315E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8358803E-04 -0.2000000E+00
-   01  0.8348321E+00  0.1999188E+00 -0.1816641E-04  0.1442437E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8123156E-04 -0.2000000E+00
-   01  0.8445296E+00  0.1999189E+00 -0.1800996E-04  0.9216661E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8106373E-04 -0.2000000E+00
-   01  0.8542271E+00  0.1999162E+00 -0.2075374E-04  0.2269356E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8383724E-04 -0.2000000E+00
-   01  0.8639247E+00  0.1999118E+00 -0.2488180E-04 -0.6596251E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8817111E-04 -0.2000000E+00
-   01  0.8736224E+00  0.1999074E+00 -0.2936793E-04 -0.1612463E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9262434E-04 -0.2000000E+00
-   01  0.8833201E+00  0.1999032E+00 -0.3348732E-04 -0.2580015E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9676413E-04 -0.2000000E+00
-   01  0.8930179E+00  0.1999003E+00 -0.3690143E-04 -0.3398847E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9973078E-04 -0.2000000E+00
-   01  0.9027157E+00  0.1998990E+00 -0.3926615E-04 -0.3954182E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1009598E-03 -0.2000000E+00
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+   01  0.9025023E+00  0.2000736E+00  0.1055735E-03  0.2202755E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7355994E-04 -0.2000000E+00
+   01  0.9121994E+00  0.2000752E+00  0.9779990E-04  0.2905447E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7518264E-04 -0.2000000E+00
+   01  0.9218967E+00  0.2000777E+00  0.8979142E-04  0.3982541E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7771820E-04 -0.2000000E+00
+   01  0.9315940E+00  0.2000851E+00  0.8748203E-04  0.5446073E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.8514698E-04 -0.2000000E+00
+   01  0.9412913E+00  0.2001002E+00  0.9524218E-04  0.7241353E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1002419E-03 -0.2000000E+00
+   01  0.9509886E+00  0.2001238E+00  0.1143718E-03  0.9556668E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1237976E-03 -0.2000000E+00
+   01  0.9606858E+00  0.2001476E+00  0.1361203E-03  0.1217531E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1475829E-03 -0.2000000E+00
+   01  0.9703831E+00  0.2001646E+00  0.1552890E-03  0.1428648E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1646063E-03 -0.2000000E+00
+   01  0.9800803E+00  0.2001720E+00  0.1653492E-03  0.1544302E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1719500E-03 -0.2000000E+00
+   01  0.9897776E+00  0.2001704E+00  0.1642518E-03  0.1568039E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1704085E-03 -0.2000000E+00
+   01  0.9994750E+00  0.2001592E+00  0.1518667E-03  0.1519824E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1591584E-03 -0.2000000E+00
diff --git a/tests/multilayer/setplot.py b/tests/multilayer/setplot.py
index 6e05dfa..eee13ad 100644
--- a/tests/multilayer/setplot.py
+++ b/tests/multilayer/setplot.py
@@ -1,67 +1,68 @@
 
-""" 
+"""
 Set up the plot figures, axes, and items to be done for each frame.
 
 This module is imported by the plotting routines and then the
 function setplot is called to set the plot parameters.
-    
-""" 
-    
+
+"""
+
 from __future__ import absolute_import
-def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,  
-                       bathy_left=-1.0,      bathy_right=-0.2):
-    """Setup the plotting data objects.
+from __future__ import print_function
 
-    Input:  plotdata, an instance of pyclaw.plotters.data.ClawPlotData.
-    Output: a modified version of plotdata.
-    
-    returns plotdata object
+import os
+
+import numpy as np
+import matplotlib.pyplot as plt
 
-    """ 
+from clawpack.visclaw import geoplot, gaugetools
 
-    import os
+import clawpack.clawutil.data as clawutil
+import clawpack.amrclaw.data as amrclaw
+import clawpack.geoclaw.data
 
-    import numpy as np
-    import matplotlib.pyplot as plt
+import clawpack.geoclaw.multilayer.plot as ml_plot
 
-    from clawpack.visclaw import geoplot, gaugetools
 
-    import clawpack.clawutil.data as clawutil
-    import clawpack.amrclaw.data as amrclaw
-    import clawpack.geoclaw.data
+def setplot(plotdata=None, bathy_location=0.15, bathy_angle=0.0,
+            bathy_left=-1.0, bathy_right=-0.2):
+    """Setup the plotting data objects.
+
+    Input:  plotdata, an instance of pyclaw.plotters.data.ClawPlotData.
+    Output: a modified version of plotdata.
+
+    returns plotdata object
+
+    """
 
-    import clawpack.geoclaw.multilayer.plot as ml_plot
+    if plotdata is None:
+        from clawpack.visclaw.data import ClawPlotData
+        plotdata = ClawPlotData()
 
     # Load data from output
     clawdata = clawutil.ClawInputData(2)
-    clawdata.read(os.path.join(plotdata.outdir,'claw.data'))
-    amrdata = amrclaw.AmrclawInputData(clawdata)
-    amrdata.read(os.path.join(plotdata.outdir,'amr.data'))
-    geodata = clawpack.geoclaw.data.GeoClawData()
-    geodata.read(os.path.join(plotdata.outdir,'geoclaw.data'))
+    clawdata.read(os.path.join(plotdata.outdir, 'claw.data'))
     multilayer_data = clawpack.geoclaw.data.MultilayerData()
-    multilayer_data.read(os.path.join(plotdata.outdir,'multilayer.data'))
+    multilayer_data.read(os.path.join(plotdata.outdir, 'multilayer.data'))
 
-    def transform_c2p(x,y,x0,y0,theta):
+    def transform_c2p(x, y, x0, y0, theta):
         return ((x+x0)*np.cos(theta) - (y+y0)*np.sin(theta),
                 (x+x0)*np.sin(theta) + (y+y0)*np.cos(theta))
 
-    def transform_p2c(x,y,x0,y0,theta):
-        return ( x*np.cos(theta) + y*np.sin(theta) - x0,
+    def transform_p2c(x, y, x0, y0, theta):
+        return (x*np.cos(theta) + y*np.sin(theta) - x0,
                 -x*np.sin(theta) + y*np.cos(theta) - y0)
-        
-    
+
     # Setup bathymetry reference lines
-    with open(os.path.join(plotdata.outdir,"bathy_geometry.data"), 'r') as bathy_geometry_file:
+    with open(os.path.join(plotdata.outdir, "bathy_geometry.data"), 'r') \
+            as bathy_geometry_file:
         bathy_location = float(bathy_geometry_file.readline())
         bathy_angle = float(bathy_geometry_file.readline())
-    x = [0.0,0.0]
-    y = [0.0,1.0]
-    x1,y1 = transform_c2p(x[0],y[0],bathy_location,
-                                0.0,bathy_angle)
-    x2,y2 = transform_c2p(x[1],y[1],bathy_location,
-                                0.0,bathy_angle)
-    
+    x = [0.0, 0.0]
+    y = [0.0, 1.0]
+    x1, y1 = transform_c2p(x[0], y[0], bathy_location, 0.0, bathy_angle)
+    x2, y2 = transform_c2p(x[1], y[1], bathy_location, 0.0, bathy_angle)
+
     if abs(x1 - x2) < 10**-3:
         x = [x1, x1]
         y = [clawdata.lower[1], clawdata.upper[1]]
@@ -71,78 +72,57 @@ def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,
         y[0] = clawdata.lower[1]
         x[1] = (clawdata.upper[1] - y1) / m + x1
         y[1] = clawdata.upper[1]
-    ref_lines = [((x[0],y[0]),(x[1],y[1]))]
+    ref_lines = [((x[0], y[0]), (x[1], y[1]))]
 
     plotdata.clearfigures()
-    
     plotdata.save_frames = False
-    
+
     # ========================================================================
     #  Generic helper functions
-    # ========================================================================
     def pcolor_afteraxes(current_data):
         bathy_ref_lines(current_data)
-        gauge_locations(current_data)
-        
+
     def contour_afteraxes(current_data):
-        # gauge_locations(current_data)
-        # m_to_km_labels()
-        plt.hold(True)
+        axes = plt.gca()
         pos = -80.0 * (23e3 / 180) + 500e3 - 5e3
-        plt.plot([pos,pos],[-300e3,300e3],'b',[pos-5e3,pos-5e3],[-300e3,300e3],'y')
-        plt.hold(False)
+        axes.plot([pos, pos], [-300e3, 300e3], 'b',
+                  [pos-5e3, pos-5e3], [-300e3, 300e3], 'y')
         wind_contours(current_data)
         bathy_ref_lines(current_data)
-        
+
     def profile_afteraxes(current_data):
         pass
-        
+
     def bathy_ref_lines(current_data):
-        plt.hold(True)
+        axes = plt.gca()
         for ref_line in ref_lines:
             x1 = ref_line[0][0]
             y1 = ref_line[0][1]
             x2 = ref_line[1][0]
-            y2 =  ref_line[1][1]
-            plt.plot([x1,x2],[y1,y2],'y--',linewidth=1)
-        plt.hold(False)
-        
-    def gauge_locations(current_data,gaugenos='all'):
-        plt.hold(True)
-        gaugetools.plot_gauge_locations(current_data.plotdata, \
-             gaugenos=gaugenos, format_string='kx', add_labels=True)
-        plt.hold(False)
-
+            y2 = ref_line[1][1]
+            axes.plot([x1, x2], [y1, y2], 'y--', linewidth=1)
 
     # ========================================================================
     # Axis limits
-    #xlimits = [amrdata.xlower,amrdata.xupper]
-    xlimits = [-0.5,0.5]
-    #ylimits = [amrdata.ylower,amrdata.yupper]
-    ylimits = [-0.5,0.5]
-    eta = [multilayer_data.eta[0],multilayer_data.eta[1]]
-    top_surface_limits = [eta[0]-0.03,eta[0]+0.03]
-    internal_surface_limits = [eta[1]-0.015,eta[1]+0.015]
-    # top_surface_limits = [eta[0]-0.3,eta[0]+0.3]
-    # internal_surface_limits = [eta[1]-0.15,eta[1]+0.15]
-    top_speed_limits = [0.0,0.1]
-    internal_speed_limits = [0.0,0.03]
-    
-    # Single layer test limits
-    # top_surface_limits = [eta[0]-2.5,eta[0]+2.5]
-    # top_speed_limits = [0.0,6.0]
-    
+
+    xlimits = [-0.2, 0.4]
+    ylimits = [-0.2, 0.4]
+    eta = [multilayer_data.eta[0], multilayer_data.eta[1]]
+    top_surface_limits = [eta[0] - 0.03, eta[0] + 0.03]
+    internal_surface_limits = [eta[1] - 0.015, eta[1] + 0.015]
+    top_speed_limits = [0.0, 0.1]
+    internal_speed_limits = [0.0, 0.03]
+
     # ========================================================================
     #  Surface Elevations
-    # ========================================================================
-    plotfigure = plotdata.new_plotfigure(name='Surface', figno=0)
+    plotfigure = plotdata.new_plotfigure(name='Surface')
     plotfigure.show = True
-    plotfigure.kwargs = {'figsize':(14,4)}
-    
+    plotfigure.kwargs = {'figsize': (14, 4)}
+
     # Top surface
     plotaxes = plotfigure.new_plotaxes()
     plotaxes.title = 'Top Surface'
-    plotaxes.axescmd = 'subplot(1,2,1)'
+    plotaxes.axescmd = 'subplot(1, 2, 1)'
     plotaxes.scaled = True
     plotaxes.xlimits = xlimits
     plotaxes.ylimits = ylimits
@@ -196,10 +176,9 @@ def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,
     
     # ========================================================================
     #  Water Speed
-    # ========================================================================
-    plotfigure = plotdata.new_plotfigure(name='speed', figno=1)
+    plotfigure = plotdata.new_plotfigure(name='speed')
     plotfigure.show = True
-    plotfigure.kwargs = {'figsize':(14,4)}
+    plotfigure.kwargs = {'figsize': (14, 4)}
 
     # Top layer speed
     plotaxes = plotfigure.new_plotaxes()
@@ -207,13 +186,11 @@ def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,
     plotaxes.scaled = True
     plotaxes.xlimits = xlimits
     plotaxes.ylimits = ylimits
-    plotaxes.axescmd = 'subplot(1,2,1)'
+    plotaxes.axescmd = 'subplot(1, 2, 1)'
     plotaxes.afteraxes = pcolor_afteraxes
-    # add_speed(plotaxes,1,bounds=[0.00,0.2])
-    ml_plot.add_speed(plotaxes,1,bounds=top_speed_limits)
-    # add_speed(plotaxes,1)
+    ml_plot.add_speed(plotaxes, 1, bounds=top_speed_limits)
     ml_plot.add_land(plotaxes, 1)
-    
+
     # Bottom layer speed
     plotaxes = plotfigure.new_plotaxes()
     plotaxes.title = 'Currents - Bottom Layer'
@@ -276,147 +253,83 @@ def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,
     plotaxes.afteraxes = pcolor_afteraxes
     # add_y_velocity(plotaxes,2,bounds=[-0.8e-6,.8e-6])
     ml_plot.add_y_velocity(plotaxes,2)
-    ml_plot.add_land(plotaxes, 2)
 
+    ml_plot.add_land(plotaxes, 2)
     # ========================================================================
     #  Profile Plots
-    # ========================================================================
-    plotfigure = plotdata.new_plotfigure(name='profile', figno=4)
+    #  Note that these are not currently plotted by default - set
+    # `plotfigure.show = True` is you want this to be plotted
+    plotfigure = plotdata.new_plotfigure(name='profile')
     plotfigure.show = False
-    
+
     # Top surface
     plotaxes = plotfigure.new_plotaxes()
     plotaxes.xlimits = xlimits
-    plotaxes.ylimits = [-2000,20]
+    plotaxes.ylimits = [-1.1, 0.1]
     plotaxes.title = "Profile of depth"
     plotaxes.afteraxes = profile_afteraxes
-    
+
     slice_index = 30
-    
+
     # Internal surface
     def bathy_profile(current_data):
-        return current_data.x[:,slice_index], b(current_data)[:,slice_index]
-    
+        return current_data.x[:, slice_index], b(current_data)[:, slice_index]
+
     def lower_surface(current_data):
         if multilayer_data.init_type == 2:
-            return current_data.x[:,slice_index], eta2(current_data)[:,slice_index]
+            return current_data.x[:, slice_index],    \
+                    eta2(current_data)[:, slice_index]
         elif multilayer_data.init_type == 6:
-            return current_data.y[slice_index,:], eta2(current_data)[slice_index,:]
-        
-    
+            return current_data.y[slice_index, :],    \
+                    eta2(current_data)[slice_index, :]
+
     def upper_surface(current_data):
         if multilayer_data.init_type == 2:
-            return current_data.x[:,slice_index], eta1(current_data)[:,slice_index]
+            return current_data.x[:, slice_index],    \
+                    eta1(current_data)[:, slice_index]
         elif multilayer_data.init_type == 6:
-            return current_data.y[slice_index,:], eta1(current_data)[slice_index,:]
-        
-        
+            return current_data.y[slice_index, :],    \
+                    eta1(current_data)[slice_index, :]
+
     def top_speed(current_data):
         if multilayer_data.init_type == 2:
-            return current_data.x[:,slice_index], water_u1(current_data)[:,slice_index]
+            return current_data.x[:, slice_index],    \
+                    water_u1(current_data)[:, slice_index]
         elif multilayer_data.init_type == 6:
-            return current_data.y[slice_index,:], water_u1(current_data)[slice_index,:]
-        
+            return current_data.y[slice_index, :],    \
+                    water_u1(current_data)[slice_index, :]
+
     def bottom_speed(current_data):
         if multilayer_data.init_type == 2:
-            return current_data.x[:,slice_index], water_u2(current_data)[:,slice_index]
+            return current_data.x[:, slice_index],    \
+                    water_u2(current_data)[:, slice_index]
         elif multilayer_data.init_type == 6:
-            return current_data.y[slice_index,:], water_u2(current_data)[slice_index,:]
-    
+            return current_data.y[slice_index, :],    \
+                    water_u2(current_data)[slice_index, :]
+
     # Bathy
     plotitem = plotaxes.new_plotitem(plot_type='1d_from_2d_data')
     plotitem.map_2d_to_1d = bathy_profile
     plotitem.plot_var = 0
-    plotitem.amr_plotstyle = ['-','+','x']
+    plotitem.amr_plotstyle = ['-', '+', 'x']
     plotitem.color = 'k'
     plotitem.show = True
-    
+
     # Internal Interface
     plotitem = plotaxes.new_plotitem(plot_type='1d_from_2d_data')
     plotitem.map_2d_to_1d = lower_surface
     plotitem.plot_var = 7
-    plotitem.amr_plotstyle = ['-','+','x']
+    plotitem.amr_plotstyle = ['-', '+', 'x']
     plotitem.color = 'b'
     plotitem.show = True
-    
+
     # Upper Interface
     plotitem = plotaxes.new_plotitem(plot_type='1d_from_2d_data')
     plotitem.map_2d_to_1d = upper_surface
     plotitem.plot_var = 6
-    plotitem.amr_plotstyle = ['-','+','x']
-    plotitem.color = (0.2,0.8,1.0)
+    plotitem.amr_plotstyle = ['-', '+', 'x']
+    plotitem.color = (0.2, 0.8, 1.0)
     plotitem.show = True
-    
-    # ========================================================================
-    #  Combined Profile Plot
-    # ========================================================================
-    # add_combined_profile_plot(plotdata,0.25,direction='y',figno=120)
-    # add_combined_profile_plot(plotdata,0.8,direction='y',figno=121)
-    # 
-    # add_velocities_profile_plot(plotdata,0.25,direction='y',figno=130)
-    # add_velocities_profile_plot(plotdata,0.8,direction='y',figno=131)
-    
-        
-    # ========================================================================
-    #  Bathy Profile
-    # ========================================================================
-    plotfigure = plotdata.new_plotfigure(name='bathy_profile',figno=20)
-    plotfigure.show = False
-    
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.xlimits = xlimits
-    plotaxes.title = "Bathymetry Profile"
-    plotaxes.scaled = 'equal'
-    
-    plotitem = plotaxes.new_plotitem(plot_type='2d_imshow')
-    plotitem.plot_var = ml_plot.b
-    plotitem.imshow_cmin = -4000
-    plotitem.imshow_cmax = 10
-    plotitem.add_colorbar = True
-    plotitem.amr_celledges_show = [0,0,0]
-    plotitem.amr_patchedges_show = [1,1,1]
-    plotitem.show = True
-    
-    # ========================================================================
-    # Figures for momentum
-    # ========================================================================
-    plotfigure = plotdata.new_plotfigure(name='x-momentum', figno=13)
-    plotfigure.show = False
-
-    # Set up for axes in this figure:
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'X-Velocity'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = pcolor_afteraxes
-    
-    # Water
-    # plotitem = plotaxes.new_plotitem(plot_type='2d_pcolor')
-    # # plotitem.plot_var = geoplot.surface
-    # plotitem.plot_var = water_u
-    # plotitem.pcolor_cmap = colormaps.make_colormap({1.0:'r',0.5:'w',0.0:'b'})
-    # # plotitem.pcolor_cmin = -1.e-10
-    # # plotitem.pcolor_cmax = 1.e-10
-    # # plotitem.pcolor_cmin = -2.5 # -3.0
-    # # plotitem.pcolor_cmax = 2.5 # 3.0
-    # plotitem.add_colorbar = True
-    # plotitem.amr_celledges_show = [0,0,0]
-    # plotitem.amr_patchedges_show = [1,1,1]
-
-    # Land
-    plotitem = plotaxes.new_plotitem(plot_type='2d_pcolor')
-    plotitem.show = True
-    plotitem.plot_var = geoplot.land
-    plotitem.pcolor_cmap = geoplot.land_colors
-    plotitem.pcolor_cmin = 0.0
-    plotitem.pcolor_cmax = 80.0
-    plotitem.add_colorbar = False
-    plotitem.amr_celledges_show = [0,0,0]
-    plotitem.amr_patchedges_show = [1,1,1]
-    
-    plotfigure = plotdata.new_plotfigure(name='y-momentum', figno=14)
-    plotfigure.show = False
 
     # Set up for axes in this figure:
     plotaxes = plotfigure.new_plotaxes()
@@ -460,7 +373,7 @@ def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,
     plotaxes.ylimits = ylimits
     plotaxes.afteraxes = contour_afteraxes
     ml_plot.add_surface_elevation(plotaxes,plot_type='contour',surface=1,bounds=[-2.5,-1.5,-0.5,0.5,1.5,2.5])
-    ml_plot.add_land(plotaxes,1,plot_type='contour')
+    ml_plot.add_land(plotaxes, 1, plot_type='contour')
     
     # Internal Surface
     plotaxes = plotfigure.new_plotaxes()
@@ -471,7 +384,7 @@ def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,
     plotaxes.ylimits = ylimits
     plotaxes.afteraxes = contour_afteraxes
     ml_plot.add_surface_elevation(plotaxes,plot_type='contour',surface=2,bounds=[-2.5,-1.5,-0.5,0.5,1.5,2.5])
-    ml_plot.add_land(plotaxes,2,plot_type='contour')
+    ml_plot.add_land(plotaxes, 2, plot_type='contour')
     
     # ========================================================================
     #  Contour plot for speed
@@ -513,6 +426,26 @@ def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,
     plotitem.amr_celledges_show = 0
     plotitem.amr_patchedges_show = 0
     plotitem.show = True
+
+    # ========================================================================
+    #  Grid Cells
+    # ========================================================================
+    
+    # Figure for grid cells
+    plotfigure = plotdata.new_plotfigure(name='cells', figno=2)
+
+    # Set up for axes in this figure:
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.xlimits = xlimits
+    plotaxes.ylimits = ylimits
+    plotaxes.title = 'Grid patches'
+    plotaxes.scaled = True
+
+    # Set up for item on these axes:
+    plotitem = plotaxes.new_plotitem(plot_type='2d_patch')
+    plotitem.amr_patch_bgcolor = ['#ffeeee', '#eeeeff', '#eeffee']
+    plotitem.amr_celledges_show = [1,1,1]
+    plotitem.amr_patchedges_show = [1,1,1]
     
     # ========================================================================
     #  Vorticity Plot
@@ -547,68 +480,92 @@ def setplot(plotdata,  bathy_location=0.15,  bathy_angle=0.0,
     # plotitem.pcolor_cmax = 80.0
     # plotitem.add_colorbar = False
     # plotitem.amr_celledges_show = [0,0,0]
-    
+
     # ========================================================================
     #  Figures for gauges
-    # ========================================================================
-    def plot_regression_gauges(cd, plot_var=(3, 7)):
-        import clawpack.pyclaw.gauges as gauges
-        import numpy
-
-        fig = plt.gcf()
-        gauge = gauges.GaugeSolution(cd.gaugeno, path="./regression_data")
-        for (i, n) in enumerate(plot_var):
-            fig.axes[i].plot(gauge.t, gauge.q[n, :], 'k-')
 
     # Top
-    plotfigure = plotdata.new_plotfigure(name='Surface & topo', figno=300, \
-                    type='each_gauge')
+    plotfigure = plotdata.new_plotfigure(name='Surface & topo',
+                                         type='each_gauge',
+                                         figno=301)
     plotfigure.show = True
     plotfigure.clf_each_gauge = True
+    plotfigure.kwargs = {'figsize': (14, 4)}
 
     # Set up for axes in this figure:
     plotaxes = plotfigure.new_plotaxes()
-    plotaxes.xlimits = [0.0,1.0]
-    # plotaxes.ylimits = top_surface_limits
+    plotaxes.axescmd = 'subplot(1, 2, 1)'
+    plotaxes.xlimits = [0.0, 1.0]
+    plotaxes.ylimits = top_surface_limits
     plotaxes.title = 'Top Surface'
-    plotaxes.axescmd = "subplot(1, 2, 1)"
 
-    # Plot surfaces:
+    # Plot surface as blue curve:
     plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
-    plotitem.plot_var = 3
-    plotitem.plotstyle = 'ro'
+    plotitem.plot_var = 6
+    plotitem.plotstyle = 'b-'
 
-    # Bottom
+    # Set up for axes in this figure:
     plotaxes = plotfigure.new_plotaxes()
-    plotaxes.xlimits = [0.0,1.0]
+    plotaxes.axescmd = 'subplot(1, 2, 2)'
+    plotaxes.xlimits = [0.0, 1.0]
+    plotaxes.ylimits = internal_surface_limits
     plotaxes.title = 'Bottom Surface'
-    plotaxes.axescmd = "subplot(1, 2, 2)"
-    plotaxes.afteraxes = plot_regression_gauges
 
+    # Plot surface as blue curve:
     plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
     plotitem.plot_var = 7
-    plotitem.plotstyle = 'ro'
+    plotitem.plotstyle = 'b-'
 
-    # Plot topo as green curve:
-    # plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
-    # plotitem.plot_var = geoplot.gaugetopo
-    # plotitem.plotstyle = 'g+'
-    
-    #-----------------------------------------
-    
+    # =========================================================================
+    #  Other plots
+
+    # Gauge Locations - Enable to see where gauges are located
+    def locations_afteraxes(current_data, gaugenos='all'):
+        gaugetools.plot_gauge_locations(current_data.plotdata,
+                                        gaugenos=gaugenos,
+                                        format_string='kx',
+                                        add_labels=True)
+        pcolor_afteraxes(current_data)
+
+    plotfigure = plotdata.new_plotfigure(name='Gauge Locations')
+    plotfigure.show = False
+    plotfigure.kwargs = {'figsize': (14, 4)}
+
+    # Top surface
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.title = 'Top Surface'
+    plotaxes.axescmd = 'subplot(1, 2, 1)'
+    plotaxes.scaled = True
+    plotaxes.xlimits = xlimits
+    plotaxes.ylimits = ylimits
+    plotaxes.afteraxes = locations_afteraxes
+    ml_plot.add_surface_elevation(plotaxes, 1, bounds=top_surface_limits)
+    ml_plot.add_land(plotaxes, 1)
+
+    # Bottom surface
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.title = 'Internal Surface'
+    plotaxes.axescmd = 'subplot(1, 2, 2)'
+    plotaxes.scaled = True
+    plotaxes.xlimits = xlimits
+    plotaxes.ylimits = ylimits
+    plotaxes.afteraxes = locations_afteraxes
+    ml_plot.add_surface_elevation(plotaxes, 2, bounds=internal_surface_limits)
+    ml_plot.add_land(plotaxes, 2)
+
+    # -----------------------------------------
     # Parameters used only when creating html and/or latex hardcopy
     # e.g., via pyclaw.plotters.frametools.printframes:
 
-    plotdata.printfigs = True                # print figures
-    plotdata.print_format = 'png'            # file format
-    plotdata.print_framenos = 'all'          # list of frames to print
-    plotdata.print_fignos = 'all'            # list of figures to print
+    plotdata.printfigs = True               # print figures
+    plotdata.print_format = 'png'           # file format
+    plotdata.print_framenos = 'all'         # list of frames to print
+    plotdata.print_fignos = 'all'           # list of figures to print
     plotdata.html = True                    # create html files of plots?
-    plotdata.latex = False                   # create latex file of plots?
-    plotdata.latex_figsperline = 2           # layout of plots
-    plotdata.latex_framesperline = 1         # layout of plots
-    plotdata.latex_makepdf = False           # also run pdflatex?
+    plotdata.latex = False                  # create latex file of plots?
+    plotdata.latex_figsperline = 2          # layout of plots
+    plotdata.latex_framesperline = 1        # layout of plots
+    plotdata.latex_makepdf = False          # also run pdflatex?
+    plotdata.parallel = True                # make multiple frame png's at once
 
     return plotdata
-
-    
diff --git a/tests/multilayer/setrun.py b/tests/multilayer/setrun.py
index 8e2d922..0dfcf47 100644
--- a/tests/multilayer/setrun.py
+++ b/tests/multilayer/setrun.py
@@ -334,12 +334,12 @@ def setrun(claw_pkg='geoclaw'):
     amrdata = rundata.amrdata
 
     # max number of refinement levels:
-    amrdata.amr_levels_max = 1
+    amrdata.amr_levels_max = 3
 
     # List of refinement ratios at each level (length at least mxnest-1)
-    amrdata.refinement_ratios_x = [2,6]
-    amrdata.refinement_ratios_y = [2,6]
-    amrdata.refinement_ratios_t = [2,6]
+    amrdata.refinement_ratios_x = [2, 6]
+    amrdata.refinement_ratios_y = [2, 6]
+    amrdata.refinement_ratios_t = [2, 6]
 
 
     # Specify type of each aux variable in amrdata.auxtype.
diff --git a/tests/multilayer_amr/Makefile b/tests/multilayer_amr/Makefile
deleted file mode 100644
index 91fb8dc..0000000
--- a/tests/multilayer_amr/Makefile
+++ /dev/null
@@ -1,102 +0,0 @@
-# Makefile for Clawpack code in this directory.
-# This version only sets the local files and frequently changed
-# options, and then includes the standard makefile pointed to by CLAWMAKE.
-CLAWMAKE = $(CLAW)/clawutil/src/Makefile.common
-
-# See the above file for details and a list of make options, or type
-#   make .help
-# at the unix prompt.
-
-
-# Adjust these variables if desired:
-# ----------------------------------
-
-CLAW_PKG = geoclaw                  # Clawpack package to use
-EXE = xgeoclaw                 # Executable to create
-SETRUN_FILE = setrun.py        # File containing function to make data
-OUTDIR = _output               # Directory for output
-SETPLOT_FILE = setplot.py      # File containing function to set plots
-PLOTDIR = _plots               # Directory for plots
-
-RESTART = False
-
-# Environment variable FC should be set to fortran compiler, e.g. gfortran
-
-# Compiler flags can be specified here or set as an environment variable
-FFLAGS ?=
-
-# Include flags for LAPACK linking
-UNAME = $(shell uname)
-ifeq ($(UNAME), Darwin)
-	ifndef LFLAGS
-		LFLAGS = -framework accelerate $(FFLAGS)
-	else
-		LFLAGS += -framework accelerate $(FFLAGS)
-	endif
-else ifeq ($(UNAME), Linux)
-	ifeq ($(FC), ifort)
-		# Created using Intel MKL Link Line Advisor
-		# Please refer to 
-		# http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/
-		# for other installation types
-		FFLAGS += -I$(MKLROOT)/include
-		ifndef LFLAGS                                                                                                                                    
-		    LFLAGS =  -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_sequential.a -Wl,--end-group -lpthread -lm $(FFLAGS)
-		else
-		    LFLAGS +=  -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_ilp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_sequential.a -Wl,--end-group -lpthread -lm $(FFLAGS)
-		endif
-	else ifeq ($(FC), gfortran)
-		ifndef LFLAGS
-			LFLAGS = -llapack $(FFLAGS)
-		else
-			LFLAGS += -llapack $(FFLAGS)
-		endif
-	endif
-endif
-
-# ---------------------------------
-# package sources for this program:
-# ---------------------------------
-
-GEOLIB = $(CLAW)/geoclaw/src/2d/shallow
-include $(GEOLIB)/Makefile.geoclaw
-
-# ---------------------------------------
-# package sources specifically to exclude
-# (i.e. if a custom replacement source 
-#  under a different name is provided)
-# ---------------------------------------
-
-EXCLUDE_MODULES = \
-
-EXCLUDE_SOURCES = \
-
-# ----------------------------------------
-# List of custom sources for this program:
-# ----------------------------------------
-
-MODULES = \
- $(GEOLIB)/multilayer/gauges_module.f90 \
- ./qinit_module.f90
-
-SOURCES = \
-  ./qinit.f90 \
-  $(GEOLIB)/multilayer/setaux.f90 \
-  $(GEOLIB)/multilayer/b4step2.f90 \
-  $(GEOLIB)/multilayer/getmaxspeed.f90 \
-  $(GEOLIB)/multilayer/stepgrid.f \
-  $(GEOLIB)/multilayer/valout.f \
-  $(GEOLIB)/multilayer/src2.f90 \
-  $(GEOLIB)/multilayer/filpatch.f90 \
-  $(GEOLIB)/multilayer/filval.f90 \
-  $(GEOLIB)/multilayer/flag2refine2.f90 \
-  $(GEOLIB)/multilayer/step2.f90 \
-  $(GEOLIB)/multilayer/upbnd.f \
-  $(GEOLIB)/multilayer/update.f90 \
-  $(CLAW)/riemann/src/rpn2_layered_shallow_water.f90 \
-  $(CLAW)/riemann/src/rpt2_layered_shallow_water.f90 \
-  $(CLAW)/riemann/src/geoclaw_riemann_utils.f
-
-#-------------------------------------------------------------------
-# Include Makefile containing standard definitions and make options:
-include $(CLAWMAKE)
diff --git a/tests/multilayer_amr/__init__.py b/tests/multilayer_amr/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/tests/multilayer_amr/qinit.f90 b/tests/multilayer_amr/qinit.f90
deleted file mode 100644
index 910f307..0000000
--- a/tests/multilayer_amr/qinit.f90
+++ /dev/null
@@ -1,52 +0,0 @@
-subroutine qinit(meqn,mbc,mx,my,xlower,ylower,dx,dy,q,maux,aux)
-    
-    use qinit_module, only: qinit_type, add_perturbation, set_qinit
-    use geoclaw_module, only: rho
-    use multilayer_module, only: num_layers, eta_init
-    
-    implicit none
-    
-    ! Subroutine arguments
-    integer, intent(in) :: meqn,mbc,mx,my,maux
-    real(kind=8), intent(in) :: xlower,ylower,dx,dy
-    real(kind=8), intent(inout) :: q(meqn,1-mbc:mx+mbc,1-mbc:my+mbc)
-    real(kind=8), intent(inout) :: aux(maux,1-mbc:mx+mbc,1-mbc:my+mbc)
-    
-    ! Locals
-    integer :: i,j,m,layer_index
-    real(kind=8) :: eta_below
-    
-    ! Set flat state based on eta_init
-    q = 0.d0
-    do j=1,my
-        do i=1,mx
-            ! Start with bottom layer and work up, set surface below for h
-            eta_below = aux(1,i,j)
-            do m=num_layers,1,-1
-                layer_index = 3 * (m-1) + 1
-                q(layer_index,i,j) = max(0.d0,eta_init(m) - eta_below)
-                eta_below = q(layer_index,i,j) + eta_below
-                q(layer_index,i,j) = q(layer_index,i,j) * rho(m)
-            enddo
-        enddo
-    enddo
-    
-    ! Add perturbation to initial conditions
-    if (qinit_type > 0) then
-!         call set_qinit()
-        call add_perturbation(meqn,mbc,mx,my,xlower,ylower,dx,dy,q,maux,aux)
-    endif
-
-    if (.false.) then
-        open(23, file='fort.aux',status='unknown',form='formatted')
-        print *,'Writing out aux arrays'
-        print *,' '
-        do j=1,my
-            do i=1,mx
-                write(23,*) i,j,(q(m,i,j),m=1,meqn)
-            enddo
-        enddo
-        close(23)
-    endif
-    
-end subroutine qinit
\ No newline at end of file
diff --git a/tests/multilayer_amr/qinit_module.f90 b/tests/multilayer_amr/qinit_module.f90
deleted file mode 100644
index 8a637f8..0000000
--- a/tests/multilayer_amr/qinit_module.f90
+++ /dev/null
@@ -1,313 +0,0 @@
-module qinit_module
-
-    implicit none
-    save
-
-    logical, private :: module_setup = .false.
-    
-    ! Type of q initialization
-    integer, public :: qinit_type
-
-    integer, public :: min_level_qinit
-    integer, public :: max_level_qinit
-
-    ! Geometry
-    real(kind=8), public :: x_low_qinit
-    real(kind=8), public :: y_low_qinit
-    real(kind=8), public :: t_low_qinit
-    real(kind=8), public :: x_hi_qinit
-    real(kind=8), public :: y_hi_qinit
-    real(kind=8), public :: t_hi_qinit
-    real(kind=8), public :: dx_qinit
-    real(kind=8), public :: dy_qinit
-    
-    ! Work array
-    real(kind=8), private, allocatable :: qinit(:)
-
-    integer, private :: mx_qinit
-    integer, private :: my_qinit
-
-    ! Specifc types of intialization    
-    ! Type of perturbation to add
-    integer, private :: wave_family
-    real(kind=8), private :: init_location(2), epsilon
-    real(kind=8), private :: angle, sigma
-
-contains
-
-    subroutine set_qinit(fname)
-    
-        use geoclaw_module, only: GEO_PARM_UNIT
-    
-        implicit none
-        
-        ! Subroutine arguments
-        character(len=*), optional, intent(in) :: fname
-        
-        ! File handling
-        character(len=150) :: qinit_fname
-        integer, parameter :: unit = 7
-        character(len=150) :: x
-        
-        if (.not.module_setup) then
-
-            write(GEO_PARM_UNIT,*) ' '
-            write(GEO_PARM_UNIT,*) '--------------------------------------------'
-            write(GEO_PARM_UNIT,*) 'SETQINIT:'
-            write(GEO_PARM_UNIT,*) '-------------'
-            
-            ! Open the data file
-            if (present(fname)) then
-                call opendatafile(unit,fname)
-            else
-                call opendatafile(unit,"qinit.data")
-            endif
-            
-            read(unit,"(i1)") qinit_type
-            if (qinit_type == 0) then
-                ! No perturbation specified
-                write(GEO_PARM_UNIT,*)  '  qinit_type = 0, no perturbation'
-                print *,'  qinit_type = 0, no perturbation'
-                return
-            else if (qinit_type > 0 .and. qinit_type < 5) then
-                read(unit,*) qinit_fname
-                read(unit,"(2i2)") min_level_qinit, max_level_qinit
-
-                write(GEO_PARM_UNIT,*) '   min_level, max_level, qinit_fname:'
-                write(GEO_PARM_UNIT,*)  min_level_qinit, max_level_qinit, qinit_fname
-                
-                call read_qinit(qinit_fname)
-            else if (qinit_type >= 5) then
-                read(unit,*) epsilon
-                read(unit,*) init_location
-                read(unit,*) wave_family
-                read(unit,*) angle
-                read(unit,*) sigma
-
-                write(GEO_PARM_UNIT,*) " epsilon = ",  epsilon
-                write(GEO_PARM_UNIT,*) " init_location = ",  init_location
-                write(GEO_PARM_UNIT,*) " wave_family = ",  wave_family
-                write(GEO_PARM_UNIT,*) " angle = ",  angle
-                write(GEO_PARM_UNIT,*) " sigma = ",  sigma
-            endif
-
-            close(unit)
-
-            module_setup = .true.
-        end if
-
-    end subroutine set_qinit
-
-
-
-    subroutine add_perturbation(meqn,mbc,mx,my,xlower,ylower,dx,dy,q,maux,aux)
-    
-        use geoclaw_module, only: sea_level, pi, g => grav, rho
-        use multilayer_module, only: aux_layer_index, r, eta_init
-    
-        implicit none
-    
-        ! Subroutine arguments
-        integer, intent(in) :: meqn,mbc,mx,my,maux
-        real(kind=8), intent(in) :: xlower,ylower,dx,dy
-        real(kind=8), intent(inout) :: q(meqn,1-mbc:mx+mbc,1-mbc:my+mbc)
-        real(kind=8), intent(inout) :: aux(maux,1-mbc:mx+mbc,1-mbc:my+mbc)
-        
-        ! Local
-        integer :: i,j
-        real(kind=8) :: ximc,xim,x,xc,xip,xipc,yjmc,yjm,y,yc,yjp,yjpc,dq
-
-        real(kind=8) :: xmid,m,x_c,y_c, effective_b
-        real(kind=8) :: eigen_vector(6),gamma,lambda,alpha,h_1,h_2,deta
-        
-        ! Topography integral function
-        real(kind=8) :: topointegral
-
-        if (qinit_type == 4) then
-            do i = 1-mbc, mx+mbc
-                x = xlower + (i - 0.5d0)*dx
-                xim = x - 0.5d0 * dx
-                xip = x + 0.5d0 * dx
-                do j = 1-mbc, my+mbc
-                    y = ylower + (j - 0.5d0) * dy
-                    yjm = y - 0.5d0 * dy
-                    yjp = y + 0.5d0 * dy
-
-                    ! Check to see if we are in the qinit region at this grid point
-                    if ((xip > x_low_qinit).and.(xim < x_hi_qinit).and.  &
-                        (yjp > y_low_qinit).and.(yjm < y_hi_qinit)) then
-
-                        xipc = min(xip, x_hi_qinit)
-                        ximc = max(xim, x_low_qinit)
-
-                        yjpc=min(yjp,y_hi_qinit)
-                        yjmc=max(yjm,y_low_qinit)
-
-                        dq = topointegral(ximc,xipc,yjmc,yjpc,x_low_qinit, &
-                                          y_low_qinit,dx_qinit,dy_qinit,mx_qinit, &
-                                          my_qinit,qinit,1)
-                        dq = dq / ((xipc-ximc)*(yjpc-yjmc))
-
-                        effective_b = max(aux(1,i,j), eta_init(2))
-                        q(1,i,j) = max((dq-effective_b) * rho(1),0.d0)
-                    endif
-                enddo
-            enddo
-
-        else if (qinit_type > 4) then
-            do i=1,mx
-                x = xlower + (i - 0.5d0) * dx
-                do j=1,my
-                    y = ylower + (j - 0.5d0) * dy
-                    
-                    ! Test perturbations - these only work in the x-direction
-                    if (qinit_type == 5 .or. qinit_type == 6) then
-                        ! Calculate wave family for perturbation
-                        gamma = aux(aux_layer_index+1,i,j) / aux(aux_layer_index,i,j)
-                        select case(wave_family)
-                            case(1) ! Shallow water, left-going
-                                alpha = 0.5d0 * (gamma - 1.d0 + sqrt((gamma-1.d0)**2+4.d0*r*gamma))
-                                lambda = -sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
-                            case(2) ! Internal wave, left-going
-                                alpha = 0.5d0 * (gamma - 1.d0 - sqrt((gamma-1.d0)**2+4.d0*r*gamma))
-                                lambda = -sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
-                            case(3) ! Internal wave, right-going
-                                alpha = 0.5d0 * (gamma - 1.d0 - sqrt((gamma-1.d0)**2+4.d0*r*gamma))
-                                lambda = sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
-                            case(4) ! Shallow water, right-going
-                                alpha = 0.5d0 * (gamma - 1.d0 + sqrt((gamma-1.d0)**2+4.d0*r*gamma))
-                                lambda = sqrt(g*aux(aux_layer_index,i,j)*(1.d0+alpha))
-                        end select
-                        eigen_vector = [1.d0,lambda,0.d0,alpha,lambda*alpha,0.d0]
-
-                        if (qinit_type == 5) then
-                            ! Add perturbation
-                            if ((x < init_location(1)).and.(wave_family >= 3)) then
-                                q(1:3,i,j) = q(1:3,i,j) + rho(1) * epsilon * eigen_vector(1:3)
-                                q(4:6,i,j) = q(4:6,i,j) + rho(2) * epsilon * eigen_vector(4:6)
-                            else if ((x > init_location(1)).and.(wave_family < 3)) then
-                                q(1:2,i,j) = q(1:2,i,j) + rho(1) * epsilon * eigen_vector(1:2)
-                                q(4:5,i,j) = q(4:5,i,j) + rho(2) * epsilon * eigen_vector(4:5)
-                            endif
-                        ! Gaussian wave along a direction on requested wave family
-                        else if (qinit_type == 6) then
-                            ! Transform back to computational coordinates
-                            x_c = x * cos(angle) + y * sin(angle) - init_location(1)
-                            deta = epsilon * exp(-(x_c/sigma)**2)
-                            q(1,i,j) = q(1,i,j) + rho(1) * deta
-                            q(4,i,j) = q(4,i,j) + rho(2) * alpha * deta
-                        endif
-                    ! Symmetric gaussian hump
-                    else if (qinit_type == 7) then
-                        deta = epsilon * exp(-((x-init_location(1))/sigma)**2)  &
-                                       * exp(-((y-init_location(2))/sigma)**2)
-                        q(1,i,j) = q(1,i,j) + rho(1) * deta
-                    ! Shelf conditions from AN paper
-                    else if (qinit_type == 8) then
-                        alpha = 0.d0
-                        xmid = 0.5d0*(-180.e3 - 80.e3)
-                        if ((x > -130.e3).and.(x < -80.e3)) then
-                            deta = epsilon * sin((x-xmid)*pi/(-80.e3-xmid))
-                            q(4,i,j) = q(4,i,j) + rho(2) * alpha * deta
-                            q(1,i,j) = q(1,i,j) + rho(1) * deta * (1.d0 - alpha)
-                        endif
-                    ! Inundation test
-                    else if (qinit_type == 9) then
-                        x_c = (x - init_location(1)) * cos(angle) &
-                            + (y - init_location(2)) * sin(angle)
-                        deta = epsilon * exp(-(x_c/sigma)**2)
-                        q(1,i,j) = q(1,i,j) + rho(1) * deta
-                    endif
-                enddo
-            enddo
-
-        endif
-        
-    end subroutine add_perturbation
-
-        
-    ! currently only supports one file type:
-    ! x,y,z values, one per line in standard order from NW corner to SE
-    ! z is perturbation from standard depth h,hu,hv set in qinit_geo,
-    ! if iqinit = 1,2, or 3 respectively.
-    ! if iqinit = 4, the z column corresponds to the definition of the 
-    ! surface elevation eta. The depth is then set as q(i,j,1)=max(eta-b,0)
-    subroutine read_qinit(fname)
-    
-        use geoclaw_module, only: GEO_PARM_UNIT
-        
-        implicit none
-        
-        ! Subroutine arguments
-        character(len=150) :: fname
-        
-        ! Data file opening
-        integer, parameter :: unit = 19
-        integer :: i,num_points,status
-        double precision :: x,y
-        
-        print *,'  '
-        print *,'Reading qinit data from file  ', fname
-        print *,'  '
-
-        write(GEO_PARM_UNIT,*) '  '
-        write(GEO_PARM_UNIT,*) 'Reading qinit data from'
-        write(GEO_PARM_UNIT,*) fname
-        write(GEO_PARM_UNIT,*) '  '
-        
-        open(unit=unit, file=fname, iostat=status, status="unknown", &
-             form='formatted',action="read")
-        if ( status /= 0 ) then
-            print *,"Error opening file", fname
-            stop
-        endif
-        
-        ! Initialize counters
-        num_points = 0
-        mx_qinit = 0
-        
-        ! Read in first values, determines x_low and y_hi
-        read(unit,*) x_low_qinit,y_hi_qinit
-        num_points = num_points + 1
-        mx_qinit = mx_qinit + 1
-        
-        ! Sweep through first row figuring out mx
-        y = y_hi_qinit
-        do while (y_hi_qinit == y)
-            read(unit,*) x,y
-            num_points = num_points + 1
-            mx_qinit = mx_qinit + 1
-        enddo
-        ! We over count by one in the above loop
-        mx_qinit = mx_qinit - 1
-        
-        ! Continue to count the rest of the lines
-        do
-            read(unit,*,iostat=status) x,y
-            if (status /= 0) exit
-            num_points = num_points + 1
-        enddo
-        if (status > 0) then
-            print *,"ERROR:  Error reading qinit file ",fname
-            stop
-        endif
-        
-        ! Extract rest of geometry
-        x_hi_qinit = x
-        y_low_qinit = y
-        my_qinit = num_points / mx_qinit
-        dx_qinit = (x_hi_qinit - x_low_qinit) / (mx_qinit-1)
-        dy_qinit = (y_hi_qinit - y_low_qinit) / (my_qinit-1)
-        
-        rewind(unit)
-        allocate(qinit(num_points))
-        
-        ! Read and store the data this time
-        do i=1,num_points
-            read(unit,*) x,y,qinit(i)
-        enddo
-        close(unit)
-        
-    end subroutine read_qinit
-
-end module qinit_module
\ No newline at end of file
diff --git a/tests/multilayer_amr/regression_data/claw_git_status.txt b/tests/multilayer_amr/regression_data/claw_git_status.txt
deleted file mode 100644
index 14c4952..0000000
--- a/tests/multilayer_amr/regression_data/claw_git_status.txt
+++ /dev/null
@@ -1,96 +0,0 @@
-Clawpack Git Status 
-Diffs can be found in /Users/avischwarzschild/amr/clawpack/geoclaw/tests/multilayer_new/regression_data/claw_git_diffs.txt
-
-Sun, 22 Oct 2017 16:59:18 PDT
-$CLAW = /Users/avischwarzschild/amr/clawpack
-$FC = gfortran
-
-
-===========
-classic
-===========
-/Users/avischwarzschild/amr/clawpack/classic
-
---- last commit ---
-606424b Merge pull request #80 from rjleveque/wcblast
-
---- branch and status ---
-## master...origin/master
-
-
-===========
-amrclaw
-===========
-/Users/avischwarzschild/amr/clawpack/amrclaw
-
---- last commit ---
-90d404f Merge pull request #205 from rjleveque/regions_data_format
-
---- branch and status ---
-## master...origin/master
-M  src/2d/prefilp.f90
-
-
-===========
-clawutil
-===========
-/Users/avischwarzschild/amr/clawpack/clawutil
-
---- last commit ---
-5c6bd99 Merge pull request #122 from rjleveque/convert_readme_string
-
---- branch and status ---
-## master...origin/master
-
-
-===========
-pyclaw
-===========
-/Users/avischwarzschild/amr/clawpack/pyclaw
-
---- last commit ---
-696f3c73 Merge pull request #584 from rjleveque/catch_wrong_format_errors
-
---- branch and status ---
-## master...origin/master
-
-
-===========
-visclaw
-===========
-/Users/avischwarzschild/amr/clawpack/visclaw
-
---- last commit ---
-95b9545 merged from visclaw
-
---- branch and status ---
-## master...origin/master [ahead 2]
-
-
-===========
-riemann
-===========
-/Users/avischwarzschild/amr/clawpack/riemann
-
---- last commit ---
-3e44723 Revert "Removing hard coded size for aux arrays in variable acoustics solver." (#130)
-
---- branch and status ---
-## master...origin/master
-
-
-===========
-geoclaw
-===========
-/Users/avischwarzschild/amr/clawpack/geoclaw
-
---- last commit ---
-0742057 update routines (both single and multi layer) are running well in parallel now. This is only a workaround, there might exist a better solution.
-
---- branch and status ---
-## conflict-resolution
- M examples/multi-layer/plane_wave/Makefile
- M examples/tsunami/bowl-slosh/Makefile
- M examples/tsunami/chile2010/Makefile
- M tests/multilayer_amr/Makefile
- M tests/multilayer_amr/regression_tests.py
diff --git a/tests/multilayer_amr/regression_data/gauge00000.txt b/tests/multilayer_amr/regression_data/gauge00000.txt
deleted file mode 100644
index b753b49..0000000
--- a/tests/multilayer_amr/regression_data/gauge00000.txt
+++ /dev/null
@@ -1,107 +0,0 @@
-# gauge_id=     0 location=(  -0.1000000E+00  -0.0000000E+00 ) num_var=  8
- # level, time, q[  1  2  3  4  5  6], eta[  1  2], aux[]
-   01  0.0000000E+00  0.6057245E+00  0.0000000E+00  0.0000000E+00  0.4035816E+00  0.0000000E+00  0.0000000E+00  0.9306084E-02 -0.5964184E+00
-   01  0.2250000E-02  0.6057090E+00  0.3312530E-02  0.3312530E-02  0.4035721E+00  0.2082980E-02  0.2082980E-02  0.9281188E-02 -0.5964279E+00
-   01  0.1184747E-01  0.6047823E+00  0.9989230E-02  0.9989230E-02  0.4029792E+00  0.6581997E-02  0.6581997E-02  0.7761531E-02 -0.5970208E+00
-   01  0.2145348E-01  0.6027045E+00  0.6318261E-02  0.6318261E-02  0.4014181E+00  0.4474442E-02  0.4474442E-02  0.4122614E-02 -0.5985819E+00
-   01  0.3110065E-01  0.6008106E+00  0.1108826E-02  0.1108826E-02  0.4001259E+00  0.1154033E-02  0.1154033E-02  0.9364543E-03 -0.5998741E+00
-   01  0.4075282E-01  0.6000815E+00 -0.8045197E-03 -0.8045197E-03  0.3996152E+00 -0.2792774E-03 -0.2792774E-03 -0.3033499E-03 -0.6003848E+00
-   01  0.5040813E-01  0.6001733E+00 -0.4760059E-03 -0.4760059E-03  0.3996022E+00 -0.2158234E-03 -0.2158234E-03 -0.2245516E-03 -0.6003978E+00
-   01  0.6006567E-01  0.6003658E+00  0.1210938E-04  0.1210763E-04  0.3996822E+00  0.3248118E-04  0.3248383E-04  0.4797916E-04 -0.6003178E+00
-   01  0.6972503E-01  0.6004099E+00  0.1500562E-03  0.1500635E-03  0.3996670E+00  0.8484014E-04  0.8484723E-04  0.7681979E-04 -0.6003330E+00
-   01  0.7938586E-01  0.6003873E+00  0.6021765E-04  0.6021820E-04  0.3996391E+00 -0.1219540E-04 -0.1219497E-04  0.2640991E-04 -0.6003609E+00
-   01  0.8904792E-01  0.6003571E+00  0.4268844E-04  0.4046597E-04  0.3996271E+00 -0.6670445E-04 -0.6777582E-04 -0.1575514E-04 -0.6003729E+00
-   01  0.9871105E-01  0.6003477E+00  0.7442227E-04  0.5694350E-04  0.3996351E+00 -0.7817407E-04 -0.8887647E-04 -0.1720932E-04 -0.6003649E+00
-   01  0.1083751E+00  0.6003475E+00  0.8788532E-04  0.9145195E-04  0.3996555E+00 -0.8715128E-04 -0.8743818E-04  0.3003946E-05 -0.6003445E+00
-   01  0.1180400E+00  0.6003633E+00 -0.5723966E-05  0.9764158E-04  0.3996987E+00 -0.1518238E-03 -0.9479639E-04  0.6203017E-04 -0.6003013E+00
-   01  0.1277057E+00  0.6004356E+00 -0.3106975E-03  0.1039717E-03  0.3997837E+00 -0.3379185E-03 -0.9699898E-04  0.2193683E-03 -0.6002163E+00
-   01  0.1373720E+00  0.6006293E+00 -0.1027544E-02  0.1093288E-03  0.3999587E+00 -0.7713560E-03 -0.9412336E-04  0.5879904E-03 -0.6000413E+00
-   01  0.1470390E+00  0.6009269E+00 -0.2048670E-02  0.1382187E-03  0.4001919E+00 -0.1403289E-02 -0.7288328E-04  0.1118832E-02 -0.5998081E+00
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-   01  0.2340659E+00  0.5996356E+00  0.9889355E-03 -0.7412217E-03  0.3996810E+00  0.5733782E-03 -0.4999863E-03 -0.6834595E-03 -0.6003190E+00
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-   01  0.2630832E+00  0.5992711E+00  0.1646814E-02 -0.9610740E-03  0.3995078E+00  0.1037862E-02 -0.6048297E-03 -0.1221092E-02 -0.6004922E+00
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-   01  0.3114483E+00  0.5996224E+00  0.1056706E-02 -0.8156901E-03  0.3997708E+00  0.6973385E-03 -0.4938923E-03 -0.6068260E-03 -0.6002292E+00
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-   01  0.6891925E+00  0.5994117E+00  0.4601655E-03  0.1033059E-03  0.4005015E+00 -0.8539237E-04 -0.1571445E-03 -0.8678772E-04 -0.5994985E+00
-   01  0.6988874E+00  0.5995643E+00  0.3945969E-03  0.6929385E-04  0.4003664E+00 -0.2865593E-04 -0.1291955E-03 -0.6928905E-04 -0.5996336E+00
-   01  0.7085822E+00  0.5997131E+00  0.3264037E-03  0.3706658E-04  0.4002382E+00  0.2187927E-04 -0.9984152E-04 -0.4866493E-04 -0.5997618E+00
-   01  0.7182769E+00  0.5998543E+00  0.2562297E-03  0.8096048E-05  0.4001198E+00  0.6429423E-04 -0.6872586E-04 -0.2594612E-04 -0.5998802E+00
-   01  0.7279716E+00  0.5999857E+00  0.1857561E-03 -0.1558307E-04  0.4000114E+00  0.9871746E-04 -0.3596132E-04 -0.2970024E-05 -0.5999886E+00
-   01  0.7376665E+00  0.6001036E+00  0.1161084E-03 -0.3376281E-04  0.3999155E+00  0.1244738E-03 -0.2917679E-05  0.1908785E-04 -0.6000845E+00
-   01  0.7473618E+00  0.6002038E+00  0.5386184E-04 -0.4891683E-04  0.3998353E+00  0.1428486E-03  0.2785013E-04  0.3905621E-04 -0.6001647E+00
-   01  0.7570571E+00  0.6002870E+00  0.3753458E-06 -0.6155291E-04  0.3997705E+00  0.1556770E-03  0.5495852E-04  0.5752835E-04 -0.6002295E+00
-   01  0.7667526E+00  0.6003543E+00 -0.4435337E-04 -0.7140207E-04  0.3997197E+00  0.1634716E-03  0.7874371E-04  0.7400855E-04 -0.6002803E+00
-   01  0.7764481E+00  0.6004066E+00 -0.7884891E-04 -0.7709120E-04  0.3996819E+00  0.1667258E-03  0.1004660E-03  0.8852099E-04 -0.6003181E+00
-   01  0.7861434E+00  0.6004473E+00 -0.1048053E-03 -0.7807115E-04  0.3996545E+00  0.1676939E-03  0.1208502E-03  0.1018214E-03 -0.6003455E+00
-   01  0.7958388E+00  0.6004795E+00 -0.1221264E-03 -0.7456019E-04  0.3996358E+00  0.1684699E-03  0.1400273E-03  0.1153011E-03 -0.6003642E+00
-   01  0.8055344E+00  0.6005039E+00 -0.1295035E-03 -0.6604793E-04  0.3996263E+00  0.1702465E-03  0.1584086E-03  0.1302600E-03 -0.6003737E+00
-   01  0.8152304E+00  0.6005224E+00 -0.1241245E-03 -0.5209523E-04  0.3996264E+00  0.1747049E-03  0.1773036E-03  0.1488846E-03 -0.6003736E+00
-   01  0.8249268E+00  0.6005370E+00 -0.1081300E-03 -0.3271548E-04  0.3996343E+00  0.1821525E-03  0.1972082E-03  0.1713875E-03 -0.6003657E+00
-   01  0.8346234E+00  0.6005465E+00 -0.8494866E-04 -0.9974891E-05  0.3996488E+00  0.1907033E-03  0.2168847E-03  0.1952360E-03 -0.6003512E+00
-   01  0.8443201E+00  0.6005447E+00 -0.6256223E-04  0.9181928E-05  0.3996694E+00  0.1957282E-03  0.2302405E-03  0.2141385E-03 -0.6003306E+00
-   01  0.8540168E+00  0.6005252E+00 -0.5017566E-04  0.1742911E-04  0.3996963E+00  0.1903758E-03  0.2314800E-03  0.2214752E-03 -0.6003037E+00
-   01  0.8637136E+00  0.6004870E+00 -0.4776987E-04  0.1399643E-04  0.3997274E+00  0.1738991E-03  0.2198243E-03  0.2143805E-03 -0.6002726E+00
-   01  0.8734107E+00  0.6004299E+00 -0.5798350E-04 -0.3898899E-05  0.3997612E+00  0.1441817E-03  0.1948601E-03  0.1911415E-03 -0.6002388E+00
-   01  0.8831079E+00  0.6003562E+00 -0.7574303E-04 -0.3285683E-04  0.3997983E+00  0.1038355E-03  0.1587766E-03  0.1544750E-03 -0.6002017E+00
-   01  0.8928051E+00  0.6002715E+00 -0.9172952E-04 -0.6241532E-04  0.3998410E+00  0.5919369E-04  0.1182280E-03  0.1124453E-03 -0.6001590E+00
-   01  0.9025022E+00  0.6001850E+00 -0.9516239E-04 -0.7999409E-04  0.3998909E+00  0.1833325E-04  0.8181973E-04  0.7584390E-04 -0.6001091E+00
-   01  0.9121994E+00  0.6001028E+00 -0.7520241E-04 -0.7751816E-04  0.3999493E+00 -0.1068959E-04  0.5564645E-04  0.5207211E-04 -0.6000507E+00
-   01  0.9218966E+00  0.6000268E+00 -0.3805725E-04 -0.5689093E-04  0.4000155E+00 -0.3005783E-04  0.3914643E-04  0.4227589E-04 -0.5999845E+00
-   01  0.9315939E+00  0.5999563E+00  0.8466260E-05 -0.2546542E-04  0.4000854E+00 -0.4246618E-04  0.2814040E-04  0.4171174E-04 -0.5999146E+00
-   01  0.9412913E+00  0.5998894E+00  0.5346635E-04  0.6810582E-05  0.4001542E+00 -0.5340154E-04  0.1736160E-04  0.4363143E-04 -0.5998458E+00
-   01  0.9509886E+00  0.5998259E+00  0.8926405E-04  0.3234982E-04  0.4002184E+00 -0.6711051E-04  0.3697187E-05  0.4428845E-04 -0.5997816E+00
-   01  0.9606858E+00  0.5997687E+00  0.1117538E-03  0.4867927E-04  0.4002741E+00 -0.8496406E-04 -0.1304754E-04  0.4278679E-04 -0.5997259E+00
-   01  0.9703830E+00  0.5997208E+00  0.1219120E-03  0.5797603E-04  0.4003208E+00 -0.1052275E-03 -0.3128138E-04  0.4160999E-04 -0.5996792E+00
-   01  0.9800803E+00  0.5996827E+00  0.1240465E-03  0.6320913E-04  0.4003601E+00 -0.1254163E-03 -0.4917406E-04  0.4277953E-04 -0.5996399E+00
-   01  0.9897776E+00  0.5996543E+00  0.1234244E-03  0.6665351E-04  0.4003928E+00 -0.1422421E-03 -0.6524618E-04  0.4712570E-04 -0.5996072E+00
-   01  0.9994750E+00  0.5996345E+00  0.1238387E-03  0.6958532E-04  0.4004192E+00 -0.1535235E-03 -0.7864020E-04  0.5365065E-04 -0.5995808E+00
diff --git a/tests/multilayer_amr/regression_data/gauge00001.txt b/tests/multilayer_amr/regression_data/gauge00001.txt
deleted file mode 100644
index 88745ca..0000000
--- a/tests/multilayer_amr/regression_data/gauge00001.txt
+++ /dev/null
@@ -1,107 +0,0 @@
-# gauge_id=     1 location=(   0.0000000E+00   0.0000000E+00 ) num_var=  8
- # level, time, q[  1  2  3  4  5  6], eta[  1  2], aux[]
-   01  0.0000000E+00  0.6000000E+00  0.0000000E+00  0.0000000E+00  0.4000000E+00  0.0000000E+00  0.0000000E+00  0.2117894E-07 -0.6000000E+00
-   01  0.2250000E-02  0.6000167E+00  0.2598827E-04  0.2598827E-04  0.4000104E+00  0.1486537E-04  0.1486537E-04  0.2705976E-04 -0.5999896E+00
-   01  0.1184747E-01  0.6006796E+00  0.1235182E-02  0.1235182E-02  0.4004090E+00  0.7052776E-03  0.7052776E-03  0.1088574E-02 -0.5995910E+00
-   01  0.2145348E-01  0.6022834E+00  0.5281054E-02  0.5281054E-02  0.4015686E+00  0.3174879E-02  0.3174879E-02  0.3852007E-02 -0.5984314E+00
-   01  0.3110065E-01  0.6035474E+00  0.8380131E-02  0.8380131E-02  0.4024588E+00  0.5198318E-02  0.5198318E-02  0.6006219E-02 -0.5975412E+00
-   01  0.4075282E-01  0.6031453E+00  0.7219564E-02  0.7219555E-02  0.4021710E+00  0.4635713E-02  0.4635714E-02  0.5316283E-02 -0.5978290E+00
-   01  0.5040813E-01  0.6015144E+00  0.3442637E-02  0.3442477E-02  0.4011292E+00  0.2353589E-02  0.2353608E-02  0.2643545E-02 -0.5988708E+00
-   01  0.6006567E-01  0.6000996E+00  0.4149433E-03  0.4115392E-03  0.4003246E+00  0.4224236E-03  0.4223031E-03  0.4242204E-03 -0.5996754E+00
-   01  0.6972503E-01  0.5995559E+00 -0.4938148E-03 -0.5148398E-03  0.4000830E+00 -0.2062011E-03 -0.2133986E-03 -0.3611617E-03 -0.5999170E+00
-   01  0.7938586E-01  0.5995975E+00 -0.3609462E-03 -0.3320410E-03  0.4001830E+00 -0.1290337E-03 -0.1081913E-03 -0.2195149E-03 -0.5998170E+00
-   01  0.8904792E-01  0.5998055E+00 -0.3016910E-03 -0.4962596E-04  0.4003108E+00 -0.6786972E-04  0.8461391E-04  0.1163150E-03 -0.5996892E+00
-   01  0.9871105E-01  0.5999950E+00 -0.7045856E-03 -0.4884958E-05  0.4004054E+00 -0.2990061E-03  0.1234501E-03  0.4003343E-03 -0.5995946E+00
-   01  0.1083751E+00  0.6002398E+00 -0.1562724E-02 -0.6180136E-04  0.4005331E+00 -0.8208535E-03  0.8744213E-04  0.7728916E-03 -0.5994669E+00
-   01  0.1180400E+00  0.6005697E+00 -0.2606787E-02 -0.6676881E-04  0.4007035E+00 -0.1474570E-02  0.7535243E-04  0.1273136E-02 -0.5992965E+00
-   01  0.1277057E+00  0.6008356E+00 -0.3377010E-02  0.2503004E-04  0.4008283E+00 -0.1972826E-02  0.1199872E-03  0.1663931E-02 -0.5991717E+00
-   01  0.1373720E+00  0.6009269E+00 -0.3552932E-02  0.1180821E-03  0.4008368E+00 -0.2116963E-02  0.1651781E-03  0.1763623E-02 -0.5991632E+00
-   01  0.1470390E+00  0.6008383E+00 -0.3142856E-02  0.1086686E-03  0.4007252E+00 -0.1896295E-02  0.1466957E-03  0.1563455E-02 -0.5992748E+00
-   01  0.1567065E+00  0.6006550E+00 -0.2448408E-02 -0.7202094E-05  0.4005724E+00 -0.1496811E-02  0.5859896E-04  0.1227367E-02 -0.5994276E+00
-   01  0.1663747E+00  0.6004328E+00 -0.1607848E-02 -0.1971098E-03  0.4003988E+00 -0.1005386E-02 -0.7935465E-04  0.8316515E-03 -0.5996012E+00
-   01  0.1760433E+00  0.6002268E+00 -0.8410719E-03 -0.3863321E-03  0.4002435E+00 -0.5567871E-03 -0.2197619E-03  0.4702954E-03 -0.5997565E+00
-   01  0.1857125E+00  0.6000352E+00 -0.1866233E-03 -0.5213787E-03  0.4001092E+00 -0.1850900E-03 -0.3290583E-03  0.1443440E-03 -0.5998908E+00
-   01  0.1953822E+00  0.5998390E+00  0.3687635E-03 -0.6166372E-03  0.3999922E+00  0.1141776E-03 -0.4138873E-03 -0.1687967E-03 -0.6000078E+00
-   01  0.2050523E+00  0.5996357E+00  0.8367993E-03 -0.7264659E-03  0.3998947E+00  0.3512486E-03 -0.5064383E-03 -0.4695936E-03 -0.6001053E+00
-   01  0.2147230E+00  0.5994370E+00  0.1216642E-02 -0.8701904E-03  0.3998204E+00  0.5261075E-03 -0.6217628E-03 -0.7426208E-03 -0.6001796E+00
-   01  0.2243942E+00  0.5992508E+00  0.1493734E-02 -0.1009718E-02  0.3997797E+00  0.6301331E-03 -0.7362317E-03 -0.9694606E-03 -0.6002203E+00
-   01  0.2340659E+00  0.5990864E+00  0.1655240E-02 -0.1076656E-02  0.3997808E+00  0.6535559E-03 -0.8078925E-03 -0.1132796E-02 -0.6002192E+00
-   01  0.2437382E+00  0.5989662E+00  0.1720234E-02 -0.1052127E-02  0.3998221E+00  0.6138825E-03 -0.8221739E-03 -0.1211710E-02 -0.6001779E+00
-   01  0.2534107E+00  0.5988864E+00  0.1738329E-02 -0.9874271E-03  0.3999072E+00  0.5411527E-03 -0.8076885E-03 -0.1206357E-02 -0.6000928E+00
-   01  0.2630832E+00  0.5988388E+00  0.1734007E-02 -0.9040249E-03  0.4000309E+00  0.4507091E-03 -0.7798207E-03 -0.1130355E-02 -0.5999691E+00
-   01  0.2727559E+00  0.5988169E+00  0.1707477E-02 -0.8233156E-03  0.4001860E+00  0.3442869E-03 -0.7507388E-03 -0.9970493E-03 -0.5998140E+00
-   01  0.2824287E+00  0.5988132E+00  0.1659885E-02 -0.7406893E-03  0.4003610E+00  0.2265795E-03 -0.7191798E-03 -0.8257782E-03 -0.5996390E+00
-   01  0.2921017E+00  0.5988105E+00  0.1587083E-02 -0.6390887E-03  0.4005364E+00  0.9970094E-04 -0.6748717E-03 -0.6530624E-03 -0.5994636E+00
-   01  0.3017749E+00  0.5987964E+00  0.1494473E-02 -0.4986564E-03  0.4006984E+00 -0.3134105E-04 -0.6042673E-03 -0.5051944E-03 -0.5993016E+00
-   01  0.3114483E+00  0.5987712E+00  0.1383693E-02 -0.3293366E-03  0.4008429E+00 -0.1643749E-03 -0.5132615E-03 -0.3858997E-03 -0.5991571E+00
-   01  0.3211218E+00  0.5987396E+00  0.1257896E-02 -0.1513521E-03  0.4009701E+00 -0.2967349E-03 -0.4140917E-03 -0.2903036E-03 -0.5990299E+00
-   01  0.3307954E+00  0.5987021E+00  0.1121524E-02  0.2552346E-04  0.4010816E+00 -0.4265822E-03 -0.3144755E-03 -0.2163026E-03 -0.5989184E+00
-   01  0.3404692E+00  0.5986674E+00  0.9824696E-03  0.1765681E-03  0.4011805E+00 -0.5487626E-03 -0.2299167E-03 -0.1520868E-03 -0.5988195E+00
-   01  0.3501430E+00  0.5986395E+00  0.8540162E-03  0.2877093E-03  0.4012726E+00 -0.6572921E-03 -0.1697190E-03 -0.8785192E-04 -0.5987274E+00
-   01  0.3598170E+00  0.5986250E+00  0.7464181E-03  0.3577956E-03  0.4013566E+00 -0.7445982E-03 -0.1345927E-03 -0.1841998E-04 -0.5986434E+00
-   01  0.3694912E+00  0.5986310E+00  0.6651636E-03  0.3866087E-03  0.4014273E+00 -0.8027110E-03 -0.1239200E-03  0.5831662E-04 -0.5985727E+00
-   01  0.3791655E+00  0.5986591E+00  0.6215163E-03  0.3694467E-03  0.4014823E+00 -0.8224662E-03 -0.1406097E-03  0.1414377E-03 -0.5985177E+00
-   01  0.3888399E+00  0.5987149E+00  0.6270931E-03  0.3001255E-03  0.4015199E+00 -0.7945097E-03 -0.1870359E-03  0.2348265E-03 -0.5984801E+00
-   01  0.3985145E+00  0.5987957E+00  0.6904093E-03  0.1889180E-03  0.4015440E+00 -0.7161537E-03 -0.2568615E-03  0.3396586E-03 -0.5984560E+00
-   01  0.4081894E+00  0.5988934E+00  0.7901628E-03  0.5694768E-04  0.4015523E+00 -0.6007582E-03 -0.3379826E-03  0.4456591E-03 -0.5984477E+00
-   01  0.4178642E+00  0.5989926E+00  0.8808795E-03 -0.5964519E-04  0.4015358E+00 -0.4775509E-03 -0.4081613E-03  0.5283888E-03 -0.5984642E+00
-   01  0.4275371E+00  0.5990780E+00  0.9037555E-03 -0.1202217E-03  0.4014852E+00 -0.3840086E-03 -0.4416030E-03  0.5631709E-03 -0.5985148E+00
-   01  0.4372096E+00  0.5991404E+00  0.8294674E-03 -0.1069317E-03  0.4013962E+00 -0.3413658E-03 -0.4245925E-03  0.5366836E-03 -0.5986038E+00
-   01  0.4468820E+00  0.5991801E+00  0.6720366E-03 -0.2839557E-04  0.4012775E+00 -0.3478784E-03 -0.3639159E-03  0.4576340E-03 -0.5987225E+00
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-   01  0.4662435E+00  0.5992705E+00  0.2706491E-03  0.1224206E-03  0.4010210E+00 -0.4102525E-03 -0.2383883E-03  0.2914854E-03 -0.5989790E+00
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-   01  0.7861434E+00  0.6000319E+00  0.1098045E-03 -0.3709912E-04  0.4000773E+00 -0.8266235E-04  0.8697449E-04  0.1092085E-03 -0.5999227E+00
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-   01  0.8540168E+00  0.5998511E+00  0.1731304E-03  0.9795293E-04  0.4003107E+00 -0.9125862E-04  0.3325737E-04  0.1617961E-03 -0.5996893E+00
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-   01  0.8734107E+00  0.5998315E+00  0.2162170E-03  0.1497119E-03  0.4003475E+00 -0.4879851E-04  0.3292070E-04  0.1789571E-03 -0.5996525E+00
-   01  0.8831079E+00  0.5998164E+00  0.2166946E-03  0.1554865E-03  0.4003546E+00 -0.3790809E-04  0.2218358E-04  0.1710190E-03 -0.5996454E+00
-   01  0.8928051E+00  0.5997965E+00  0.1981453E-03  0.1445342E-03  0.4003538E+00 -0.3758734E-04  0.2645820E-05  0.1502777E-03 -0.5996462E+00
-   01  0.9025022E+00  0.5997731E+00  0.1607566E-03  0.1165680E-03  0.4003452E+00 -0.4760676E-04 -0.2584601E-04  0.1183010E-03 -0.5996548E+00
-   01  0.9121994E+00  0.5997501E+00  0.1127352E-03  0.7950891E-04  0.4003306E+00 -0.6333256E-04 -0.5831886E-04  0.8070416E-04 -0.5996694E+00
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-   01  0.9994750E+00  0.5999466E+00 -0.3492419E-04  0.7033081E-04  0.4001135E+00  0.1030687E-04 -0.1002771E-03  0.6006517E-04 -0.5998865E+00
diff --git a/tests/multilayer_amr/regression_data/gauge00002.txt b/tests/multilayer_amr/regression_data/gauge00002.txt
deleted file mode 100644
index 53e34ae..0000000
--- a/tests/multilayer_amr/regression_data/gauge00002.txt
+++ /dev/null
@@ -1,107 +0,0 @@
-# gauge_id=     2 location=(   0.1000000E+00   0.0000000E+00 ) num_var=  8
- # level, time, q[  1  2  3  4  5  6], eta[  1  2], aux[]
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-   01  0.5040813E-01  0.6032667E+00  0.7515551E-02  0.7480174E-02  0.4020817E+00  0.4642381E-02  0.4582055E-02  0.5348323E-02 -0.5979183E+00
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-   01  0.4275371E+00  0.6010703E+00 -0.4063274E-03 -0.3215828E-03  0.3993372E+00  0.2898780E-03 -0.3708648E-04  0.4074656E-03 -0.6006628E+00
-   01  0.4372096E+00  0.6009734E+00 -0.1588356E-03 -0.4240365E-03  0.3994993E+00  0.3508101E-03 -0.1575340E-03  0.4727924E-03 -0.6005007E+00
-   01  0.4468820E+00  0.6008472E+00  0.7932181E-04 -0.4940886E-03  0.3996758E+00  0.3900759E-03 -0.2579286E-03  0.5229892E-03 -0.6003242E+00
-   01  0.4565585E+00  0.6006682E+00  0.2499043E-03 -0.4965775E-03  0.3998653E+00  0.3676119E-03 -0.3161143E-03  0.5335345E-03 -0.6001347E+00
-   01  0.4662435E+00  0.6004641E+00  0.3116572E-03 -0.4475523E-03  0.4000485E+00  0.2731628E-03 -0.3408954E-03  0.5126508E-03 -0.5999515E+00
-   01  0.4759341E+00  0.6002588E+00  0.3080771E-03 -0.3581292E-03  0.4002117E+00  0.1406616E-03 -0.3361154E-03  0.4705257E-03 -0.5997883E+00
-   01  0.4856250E+00  0.6000658E+00  0.2379974E-03 -0.2413683E-03  0.4003520E+00 -0.2389307E-04 -0.3086553E-03  0.4178444E-03 -0.5996480E+00
-   01  0.4953168E+00  0.5999158E+00  0.1767983E-03 -0.1287920E-03  0.4004597E+00 -0.1639743E-03 -0.2742943E-03  0.3754418E-03 -0.5995403E+00
-   01  0.5050091E+00  0.5998218E+00  0.1703616E-03 -0.4929603E-04  0.4005391E+00 -0.2482778E-03 -0.2502414E-03  0.3608894E-03 -0.5994609E+00
-   01  0.5147016E+00  0.5997756E+00  0.2124991E-03  0.1132872E-04  0.4005850E+00 -0.2770024E-03 -0.2304004E-03  0.3605371E-03 -0.5994150E+00
-   01  0.5243940E+00  0.5997479E+00  0.2831173E-03  0.7027345E-04  0.4006107E+00 -0.2749740E-03 -0.2034329E-03  0.3585713E-03 -0.5993893E+00
-   01  0.5340867E+00  0.5997291E+00  0.3484061E-03  0.1310997E-03  0.4006149E+00 -0.2628713E-03 -0.1680278E-03  0.3440086E-03 -0.5993851E+00
-   01  0.5437794E+00  0.5997061E+00  0.3918284E-03  0.1879449E-03  0.4006059E+00 -0.2560242E-03 -0.1288246E-03  0.3120048E-03 -0.5993941E+00
-   01  0.5534720E+00  0.5996765E+00  0.4119889E-03  0.2208188E-03  0.4005920E+00 -0.2551426E-03 -0.9886528E-04  0.2685338E-03 -0.5994080E+00
-   01  0.5631649E+00  0.5996480E+00  0.4150830E-03  0.2333471E-03  0.4005708E+00 -0.2561095E-03 -0.7606161E-04  0.2188703E-03 -0.5994292E+00
-   01  0.5728584E+00  0.5996220E+00  0.4088473E-03  0.2237426E-03  0.4005409E+00 -0.2539667E-03 -0.6244269E-04  0.1628886E-03 -0.5994591E+00
-   01  0.5825524E+00  0.5996018E+00  0.4025108E-03  0.1935529E-03  0.4005010E+00 -0.2443407E-03 -0.5795173E-04  0.1028384E-03 -0.5994990E+00
-   01  0.5922468E+00  0.5995931E+00  0.3984032E-03  0.1510436E-03  0.4004506E+00 -0.2249736E-03 -0.5768709E-04  0.4375443E-04 -0.5995494E+00
-   01  0.6019412E+00  0.5995980E+00  0.3991566E-03  0.1034065E-03  0.4003934E+00 -0.1973002E-03 -0.5650553E-04 -0.8635347E-05 -0.5996066E+00
-   01  0.6116356E+00  0.5996170E+00  0.4043610E-03  0.5475208E-04  0.4003344E+00 -0.1625298E-03 -0.5307312E-04 -0.4864001E-04 -0.5996656E+00
-   01  0.6213299E+00  0.5996493E+00  0.4127037E-03  0.8136092E-05  0.4002767E+00 -0.1214785E-03 -0.4765935E-04 -0.7395784E-04 -0.5997233E+00
-   01  0.6310242E+00  0.5996951E+00  0.4218896E-03 -0.3709765E-04  0.4002198E+00 -0.7599234E-04 -0.4021711E-04 -0.8509828E-04 -0.5997802E+00
-   01  0.6407186E+00  0.5997472E+00  0.4265616E-03 -0.8103038E-04  0.4001671E+00 -0.3322765E-04 -0.3155924E-04 -0.8567027E-04 -0.5998329E+00
-   01  0.6504131E+00  0.5998021E+00  0.4237443E-03 -0.1183581E-03  0.4001189E+00  0.3649542E-05 -0.1928191E-04 -0.7899239E-04 -0.5998811E+00
-   01  0.6601077E+00  0.5998560E+00  0.4088460E-03 -0.1466406E-03  0.4000765E+00  0.3239013E-04 -0.4222349E-05 -0.6746286E-04 -0.5999235E+00
-   01  0.6698025E+00  0.5999093E+00  0.3780841E-03 -0.1597518E-03  0.4000387E+00  0.5336192E-04  0.1629717E-04 -0.5194047E-04 -0.5999613E+00
-   01  0.6794975E+00  0.5999624E+00  0.3326302E-03 -0.1574453E-03  0.4000044E+00  0.6731474E-04  0.4261638E-04 -0.3323160E-04 -0.5999956E+00
-   01  0.6891925E+00  0.6000121E+00  0.2779337E-03 -0.1434429E-03  0.3999750E+00  0.7615867E-04  0.7252759E-04 -0.1284819E-04 -0.6000250E+00
-   01  0.6988874E+00  0.6000552E+00  0.2177938E-03 -0.1231230E-03  0.3999532E+00  0.8164192E-04  0.1010094E-03  0.8382956E-05 -0.6000468E+00
-   01  0.7085822E+00  0.6000917E+00  0.1576441E-03 -0.1014904E-03  0.3999376E+00  0.8639714E-04  0.1245434E-03  0.2934977E-04 -0.6000624E+00
-   01  0.7182769E+00  0.6001249E+00  0.1015893E-03 -0.8296282E-04  0.3999249E+00  0.9231748E-04  0.1429120E-03  0.4985468E-04 -0.6000751E+00
-   01  0.7279716E+00  0.6001544E+00  0.5080725E-04 -0.6926624E-04  0.3999153E+00  0.9922994E-04  0.1550440E-03  0.6975162E-04 -0.6000847E+00
-   01  0.7376665E+00  0.6001788E+00  0.5757482E-05 -0.5993818E-04  0.3999098E+00  0.1064866E-03  0.1614515E-03  0.8864930E-04 -0.6000902E+00
-   01  0.7473618E+00  0.6002009E+00 -0.3051892E-04 -0.5508799E-04  0.3999054E+00  0.1105732E-03  0.1628646E-03  0.1063340E-03 -0.6000946E+00
-   01  0.7570571E+00  0.6002182E+00 -0.5878926E-04 -0.5428592E-04  0.3999032E+00  0.1115912E-03  0.1602271E-03  0.1214251E-03 -0.6000968E+00
-   01  0.7667526E+00  0.6002261E+00 -0.7953302E-04 -0.5712084E-04  0.3999067E+00  0.1067837E-03  0.1537409E-03  0.1327744E-03 -0.6000933E+00
-   01  0.7764481E+00  0.6002277E+00 -0.9503996E-04 -0.6329586E-04  0.3999132E+00  0.9741251E-04  0.1436485E-03  0.1409032E-03 -0.6000868E+00
-   01  0.7861434E+00  0.6002213E+00 -0.1071856E-03 -0.7235536E-04  0.3999239E+00  0.8393880E-04  0.1303264E-03  0.1451355E-03 -0.6000761E+00
-   01  0.7958388E+00  0.6002072E+00 -0.1174268E-03 -0.8146516E-04  0.3999382E+00  0.6700687E-04  0.1156349E-03  0.1453613E-03 -0.6000618E+00
-   01  0.8055344E+00  0.6001860E+00 -0.1254397E-03 -0.8832767E-04  0.3999564E+00  0.4744257E-04  0.1002650E-03  0.1423397E-03 -0.6000436E+00
-   01  0.8152304E+00  0.6001587E+00 -0.1291648E-03 -0.9135564E-04  0.3999780E+00  0.2687846E-04  0.8492949E-04  0.1366957E-03 -0.6000220E+00
-   01  0.8249268E+00  0.6001325E+00 -0.1278579E-03 -0.9022172E-04  0.3999975E+00  0.8947862E-05  0.7044192E-04  0.1300089E-03 -0.6000025E+00
-   01  0.8346234E+00  0.6001070E+00 -0.1199505E-03 -0.8386381E-04  0.4000160E+00 -0.4105865E-05  0.5772319E-04  0.1230235E-03 -0.5999840E+00
-   01  0.8443201E+00  0.6000852E+00 -0.1041092E-03 -0.7208094E-04  0.4000322E+00 -0.1059193E-04  0.4691099E-04  0.1173582E-03 -0.5999678E+00
-   01  0.8540168E+00  0.6000708E+00 -0.7838703E-04 -0.5427615E-04  0.4000457E+00 -0.9925360E-05  0.4011451E-04  0.1165206E-03 -0.5999543E+00
-   01  0.8637136E+00  0.6000646E+00 -0.4073936E-04 -0.3062775E-04  0.4000582E+00 -0.1848966E-05  0.3704314E-04  0.1228074E-03 -0.5999418E+00
-   01  0.8734107E+00  0.6000666E+00  0.5704459E-05 -0.1859131E-05  0.4000686E+00  0.1178289E-04  0.3706896E-04  0.1352214E-03 -0.5999314E+00
-   01  0.8831079E+00  0.6000750E+00  0.5485478E-04  0.2859196E-04  0.4000755E+00  0.2694374E-04  0.3927332E-04  0.1505088E-03 -0.5999245E+00
-   01  0.8928051E+00  0.6000866E+00  0.9520365E-04  0.5222619E-04  0.4000763E+00  0.3721637E-04  0.3880445E-04  0.1629591E-03 -0.5999237E+00
-   01  0.9025022E+00  0.6000970E+00  0.1131538E-03  0.6349940E-04  0.4000709E+00  0.3556079E-04  0.3006799E-04  0.1679133E-03 -0.5999291E+00
-   01  0.9121994E+00  0.6001034E+00  0.1041276E-03  0.5946165E-04  0.4000582E+00  0.1932253E-04  0.1026723E-04  0.1616533E-03 -0.5999418E+00
-   01  0.9218966E+00  0.6001063E+00  0.7162347E-04  0.4162689E-04  0.4000380E+00 -0.9748356E-05 -0.2096305E-04  0.1442290E-03 -0.5999620E+00
-   01  0.9315939E+00  0.6001088E+00  0.2173580E-04  0.1641013E-04  0.4000087E+00 -0.4636504E-04 -0.5995306E-04  0.1175194E-03 -0.5999913E+00
-   01  0.9412913E+00  0.6001180E+00 -0.2993546E-04 -0.5804837E-05  0.3999688E+00 -0.7810389E-04 -0.1001966E-03  0.8677057E-04 -0.6000312E+00
-   01  0.9509886E+00  0.6001365E+00 -0.6761657E-04 -0.1477681E-04  0.3999240E+00 -0.9493397E-04 -0.1349981E-03  0.6052699E-04 -0.6000760E+00
-   01  0.9606858E+00  0.6001652E+00 -0.7760497E-04 -0.7777636E-06  0.3998798E+00 -0.9046041E-04 -0.1569805E-03  0.4503937E-04 -0.6001202E+00
-   01  0.9703830E+00  0.6001987E+00 -0.6390812E-04  0.3143593E-04  0.3998392E+00 -0.6617454E-04 -0.1677033E-03  0.3794246E-04 -0.6001608E+00
-   01  0.9800803E+00  0.6002353E+00 -0.3484318E-04  0.6852656E-04  0.3998004E+00 -0.2795750E-04 -0.1746722E-03  0.3568228E-04 -0.6001996E+00
-   01  0.9897776E+00  0.6002732E+00 -0.1248014E-05  0.1020409E-03  0.3997603E+00  0.1587331E-04 -0.1831219E-03  0.3349656E-04 -0.6002397E+00
-   01  0.9994750E+00  0.6003128E+00  0.2528782E-04  0.1271682E-03  0.3997184E+00  0.5681987E-04 -0.1955059E-03  0.3119586E-04 -0.6002816E+00
diff --git a/tests/multilayer_amr/regression_data/gauge00003.txt b/tests/multilayer_amr/regression_data/gauge00003.txt
deleted file mode 100644
index 6cf20c8..0000000
--- a/tests/multilayer_amr/regression_data/gauge00003.txt
+++ /dev/null
@@ -1,107 +0,0 @@
-# gauge_id=     3 location=(   0.2000000E+00   0.0000000E+00 ) num_var=  8
- # level, time, q[  1  2  3  4  5  6], eta[  1  2], aux[]
-   01  0.0000000E+00  0.2497754E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4977544E-01 -0.2000000E+00
-   01  0.2250000E-02  0.2497754E+00  0.8706804E-18  0.1914591E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4977544E-01 -0.2000000E+00
-   01  0.1184747E-01  0.2497754E+00 -0.4931455E-16 -0.2105883E-16  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4977544E-01 -0.2000000E+00
-   01  0.2145348E-01  0.2497754E+00 -0.1508822E-07 -0.1469438E-07  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4977543E-01 -0.2000000E+00
-   01  0.3110065E-01  0.2497761E+00  0.1014026E-05  0.6639796E-06  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4977612E-01 -0.2000000E+00
-   01  0.4075282E-01  0.2498052E+00  0.4055962E-04  0.3160080E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4980518E-01 -0.2000000E+00
-   01  0.5040813E-01  0.2501413E+00  0.4431712E-03  0.4004033E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5014126E-01 -0.2000000E+00
-   01  0.6006567E-01  0.2515930E+00  0.2103022E-02  0.1774045E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5159296E-01 -0.2000000E+00
-   01  0.6972503E-01  0.2541791E+00  0.5210432E-02  0.3985659E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5417912E-01 -0.2000000E+00
-   01  0.7938586E-01  0.2565772E+00  0.8028132E-02  0.6063806E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5657715E-01 -0.2000000E+00
-   01  0.8904792E-01  0.2568571E+00  0.8309380E-02  0.6216694E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5685709E-01 -0.2000000E+00
-   01  0.9871105E-01  0.2553229E+00  0.6317232E-02  0.5025632E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5532286E-01 -0.2000000E+00
-   01  0.1083751E+00  0.2528928E+00  0.3304595E-02  0.2933414E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5289280E-01 -0.2000000E+00
-   01  0.1180400E+00  0.2507274E+00  0.7336243E-03  0.1216899E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5072745E-01 -0.2000000E+00
-   01  0.1277057E+00  0.2494482E+00 -0.7434822E-03  0.3590730E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4944820E-01 -0.2000000E+00
-   01  0.1373720E+00  0.2488221E+00 -0.1402945E-02 -0.9889381E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4882214E-01 -0.2000000E+00
-   01  0.1470390E+00  0.2486529E+00 -0.1556928E-02 -0.2651577E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4865288E-01 -0.2000000E+00
-   01  0.1567065E+00  0.2487605E+00 -0.1396324E-02 -0.2887430E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4876045E-01 -0.2000000E+00
-   01  0.1663747E+00  0.2488939E+00 -0.1167191E-02 -0.3626628E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4889389E-01 -0.2000000E+00
-   01  0.1760433E+00  0.2489924E+00 -0.9515969E-03 -0.5111875E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4899237E-01 -0.2000000E+00
-   01  0.1857125E+00  0.2490188E+00 -0.8107272E-03 -0.7367430E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4901882E-01 -0.2000000E+00
-   01  0.1953822E+00  0.2489546E+00 -0.7495783E-03 -0.1008330E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4895459E-01 -0.2000000E+00
-   01  0.2050523E+00  0.2488303E+00 -0.7555974E-03 -0.1291269E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4883029E-01 -0.2000000E+00
-   01  0.2147230E+00  0.2487207E+00 -0.7739807E-03 -0.1516875E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4872066E-01 -0.2000000E+00
-   01  0.2243942E+00  0.2486658E+00 -0.7595075E-03 -0.1646346E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4866575E-01 -0.2000000E+00
-   01  0.2340659E+00  0.2486878E+00 -0.6935374E-03 -0.1665684E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4868781E-01 -0.2000000E+00
-   01  0.2437382E+00  0.2487893E+00 -0.5784767E-03 -0.1572799E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4878934E-01 -0.2000000E+00
-   01  0.2534107E+00  0.2489410E+00 -0.4286098E-03 -0.1401124E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4894101E-01 -0.2000000E+00
-   01  0.2630832E+00  0.2491160E+00 -0.2662723E-03 -0.1179404E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4911602E-01 -0.2000000E+00
-   01  0.2727559E+00  0.2492981E+00 -0.1102844E-03 -0.9187793E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4929807E-01 -0.2000000E+00
-   01  0.2824287E+00  0.2494751E+00  0.3690185E-04 -0.6463227E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4947510E-01 -0.2000000E+00
-   01  0.2921017E+00  0.2496404E+00  0.1747433E-03 -0.3929524E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4964036E-01 -0.2000000E+00
-   01  0.3017749E+00  0.2497948E+00  0.3188387E-03 -0.1791523E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4979485E-01 -0.2000000E+00
-   01  0.3114483E+00  0.2499400E+00  0.4711822E-03 -0.2271102E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4994000E-01 -0.2000000E+00
-   01  0.3211218E+00  0.2500696E+00  0.6160153E-03  0.8857737E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5006955E-01 -0.2000000E+00
-   01  0.3307954E+00  0.2501707E+00  0.7327865E-03  0.1653349E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5017066E-01 -0.2000000E+00
-   01  0.3404692E+00  0.2502379E+00  0.8064743E-03  0.2217918E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5023789E-01 -0.2000000E+00
-   01  0.3501430E+00  0.2502685E+00  0.8322068E-03  0.2712250E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5026853E-01 -0.2000000E+00
-   01  0.3598170E+00  0.2502663E+00  0.8158645E-03  0.3155398E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5026632E-01 -0.2000000E+00
-   01  0.3694912E+00  0.2502322E+00  0.7625029E-03  0.3510617E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5023221E-01 -0.2000000E+00
-   01  0.3791655E+00  0.2501754E+00  0.6798505E-03  0.3761888E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5017540E-01 -0.2000000E+00
-   01  0.3888399E+00  0.2501090E+00  0.5852427E-03  0.3886125E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5010897E-01 -0.2000000E+00
-   01  0.3985145E+00  0.2500379E+00  0.4835425E-03  0.3885066E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5003790E-01 -0.2000000E+00
-   01  0.4081894E+00  0.2499748E+00  0.3885447E-03  0.3749183E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4997478E-01 -0.2000000E+00
-   01  0.4178642E+00  0.2499259E+00  0.3137851E-03  0.3437850E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4992587E-01 -0.2000000E+00
-   01  0.4275371E+00  0.2498955E+00  0.2630249E-03  0.3020552E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4989548E-01 -0.2000000E+00
-   01  0.4372096E+00  0.2498938E+00  0.2488929E-03  0.2578244E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4989376E-01 -0.2000000E+00
-   01  0.4468820E+00  0.2499233E+00  0.2709924E-03  0.2187526E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4992332E-01 -0.2000000E+00
-   01  0.4565585E+00  0.2499864E+00  0.3338780E-03  0.1826717E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4998642E-01 -0.2000000E+00
-   01  0.4662435E+00  0.2500798E+00  0.4360487E-03  0.1530501E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5007977E-01 -0.2000000E+00
-   01  0.4759341E+00  0.2501860E+00  0.5537864E-03  0.1359556E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5018603E-01 -0.2000000E+00
-   01  0.4856250E+00  0.2502666E+00  0.6280927E-03  0.1390343E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5026661E-01 -0.2000000E+00
-   01  0.4953168E+00  0.2503081E+00  0.6439550E-03  0.1495871E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5030813E-01 -0.2000000E+00
-   01  0.5050091E+00  0.2502985E+00  0.5844665E-03  0.1735844E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5029851E-01 -0.2000000E+00
-   01  0.5147016E+00  0.2502465E+00  0.4630342E-03  0.2069743E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5024653E-01 -0.2000000E+00
-   01  0.5243940E+00  0.2501833E+00  0.3326945E-03  0.2342225E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5018327E-01 -0.2000000E+00
-   01  0.5340867E+00  0.2501213E+00  0.2172367E-03  0.2388474E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5012127E-01 -0.2000000E+00
-   01  0.5437794E+00  0.2500724E+00  0.1303093E-03  0.2297791E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5007241E-01 -0.2000000E+00
-   01  0.5534720E+00  0.2500346E+00  0.7591052E-04  0.1995618E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5003461E-01 -0.2000000E+00
-   01  0.5631649E+00  0.2499957E+00  0.3653635E-04  0.1510442E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4999570E-01 -0.2000000E+00
-   01  0.5728584E+00  0.2499503E+00  0.1177509E-05  0.8757862E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4995027E-01 -0.2000000E+00
-   01  0.5825524E+00  0.2498969E+00 -0.3992520E-04  0.1742884E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4989691E-01 -0.2000000E+00
-   01  0.5922468E+00  0.2498388E+00 -0.8782346E-04 -0.5000502E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4983883E-01 -0.2000000E+00
-   01  0.6019412E+00  0.2497820E+00 -0.1365268E-03 -0.1103828E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4978196E-01 -0.2000000E+00
-   01  0.6116356E+00  0.2497334E+00 -0.1762132E-03 -0.1585424E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4973341E-01 -0.2000000E+00
-   01  0.6213299E+00  0.2496954E+00 -0.2026636E-03 -0.1939251E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4969535E-01 -0.2000000E+00
-   01  0.6310242E+00  0.2496725E+00 -0.2129670E-03 -0.2134564E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4967250E-01 -0.2000000E+00
-   01  0.6407186E+00  0.2496671E+00 -0.2055951E-03 -0.2192038E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4966713E-01 -0.2000000E+00
-   01  0.6504131E+00  0.2496769E+00 -0.1819638E-03 -0.2133788E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4967690E-01 -0.2000000E+00
-   01  0.6601077E+00  0.2496994E+00 -0.1427934E-03 -0.2005164E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4969936E-01 -0.2000000E+00
-   01  0.6698025E+00  0.2497317E+00 -0.9263639E-04 -0.1821093E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4973167E-01 -0.2000000E+00
-   01  0.6794975E+00  0.2497713E+00 -0.3527840E-04 -0.1583725E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4977133E-01 -0.2000000E+00
-   01  0.6891925E+00  0.2498117E+00  0.2064314E-04 -0.1297677E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4981165E-01 -0.2000000E+00
-   01  0.6988874E+00  0.2498469E+00  0.6820380E-04 -0.9875986E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4984691E-01 -0.2000000E+00
-   01  0.7085822E+00  0.2498748E+00  0.1041222E-03 -0.6640515E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4987480E-01 -0.2000000E+00
-   01  0.7182769E+00  0.2498955E+00  0.1275670E-03 -0.3374045E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4989547E-01 -0.2000000E+00
-   01  0.7279716E+00  0.2499098E+00  0.1394348E-03 -0.2389538E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4990980E-01 -0.2000000E+00
-   01  0.7376665E+00  0.2499205E+00  0.1450084E-03  0.2591602E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4992045E-01 -0.2000000E+00
-   01  0.7473618E+00  0.2499294E+00  0.1462556E-03  0.4910733E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4992945E-01 -0.2000000E+00
-   01  0.7570571E+00  0.2499371E+00  0.1445534E-03  0.6581038E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4993711E-01 -0.2000000E+00
-   01  0.7667526E+00  0.2499436E+00  0.1409533E-03  0.7677372E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4994360E-01 -0.2000000E+00
-   01  0.7764481E+00  0.2499484E+00  0.1356396E-03  0.8256660E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4994836E-01 -0.2000000E+00
-   01  0.7861434E+00  0.2499504E+00  0.1278418E-03  0.8350269E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4995035E-01 -0.2000000E+00
-   01  0.7958388E+00  0.2499493E+00  0.1177500E-03  0.8041705E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4994929E-01 -0.2000000E+00
-   01  0.8055344E+00  0.2499447E+00  0.1047916E-03  0.7436274E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4994473E-01 -0.2000000E+00
-   01  0.8152304E+00  0.2499353E+00  0.8911951E-04  0.6593413E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4993530E-01 -0.2000000E+00
-   01  0.8249268E+00  0.2499213E+00  0.7198054E-04  0.5630411E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4992128E-01 -0.2000000E+00
-   01  0.8346234E+00  0.2499036E+00  0.5411659E-04  0.4697429E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4990364E-01 -0.2000000E+00
-   01  0.8443201E+00  0.2498844E+00  0.3669168E-04  0.4050714E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4988438E-01 -0.2000000E+00
-   01  0.8540168E+00  0.2498658E+00  0.2120058E-04  0.3766848E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4986583E-01 -0.2000000E+00
-   01  0.8637136E+00  0.2498515E+00  0.1014605E-04  0.4042697E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4985151E-01 -0.2000000E+00
-   01  0.8734107E+00  0.2498442E+00  0.5383671E-05  0.4961188E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4984423E-01 -0.2000000E+00
-   01  0.8831079E+00  0.2498478E+00  0.1079041E-04  0.6634011E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4984778E-01 -0.2000000E+00
-   01  0.8928051E+00  0.2498630E+00  0.2778056E-04  0.9143204E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4986297E-01 -0.2000000E+00
-   01  0.9025022E+00  0.2498884E+00  0.5457463E-04  0.1230791E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4988840E-01 -0.2000000E+00
-   01  0.9121994E+00  0.2499177E+00  0.8355148E-04  0.1551644E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4991773E-01 -0.2000000E+00
-   01  0.9218966E+00  0.2499425E+00  0.1056679E-03  0.1801432E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4994247E-01 -0.2000000E+00
-   01  0.9315939E+00  0.2499542E+00  0.1104387E-03  0.1938135E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4995418E-01 -0.2000000E+00
-   01  0.9412913E+00  0.2499476E+00  0.9465261E-04  0.1911961E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4994761E-01 -0.2000000E+00
-   01  0.9509886E+00  0.2499215E+00  0.5878075E-04  0.1705958E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4992150E-01 -0.2000000E+00
-   01  0.9606858E+00  0.2498802E+00  0.2408589E-05  0.1405934E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4988016E-01 -0.2000000E+00
-   01  0.9703830E+00  0.2498292E+00 -0.6133611E-04  0.1041841E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4982916E-01 -0.2000000E+00
-   01  0.9800803E+00  0.2497879E+00 -0.1105418E-03  0.7411317E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4978790E-01 -0.2000000E+00
-   01  0.9897776E+00  0.2497638E+00 -0.1370504E-03  0.5562894E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4976376E-01 -0.2000000E+00
-   01  0.9994750E+00  0.2497565E+00 -0.1389741E-03  0.4681198E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4975649E-01 -0.2000000E+00
diff --git a/tests/multilayer_amr/regression_data/gauge00004.txt b/tests/multilayer_amr/regression_data/gauge00004.txt
deleted file mode 100644
index ca1684a..0000000
--- a/tests/multilayer_amr/regression_data/gauge00004.txt
+++ /dev/null
@@ -1,107 +0,0 @@
-# gauge_id=     4 location=(   0.3000000E+00   0.0000000E+00 ) num_var=  8
- # level, time, q[  1  2  3  4  5  6], eta[  1  2], aux[]
-   01  0.0000000E+00  0.2000000E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.2250000E-02  0.2000000E+00 -0.1413392E-32  0.2318458E-18  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.1184747E-01  0.2000000E+00  0.1794110E-18  0.1220633E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.2145348E-01  0.2000000E+00  0.1039888E-17  0.2242488E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.3110065E-01  0.2000000E+00  0.2258260E-17  0.3331249E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.4075282E-01  0.2000000E+00  0.3684217E-17  0.4765266E-17  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2775558E-16 -0.2000000E+00
-   01  0.5040813E-01  0.2000000E+00 -0.1707116E-08 -0.2915847E-09  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1426916E-08 -0.2000000E+00
-   01  0.6006567E-01  0.2000000E+00  0.9460739E-08  0.1312289E-08  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.8173653E-08 -0.2000000E+00
-   01  0.6972503E-01  0.2000005E+00  0.5394627E-06  0.1278703E-06  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4716761E-06 -0.2000000E+00
-   01  0.7938586E-01  0.2000067E+00  0.7539667E-05  0.2167535E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.6672264E-05 -0.2000000E+00
-   01  0.8904792E-01  0.2000438E+00  0.4977540E-04  0.1663031E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4377041E-04 -0.2000000E+00
-   01  0.9871105E-01  0.2003461E+00  0.4111662E-03  0.1111910E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3460877E-03 -0.2000000E+00
-   01  0.1083751E+00  0.2015793E+00  0.1762603E-02  0.7683077E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1579279E-02 -0.2000000E+00
-   01  0.1180400E+00  0.2034564E+00  0.3878271E-02  0.2133422E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3456443E-02 -0.2000000E+00
-   01  0.1277057E+00  0.2050689E+00  0.5859912E-02  0.3456295E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5068883E-02 -0.2000000E+00
-   01  0.1373720E+00  0.2055986E+00  0.6605598E-02  0.4178217E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5598642E-02 -0.2000000E+00
-   01  0.1470390E+00  0.2050623E+00  0.6066554E-02  0.4099730E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5062280E-02 -0.2000000E+00
-   01  0.1567065E+00  0.2040363E+00  0.4918333E-02  0.3466876E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4036300E-02 -0.2000000E+00
-   01  0.1663747E+00  0.2025328E+00  0.3180632E-02  0.2485894E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.2532809E-02 -0.2000000E+00
-   01  0.1760433E+00  0.2009946E+00  0.1377350E-02  0.1360684E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.9945634E-03 -0.2000000E+00
-   01  0.1857125E+00  0.1998982E+00  0.6218819E-05  0.4653211E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1018480E-03 -0.2000000E+00
-   01  0.1953822E+00  0.1993083E+00 -0.7442811E-03 -0.1522427E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.6917111E-03 -0.2000000E+00
-   01  0.2050523E+00  0.1990415E+00 -0.1020533E-02 -0.5333667E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9584513E-03 -0.2000000E+00
-   01  0.2147230E+00  0.1989155E+00 -0.1087648E-02 -0.8208679E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1084507E-02 -0.2000000E+00
-   01  0.2243942E+00  0.1988387E+00 -0.1094292E-02 -0.1051182E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1161292E-02 -0.2000000E+00
-   01  0.2340659E+00  0.1987743E+00 -0.1086016E-02 -0.1239940E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1225663E-02 -0.2000000E+00
-   01  0.2437382E+00  0.1987301E+00 -0.1059381E-02 -0.1382072E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1269873E-02 -0.2000000E+00
-   01  0.2534107E+00  0.1987089E+00 -0.1020930E-02 -0.1463308E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1291136E-02 -0.2000000E+00
-   01  0.2630832E+00  0.1987237E+00 -0.9625436E-03 -0.1491086E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1276334E-02 -0.2000000E+00
-   01  0.2727559E+00  0.1987969E+00 -0.8792750E-03 -0.1444210E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1203076E-02 -0.2000000E+00
-   01  0.2824287E+00  0.1989172E+00 -0.7573765E-03 -0.1329776E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1082818E-02 -0.2000000E+00
-   01  0.2921017E+00  0.1990866E+00 -0.5988593E-03 -0.1147264E-02  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9133622E-03 -0.2000000E+00
-   01  0.3017749E+00  0.1993028E+00 -0.4181649E-03 -0.9114911E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.6972146E-03 -0.2000000E+00
-   01  0.3114483E+00  0.1995387E+00 -0.2301330E-03 -0.6347540E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.4613196E-03 -0.2000000E+00
-   01  0.3211218E+00  0.1997516E+00 -0.5976452E-04 -0.3500067E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2484115E-03 -0.2000000E+00
-   01  0.3307954E+00  0.1999224E+00  0.7208878E-04 -0.9290766E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.7755372E-04 -0.2000000E+00
-   01  0.3404692E+00  0.2000592E+00  0.1723730E-03  0.1192459E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5919425E-04 -0.2000000E+00
-   01  0.3501430E+00  0.2001708E+00  0.2552132E-03  0.2863304E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1707672E-03 -0.2000000E+00
-   01  0.3598170E+00  0.2002654E+00  0.3228760E-03  0.4122914E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.2653841E-03 -0.2000000E+00
-   01  0.3694912E+00  0.2003447E+00  0.3828390E-03  0.4927158E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3447282E-03 -0.2000000E+00
-   01  0.3791655E+00  0.2004168E+00  0.4389302E-03  0.5313561E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4167720E-03 -0.2000000E+00
-   01  0.3888399E+00  0.2004816E+00  0.4829951E-03  0.5431940E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4815972E-03 -0.2000000E+00
-   01  0.3985145E+00  0.2005242E+00  0.5091222E-03  0.5417271E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5241845E-03 -0.2000000E+00
-   01  0.4081894E+00  0.2005395E+00  0.5078661E-03  0.5341395E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5395219E-03 -0.2000000E+00
-   01  0.4178642E+00  0.2005349E+00  0.4873804E-03  0.5173873E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5349052E-03 -0.2000000E+00
-   01  0.4275371E+00  0.2005163E+00  0.4550029E-03  0.4902769E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5162928E-03 -0.2000000E+00
-   01  0.4372096E+00  0.2004716E+00  0.3988187E-03  0.4533550E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4715796E-03 -0.2000000E+00
-   01  0.4468820E+00  0.2004021E+00  0.3161598E-03  0.4065614E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4021394E-03 -0.2000000E+00
-   01  0.4565585E+00  0.2003178E+00  0.2172368E-03  0.3489576E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3178115E-03 -0.2000000E+00
-   01  0.4662435E+00  0.2002403E+00  0.1297800E-03  0.2845833E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.2403131E-03 -0.2000000E+00
-   01  0.4759341E+00  0.2001910E+00  0.7674714E-04  0.2303008E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1909673E-03 -0.2000000E+00
-   01  0.4856250E+00  0.2001727E+00  0.5983930E-04  0.1866626E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1726971E-03 -0.2000000E+00
-   01  0.4953168E+00  0.2001677E+00  0.5821503E-04  0.1517419E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1676595E-03 -0.2000000E+00
-   01  0.5050091E+00  0.2001849E+00  0.8313845E-04  0.1242386E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1849096E-03 -0.2000000E+00
-   01  0.5147016E+00  0.2002390E+00  0.1574366E-03  0.1066472E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.2390250E-03 -0.2000000E+00
-   01  0.5243940E+00  0.2003284E+00  0.2774759E-03  0.1024253E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3283557E-03 -0.2000000E+00
-   01  0.5340867E+00  0.2004213E+00  0.4043008E-03  0.1119152E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4212504E-03 -0.2000000E+00
-   01  0.5437794E+00  0.2004830E+00  0.4878267E-03  0.1348066E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4830308E-03 -0.2000000E+00
-   01  0.5534720E+00  0.2005097E+00  0.5222048E-03  0.1622427E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5097172E-03 -0.2000000E+00
-   01  0.5631649E+00  0.2005107E+00  0.5225170E-03  0.1860347E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.5107350E-03 -0.2000000E+00
-   01  0.5728584E+00  0.2004994E+00  0.5095080E-03  0.2022123E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4994468E-03 -0.2000000E+00
-   01  0.5825524E+00  0.2004675E+00  0.4686674E-03  0.2097385E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4675149E-03 -0.2000000E+00
-   01  0.5922468E+00  0.2004151E+00  0.4039997E-03  0.2035234E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.4151321E-03 -0.2000000E+00
-   01  0.6019412E+00  0.2003452E+00  0.3208109E-03  0.1795424E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3452250E-03 -0.2000000E+00
-   01  0.6116356E+00  0.2002709E+00  0.2343027E-03  0.1385586E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.2709101E-03 -0.2000000E+00
-   01  0.6213299E+00  0.2001911E+00  0.1489102E-03  0.8335920E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1911231E-03 -0.2000000E+00
-   01  0.6310242E+00  0.2001100E+00  0.6926469E-04  0.2070638E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1100255E-03 -0.2000000E+00
-   01  0.6407186E+00  0.2000384E+00 -0.1587567E-05 -0.3481419E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3837043E-04 -0.2000000E+00
-   01  0.6504131E+00  0.1999798E+00 -0.6329699E-04 -0.7521995E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.2020930E-04 -0.2000000E+00
-   01  0.6601077E+00  0.1999346E+00 -0.1117266E-03 -0.9702587E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.6542013E-04 -0.2000000E+00
-   01  0.6698025E+00  0.1999048E+00 -0.1479473E-03 -0.1002670E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9523700E-04 -0.2000000E+00
-   01  0.6794975E+00  0.1998958E+00 -0.1620255E-03 -0.8959308E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1042308E-03 -0.2000000E+00
-   01  0.6891925E+00  0.1999010E+00 -0.1644885E-03 -0.6697076E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.9899729E-04 -0.2000000E+00
-   01  0.6988874E+00  0.1999171E+00 -0.1641919E-03 -0.3410569E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.8291954E-04 -0.2000000E+00
-   01  0.7085822E+00  0.1999424E+00 -0.1624843E-03  0.7917266E-05  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.5763004E-04 -0.2000000E+00
-   01  0.7182769E+00  0.1999807E+00 -0.1533622E-03  0.5883939E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00 -0.1932483E-04 -0.2000000E+00
-   01  0.7279716E+00  0.2000289E+00 -0.1338070E-03  0.1098875E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.2887909E-04 -0.2000000E+00
-   01  0.7376665E+00  0.2000801E+00 -0.1060958E-03  0.1510105E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.8005249E-04 -0.2000000E+00
-   01  0.7473618E+00  0.2001228E+00 -0.7590706E-04  0.1787898E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1228346E-03 -0.2000000E+00
-   01  0.7570571E+00  0.2001542E+00 -0.4794119E-04  0.1939284E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1541940E-03 -0.2000000E+00
-   01  0.7667526E+00  0.2001714E+00 -0.2551164E-04  0.1970785E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1714122E-03 -0.2000000E+00
-   01  0.7764481E+00  0.2001772E+00 -0.7792619E-05  0.1923158E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1772232E-03 -0.2000000E+00
-   01  0.7861434E+00  0.2001731E+00  0.7318335E-05  0.1794691E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1730985E-03 -0.2000000E+00
-   01  0.7958388E+00  0.2001611E+00  0.2269198E-04  0.1590761E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1610918E-03 -0.2000000E+00
-   01  0.8055344E+00  0.2001434E+00  0.3857721E-04  0.1324285E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1433721E-03 -0.2000000E+00
-   01  0.8152304E+00  0.2001237E+00  0.5478616E-04  0.1022012E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1237197E-03 -0.2000000E+00
-   01  0.8249268E+00  0.2001061E+00  0.7137465E-04  0.7328580E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1061483E-03 -0.2000000E+00
-   01  0.8346234E+00  0.2000924E+00  0.8678124E-04  0.4921797E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.9239086E-04 -0.2000000E+00
-   01  0.8443201E+00  0.2000829E+00  0.1004848E-03  0.3140808E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.8289976E-04 -0.2000000E+00
-   01  0.8540168E+00  0.2000769E+00  0.1108387E-03  0.1995258E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7692480E-04 -0.2000000E+00
-   01  0.8637136E+00  0.2000724E+00  0.1166061E-03  0.1354610E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7238948E-04 -0.2000000E+00
-   01  0.8734107E+00  0.2000701E+00  0.1185220E-03  0.1198385E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7014350E-04 -0.2000000E+00
-   01  0.8831079E+00  0.2000703E+00  0.1178819E-03  0.1425623E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7030076E-04 -0.2000000E+00
-   01  0.8928051E+00  0.2000715E+00  0.1145379E-03  0.1871982E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7151175E-04 -0.2000000E+00
-   01  0.9025022E+00  0.2000730E+00  0.1084445E-03  0.2425283E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7298529E-04 -0.2000000E+00
-   01  0.9121994E+00  0.2000747E+00  0.1006733E-03  0.3136426E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7472000E-04 -0.2000000E+00
-   01  0.9218966E+00  0.2000773E+00  0.9261675E-04  0.4220401E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.7726190E-04 -0.2000000E+00
-   01  0.9315939E+00  0.2000847E+00  0.9026287E-04  0.5685679E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.8468546E-04 -0.2000000E+00
-   01  0.9412913E+00  0.2000998E+00  0.9796216E-04  0.7483695E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.9975900E-04 -0.2000000E+00
-   01  0.9509886E+00  0.2001233E+00  0.1170342E-03  0.9805377E-04  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1233414E-03 -0.2000000E+00
-   01  0.9606858E+00  0.2001471E+00  0.1387254E-03  0.1241916E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1470708E-03 -0.2000000E+00
-   01  0.9703830E+00  0.2001641E+00  0.1579007E-03  0.1452562E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1640726E-03 -0.2000000E+00
-   01  0.9800803E+00  0.2001714E+00  0.1679455E-03  0.1567805E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1713758E-03 -0.2000000E+00
-   01  0.9897776E+00  0.2001698E+00  0.1668462E-03  0.1590887E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1697942E-03 -0.2000000E+00
-   01  0.9994750E+00  0.2001585E+00  0.1544692E-03  0.1542338E-03  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.1585306E-03 -0.2000000E+00
diff --git a/tests/multilayer_amr/regression_tests.py b/tests/multilayer_amr/regression_tests.py
deleted file mode 100644
index ddf3bca..0000000
--- a/tests/multilayer_amr/regression_tests.py
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env python
-
-r"""Multilayer Shallow Water Test Case
-
-To create new regression data use
-    `python regression_tests.py True`
-"""
-
-from __future__ import absolute_import
-import os
-import sys
-import unittest
-
-import numpy
-
-import clawpack.geoclaw.test as test
-import clawpack.geoclaw.topotools as topotools
-
-
-def transform_p2c(x,y,x0,y0,theta):
-    return ( x*numpy.cos(theta) + y*numpy.sin(theta) - x0,
-            -x*numpy.sin(theta) + y*numpy.cos(theta) - y0)
-
-# Bathymetry
-def bathy_step(x, y, location=0.15, angle=0.0, left=-1.0, right=-0.2):
-    x_c,y_c = transform_p2c(x, y, location, 0.0, angle)
-    return ((x_c <= 0.0) * left 
-          + (x_c >  0.0) * right)
-
-
-class MultilayerTest(test.GeoClawRegressionTest):
-
-    r"""Multilayer plane-wave regression test for GeoClaw
-
-    initial condition angle = numpy.pi / 4.0
-    bathy_angle = numpy.pi / 8.0
-
-    """
-
-    def setUp(self):
-
-        super(MultilayerTest, self).setUp()
-
-        # Make topography
-        topo_func = lambda x, y: bathy_step(x, y, location=0.15, 
-                                                  angle=numpy.pi / 8.0, 
-                                                  left=-1.0, right=-0.2)
-        topo = topotools.Topography(topo_func=topo_func)
-        topo.x = numpy.linspace(-1.16, 2.16, 166)
-        topo.y = numpy.linspace(-1.16, 2.16, 166)
-        topo.write(os.path.join(self.temp_path, "jump_topo.topotype2"))
-
-
-    def runTest(self, save=False):
-        r"""Test multi-layer basic plane-waves."""
-
-        # Load and write data, change init-condition's starting angle
-        self.load_rundata()
-        self.rundata.qinit_data.angle = numpy.pi / 4.0
-        self.write_rundata_objects()
-
-        # Run code and check surfaces
-        self.run_code()
-        self.check_gauges(save=save, gauge_id=0, indices=(6, 7))
-        self.check_gauges(save=save, gauge_id=1, indices=(6, 7))
-        self.check_gauges(save=save, gauge_id=2, indices=(6, 7))
-        self.check_gauges(save=save, gauge_id=3, indices=(6, 7))
-        self.check_gauges(save=save, gauge_id=4, indices=(6, 7))
-
-        # If we have gotten here then we do not need to copy the run results
-        self.success = True
-
-
-if __name__=="__main__":
-    if len(sys.argv) > 1:
-        if bool(sys.argv[1]):
-            # Fake the setup and save out output
-            test = MultilayerTest()
-            try:
-                test.setUp()
-                test.runTest(save=True)
-            finally:
-                test.tearDown()
-            sys.exit(0)
-    unittest.main()
diff --git a/tests/multilayer_amr/setplot.py b/tests/multilayer_amr/setplot.py
deleted file mode 100644
index eee13ad..0000000
--- a/tests/multilayer_amr/setplot.py
+++ /dev/null
@@ -1,571 +0,0 @@
-
-"""
-Set up the plot figures, axes, and items to be done for each frame.
-
-This module is imported by the plotting routines and then the
-function setplot is called to set the plot parameters.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import print_function
-
-import os
-
-import numpy as np
-import matplotlib.pyplot as plt
-
-from clawpack.visclaw import geoplot, gaugetools
-
-import clawpack.clawutil.data as clawutil
-import clawpack.amrclaw.data as amrclaw
-import clawpack.geoclaw.data
-
-import clawpack.geoclaw.multilayer.plot as ml_plot
-
-
-def setplot(plotdata=None, bathy_location=0.15, bathy_angle=0.0,
-            bathy_left=-1.0, bathy_right=-0.2):
-    """Setup the plotting data objects.
-
-    Input:  plotdata, an instance of pyclaw.plotters.data.ClawPlotData.
-    Output: a modified version of plotdata.
-
-    returns plotdata object
-
-    """
-
-    if plotdata is None:
-        from clawpack.visclaw.data import ClawPlotData
-        plotdata = ClawPlotData()
-
-    # Load data from output
-    clawdata = clawutil.ClawInputData(2)
-    clawdata.read(os.path.join(plotdata.outdir, 'claw.data'))
-    multilayer_data = clawpack.geoclaw.data.MultilayerData()
-    multilayer_data.read(os.path.join(plotdata.outdir, 'multilayer.data'))
-
-    def transform_c2p(x, y, x0, y0, theta):
-        return ((x+x0)*np.cos(theta) - (y+y0)*np.sin(theta),
-                (x+x0)*np.sin(theta) + (y+y0)*np.cos(theta))
-
-    def transform_p2c(x, y, x0, y0, theta):
-        return (x*np.cos(theta) + y*np.sin(theta) - x0,
-                -x*np.sin(theta) + y*np.cos(theta) - y0)
-
-    # Setup bathymetry reference lines
-    with open(os.path.join(plotdata.outdir, "bathy_geometry.data"), 'r') \
-            as bathy_geometry_file:
-        bathy_location = float(bathy_geometry_file.readline())
-        bathy_angle = float(bathy_geometry_file.readline())
-    x = [0.0, 0.0]
-    y = [0.0, 1.0]
-    x1, y1 = transform_c2p(x[0], y[0], bathy_location, 0.0, bathy_angle)
-    x2, y2 = transform_c2p(x[1], y[1], bathy_location, 0.0, bathy_angle)
-
-    if abs(x1 - x2) < 10**-3:
-        x = [x1, x1]
-        y = [clawdata.lower[1], clawdata.upper[1]]
-    else:
-        m = (y1 - y2) / (x1 - x2)
-        x[0] = (clawdata.lower[1] - y1) / m + x1
-        y[0] = clawdata.lower[1]
-        x[1] = (clawdata.upper[1] - y1) / m + x1
-        y[1] = clawdata.upper[1]
-    ref_lines = [((x[0], y[0]), (x[1], y[1]))]
-
-    plotdata.clearfigures()
-    plotdata.save_frames = False
-
-    # ========================================================================
-    #  Generic helper functions
-    def pcolor_afteraxes(current_data):
-        bathy_ref_lines(current_data)
-
-    def contour_afteraxes(current_data):
-        axes = plt.gca()
-        pos = -80.0 * (23e3 / 180) + 500e3 - 5e3
-        axes.plot([pos, pos], [-300e3, 300e3], 'b',
-                  [pos-5e3, pos-5e3], [-300e3, 300e3], 'y')
-        wind_contours(current_data)
-        bathy_ref_lines(current_data)
-
-    def profile_afteraxes(current_data):
-        pass
-
-    def bathy_ref_lines(current_data):
-        axes = plt.gca()
-        for ref_line in ref_lines:
-            x1 = ref_line[0][0]
-            y1 = ref_line[0][1]
-            x2 = ref_line[1][0]
-            y2 = ref_line[1][1]
-            axes.plot([x1, x2], [y1, y2], 'y--', linewidth=1)
-
-    # ========================================================================
-    # Axis limits
-
-    xlimits = [-0.2, 0.4]
-    ylimits = [-0.2, 0.4]
-    eta = [multilayer_data.eta[0], multilayer_data.eta[1]]
-    top_surface_limits = [eta[0] - 0.03, eta[0] + 0.03]
-    internal_surface_limits = [eta[1] - 0.015, eta[1] + 0.015]
-    top_speed_limits = [0.0, 0.1]
-    internal_speed_limits = [0.0, 0.03]
-
-    # ========================================================================
-    #  Surface Elevations
-    plotfigure = plotdata.new_plotfigure(name='Surface')
-    plotfigure.show = True
-    plotfigure.kwargs = {'figsize': (14, 4)}
-
-    # Top surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Top Surface'
-    plotaxes.axescmd = 'subplot(1, 2, 1)'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = pcolor_afteraxes
-    ml_plot.add_surface_elevation(plotaxes,1,bounds=top_surface_limits)
-    # ml_plot.add_surface_elevation(plotaxes,1,bounds=[-0.06,0.06])
-    # ml_plot.add_surface_elevation(plotaxes,1)
-    ml_plot.add_land(plotaxes, 1)
-    
-    # Bottom surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Internal Surface'
-    plotaxes.axescmd = 'subplot(1,2,2)'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = pcolor_afteraxes
-    # ml_plot.add_surface_elevation(plotaxes,2,bounds=[-300-0.5,-300+0.5])
-    ml_plot.add_surface_elevation(plotaxes,2,bounds=internal_surface_limits)
-    # ml_plot.add_surface_elevation(plotaxes,2)
-    ml_plot.add_land(plotaxes, 2)
-    
-    # ========================================================================
-    #  Depths
-    # ========================================================================
-    plotfigure = plotdata.new_plotfigure(name='Depths', figno=42)
-    plotfigure.show = False
-    plotfigure.kwargs = {'figsize':(14,4)}
-    
-    # Top surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Top Layer Depth'
-    plotaxes.axescmd = 'subplot(1,2,1)'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = pcolor_afteraxes
-    ml_plot.add_layer_depth(plotaxes,1,bounds=[-0.1,1.1])
-    ml_plot.add_land(plotaxes, 1)
-    
-    # Bottom surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Bottom Layer Depth'
-    plotaxes.axescmd = 'subplot(1,2,2)'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = pcolor_afteraxes
-    ml_plot.add_layer_depth(plotaxes,2,bounds=[-0.1,0.7])
-    ml_plot.add_land(plotaxes, 2)
-    
-    # ========================================================================
-    #  Water Speed
-    plotfigure = plotdata.new_plotfigure(name='speed')
-    plotfigure.show = True
-    plotfigure.kwargs = {'figsize': (14, 4)}
-
-    # Top layer speed
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Currents - Top Layer'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.axescmd = 'subplot(1, 2, 1)'
-    plotaxes.afteraxes = pcolor_afteraxes
-    ml_plot.add_speed(plotaxes, 1, bounds=top_speed_limits)
-    ml_plot.add_land(plotaxes, 1)
-
-    # Bottom layer speed
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Currents - Bottom Layer'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.axescmd = 'subplot(1,2,2)'
-    plotaxes.afteraxes = pcolor_afteraxes
-    # add_speed(plotaxes,2,bounds=[0.0,1e-10])
-    ml_plot.add_speed(plotaxes,2,bounds=internal_speed_limits)
-    # add_speed(plotaxes,2)
-    ml_plot.add_land(plotaxes, 2)
-    
-    # Individual components
-    plotfigure = plotdata.new_plotfigure(name='speed_components',figno=401)
-    plotfigure.show = False
-    plotfigure.kwargs = {'figsize':(14,14)}
-    
-    # Top layer
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = "X-Velocity - Top Layer"
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.axescmd = 'subplot(2,2,1)'
-    plotaxes.afteraxes = pcolor_afteraxes
-    # add_x_velocity(plotaxes,1,bounds=[-1e-10,1e-10])
-    ml_plot.add_x_velocity(plotaxes,1)
-    ml_plot.add_land(plotaxes, 1)
-    
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = "Y-Velocity - Top Layer"
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.axescmd = 'subplot(2,2,2)'
-    plotaxes.afteraxes = pcolor_afteraxes
-    # add_y_velocity(plotaxes,1,bounds=[-0.000125,0.000125])
-    ml_plot.add_y_velocity(plotaxes,1)
-    ml_plot.add_land(plotaxes, 1)
-    
-    # Bottom layer
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = "X-Velocity - Bottom Layer"
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.axescmd = 'subplot(2,2,3)'
-    plotaxes.afteraxes = pcolor_afteraxes
-    # add_x_velocity(plotaxes,2,bounds=[-1e-10,1e-10])
-    ml_plot.add_x_velocity(plotaxes,2)
-    ml_plot.add_land(plotaxes, 2)
-    
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = "Y-Velocity - Bottom Layer"
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.axescmd = 'subplot(2,2,4)'
-    plotaxes.afteraxes = pcolor_afteraxes
-    # add_y_velocity(plotaxes,2,bounds=[-0.8e-6,.8e-6])
-    ml_plot.add_y_velocity(plotaxes,2)
-
-    ml_plot.add_land(plotaxes, 2)
-    # ========================================================================
-    #  Profile Plots
-    #  Note that these are not currently plotted by default - set
-    # `plotfigure.show = True` is you want this to be plotted
-    plotfigure = plotdata.new_plotfigure(name='profile')
-    plotfigure.show = False
-
-    # Top surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = [-1.1, 0.1]
-    plotaxes.title = "Profile of depth"
-    plotaxes.afteraxes = profile_afteraxes
-
-    slice_index = 30
-
-    # Internal surface
-    def bathy_profile(current_data):
-        return current_data.x[:, slice_index], b(current_data)[:, slice_index]
-
-    def lower_surface(current_data):
-        if multilayer_data.init_type == 2:
-            return current_data.x[:, slice_index],    \
-                    eta2(current_data)[:, slice_index]
-        elif multilayer_data.init_type == 6:
-            return current_data.y[slice_index, :],    \
-                    eta2(current_data)[slice_index, :]
-
-    def upper_surface(current_data):
-        if multilayer_data.init_type == 2:
-            return current_data.x[:, slice_index],    \
-                    eta1(current_data)[:, slice_index]
-        elif multilayer_data.init_type == 6:
-            return current_data.y[slice_index, :],    \
-                    eta1(current_data)[slice_index, :]
-
-    def top_speed(current_data):
-        if multilayer_data.init_type == 2:
-            return current_data.x[:, slice_index],    \
-                    water_u1(current_data)[:, slice_index]
-        elif multilayer_data.init_type == 6:
-            return current_data.y[slice_index, :],    \
-                    water_u1(current_data)[slice_index, :]
-
-    def bottom_speed(current_data):
-        if multilayer_data.init_type == 2:
-            return current_data.x[:, slice_index],    \
-                    water_u2(current_data)[:, slice_index]
-        elif multilayer_data.init_type == 6:
-            return current_data.y[slice_index, :],    \
-                    water_u2(current_data)[slice_index, :]
-
-    # Bathy
-    plotitem = plotaxes.new_plotitem(plot_type='1d_from_2d_data')
-    plotitem.map_2d_to_1d = bathy_profile
-    plotitem.plot_var = 0
-    plotitem.amr_plotstyle = ['-', '+', 'x']
-    plotitem.color = 'k'
-    plotitem.show = True
-
-    # Internal Interface
-    plotitem = plotaxes.new_plotitem(plot_type='1d_from_2d_data')
-    plotitem.map_2d_to_1d = lower_surface
-    plotitem.plot_var = 7
-    plotitem.amr_plotstyle = ['-', '+', 'x']
-    plotitem.color = 'b'
-    plotitem.show = True
-
-    # Upper Interface
-    plotitem = plotaxes.new_plotitem(plot_type='1d_from_2d_data')
-    plotitem.map_2d_to_1d = upper_surface
-    plotitem.plot_var = 6
-    plotitem.amr_plotstyle = ['-', '+', 'x']
-    plotitem.color = (0.2, 0.8, 1.0)
-    plotitem.show = True
-
-    # Set up for axes in this figure:
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Y-Velocity'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = pcolor_afteraxes
-    
-    # Water
-    # plotitem = plotaxes.new_plotitem(plot_type='2d_pcolor')
-    # # plotitem.plot_var = geoplot.surface
-    # plotitem.plot_var = water_v
-    # plotitem.pcolor_cmap = colormaps.make_colormap({1.0:'r',0.5:'w',0.0:'b'})
-    # # plotitem.pcolor_cmin = -1.e-10
-    # # plotitem.pcolor_cmax = 1.e-10
-    # # plotitem.pcolor_cmin = -2.5 # -3.0
-    # # plotitem.pcolor_cmax = 2.5 # 3.0
-    # plotitem.add_colorbar = True
-    # plotitem.amr_celledges_show = [0,0,0]
-    # plotitem.amr_patchedges_show = [1,1,1]
-
-    # Land
-    ml_plot.add_land(plotaxes, 1)
-    
-    # ========================================================================
-    #  Contour plot for surface
-    # ========================================================================
-    plotfigure = plotdata.new_plotfigure(name='contour_surface',figno=15)
-    plotfigure.show = False
-    plotfigure.kwargs = {'figsize':(14,4)}
-    
-    # Set up for axes in this figure:
-    
-    # Top Surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Top Surface'
-    plotaxes.axescmd = 'subplot(1,2,1)'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = contour_afteraxes
-    ml_plot.add_surface_elevation(plotaxes,plot_type='contour',surface=1,bounds=[-2.5,-1.5,-0.5,0.5,1.5,2.5])
-    ml_plot.add_land(plotaxes, 1, plot_type='contour')
-    
-    # Internal Surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Internal Surface'
-    plotaxes.axescmd = 'subplot(1,2,2)'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = contour_afteraxes
-    ml_plot.add_surface_elevation(plotaxes,plot_type='contour',surface=2,bounds=[-2.5,-1.5,-0.5,0.5,1.5,2.5])
-    ml_plot.add_land(plotaxes, 2, plot_type='contour')
-    
-    # ========================================================================
-    #  Contour plot for speed
-    # ========================================================================
-    plotfigure = plotdata.new_plotfigure(name='contour_speed',figno=16)
-    plotfigure.show = False
-    plotfigure.kwargs = {'figsize':(14,4)}
-    
-    # Set up for axes in this figure:
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Current'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = contour_afteraxes
-    
-    # Surface
-    plotitem = plotaxes.new_plotitem(plot_type='2d_contour')
-    plotitem.plot_var = ml_plot.water_speed_depth_ave
-    plotitem.kwargs = {'linewidths':1}
-    # plotitem.contour_levels = [1.0,2.0,3.0,4.0,5.0,6.0]
-    plotitem.contour_levels = [0.5,1.5,3,4.5,6.0]
-    plotitem.amr_contour_show = [1,1,1]
-    plotitem.amr_celledges_show = [0,0,0]
-    plotitem.amr_patchedges_show = [1,1,1]
-    plotitem.amr_contour_colors = 'k'
-    # plotitem.amr_contour_colors = ['r','k','b']  # color on each level
-    # plotitem.amr_grid_bgcolor = ['#ffeeee', '#eeeeff', '#eeffee']
-    plotitem.show = True 
-    
-    # Land
-    plotitem = plotaxes.new_plotitem(plot_type='2d_contour')
-    plotitem.plot_var = geoplot.land
-    plotitem.contour_nlevels = 40
-    plotitem.contour_min = 0.0
-    plotitem.contour_max = 100.0
-    plotitem.amr_contour_colors = ['g']  # color on each level
-    plotitem.amr_patch_bgcolor = ['#ffeeee', '#eeeeff', '#eeffee']
-    plotitem.amr_celledges_show = 0
-    plotitem.amr_patchedges_show = 0
-    plotitem.show = True
-
-    # ========================================================================
-    #  Grid Cells
-    # ========================================================================
-    
-    # Figure for grid cells
-    plotfigure = plotdata.new_plotfigure(name='cells', figno=2)
-
-    # Set up for axes in this figure:
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.title = 'Grid patches'
-    plotaxes.scaled = True
-
-    # Set up for item on these axes:
-    plotitem = plotaxes.new_plotitem(plot_type='2d_patch')
-    plotitem.amr_patch_bgcolor = ['#ffeeee', '#eeeeff', '#eeffee']
-    plotitem.amr_celledges_show = [1,1,1]
-    plotitem.amr_patchedges_show = [1,1,1]
-    
-    # ========================================================================
-    #  Vorticity Plot
-    # ========================================================================
-    # plotfigure = plotdata.new_plotfigure(name='vorticity',figno=17)
-    # plotfigure.show = False
-    # plotaxes = plotfigure.new_plotaxes()
-    # plotaxes.title = "Vorticity"
-    # plotaxes.scaled = True
-    # plotaxes.xlimits = xlimits
-    # plotaxes.ylimits = ylimits
-    # plotaxes.afteraxes = pcolor_afteraxes
-    # 
-    # # Vorticity
-    # plotitem = plotaxes.new_plotitem(plot_type='2d_imshow')
-    # plotitem.plot_var = 9
-    # plotitem.imshow_cmap = plt.get_cmap('PRGn')
-    # # plotitem.pcolor_cmap = plt.get_cmap('PuBu')
-    # # plotitem.pcolor_cmin = 0.0
-    # # plotitem.pcolor_cmax = 6.0
-    # plotitem.imshow_cmin = -1.e-2
-    # plotitem.imshow_cmax = 1.e-2
-    # plotitem.add_colorbar = True
-    # plotitem.amr_celledges_show = [0,0,0]
-    # plotitem.amr_patchedges_show = [1]
-    # 
-    # # Land
-    # plotitem = plotaxes.new_plotitem(plot_type='2d_pcolor')
-    # plotitem.plot_var = geoplot.land
-    # plotitem.pcolor_cmap = geoplot.land_colors
-    # plotitem.pcolor_cmin = 0.0
-    # plotitem.pcolor_cmax = 80.0
-    # plotitem.add_colorbar = False
-    # plotitem.amr_celledges_show = [0,0,0]
-
-    # ========================================================================
-    #  Figures for gauges
-
-    # Top
-    plotfigure = plotdata.new_plotfigure(name='Surface & topo',
-                                         type='each_gauge',
-                                         figno=301)
-    plotfigure.show = True
-    plotfigure.clf_each_gauge = True
-    plotfigure.kwargs = {'figsize': (14, 4)}
-
-    # Set up for axes in this figure:
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.axescmd = 'subplot(1, 2, 1)'
-    plotaxes.xlimits = [0.0, 1.0]
-    plotaxes.ylimits = top_surface_limits
-    plotaxes.title = 'Top Surface'
-
-    # Plot surface as blue curve:
-    plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
-    plotitem.plot_var = 6
-    plotitem.plotstyle = 'b-'
-
-    # Set up for axes in this figure:
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.axescmd = 'subplot(1, 2, 2)'
-    plotaxes.xlimits = [0.0, 1.0]
-    plotaxes.ylimits = internal_surface_limits
-    plotaxes.title = 'Bottom Surface'
-
-    # Plot surface as blue curve:
-    plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
-    plotitem.plot_var = 7
-    plotitem.plotstyle = 'b-'
-
-    # =========================================================================
-    #  Other plots
-
-    # Gauge Locations - Enable to see where gauges are located
-    def locations_afteraxes(current_data, gaugenos='all'):
-        gaugetools.plot_gauge_locations(current_data.plotdata,
-                                        gaugenos=gaugenos,
-                                        format_string='kx',
-                                        add_labels=True)
-        pcolor_afteraxes(current_data)
-
-    plotfigure = plotdata.new_plotfigure(name='Gauge Locations')
-    plotfigure.show = False
-    plotfigure.kwargs = {'figsize': (14, 4)}
-
-    # Top surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Top Surface'
-    plotaxes.axescmd = 'subplot(1, 2, 1)'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = locations_afteraxes
-    ml_plot.add_surface_elevation(plotaxes, 1, bounds=top_surface_limits)
-    ml_plot.add_land(plotaxes, 1)
-
-    # Bottom surface
-    plotaxes = plotfigure.new_plotaxes()
-    plotaxes.title = 'Internal Surface'
-    plotaxes.axescmd = 'subplot(1, 2, 2)'
-    plotaxes.scaled = True
-    plotaxes.xlimits = xlimits
-    plotaxes.ylimits = ylimits
-    plotaxes.afteraxes = locations_afteraxes
-    ml_plot.add_surface_elevation(plotaxes, 2, bounds=internal_surface_limits)
-    ml_plot.add_land(plotaxes, 2)
-
-    # -----------------------------------------
-    # Parameters used only when creating html and/or latex hardcopy
-    # e.g., via pyclaw.plotters.frametools.printframes:
-
-    plotdata.printfigs = True               # print figures
-    plotdata.print_format = 'png'           # file format
-    plotdata.print_framenos = 'all'         # list of frames to print
-    plotdata.print_fignos = 'all'           # list of figures to print
-    plotdata.html = True                    # create html files of plots?
-    plotdata.latex = False                  # create latex file of plots?
-    plotdata.latex_figsperline = 2          # layout of plots
-    plotdata.latex_framesperline = 1        # layout of plots
-    plotdata.latex_makepdf = False          # also run pdflatex?
-    plotdata.parallel = True                # make multiple frame png's at once
-
-    return plotdata
diff --git a/tests/multilayer_amr/setrun.py b/tests/multilayer_amr/setrun.py
deleted file mode 100644
index 5bef557..0000000
--- a/tests/multilayer_amr/setrun.py
+++ /dev/null
@@ -1,534 +0,0 @@
-"""
-Module to set up run time parameters for Clawpack.
-
-The values set in the function setrun are then written out to data files
-that will be read in by the Fortran code.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import print_function
-import os
-
-import numpy as numpy
-
-import clawpack.geoclaw.data
-import clawpack.geoclaw.topotools as tt
-
-# Rotation transformations
-def transform_c2p(x,y,x0,y0,theta):
-    return ((x+x0)*numpy.cos(theta) - (y+y0)*numpy.sin(theta),
-            (x+x0)*numpy.sin(theta) + (y+y0)*numpy.cos(theta))
-
-def transform_p2c(x,y,x0,y0,theta):
-    return ( x*numpy.cos(theta) + y*numpy.sin(theta) - x0,
-            -x*numpy.sin(theta) + y*numpy.cos(theta) - y0)
-
-
-# Class containing some setup for the qinit especially for multilayer tests 
-class QinitMultilayerData(clawpack.geoclaw.data.QinitData):
-    r"""
-    Modified Qinit data object for multiple layers
-
-    """
-
-    def __init__(self):
-        super(QinitMultilayerData, self).__init__()
-
-        # Test qinit data > 4
-        self.add_attribute("init_location", [0.0, 0.0])
-        self.add_attribute("wave_family", 1)
-        self.add_attribute("epsilon", 0.02)
-        self.add_attribute("angle", 0.0)
-        self.add_attribute("sigma", 0.02)
-
-    def write(self, data_source='setrun.py'):
-
-        # Initial perturbation
-        self.open_data_file('qinit.data',data_source)
-        self.data_write('qinit_type')
-
-        # Perturbation requested
-        if self.qinit_type == 0:
-            pass
-        elif 0 < self.qinit_type < 5:
-            # Check to see if each qinit file is present and then write the data
-            for tfile in self.qinitfiles:
-                try:
-                    fname = "'%s'" % os.path.abspath(tfile[-1])
-                except:
-                    raise Warning("File %s was not found." % fname)
-                    # raise MissingFile("file not found")
-                self._out_file.write("\n%s  \n" % fname)
-                self._out_file.write("%3i %3i \n" % tuple(tfile[:-1]))
-        elif self.qinit_type >= 5 and self.qinit_type <= 9:
-            self.data_write('epsilon')
-            self.data_write("init_location")
-            self.data_write("wave_family")
-            self.data_write("angle")
-            self.data_write("sigma")
-        else:
-            raise ValueError("Invalid qinit_type parameter %s." % self.qinit_type)
-        self.close_data_file()
-
-
-
-#------------------------------
-def setrun(claw_pkg='geoclaw'):
-#------------------------------
-
-    """
-    Define the parameters used for running Clawpack.
-
-    INPUT:
-        claw_pkg expected to be "geoclaw" for this setrun.
-
-    OUTPUT:
-        rundata - object of class ClawRunData
-
-    """
-
-    from clawpack.clawutil import data
-
-    assert claw_pkg.lower() == 'geoclaw',  "Expected claw_pkg = 'geoclaw'"
-
-    num_dim = 2
-    rundata = data.ClawRunData(claw_pkg, num_dim)
-
-    #------------------------------------------------------------------
-    # GeoClaw specific parameters:
-    #------------------------------------------------------------------
-    rundata = setgeo(rundata)
-
-    set_multilayer(rundata)
-
-    #------------------------------------------------------------------
-    # Standard Clawpack parameters to be written to claw.data:
-    #   (or to amr2ez.data for AMR)
-    #------------------------------------------------------------------
-    clawdata = rundata.clawdata  # initialized when rundata instantiated
-
-
-    # Set single grid parameters first.
-    # See below for AMR parameters.
-
-
-    # ---------------
-    # Spatial domain:
-    # ---------------
-
-    # Number of space dimensions:
-    clawdata.num_dim = num_dim
-
-    # Lower and upper edge of computational domain:
-    clawdata.lower[0] = -1      # west longitude
-    clawdata.upper[0] = 2.0       # east longitude
-
-    clawdata.lower[1] = -1.0       # south latitude
-    clawdata.upper[1] = 2.0         # north latitude
-
-
-
-    # Number of grid cells: Coarsest grid
-    clawdata.num_cells[0] = 75
-    clawdata.num_cells[1] = 75
-
-    # ---------------
-    # Size of system:
-    # ---------------
-
-    # Number of equations in the system:
-    clawdata.num_eqn = 6
-
-    # Number of auxiliary variables in the aux array (initialized in setaux)
-    clawdata.num_aux = 1 + rundata.multilayer_data.num_layers
-
-    # Index of aux array corresponding to capacity function, if there is one:
-    clawdata.capa_index = 0
-
-    
-    
-    # -------------
-    # Initial time:
-    # -------------
-
-    clawdata.t0 = 0.0
-
-
-    # Restart from checkpoint file of a previous run?
-    # Note: If restarting, you must also change the Makefile to set:
-    #    RESTART = True
-    # If restarting, t0 above should be from original run, and the
-    # restart_file 'fort.chkNNNNN' specified below should be in 
-    # the OUTDIR indicated in Makefile.
-
-    clawdata.restart = False               # True to restart from prior results
-    clawdata.restart_file = 'fort.chk00036'  # File to use for restart data
-
-    # -------------
-    # Output times:
-    #--------------
-
-    # Specify at what times the results should be written to fort.q files.
-    # Note that the time integration stops after the final output time.
-    # The solution at initial time t0 is always written in addition.
-
-    clawdata.output_style = 1
-
-    if clawdata.output_style==1:
-        # Output nout frames at equally spaced times up to tfinal:
-        clawdata.num_output_times = 1
-        clawdata.tfinal = 1.0
-        clawdata.output_t0 = True  # output at initial (or restart) time?
-
-    elif clawdata.output_style == 2:
-        # Specify a list of output times.
-        clawdata.output_times = [0.5, 1.0]
-
-    elif clawdata.output_style == 3:
-        # Output every iout timesteps with a total of ntot time steps:
-        clawdata.output_step_interval = 10
-        clawdata.total_steps = 100
-        clawdata.output_t0 = True
-        
-
-    clawdata.output_format = 'ascii'      # 'ascii' or 'binary' 
-
-    clawdata.output_q_components = 'all'   # need all
-    clawdata.output_aux_components = 'all'  # eta=h+B is in q
-    clawdata.output_aux_onlyonce = False    # output aux arrays each frame
-
-
-
-    # ---------------------------------------------------
-    # Verbosity of messages to screen during integration:
-    # ---------------------------------------------------
-
-    # The current t, dt, and cfl will be printed every time step
-    # at AMR levels <= verbosity.  Set verbosity = 0 for no printing.
-    #   (E.g. verbosity == 2 means print only on levels 1 and 2.)
-    clawdata.verbosity = 1
-
-
-
-    # --------------
-    # Time stepping:
-    # --------------
-
-    # if dt_variable==1: variable time steps used based on cfl_desired,
-    # if dt_variable==0: fixed time steps dt = dt_initial will always be used.
-    clawdata.dt_variable = True
-
-    # Initial time step for variable dt.
-    # If dt_variable==0 then dt=dt_initial for all steps:
-    clawdata.dt_initial = 0.00225
-
-    # Max time step to be allowed if variable dt used:
-    clawdata.dt_max = 1e+99
-
-    # Desired Courant number if variable dt used, and max to allow without
-    # retaking step with a smaller dt:
-    clawdata.cfl_desired = 0.75
-    clawdata.cfl_max = 1.0
-    # clawdata.cfl_desired = 0.45
-    # clawdata.cfl_max = 0.5
-
-    # Maximum number of time steps to allow between output times:
-    clawdata.steps_max = 5000
-
-
-
-
-    # ------------------
-    # Method to be used:
-    # ------------------
-
-    # Order of accuracy:  1 => Godunov,  2 => Lax-Wendroff plus limiters
-    clawdata.order = 2
-    
-    # Use dimensional splitting? (not yet available for AMR)
-    #  0 or 'unsplit' or none'  ==> Unsplit
-    #  1 or 'increment'         ==> corner transport of waves
-    #  2 or 'all'               ==> corner transport of 2nd order corrections too
-    clawdata.dimensional_split = 0
-    
-    # For unsplit method, transverse_waves can be 
-    #  0 or 'none'      ==> donor cell (only normal solver used)
-    #  1 or 'increment' ==> corner transport of waves
-    #  2 or 'all'       ==> corner transport of 2nd order corrections too
-    clawdata.transverse_waves = 2
-
-    # Number of waves in the Riemann solution:
-    clawdata.num_waves = 6
-    
-    # List of limiters to use for each wave family:  
-    # Required:  len(limiter) == num_waves
-    # Some options:
-    #   0 or 'none'     ==> no limiter (Lax-Wendroff)
-    #   1 or 'minmod'   ==> minmod
-    #   2 or 'superbee' ==> superbee
-    #   3 or 'mc'       ==> MC limiter
-    #   4 or 'vanleer'  ==> van Leer
-    clawdata.limiter = ['mc', 'mc', 'mc', 'mc', 'mc', 'mc']
-
-    clawdata.use_fwaves = True    # True ==> use f-wave version of algorithms
-    
-    # Source terms splitting:
-    #   src_split == 0 or 'none'    ==> no source term (src routine never called)
-    #   src_split == 1 or 'godunov' ==> Godunov (1st order) splitting used, 
-    #   src_split == 2 or 'strang'  ==> Strang (2nd order) splitting used,  not recommended.
-    clawdata.source_split = 'godunov'
-
-
-    # --------------------
-    # Boundary conditions:
-    # --------------------
-
-    # Number of ghost cells (usually 2)
-    clawdata.num_ghost = 2
-
-    # Choice of BCs at xlower and xupper:
-    #   0 => user specified (must modify bcN.f to use this option)
-    #   1 => extrapolation (non-reflecting outflow)
-    #   2 => periodic (must specify this at both boundaries)
-    #   3 => solid wall for systems where q(2) is normal velocity
-
-    clawdata.bc_lower[0] = 'extrap'
-    clawdata.bc_upper[0] = 'extrap'
-
-    clawdata.bc_lower[1] = 'extrap'
-    clawdata.bc_upper[1] = 'extrap'
-
-
-
-    # --------------
-    # Checkpointing:
-    # --------------
-
-    # Specify when checkpoint files should be created that can be
-    # used to restart a computation.
-
-    clawdata.checkpt_style = 0
-
-    if clawdata.checkpt_style == 0:
-        # Do not checkpoint at all
-        pass
-
-    elif clawdata.checkpt_style == 1:
-        # Checkpoint only at tfinal.
-        pass
-
-    elif clawdata.checkpt_style == 2:
-        # Specify a list of checkpoint times.  
-        clawdata.checkpt_times = [0.1,0.15]
-
-    elif clawdata.checkpt_style == 3:
-        # Checkpoint every checkpt_interval timesteps (on Level 1)
-        # and at the final time.
-        clawdata.checkpt_interval = 5
-
-
-    # ---------------
-    # AMR parameters:
-    # ---------------
-    amrdata = rundata.amrdata
-
-    # max number of refinement levels:
-    amrdata.amr_levels_max = 3
-
-    # List of refinement ratios at each level (length at least mxnest-1)
-    amrdata.refinement_ratios_x = [2,6]
-    amrdata.refinement_ratios_y = [2,6]
-    amrdata.refinement_ratios_t = [2,6]
-
-
-    # Specify type of each aux variable in amrdata.auxtype.
-    # This must be a list of length maux, each element of which is one of:
-    #   'center',  'capacity', 'xleft', or 'yleft'  (see documentation).
-
-    amrdata.aux_type = ['center','center','yleft','center','center','center']
-
-
-    # Flag using refinement routine flag2refine rather than richardson error
-    amrdata.flag_richardson = False    # use Richardson?
-    amrdata.flag2refine = True
-
-    # steps to take on each level L between regriddings of level L+1:
-    amrdata.regrid_interval = 3
-
-    # width of buffer zone around flagged points:
-    # (typically the same as regrid_interval so waves don't escape):
-    amrdata.regrid_buffer_width  = 2
-
-    # clustering alg. cutoff for (# flagged pts) / (total # of cells refined)
-    # (closer to 1.0 => more small grids may be needed to cover flagged cells)
-    amrdata.clustering_cutoff = 0.700000
-
-    # print info about each regridding up to this level:
-    amrdata.verbosity_regrid = 0  
-
-    #  ----- For developers ----- 
-    # Toggle debugging print statements:
-    amrdata.dprint = False      # print domain flags
-    amrdata.eprint = False      # print err est flags
-    amrdata.edebug = False      # even more err est flags
-    amrdata.gprint = False      # grid bisection/clustering
-    amrdata.nprint = False      # proper nesting output
-    amrdata.pprint = False      # proj. of tagged points
-    amrdata.rprint = False      # print regridding summary
-    amrdata.sprint = False      # space/memory output
-    amrdata.tprint = True       # time step reporting each level
-    amrdata.uprint = False      # update/upbnd reporting
-    
-    # More AMR parameters can be set -- see the defaults in pyclaw/data.py
-
-    # ---------------
-    # Regions:
-    # ---------------
-    rundata.regiondata.regions = []
-    # to specify regions of refinement append lines of the form
-    #  [minlevel,maxlevel,t1,t2,x1,x2,y1,y2]
-
-    # ---------------
-    # Gauges:
-    # ---------------
-    rundata.gaugedata.gauges = []
-    # for gauges append lines of the form  [gaugeno, x, y, t1, t2]
-    gauge_locations = [-0.1,0.0,0.1,0.2,0.3]
-    for (i,x_c) in enumerate(gauge_locations):
-        # y0 = (self.run_data.clawdata.yupper - self.run_data.clawdata.ylower) / 2.0
-        # x_p,y_p = transform_c2p(x_c,0.0,location[0],location[1],angle)
-        x_p = x_c * numpy.cos(0.0)
-        y_p = x_c * numpy.sin(0.0)
-        # print "+=====+"
-        # print x_c,0.0
-        # print x_p,y_p
-        if (rundata.clawdata.lower[0] < x_p < rundata.clawdata.upper[0] and
-                rundata.clawdata.lower[1] < y_p < rundata.clawdata.upper[1]):
-            rundata.gaugedata.gauges.append([i, x_p, y_p, 0.0, 1e10])
-            # print "Gauge %s: (%s,%s)" % (i,x_p,y_p)
-    # print "+=====+"
-
-    return rundata
-    # end of function setrun
-    # ----------------------
-
-
-#-------------------
-def setgeo(rundata):
-#-------------------
-    """
-    Set GeoClaw specific runtime parameters.
-    For documentation see ....
-    """
-
-    try:
-        geo_data = rundata.geo_data
-    except:
-        print("*** Error, this rundata has no geo_data attribute")
-        raise AttributeError("Missing geo_data attribute")
-       
-    # == Physics ==
-    geo_data.gravity = 9.81
-    geo_data.coordinate_system = 1
-    geo_data.earth_radius = 6367.5e3
-    geo_data.rho = [0.9, 1.0]
-
-    # == Forcing Options
-    geo_data.coriolis_forcing = False
-
-    # == Algorithm and Initial Conditions ==
-    geo_data.sea_level = 0.0
-    geo_data.dry_tolerance = 1.e-3
-    geo_data.friction_forcing = True
-    geo_data.manning_coefficient = 0.025
-    geo_data.friction_depth = 1e6
-
-    # Refinement settings
-    refinement_data = rundata.refinement_data
-    refinement_data.variable_dt_refinement_ratios = True
-    refinement_data.wave_tolerance = 1.e-1
-    refinement_data.deep_depth = 1e2
-    refinement_data.max_level_deep = 3
-
-    # == settopo.data values ==
-    topo_data = rundata.topo_data
-    # for topography, append lines of the form
-    #    [topotype, minlevel, maxlevel, t1, t2, fname]
-    topo_data.topofiles.append([2, 1, 5, 0.0, 1e10, 'jump_topo.topotype2'])
-    
-    # == setdtopo.data values ==
-    dtopo_data = rundata.dtopo_data
-    # for moving topography, append lines of the form :   (<= 1 allowed for now!)
-    #   [topotype, minlevel,maxlevel,fname]
-
-    # == setqinit.data values ==
-    qinit_data = rundata.qinit_data
-
-
-
-    return rundata
-    # end of function setgeo
-    # ----------------------
-
-
-def set_multilayer(rundata):
-
-    data = rundata.multilayer_data
-
-    # Physics parameters
-    data.num_layers = 2
-    data.layer_index = 1
-    data.eta = [0.0,-0.6]
-    
-    # Algorithm parameters
-    data.eigen_method = 2
-    data.inundation_method = 2
-    data.richardson_tolerance = 0.95
-    # data.wave_tolerance = [0.1,0.1]
-    # data.dry_limit = True
-
-    # Set special initial conditions for qinit
-    rundata.replace_data('qinit_data', QinitMultilayerData())
-    rundata.qinit_data.qinit_type = 6
-    rundata.qinit_data.epsilon = 0.02
-    rundata.qinit_data.angle = numpy.pi / 4.0
-    rundata.qinit_data.sigma = 0.02
-    rundata.qinit_data.wave_family = 4
-    rundata.qinit_data.init_location = [-0.1,0.0]
-
-
-
-def bathy_step(x, y, location=0.15, angle=0.0, left=-1.0, right=-0.2):
-    x_c,y_c = transform_p2c(x, y, location, 0.0, angle)
-    return ((x_c <= 0.0) * left 
-          + (x_c >  0.0) * right)
-
-
-def write_topo_file(run_data, out_file):
-    
-    # Make topography
-    topo_func = lambda x, y: bathy_step(x, y, location=0.15, 
-                                              angle=numpy.pi / 8.0, 
-                                              left=-1.0, right=-0.2)
-    topo = tt.Topography(topo_func=topo_func)
-    topo.x = numpy.linspace(-1.16, 2.16, 166)
-    topo.y = numpy.linspace(-1.16, 2.16, 166)
-    topo.write(out_file)
-
-    # Write out simple bathy geometry file for communication to the plotting
-    with open("./bathy_geometry.data", 'w') as bathy_geometry_file:
-        bathy_geometry_file.write("%s\n%s" % (0.15, numpy.pi / 8.0) )
-
-
-if __name__ == '__main__':
-    # Set up run-time parameters and write all data files.
-    import sys
-    if len(sys.argv) == 2:
-        rundata = setrun(sys.argv[1])
-    else:
-        rundata = setrun()
-
-    rundata.write()
-
-    write_topo_file(rundata, 'jump_topo.topotype2')
\ No newline at end of file
