Wed Nov 5 15:41:40 PST 2014

Repository : https://github.com/geodynamics/pylith

On branches: baagaard/add-missing-files-dist,baagaard/add-release-2.0.2,baagaard/add-release-2.0.3,baagaard/add-release-2.1.0,baagaard/dynrup-new-lagrange,baagaard/feature-output-station-names,baagaard/feature-progress-monitor,baagaard/fix-custom-faultpc,baagaard/fix-error-messages,baagaard/fix-faults-intersect,baagaard/fix-friction-initial-state,baagaard/fix-meshing-examples-trelis,baagaard/update-autoconf,knepley/feature-petsc-fe,knepley/fix-dm-composition,knepley/upgrade-petsc-3.5,knepley/upgrade-petsc-master,maint,master,next,willic3/fix-plasticity
Link       : https://github.com/geodynamics/pylith/compare/f33c75b19fd60eedb2a3405db76a1fee333bb1d7...5b6d812b1612809fea3bd331c4e5af98c25a536a

>---------------------------------------------------------------

commit 6075897e1b7b4653533a1d569b73ff8335380143
Author: Brad Aagaard <baagaard at usgs.gov>
Date:   Sun Jun 22 09:41:04 2014 -0700

    Switched to IDless journal files. Minor cleanup.


>---------------------------------------------------------------

6075897e1b7b4653533a1d569b73ff8335380143
 examples/2d/greensfns/README                   |   3 +
 examples/2d/greensfns/reverse/geometry.jou     |  33 +++++---
 examples/2d/greensfns/reverse/gradient.jou     |  12 +--
 examples/2d/greensfns/reverse/mesh_tri3.exo    | Bin 150488 -> 149700 bytes
 examples/2d/greensfns/reverse/mesh_tri3.jou    |   2 +-
 examples/2d/greensfns/strikeslip/createbc.jou  |  18 +++--
 examples/2d/greensfns/strikeslip/geometry.jou  | 107 +++++++++++++++++++++----
 examples/2d/greensfns/strikeslip/gradient.jou  |  31 +++----
 examples/2d/greensfns/strikeslip/mesh_tri3.exo | Bin 234976 -> 234976 bytes
 examples/2d/greensfns/strikeslip/mesh_tri3.jou |   2 +-
 10 files changed, 149 insertions(+), 59 deletions(-)

diff --git a/examples/2d/greensfns/README b/examples/2d/greensfns/README
index ec9be0f..2683c52 100644
--- a/examples/2d/greensfns/README
+++ b/examples/2d/greensfns/README
@@ -44,6 +44,9 @@ Mesh generation (optional)
   recommend that you study the contents of the journal files to
   understand the mesh generation process.
 
+  NOTE: We use IDless journal files to maximize the compatibility
+  of the journal files with various versions of CUBIT and Trelis.
+
 
 Step 1. Forward simulation
 
diff --git a/examples/2d/greensfns/reverse/geometry.jou b/examples/2d/greensfns/reverse/geometry.jou
index 7f16236..d60f6a5 100644
--- a/examples/2d/greensfns/reverse/geometry.jou
+++ b/examples/2d/greensfns/reverse/geometry.jou
@@ -20,7 +20,7 @@
 # ----------------------------------------------------------------------
 # Set units to SI.
 # ----------------------------------------------------------------------
-# {Units('si')}
+${Units('si')}
 #
 # ----------------------------------------------------------------------
 # Reset geometry.
@@ -29,6 +29,11 @@ reset
 
 # Make sure undo is off to prevent errors in stitching volumes.
 undo off
+
+# Turn on IDless journal files for maximum compatibility.
+# The commands echoed to the log will replace the object ID with a
+# geometric specification of the object. Note that this means changing
+# the geometry will require changes to subsequent journal commands.
 journal idless on
 
 # ----------------------------------------------------------------------
@@ -38,24 +43,25 @@ journal idless on
 # -75.0 km <= x <= 75.0 km
 # -80.0 km <= y <= 0.0 km
 #
-#{blockWidth=150*km}
-#{blockHeight=80*km}
-#{blockLength=10*km}
-#
-#{faultWidth=30.0*km}
-#{faultDipAngle=45.0}
-#
-#{xoffset=0.5*faultWidth*cosd(faultDipAngle)}
+${blockWidth=150*km}
+${blockHeight=80*km}
+${blockLength=10*km}
+
+${faultWidth=30.0*km}
+${faultDipAngle=45.0}
+
+${xoffset=0.5*faultWidth*cosd(faultDipAngle)}
 
 brick x {blockWidth} y {blockHeight} z {blockLength}
-#{idV=Id("volume")}
+${idV=Id("volume")}
 volume {idV} move x {-xoffset} y {-blockHeight/2.0} z 0.0
 
-# create midsurface volume {idV} surface 1 2
+#create midsurface volume {idV} surface 1 2
 surface ( at -10606.6 -40000 5000 ordinal 1 ) name "surf_front"
 surface ( at -10606.6 -40000 -5000 ordinal 1 ) name "surf_back"
 create midsurface volume {idV} surface surf_front surf_back
-#{idS=Id("surface")}
+
+${idS=Id("surface")}
 delete volume {idV}
 
 # ----------------------------------------------------------------------
@@ -120,3 +126,6 @@ vertex ( at 64393.4 -80000 0 ordinal 1 ordered ) name "vertex_bot_xpos"
 
 #vertex 10 name "vertex_bot_xneg"
 vertex ( at -85606.6 -80000 0 ordinal 1 ordered ) name "vertex_bot_xneg"
+
+
+# End of file
diff --git a/examples/2d/greensfns/reverse/gradient.jou b/examples/2d/greensfns/reverse/gradient.jou
index e36cd8f..6aceb83 100644
--- a/examples/2d/greensfns/reverse/gradient.jou
+++ b/examples/2d/greensfns/reverse/gradient.jou
@@ -1,26 +1,26 @@
 # ----------------------------------------------------------------------
 # Set vertex spacing with increasing spacing away from fault
 # ----------------------------------------------------------------------
-#{bias_factor=1.05}
+${bias_factor=1.05}
 
 # Function for computing discretization size at end of curve with bias
-#{fun_dx='dxStart*bias_factor**ceil( ln(1-curveL/dxStart*(1-bias_factor))/ln(bias_factor))'}
+${fun_dx='dxStart*bias_factor**ceil( ln(1-curveL/dxStart*(1-bias_factor))/ln(bias_factor))'}
 
 # ----------------------------------------------------------------------
 # Compute sizes at curve endpoints
 # ----------------------------------------------------------------------
 
 # dxA - size at vertex_xpos
-#{dxStart=dx}{curveL=Length(Id("ground_fw"))}{execute("dxA="//fun_dx)}
+${dxStart=dx}{curveL=Length(Id("ground_fw"))}{execute("dxA="//fun_dx)}
 
 # dxB - size at vertex_xneg
-#{dxStart=dx}{curveL=Length(Id("ground_hw"))}{execute("dxB="//fun_dx)}
+${dxStart=dx}{curveL=Length(Id("ground_hw"))}{execute("dxB="//fun_dx)}
 
 # dxC - size at vertex_fault_yneg, vertex_bot_yneg
-#{dxStart=dx}{curveL=Length(Id("fault_extended"))}{execute("dxC="//fun_dx)}
+${dxStart=dx}{curveL=Length(Id("fault_extended"))}{execute("dxC="//fun_dx)}
 
 # dxD - size at vertex__xpos, vertex_top_xneg
-#{dxStart=dxA}{curveL=Length(Id("edge_xpos"))}{execute("dxD="//fun_dx)}
+${dxStart=dxA}{curveL=Length(Id("edge_xpos"))}{execute("dxD="//fun_dx)}
 
 # ----------------------------------------------------------------------
 # Reset sizes
diff --git a/examples/2d/greensfns/reverse/mesh_tri3.exo b/examples/2d/greensfns/reverse/mesh_tri3.exo
index 993ea0d..4adb89f 100644
Binary files a/examples/2d/greensfns/reverse/mesh_tri3.exo and b/examples/2d/greensfns/reverse/mesh_tri3.exo differ
diff --git a/examples/2d/greensfns/reverse/mesh_tri3.jou b/examples/2d/greensfns/reverse/mesh_tri3.jou
index bb2b3b7..03e58f0 100644
--- a/examples/2d/greensfns/reverse/mesh_tri3.jou
+++ b/examples/2d/greensfns/reverse/mesh_tri3.jou
@@ -10,7 +10,7 @@ playback 'geometry.jou'
 # ----------------------------------------------------------------------
 # Set discretization size and scheme
 # ----------------------------------------------------------------------
-#{dx=1.0*km}
+${dx=1.0*km}
 surface all scheme trimesh
 playback 'gradient.jou'
 
diff --git a/examples/2d/greensfns/strikeslip/createbc.jou b/examples/2d/greensfns/strikeslip/createbc.jou
index b35998a..63852bd 100644
--- a/examples/2d/greensfns/strikeslip/createbc.jou
+++ b/examples/2d/greensfns/strikeslip/createbc.jou
@@ -15,7 +15,7 @@
 # ----------------------------------------------------------------------
 # Create blocks for materials
 # ----------------------------------------------------------------------
-block 1 surface 8 9
+block 1 surface all
 block 1 name "elastic"
 
 # ----------------------------------------------------------------------
@@ -28,37 +28,39 @@ nodeset 10 name "fault"
 # ----------------------------------------------------------------------
 # Create nodeset for fault edge
 # ----------------------------------------------------------------------
-group "fault_edge" add node in vertex 15 16
+group "fault_edge" add node in vertex vertex_fault_ypos vertex_fault_yneg
 nodeset 11 group fault_edge
 nodeset 11 name "fault_edge"
 
 # ----------------------------------------------------------------------
 # Create nodeset for +x face
 # ----------------------------------------------------------------------
-group "face_xpos" add node in curve 14
+group "face_xpos" add node in curve edge_xpos
 nodeset 21 group face_xpos
 nodeset 21 name "face_xpos"
 
 # ----------------------------------------------------------------------
 # Create nodeset for -x face
 # ----------------------------------------------------------------------
-group "face_xneg" add node in curve 16
+group "face_xneg" add node in curve edge_xneg
 nodeset 22 group face_xneg
 nodeset 22 name "face_xneg"
 
 # ----------------------------------------------------------------------
 # Create nodeset for +y face
 # ----------------------------------------------------------------------
-group "face_ypos" add node in curve 18
-group "face_ypos" add node in curve 21
+group "face_ypos" add node in curve edge_ypos_xneg
+group "face_ypos" add node in curve edge_ypos_xpos
 nodeset 23 group face_ypos
 nodeset 23 name "face_ypos"
 
 # ----------------------------------------------------------------------
 # Create nodeset for -y face
 # ----------------------------------------------------------------------
-group "face_yneg" add node in curve 19
-group "face_yneg" add node in curve 20
+group "face_yneg" add node in curve edge_yneg_xneg
+group "face_yneg" add node in curve edge_yneg_xpos
 nodeset 24 group face_yneg
 nodeset 24 name "face_yneg"
 
+
+# End of file
diff --git a/examples/2d/greensfns/strikeslip/geometry.jou b/examples/2d/greensfns/strikeslip/geometry.jou
index 0b35478..e13cd1c 100644
--- a/examples/2d/greensfns/strikeslip/geometry.jou
+++ b/examples/2d/greensfns/strikeslip/geometry.jou
@@ -20,7 +20,7 @@
 # ----------------------------------------------------------------------
 # Set units to SI.
 # ----------------------------------------------------------------------
-# {Units('si')}
+${Units('si')}
 #
 # ----------------------------------------------------------------------
 # Reset geometry.
@@ -30,6 +30,12 @@ reset
 # Make sure undo is off to prevent errors in stitching volumes.
 undo off
 
+# Turn on IDless journal files for maximum compatibility.
+# The commands echoed to the log will replace the object ID with a
+# geometric specification of the object. Note that this means changing
+# the geometry will require changes to subsequent journal commands.
+journal idless on
+
 # ----------------------------------------------------------------------
 # Create block
 # ----------------------------------------------------------------------
@@ -37,28 +43,97 @@ undo off
 # -50.0 km <= x <= 50.0 km
 # -75.0 km <= y <= 75.0 km
 #
-#{blockWidth=100*km}
-#{blockLength=150*km}
-#{blockHeight=10*km}
-#
-#{faultLength=50.0*km}
-#
+${blockWidth=100*km}
+${blockLength=150*km}
+${blockHeight=10*km}
+
+${faultLength=50.0*km}
+
 brick x {blockWidth} y {blockLength} z {blockHeight}
-create midsurface volume 1 surface 1 2
-delete volume 1
+${idV=Id("volume")}
+
+#surface 1 name "surf_front"
+surface ( at 0 0 5000 ordinal 1 ordered ) name "surf_front"
+
+#surface 2 name "surf_back"
+surface ( at 0 0 -5000 ordinal 1 ordered ) name "surf_back"
+
+create midsurface volume {idV} surface surf_front surf_back
+${idS=Id("surface")}
+delete volume {idV}
 
 # ----------------------------------------------------------------------
 # Create interface surfaces
 # ----------------------------------------------------------------------
 
 # Create fault (yz plane) at x = 0.0
-split surface 7 across location position 0 {-blockLength/2.0} 0 location position 0 {blockLength/2.0} 0
-split curve 17 at position 0.0 {faultLength/2.0} 0.0
-split curve 23 at position 0.0 {-faultLength/2.0} 0.0
-curve 25 name "fault_surface"
+split surface {idS} across location position 0 {-blockLength/2.0} 0 location position 0 {blockLength/2.0} 0
+
+#curve 17 name "fault_ext1"
+curve ( at 0 0 0 ordinal 1 ordered ) name "fault_ext1"
+split curve fault_ext1 at position 0.0 {faultLength/2.0} 0.0
+
+#curve 23 name "fault_ext2"
+curve ( at 0 -25000 0 ordinal 1 ordered ) name "fault_ext2"
+split curve fault_ext2 at position 0.0 {-faultLength/2.0} 0.0
 
 # ----------------------------------------------------------------------
-# Imprint all volumes, merging surfaces
+# Name curves
 # ----------------------------------------------------------------------
-imprint all
-merge all
+#curve 25 name "fault_surface"
+curve ( at 0 0 0 ordinal 1 ordered ) name "fault_surface"
+
+#curve 22 name "fault_ext_ypos"
+curve ( at 0 50000 0 ordinal 1 ordered ) name "fault_ext_ypos"
+
+#curve 24 name "fault_ext_yneg"
+curve ( at 0 -50000 0 ordinal 1 ordered ) name "fault_ext_yneg"
+
+#curve 21 name "edge_ypos_xpos"
+curve ( at 25000 75000 0 ordinal 1 ordered ) name "edge_ypos_xpos"
+
+#curve 18 name "edge_ypos_xneg"
+curve ( at -25000 75000 0 ordinal 1 ordered ) name "edge_ypos_xneg"
+
+#curve 20 name "edge_yneg_xpos"
+curve ( at 25000 -75000 0 ordinal 1 ordered ) name "edge_yneg_xpos"
+
+#curve 19 name "edge_yneg_xneg"
+curve ( at -25000 -75000 0 ordinal 1 ordered ) name "edge_yneg_xneg"
+
+#curve 14 name "edge_xpos"
+curve ( at 50000 0 0 ordinal 1 ordered ) name "edge_xpos"
+
+#curve 16 name "edge_xneg"
+curve ( at -50000 0 0 ordinal 1 ordered ) name "edge_xneg"
+
+# ----------------------------------------------------------------------
+# Name vertices
+# ----------------------------------------------------------------------
+
+#vertex 15 name "vertex_fault_ypos"
+vertex ( at 0 25000 0 ordinal 1 ordered ) name "vertex_fault_ypos"
+
+#vertex 16 name "vertex_fault_yneg"
+vertex ( at 0 -25000 0 ordinal 1 ordered ) name "vertex_fault_yneg"
+
+#vertex 13 name "vertex_ypos_mid"
+vertex ( at 0 75000 0 ordinal 1 ordered ) name "vertex_ypos_mid"
+
+#vertex 11 name "vertex_ypos_xpos"
+vertex ( at 50000 75000 0 ordinal 1 ordered ) name "vertex_ypos_xpos"
+
+#vertex 12 name "vertex_ypos_xneg"
+vertex ( at -50000 75000 0 ordinal 1 ordered ) name "vertex_ypos_xneg"
+
+#vertex 14 name "vertex_yneg_mid"
+vertex ( at 0 -75000 0 ordinal 1 ordered ) name "vertex_yneg_mid"
+
+#vertex 9 name "vertex_yneg_xpos"
+vertex ( at 50000 -75000 0 ordinal 1 ordered ) name "vertex_yneg_xpos"
+
+#vertex 10 name "vertex_yneg_xneg"
+vertex ( at -50000 -75000 0 ordinal 1 ordered ) name "vertex_yneg_xneg"
+
+
+# End of file
\ No newline at end of file
diff --git a/examples/2d/greensfns/strikeslip/gradient.jou b/examples/2d/greensfns/strikeslip/gradient.jou
index e85050f..ef9c343 100644
--- a/examples/2d/greensfns/strikeslip/gradient.jou
+++ b/examples/2d/greensfns/strikeslip/gradient.jou
@@ -15,20 +15,20 @@
 # ----------------------------------------------------------------------
 # Set vertex spacing with increasing spacing away from fault
 # ----------------------------------------------------------------------
-#{bias_factor=1.05}
+${bias_factor=1.05}
 
 # Function for computing discretization size at end of curve with bias
-#{fun_dx='dxStart*bias_factor**ceil( ln(1-curveL/dxStart*(1-bias_factor))/ln(bias_factor))'}
+${fun_dx='dxStart*bias_factor**ceil( ln(1-curveL/dxStart*(1-bias_factor))/ln(bias_factor))'}
 
 # ----------------------------------------------------------------------
 # Compute sizes at curve endpoints
 # ----------------------------------------------------------------------
 
-# dxA - size at vertex 13 14
-#{dxStart=dx}{curveL=Length(22)}{execute("dxA="//fun_dx)}
+# dxA - size at vertex_ypos_mid, vertex_yneg_mid
+${dxStart=dx}{curveL=Length(Id("fault_ext_ypos"))}{execute("dxA="//fun_dx)}
 
-# dxB - size at vertex 9 10 11 12
-#{dxStart=dxA}{curveL=Length(21)}{execute("dxC="//fun_dx)}
+# dxB - size at domain corners
+${dxStart=dxA}{curveL=Length(Id("edge_ypos_xpos"))}{execute("dxC="//fun_dx)}
 
 # ----------------------------------------------------------------------
 # Reset sizes
@@ -40,21 +40,22 @@ surface all sizing function none
 curve fault_surface size {dx}
 
 # Set bias on curves extending from faults
-curve 22 scheme bias fine size {dx} factor {bias_factor} start vertex 15
-curve 24 scheme bias fine size {dx} factor {bias_factor} start vertex 16
+curve fault_ext_ypos scheme bias fine size {dx} factor {bias_factor} start vertex vertex_fault_ypos
+curve fault_ext_yneg scheme bias fine size {dx} factor {bias_factor} start vertex vertex_fault_yneg
 
 # A to B
-curve 18 scheme bias fine size {dxA} factor {bias_factor} start vertex 13
-curve 21 scheme bias fine size {dxA} factor {bias_factor} start vertex 13
-curve 19 scheme bias fine size {dxA} factor {bias_factor} start vertex 14
-curve 20 scheme bias fine size {dxA} factor {bias_factor} start vertex 14
+curve edge_ypos_xneg scheme bias fine size {dxA} factor {bias_factor} start vertex vertex_ypos_mid
+curve edge_ypos_xpos scheme bias fine size {dxA} factor {bias_factor} start vertex vertex_ypos_mid
+curve edge_yneg_xneg scheme bias fine size {dxA} factor {bias_factor} start vertex vertex_yneg_mid
+curve edge_yneg_xpos scheme bias fine size {dxA} factor {bias_factor} start vertex vertex_yneg_mid
 
 # B to B
-curve 16 size {dxC}
-curve 14 size {dxC}
+curve edge_xneg size {dxC}
+curve edge_xpos size {dxC}
 
-surface 8 9 sizing function type bias start curve fault_surface factor {bias_factor}
+surface all sizing function type bias start curve fault_surface factor {bias_factor}
 
 # End of file
 
 
+
diff --git a/examples/2d/greensfns/strikeslip/mesh_tri3.exo b/examples/2d/greensfns/strikeslip/mesh_tri3.exo
index 7819f22..605789d 100644
Binary files a/examples/2d/greensfns/strikeslip/mesh_tri3.exo and b/examples/2d/greensfns/strikeslip/mesh_tri3.exo differ
diff --git a/examples/2d/greensfns/strikeslip/mesh_tri3.jou b/examples/2d/greensfns/strikeslip/mesh_tri3.jou
index 7802398..c850e3d 100644
--- a/examples/2d/greensfns/strikeslip/mesh_tri3.jou
+++ b/examples/2d/greensfns/strikeslip/mesh_tri3.jou
@@ -24,7 +24,7 @@ playback 'geometry.jou'
 # ----------------------------------------------------------------------
 # Set discretization size and scheme
 # ----------------------------------------------------------------------
-#{dx=1.0*km}
+${dx=1.0*km}
 surface all scheme trimesh
 playback 'gradient.jou'
 

