update paper2_examples/acoustics_2d_ex3 for v5.6.1

Includes fixed versions of rpn2_vc_acoustics solvers that are not yet in Clawpack release.

paper2_examples/acoustics_2d_ex3/Makefile

@@ -24,14 +24,14 @@ 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 ?= -O2 -fopenmp 
+FFLAGS ?= 
 
 # ---------------------------------
 # package sources for this program:
 # ---------------------------------
 
-ADJLIB = $(CLAW)/amrclaw/src/2d/adjoint
-include $(ADJLIB)/Makefile.adjoint_amr_2d
+AMRLIB = $(CLAW)/amrclaw/src/2d
+include $(AMRLIB)/Makefile.amr_2d
 
 # ---------------------------------------
 # package sources specifically to exclude
@@ -53,8 +53,8 @@ SOURCES += \
   qinit.f \
   setprob.f \
   setaux.f \
-  $(CLAW)/riemann/src/rpn2_vc_acoustics.f \
-  $(CLAW)/riemann/src/rpt2_vc_acoustics.f \
+  rpn2_vc_acoustics.f90 \
+  $(CLAW)/riemann/src/rpt2_vc_acoustics.f90 \
 
 #-------------------------------------------------------------------
 # Include Makefile containing standard definitions and make options:

paper2_examples/acoustics_2d_ex3/adjoint/Makefile

@@ -53,7 +53,7 @@ SOURCES = \
   qinit.f \
   setprob.f \
   setaux.f \
-  $(CLAW)/riemann/src/rpn2_vc_acoustics_adjoint.f90 \
+  rpn2_vc_acoustics_adjoint.f90 \
   $(CLAW)/riemann/src/rpt2_vc_acoustics_adjoint.f90 \
 
 #-------------------------------------------------------------------

paper2_examples/acoustics_2d_ex3/adjoint/rpn2_vc_acoustics_adjoint.f90

@@ -0,0 +1,135 @@
+! =====================================================
+subroutine rpn2(ixy,maxm,meqn,mwaves,maux,mbc,mx,ql,qr,auxl,auxr,fwave,s,amdq,apdq)
+! =====================================================
+!     # Adjoint Riemann solver for the acoustics equations in 2d, with varying
+!     # material properties rho and kappa
+
+!     waves: 2
+!     equations: 3
+!     aux fields: 2
+
+!     Conserved quantities:
+!       1 pressure
+!       2 x_momentum
+!       3 y_momentum
+
+!     Auxiliary variables:
+!         1  density
+!         2  sound_speed
+
+!     # Note that although there are 3 eigenvectors, the second eigenvalue
+!     # is always zero and so we only need to compute 2 waves.
+!     #
+!     # solve Riemann problems along one slice of data.
+
+!     # On input, ql contains the state vector at the left edge of each cell
+!     #           qr contains the state vector at the right edge of each cell
+
+!     # Here it is assumed that auxl=auxr gives the cell values.
+
+!     # This data is along a slice in the x-direction if ixy=1
+!     #                            or the y-direction if ixy=2.
+!     # On output, wave contains the waves,
+!     #            s the speeds,
+!     #            amdq the  left-going flux difference  A^- \Delta q
+!     #            apdq the right-going flux difference  A^+ \Delta q
+
+
+!     # Note that the i'th Riemann problem has left state qr(i-1,:)
+!     #                                    and right state ql(i,:)
+!     # From the basic clawpack routines, this routine is called with ql = qr
+
+    implicit double precision (a-h,o-z)
+
+    dimension fwave(meqn, mwaves, 1-mbc:maxm+mbc)
+    dimension    s(mwaves, 1-mbc:maxm+mbc)
+    dimension   ql(meqn, 1-mbc:maxm+mbc)
+    dimension   qr(meqn, 1-mbc:maxm+mbc)
+    dimension apdq(meqn, 1-mbc:maxm+mbc)
+    dimension amdq(meqn, 1-mbc:maxm+mbc)
+    dimension auxl(maux, 1-mbc:maxm+mbc)
+    dimension auxr(maux, 1-mbc:maxm+mbc)
+
+!     local arrays
+!     ------------
+    dimension delta(3)
+
+!     # set mu to point to  the component of the system that corresponds
+!     # to velocity in the direction of this slice, mv to the orthogonal
+!     # velocity:
+
+    if (ixy == 1) then
+        mu = 2
+        mv = 3
+    else
+        mu = 3
+        mv = 2
+    endif
+
+!     # note that notation for u and v reflects assumption that the
+!     # Riemann problems are in the x-direction with u in the normal
+!     # direciton and v in the orthogonal direcion, but with the above
+!     # definitions of mu and mv the routine also works with ixy=2
+!     # in which case waves come from the
+!     # Riemann problems u_t + g(u)_y = 0 in the y-direction.
+
+
+!     # split the jump in f(q) at each interface into waves
+!     # The jump is split into a leftgoing wave traveling at speed -c
+!     # relative to the material properties to the left of the interface,
+!     # and a rightgoing wave traveling at speed +c
+!     # relative to the material properties to the right of the interface,
+
+!     # find b1 and b2, the coefficients of the 2 eigenvectors:
+    do 20 i = 2-mbc, mx+mbc
+!       # material properties
+
+!        # impedances:
+        zi = auxl(1,i)*auxl(2,i)
+        zim = auxr(1,i-1)*auxr(2,i-1)
+
+!       # sound speed
+        ci = auxl(2,i)
+        cim = auxr(2,i-1)
+
+!       # density
+        rhoi = auxl(1,i)
+        rhoim = auxr(1,i-1)
+
+!       # bulk modulus
+        bulki = rhoi*ci**2
+        bulkim = rhoim*cim**2
+
+!       # f-wave splitting
+        delta(1) = -(ql(mu,i)/rhoi - qr(mu,i-1)/rhoim)
+        delta(2) = -(bulki*ql(1,i) - bulkim*qr(1,i-1))
+
+        beta1 = (zi*delta(1) + delta(2)) / (zi+zim)
+        beta2 = (zim*delta(1) - delta(2)) / (zi+zim)
+
+!       # Compute the waves. Eigenvectors switched for adjoint:
+
+        fwave(1,1,i) = beta1
+        fwave(mu,1,i) = beta1*zim
+        fwave(mv,1,i) = 0.d0
+        s(1,i) = -cim
+
+        fwave(1,2,i) = beta2
+        fwave(mu,2,i) = -beta2*zi
+        fwave(mv,2,i) = 0.d0
+        s(2,i) = ci
+
+    20 END DO
+
+
+!     # compute the leftgoing and rightgoing flux differences:
+!     # Note s(i,1) < 0   and   s(i,2) > 0.
+
+!   # f-wave splitting, so do not multiply by wave speeds:
+    forall (m=1:meqn,  i=2-mbc: mx+mbc)
+    amdq(m,i) = fwave(m,1,i)
+    apdq(m,i) = fwave(m,2,i)
+    end forall
+
+    return
+    end subroutine rpn2

paper2_examples/acoustics_2d_ex3/rpn2_vc_acoustics.f90

@@ -0,0 +1,122 @@
+! =====================================================
+subroutine rpn2(ixy,maxm,meqn,mwaves,maux,mbc,mx,ql,qr,auxl,auxr,wave,s,amdq,apdq)
+! =====================================================
+
+! Riemann solver for the acoustics equations in 2d, with varying
+! material properties rho and kappa
+
+! waves: 2
+! equations: 3
+! aux fields: 2
+
+! Conserved quantities:
+!       1 pressure
+!       2 x_momentum
+!       3 y_momentum
+
+! Auxiliary variables:
+!         1  density
+!         2  sound_speed
+
+! Note that although there are 3 eigenvectors, the second eigenvalue
+! is always zero and so we only need to compute 2 waves.
+!
+! solve Riemann problems along one slice of data.
+
+! On input, ql contains the state vector at the left edge of each cell
+!           qr contains the state vector at the right edge of each cell
+
+! Here it is assumed that auxl=auxr gives the cell values.
+
+! On output, wave contains the waves,
+!            s the speeds,
+!            amdq the  left-going flux difference  A^- \Delta q
+!            apdq the right-going flux difference  A^+ \Delta q
+
+! This data is along a slice in the x-direction if ixy=1
+!                            or the y-direction if ixy=2.
+
+! Note that the i'th Riemann problem has left state qr(:,i-1)
+!                                    and right state ql(:,i)
+! From the basic clawpack routines, this routine is called with ql = qr
+
+
+    implicit double precision (a-h,o-z)
+
+    dimension wave(meqn, mwaves, 1-mbc:maxm+mbc)
+    dimension    s(mwaves, 1-mbc:maxm+mbc)
+    dimension   ql(meqn, 1-mbc:maxm+mbc)
+    dimension   qr(meqn, 1-mbc:maxm+mbc)
+    dimension apdq(meqn, 1-mbc:maxm+mbc)
+    dimension amdq(meqn, 1-mbc:maxm+mbc)
+    dimension auxl(maux, 1-mbc:maxm+mbc)
+    dimension auxr(maux, 1-mbc:maxm+mbc)
+
+!     local arrays
+!     ------------
+    dimension delta(3)
+
+!     # set mu to point to  the component of the system that corresponds
+!     # to velocity in the direction of this slice, mv to the orthogonal
+!     # velocity.
+
+
+    if (ixy == 1) then
+        mu = 2
+        mv = 3
+    else
+        mu = 3
+        mv = 2
+    endif
+
+!     # note that notation for u and v reflects assumption that the
+!     # Riemann problems are in the x-direction with u in the normal
+!     # direciton and v in the orthogonal direcion, but with the above
+!     # definitions of mu and mv the routine also works with ixy=2
+
+
+!     # split the jump in q at each interface into waves
+!     # The jump is split into a leftgoing wave traveling at speed -c
+!     # relative to the material properties to the left of the interface,
+!     # and a rightgoing wave traveling at speed +c
+!     # relative to the material properties to the right of the interface,
+
+!     # find a1 and a2, the coefficients of the 2 eigenvectors:
+    do 20 i = 2-mbc, mx+mbc
+        delta(1) = ql(1,i) - qr(1,i-1)
+        delta(2) = ql(mu,i) - qr(mu,i-1)
+    !        # impedances:
+        zi = auxl(1,i)*auxl(2,i)
+        zim = auxr(1,i-1)*auxr(2,i-1)
+
+        a1 = (-delta(1) + zi*delta(2)) / (zim + zi)
+        a2 =  (delta(1) + zim*delta(2)) / (zim + zi)
+
+
+    !        # Compute the waves.
+
+        wave(1,1,i) = -a1*zim
+        wave(mu,1,i) = a1
+        wave(mv,1,i) = 0.d0
+        s(1,i) = -auxr(2,i-1)
+
+        wave(1,2,i) = a2*zi
+        wave(mu,2,i) = a2
+        wave(mv,2,i) = 0.d0
+        s(2,i) = auxl(2,i)
+
+    20 END DO
+
+
+
+!     # compute the leftgoing and rightgoing flux differences:
+!     # Note s(1,i) < 0   and   s(2,i) > 0.
+
+    do 220 m=1,meqn
+        do 220 i = 2-mbc, mx+mbc
+            amdq(m,i) = s(1,i)*wave(m,1,i)
+            apdq(m,i) = s(2,i)*wave(m,2,i)
+    220 END DO
+
+    return
+    end subroutine rpn2

paper2_examples/acoustics_2d_ex3/setaux.f

@@ -11,7 +11,7 @@ subroutine setaux(mbc,mx,my,xlower,ylower,
 c
 c
       use amr_module, only : NEEDS_TO_BE_SET
-      use adjoint_module, only: innerprod_index
+      use adjoint_module, only: innerprod_index, adjoint_flagging
 
       implicit double precision (a-h,o-z)
       double precision aux(maux,1-mbc:mx+mbc,1-mbc:my+mbc)
@@ -22,7 +22,8 @@ subroutine setaux(mbc,mx,my,xlower,ylower,
         do i = 1-mbc,mx+mbc
             xcell = xlower + (i-0.5d0)*dx
 
-            if (aux(1,i,j) .eq. NEEDS_TO_BE_SET) then
+            if (adjoint_flagging .and. 
+     &             (aux(1,i,j) .eq. NEEDS_TO_BE_SET)) then
                 aux(innerprod_index,i,j) = 0.d0
             endif
 

paper2_examples/acoustics_2d_ex3/setplot.py

@@ -21,7 +21,7 @@ def setplot(plotdata):
     from clawpack.visclaw import colormaps
 
     plotdata.clearfigures()  # clear any old figures,axes,items data
-    plotdata.format = 'binary'      # 'ascii', 'binary', 'netcdf'
+    plotdata.format = 'ascii'      # 'ascii', 'binary', 'netcdf'
 
 
     # Figure for pressure
@@ -42,7 +42,7 @@ def setplot(plotdata):
     plotitem = plotaxes.new_plotitem(plot_type='2d_pcolor')
     plotitem.plot_var = 0
     plotitem.pcolor_cmap = colormaps.blue_white_red
-    plotitem.add_colorbar = False
+    plotitem.add_colorbar = True
     plotitem.show = True       # show on plot?
     plotitem.pcolor_cmin = -0.3
     plotitem.pcolor_cmax = 0.3
@@ -54,6 +54,7 @@ def setplot(plotdata):
     #-----------------------------------------
     plotfigure = plotdata.new_plotfigure(name='Inner Product', figno=1)
     plotfigure.kwargs = {'figsize': (5.5,4)}
+    #plotfigure.show = False
 
     # Set up for axes in this figure:
     plotaxes = plotfigure.new_plotaxes()
@@ -72,7 +73,7 @@ def setplot(plotdata):
     plotitem.show = True       # show on plot?
     plotitem.pcolor_cmin = 0.0     # use when plotting inner product with q
     #plotitem.pcolor_cmin = 0.0      # use when plotting inner product with error
-    plotitem.pcolor_cmax = 0.01    # use when plotting inner product with q
+    plotitem.pcolor_cmax = 0.0001    # use when plotting inner product with q
     #plotitem.pcolor_cmax = 0.00001    # use when plotting inner product with error
     plotitem.amr_patchedges_show = [0,0,0]
     plotitem.amr_celledges_show = [0,0,0]
@@ -132,6 +133,7 @@ def setplot(plotdata):
     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 frames in parallel with omp?
 
     return plotdata
 

paper2_examples/acoustics_2d_ex3/setrun.py

@@ -9,32 +9,16 @@
 import os
 import numpy as np
 
-#-----------------------------------------------
-# Set these parameters for adjoint flagging....
-
-# location of output from computing adjoint:
-adjoint_output = os.path.abspath('adjoint/_output')
-print('Will flag using adjoint solution from  %s' % adjoint_output)
 
-# Time period of interest:
-t1 = 20.5
-t2 = 21.
-
-# Determining type of adjoint flagging:
+# This version is set up for adjoint flagging
+#-----------------------------------------------
 
-# taking inner product with forward solution or Richardson error:
-flag_forward_adjoint = True
-flag_richardson_adjoint = False
 
-# tolerance for adjoint flagging:
-adjoint_flag_tolerance = 3e-4       # suggested if using forward solution
-#adjoint_flag_tolerance = 3e-3        # suggested if using Richardson error
-#-----------------------------------------------
 
 #------------------------------
 def setrun(claw_pkg='amrclaw'):
 #------------------------------
-    
+
     """ 
     Define the parameters used for running Clawpack.
 
@@ -102,7 +86,8 @@ def setrun(claw_pkg='amrclaw'):
     clawdata.num_eqn = 3
 
     # Number of auxiliary variables in the aux array (initialized in setaux)
-    # see setadjoint
+    rundata.clawdata.num_aux = 2   
+    # Note: as required for original problem - modified below for adjoint
 
     # Index of aux array corresponding to capacity function, if there is one:
     clawdata.capa_index = 0
@@ -147,12 +132,12 @@ def setrun(claw_pkg='amrclaw'):
 
     elif clawdata.output_style == 3:
         # Output every step_interval timesteps over total_steps timesteps:
-        clawdata.output_step_interval = 2
-        clawdata.total_steps = 4
+        clawdata.output_step_interval = 1
+        clawdata.total_steps = 10
         clawdata.output_t0 = True  # output at initial (or restart) time?
 
 
-    clawdata.output_format = 'binary'       # 'ascii', 'binary', 'netcdf'
+    clawdata.output_format = 'ascii'       # 'ascii', 'binary', 'netcdf'
 
     clawdata.output_q_components = 'all'   # could be list such as [True,True]
     clawdata.output_aux_components = 'all'  # could be list
@@ -308,17 +293,22 @@ def setrun(claw_pkg='amrclaw'):
     # This must be a list of length num_aux, each element of which is one of:
     #   'center',  'capacity', 'xleft', or 'yleft'  (see documentation).
 
+    rundata.amrdata.aux_type = ['center','center']
+    # Note: as required for original problem - modified below for adjoint
+
+    # set tolerances appropriate for adjoint flagging:
+
     # need 1 value, set in setadjoint
 
 
     # Flag for refinement based on Richardson error estimater:
-    amrdata.flag_richardson = False
-
+    amrdata.flag_richardson = True
+    amrdata.flag_richardson_tol = 3e-3 # suggested if using adjoint error flag
+
     # Flag for refinement using routine flag2refine:
     amrdata.flag2refine = False
+    rundata.amrdata.flag2refine_tol = 3e-4 # suggested if using adj mag flag
 
-    # see setadjoint to set tolerance for adjoint flagging
-
     # steps to take on each level L between regriddings of level L+1:
     amrdata.regrid_interval = 2       
 
@@ -340,13 +330,29 @@ def setrun(claw_pkg='amrclaw'):
     rundata.regiondata.regions = []
     # to specify regions of refinement append lines of the form
     #  [minlevel,maxlevel,t1,t2,x1,x2,y1,y2]
-    
+
     #------------------------------------------------------------------
     # Adjoint specific data:
     #------------------------------------------------------------------
-    rundata = setadjoint(rundata)
+    # Also need to set flagging method and appropriate tolerances above
+
+    adjointdata = rundata.adjointdata
+    adjointdata.use_adjoint = True
+
+    # location of adjoint solution, must first be created:
+    adjointdata.adjoint_outdir = os.path.abspath('adjoint/_output')
 
+    # time period of interest:
+    adjointdata.t1 = 20.5
+    adjointdata.t2 = 21.
 
+    if adjointdata.use_adjoint:
+        # need an additional aux variable for inner product:
+        rundata.amrdata.aux_type.append('center')
+        rundata.clawdata.num_aux = len(rundata.amrdata.aux_type)
+        adjointdata.innerprod_index = len(rundata.amrdata.aux_type)
+
+
     #  ----- For developers -----
     # Toggle debugging print statements:
     amrdata.dprint = False      # print domain flags
@@ -365,60 +371,6 @@ def setrun(claw_pkg='amrclaw'):
     # end of function setrun
     # ----------------------
 
-#-------------------
-def setadjoint(rundata):
-    #-------------------
-
-    """
-        Setting up adjoint variables and
-        reading in all of the checkpointed Adjoint files
-        """
-
-    import glob
-
-
-    # Set these parameters at top of this file:
-    # adjoint_flag_tolerance, t1, t2, adjoint_output
-    # Then you don't need to modify this function...
-
-    # flag and tolerance for adjoint flagging:
-    if flag_forward_adjoint == True:
-        # setting up taking inner product with forward solution
-        rundata.amrdata.flag2refine = True
-        rundata.amrdata.flag2refine_tol = adjoint_flag_tolerance
-    elif flag_richardson_adjoint == True:
-        # setting up taking inner product with Richardson error
-        rundata.amrdata.flag_richardson = True
-        rundata.amrdata.flag_richardson_tol = adjoint_flag_tolerance
-    else:
-        print("No refinement flag set!")
-
-    rundata.clawdata.num_aux = 3   # 3 required for adjoint flagging
-    rundata.amrdata.aux_type = ['center','center','center']
-
-    adjointdata = rundata.new_UserData(name='adjointdata',fname='adjoint.data')
-    adjointdata.add_param('adjoint_output',adjoint_output,'adjoint_output')
-    adjointdata.add_param('t1',t1,'t1, start time of interest')
-    adjointdata.add_param('t2',t2,'t2, final time of interest')
-
-    files = glob.glob(os.path.join(adjoint_output,"fort.b*"))
-    files.sort()
-
-    if (len(files) == 0):
-        print("No binary files found for adjoint output!")
-
-    adjointdata.add_param('numadjoints', len(files), 'Number of adjoint checkpoint files.')
-    adjointdata.add_param('innerprod_index', 3, 'Index for innerproduct data in aux array.')
-
-    counter = 1
-    for fname in files:
-        f = open(fname)
-        adjointdata.add_param('file' + str(counter), fname, 'Binary file' + str(counter))
-        counter = counter + 1
-
-    return rundata
-# end of function setadjoint
-# ----------------------
 
 if __name__ == '__main__':
     # Set up run-time parameters and write all data files.