From c0e1bf98e144265f3a7f3e38c01c1bd5af5af596 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Thu, 27 Feb 2020 22:51:50 -0600
Subject: [PATCH 01/18] Add some functions for wavy metrics that just return
 uniform metrics

---
 test/data_for_test.py | 45 +++++++++++++++++++++++++------------------
 test/wavy_metrics.py  | 33 +++++++++++++++++++++++++++++++
 2 files changed, 59 insertions(+), 19 deletions(-)
 create mode 100644 test/wavy_metrics.py

diff --git a/test/data_for_test.py b/test/data_for_test.py
index 483d50b..afd750a 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -1,4 +1,4 @@
-__copyright__ = "Copyright (C) 2019 Timothy A. Smith"
+__copyright__ = "Copyright (C) 2019-2020 Timothy A. Smith"
 
 __license__ = """
 Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -24,6 +24,7 @@ import numpy as np
 import pytest
 import utilities as u
 import weno_reference_implementation as ref
+import wavy_metrics as wavy
 
 
 class WindowData:
@@ -72,6 +73,9 @@ def metrics_generator():
                                dtype=np.float64,
                                order="F")
             jacobians = np.repeat(1.0, 6)
+        elif (metric_str == "wavy"):
+            metrics = wavy.metrics(ndim)
+            jacobians = wavy.jacobians(ndim)
         else:
             raise ValueError("Metric string {} not supported".format(metric_str))
         return metrics, jacobians
@@ -80,24 +84,27 @@ def metrics_generator():
 
 
 @pytest.fixture(scope="session", params=[
-    ("sine", "x", "uniform"),
-    ("sine", "y", "uniform"),
-    ("sine", "z", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
-    ("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
-    ("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
-    ("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
-    ("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
-    ("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
-    ("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
+    ("sine", "x", "wavy"),
+    ("sine", "y", "wavy"),
+    ("sine", "z", "wavy"),
+    #("sine", "x", "uniform"),
+    #("sine", "y", "uniform"),
+    #("sine", "z", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
+    #("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
+    #("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
+    #("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
+    #("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
+    #("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
+    #("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
     ])
 def window_data(request, states_generator, metrics_generator):
     states_str = request.param[0]
diff --git a/test/wavy_metrics.py b/test/wavy_metrics.py
new file mode 100644
index 0000000..672d0c1
--- /dev/null
+++ b/test/wavy_metrics.py
@@ -0,0 +1,33 @@
+__copyright__ = "Copyright (C) 2020 Timothy A. Smith"
+
+__license__ = """
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+"""
+
+import numpy as np
+
+
+def metrics(ndim):
+    return np.array([np.identity(ndim) for i in range(6)],
+                     dtype=np.float64,
+                     order="F")
+
+
+def jacobians(ndim):
+    return np.array([1.0 for i in range(6)], dtype=np.float64, order="F")
-- 
GitLab


From 3cfd088e08f7fb6ed3dcccd1dc9349b7c26be3f0 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 28 Feb 2020 19:30:57 -0600
Subject: [PATCH 02/18] refactor API to wavy metrics

---
 test/data_for_test.py                        | 14 +++++++-------
 test/{wavy_metrics.py => wavy_metrics_3d.py} | 19 +++++++++++++++----
 2 files changed, 22 insertions(+), 11 deletions(-)
 rename test/{wavy_metrics.py => wavy_metrics_3d.py} (73%)

diff --git a/test/data_for_test.py b/test/data_for_test.py
index afd750a..06f485e 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -24,7 +24,7 @@ import numpy as np
 import pytest
 import utilities as u
 import weno_reference_implementation as ref
-import wavy_metrics as wavy
+import wavy_metrics_3d as wavy3d
 
 
 class WindowData:
@@ -73,9 +73,9 @@ def metrics_generator():
                                dtype=np.float64,
                                order="F")
             jacobians = np.repeat(1.0, 6)
-        elif (metric_str == "wavy"):
-            metrics = wavy.metrics(ndim)
-            jacobians = wavy.jacobians(ndim)
+        elif (metric_str == "wavy3d"):
+            metrics = wavy3d.metrics()
+            jacobians = wavy3d.jacobians()
         else:
             raise ValueError("Metric string {} not supported".format(metric_str))
         return metrics, jacobians
@@ -84,9 +84,9 @@ def metrics_generator():
 
 
 @pytest.fixture(scope="session", params=[
-    ("sine", "x", "wavy"),
-    ("sine", "y", "wavy"),
-    ("sine", "z", "wavy"),
+    ("sine", "x", "wavy3d"),
+    ("sine", "y", "wavy3d"),
+    ("sine", "z", "wavy3d"),
     #("sine", "x", "uniform"),
     #("sine", "y", "uniform"),
     #("sine", "z", "uniform"),
diff --git a/test/wavy_metrics.py b/test/wavy_metrics_3d.py
similarity index 73%
rename from test/wavy_metrics.py
rename to test/wavy_metrics_3d.py
index 672d0c1..4096eff 100644
--- a/test/wavy_metrics.py
+++ b/test/wavy_metrics_3d.py
@@ -20,14 +20,25 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
 """
 
+# The wavy grid and curvilinear metric formulation used here was taken from
+# T. Nonomura, et al., Comput. Fluids 107 (2015) 242-255
+
 import numpy as np
 
 
-def metrics(ndim):
-    return np.array([np.identity(ndim) for i in range(6)],
+def weighted_metrics():
+    return np.array([np.identity(3) for i in range(6)],
                      dtype=np.float64,
                      order="F")
 
 
-def jacobians(ndim):
-    return np.array([1.0 for i in range(6)], dtype=np.float64, order="F")
+def inverse_jacobians():
+    return np.array([1.0 for i in range(6)], dtype=np.float64)
+
+
+def metrics():
+    return weighted_metrics()*jacobians()[:,None,None]
+
+
+def jacobians():
+    return np.reciprocal(inverse_jacobians())
-- 
GitLab


From 6109a854f60f9d2ce5db3ca748d493ac5f74ace7 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 29 Feb 2020 09:46:56 -0700
Subject: [PATCH 03/18] add some constants, setup choice of direction

---
 test/data_for_test.py   |  8 ++---
 test/wavy_metrics_3d.py | 72 +++++++++++++++++++++++++++++++++++------
 2 files changed, 66 insertions(+), 14 deletions(-)

diff --git a/test/data_for_test.py b/test/data_for_test.py
index 06f485e..1711bfd 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -67,15 +67,15 @@ def states_generator():
 def metrics_generator():
     ndim = ref.gas.ndim
 
-    def window_metrics(metric_str):
+    def window_metrics(metric_str, dim):
         if (metric_str == "uniform"):
             metrics = np.array([np.identity(ndim) for i in range(6)],
                                dtype=np.float64,
                                order="F")
             jacobians = np.repeat(1.0, 6)
         elif (metric_str == "wavy3d"):
-            metrics = wavy3d.metrics()
-            jacobians = wavy3d.jacobians()
+            metrics = wavy3d.metrics(dim)
+            jacobians = wavy3d.jacobians(dim)
         else:
             raise ValueError("Metric string {} not supported".format(metric_str))
         return metrics, jacobians
@@ -113,7 +113,7 @@ def window_data(request, states_generator, metrics_generator):
 
     return WindowData(states_generator(states_str),
                       dir_str,
-                      metrics_generator(metric_str))
+                      metrics_generator(metric_str, dir_str))
 
 
 class PairData:
diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index 4096eff..d83ce26 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -25,20 +25,72 @@ THE SOFTWARE.
 
 import numpy as np
 
+# grid parameters
+Lx = 4
+Ly = 4
+Lz = 4
 
-def weighted_metrics():
-    return np.array([np.identity(3) for i in range(6)],
-                     dtype=np.float64,
-                     order="F")
+# grid indices
+# built-in assumption is j goes from 1 to j_max, and similarly with k, l
+j_max = 21
+k_max = 21
+l_max = 21
 
+dx = Lx/(j_max - 1)
+dy = Ly/(k_max - 1)
+dz = Lz/(l_max - 1)
 
-def inverse_jacobians():
-    return np.array([1.0 for i in range(6)], dtype=np.float64)
 
+def weighted_metric_mat(j, k, l):
+    """ returns weighted metric matrix at a single grid point with indices j,k,l"""
+    arr = np.identity(3)
+    #FIXME: Shouldn't be uniform
+    return arr
 
-def metrics():
-    return weighted_metrics()*jacobians()[:,None,None]
 
+def inverse_jacobian(j, k, l):
+    """ returns inverse jacobian at a single grid point with indices j,k,l"""
+    #FIXME: Shouldn't be uniform
+    return 1.0
 
-def jacobians():
-    return np.reciprocal(inverse_jacobians())
+
+def weighted_metrics(dim):
+    if dim == "x":
+        return np.array([weighted_metric_mat(j+1,1,1) for j in range(6)],
+                         dtype=np.float64,
+                         order="F")
+    elif dim == "y":
+        return np.array([weighted_metric_mat(1,k+1,1) for k in range(6)],
+                         dtype=np.float64,
+                         order="F")
+    elif dim == "z":
+        return np.array([weighted_metric_mat(1,1,l+1) for l in range(6)],
+                         dtype=np.float64,
+                         order="F")
+    else:
+        raise ValueError("Dimension {} not supported".format(dim))
+
+
+def inverse_jacobians(dim):
+    if dim == "x":
+        return np.array([inverse_jacobian(j+1,1,1) for j in range(6)],
+                         dtype=np.float64,
+                         order="F")
+    elif dim == "y":
+        return np.array([inverse_jacobian(1,k+1,1) for k in range(6)],
+                         dtype=np.float64,
+                         order="F")
+    elif dim == "z":
+        return np.array([inverse_jacobian(1,1,l+1) for l in range(6)],
+                         dtype=np.float64,
+                         order="F")
+    else:
+        raise ValueError("Dimension {} not supported".format(dim))
+
+
+def metrics(dim):
+    return weighted_metrics(dim)*jacobians(dim)[:,None,None]
+
+
+def jacobians(dim):
+    return np.reciprocal(inverse_jacobians(dim))
-- 
GitLab


From 4f36f206e13b9ba4a1a049eda879c4bc7f990e50 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 29 Feb 2020 09:54:22 -0700
Subject: [PATCH 04/18] clean up and remove some duplication in wavy metrics

---
 test/wavy_metrics_3d.py | 33 ++++++++++-----------------------
 1 file changed, 10 insertions(+), 23 deletions(-)

diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index d83ce26..df1f801 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -54,43 +54,30 @@ def inverse_jacobian(j, k, l):
     return 1.0
 
 
-def weighted_metrics(dim):
+def array_along_dim(func, dim):
     if dim == "x":
-        return np.array([weighted_metric_mat(j+1,1,1) for j in range(6)],
+        return np.array([func(j+1,1,1) for j in range(6)],
                          dtype=np.float64,
                          order="F")
     elif dim == "y":
-        return np.array([weighted_metric_mat(1,k+1,1) for k in range(6)],
+        return np.array([func(1,k+1,1) for k in range(6)],
                          dtype=np.float64,
                          order="F")
     elif dim == "z":
-        return np.array([weighted_metric_mat(1,1,l+1) for l in range(6)],
+        return np.array([func(1,1,l+1) for l in range(6)],
                          dtype=np.float64,
                          order="F")
     else:
         raise ValueError("Dimension {} not supported".format(dim))
 
 
-def inverse_jacobians(dim):
-    if dim == "x":
-        return np.array([inverse_jacobian(j+1,1,1) for j in range(6)],
-                         dtype=np.float64,
-                         order="F")
-    elif dim == "y":
-        return np.array([inverse_jacobian(1,k+1,1) for k in range(6)],
-                         dtype=np.float64,
-                         order="F")
-    elif dim == "z":
-        return np.array([inverse_jacobian(1,1,l+1) for l in range(6)],
-                         dtype=np.float64,
-                         order="F")
-    else:
-        raise ValueError("Dimension {} not supported".format(dim))
+def weighted_metrics(dim):
+    return array_along_dim(weighted_metric_mat, dim)
 
 
-def metrics(dim):
-    return weighted_metrics(dim)*jacobians(dim)[:,None,None]
+def jacobians(dim):
+    return np.reciprocal(array_along_dim(inverse_jacobian, dim))
 
 
-def jacobians(dim):
-    return np.reciprocal(inverse_jacobians(dim))
+def metrics(dim):
+    return weighted_metrics(dim)*jacobians(dim)[:,None,None]
-- 
GitLab


From 5f901fec1557b66362f364ec260cc30c3ea21742 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 29 Feb 2020 10:14:57 -0700
Subject: [PATCH 05/18] added non-uniform jacobians

---
 test/wavy_metrics_3d.py | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index df1f801..935e0e4 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -41,17 +41,40 @@ dy = Ly/(k_max - 1)
 dz = Lz/(l_max - 1)
 
 
+def cos_x(xi):
+    return np.cos((4*np.pi*dx*xi)/Lx)
+
+def cos_y(eta):
+    return np.cos((4*np.pi*dy*eta)/Ly)
+
+def cos_z(zeta):
+    return np.cos((4*np.pi*dz*zeta)/Lz)
+
+def sin_x(xi):
+    return np.sin((4*np.pi*dx*xi)/Lx)
+
+def sin_y(eta):
+    return np.sin((4*np.pi*dy*eta)/Ly)
+
+def sin_z(zeta):
+    return np.sin((4*np.pi*dz*zeta)/Lz)
+
+
 def weighted_metric_mat(j, k, l):
     """ returns weighted metric matrix at a single grid point with indices j,k,l"""
     arr = np.identity(3)
     #FIXME: Shouldn't be uniform
     return arr
 
-
 def inverse_jacobian(j, k, l):
     """ returns inverse jacobian at a single grid point with indices j,k,l"""
-    #FIXME: Shouldn't be uniform
-    return 1.0
+    return dx*dy*dz*(
+            Lx*Ly*Lz
+            -16*(pi^2)*Ly*dx*dz*cos_z(zeta)*cos_x(xi)*sin_y(eta)^2
+            -16*(pi^2)*Lz*dx*dy*cos_y(eta)*cos_x(xi)*sin_z(zeta)^2
+            -16*(pi^2)*Lx*dz*dy*cos_y(eta)*cos_z(zeta)*sin_x(xi)^2
+            +16*(pi^3)*dx*dy*dz*sin_x(2*xi)*sin_y(2*eta)*sin_z(2*zeta)
+            )/(Lx*Ly*Lz)
 
 
 def array_along_dim(func, dim):
-- 
GitLab


From 11b7136937d9c076d37b286d865aeb483a3d39e8 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 29 Feb 2020 10:30:09 -0700
Subject: [PATCH 06/18] some more refactoring, start on weighted metric matrix

---
 test/wavy_metrics_3d.py | 58 ++++++++++++++++++++++++++++++++---------
 1 file changed, 45 insertions(+), 13 deletions(-)

diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index 935e0e4..dd39f6d 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -24,12 +24,15 @@ THE SOFTWARE.
 # T. Nonomura, et al., Comput. Fluids 107 (2015) 242-255
 
 import numpy as np
+import numpy.pi as pi
 
 # grid parameters
 Lx = 4
 Ly = 4
 Lz = 4
 
+Lprod = Lx*Ly*Lz
+
 # grid indices
 # built-in assumption is j goes from 1 to j_max, and similarly with k, l
 j_max = 21
@@ -42,39 +45,68 @@ dz = Lz/(l_max - 1)
 
 
 def cos_x(xi):
-    return np.cos((4*np.pi*dx*xi)/Lx)
+    return np.cos((4*pi*dx*xi)/Lx)
 
 def cos_y(eta):
-    return np.cos((4*np.pi*dy*eta)/Ly)
+    return np.cos((4*pi*dy*eta)/Ly)
 
 def cos_z(zeta):
-    return np.cos((4*np.pi*dz*zeta)/Lz)
+    return np.cos((4*pi*dz*zeta)/Lz)
 
 def sin_x(xi):
-    return np.sin((4*np.pi*dx*xi)/Lx)
+    return np.sin((4*pi*dx*xi)/Lx)
 
 def sin_y(eta):
-    return np.sin((4*np.pi*dy*eta)/Ly)
+    return np.sin((4*pi*dy*eta)/Ly)
 
 def sin_z(zeta):
-    return np.sin((4*np.pi*dz*zeta)/Lz)
+    return np.sin((4*pi*dz*zeta)/Lz)
+
+
+def blue_x(xi, eta, zeta):
+    return 16*(pi^2)*Lx*dz*dy*cos_y(eta)*cos_z(zeta)*sin_x(xi)^2
+
+def blue_y(xi, eta, zeta):
+    return 16*(pi^2)*Ly*dx*dz*cos_z(zeta)*cos_x(xi)*sin_y(eta)^2
+
+def blue_z(xi, eta, zeta):
+    return 16*(pi^2)*Lz*dx*dy*cos_y(eta)*cos_x(xi)*sin_z(zeta)^2
+
+
+def coords_from_indices(j, k, l):
+    return (j-1, k-1, l-1)
 
 
 def weighted_metric_mat(j, k, l):
     """ returns weighted metric matrix at a single grid point with indices j,k,l"""
-    arr = np.identity(3)
-    #FIXME: Shouldn't be uniform
+    xi, eta, zeta = coords_from_indices(j, k, l)
+    arr = np.zeros([3,3])
+
+    arr[0,0] = dy*dz*(Lprod - blue_x(xi, eta, zeta))/Lprod
+    arr[1,0] = 
+    arr[2,0] = 
+
+    arr[0,1] = 
+    arr[1,1] = dx*dz*(Lprod - blue_y(xi, eta, zeta))/Lprod
+    arr[2,1] = 
+
+    arr[0,2] = 
+    arr[1,2] = 
+    arr[2,2] = dx*dy*(Lprod - blue_z(xi, eta, zeta))/Lprod
+
     return arr
 
+
 def inverse_jacobian(j, k, l):
     """ returns inverse jacobian at a single grid point with indices j,k,l"""
+    xi, eta, zeta = coords_from_indices(j, k, l)
     return dx*dy*dz*(
-            Lx*Ly*Lz
-            -16*(pi^2)*Ly*dx*dz*cos_z(zeta)*cos_x(xi)*sin_y(eta)^2
-            -16*(pi^2)*Lz*dx*dy*cos_y(eta)*cos_x(xi)*sin_z(zeta)^2
-            -16*(pi^2)*Lx*dz*dy*cos_y(eta)*cos_z(zeta)*sin_x(xi)^2
+            Lprod
+            - blue_x(xi, eta, zeta)
+            - blue_y(xi, eta, zeta)
+            - blue_z(xi, eta, zeta)
             +16*(pi^3)*dx*dy*dz*sin_x(2*xi)*sin_y(2*eta)*sin_z(2*zeta)
-            )/(Lx*Ly*Lz)
+            )/Lprod
 
 
 def array_along_dim(func, dim):
-- 
GitLab


From 7b796888bee4eb8a3c7b31f4accca1deb5b729bf Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 17:18:00 -0700
Subject: [PATCH 07/18] initial implementation of wavy mesh complete

---
 test/wavy_metrics_3d.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index dd39f6d..6aca999 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -83,15 +83,21 @@ def weighted_metric_mat(j, k, l):
     arr = np.zeros([3,3])
 
     arr[0,0] = dy*dz*(Lprod - blue_x(xi, eta, zeta))/Lprod
-    arr[1,0] = 
-    arr[2,0] = 
+    arr[1,0] = 4*pi*dx*dy*dz*cos_x(xi)*(-Lz*sin_z(zeta)
+                + 4*pi*dz*cos_z(zeta)*sin_y(eta)*sin_x(xi))/(Lx*Lz)
+    arr[2,0] = 4*pi*dx*dy*dz*cos_x(xi)*(-Ly*sin_y(eta)
+                + 4*pi*dy*cos_y(eta)*sin_z(zeta)*sin_x(xi))/(Lx*Ly)
 
-    arr[0,1] = 
+    arr[0,1] = 4*pi*dx*dy*dz*cos_y(eta)*(-Lz*sin_z(zeta)
+                + 4*pi*dz*cos_z(zeta)*sin_x(xi)*sin_y(eta))/(Ly*Lz)
     arr[1,1] = dx*dz*(Lprod - blue_y(xi, eta, zeta))/Lprod
-    arr[2,1] = 
+    arr[2,1] = 4*pi*dx*dy*dz*cos_y(eta)*(-Lx*sin_x(xi)
+                + 4*pi*dx*cos_x(xi)*sin_z(zeta)*sin_y(eta))/(Ly*Lx)
 
-    arr[0,2] = 
-    arr[1,2] = 
+    arr[0,2] = 4*pi*dx*dy*dz*cos_z(zeta)*(-Ly*sin_y(eta)
+                + 4*pi*dy*cos_y(eta)*sin_x(xi)*sin_z(zeta))/(Lz*Ly)
+    arr[1,2] = 4*pi*dx*dy*dz*cos_z(zeta)*(-Lx*sin_x(xi)
+                + 4*pi*dx*cos_x(xi)*sin_y(eta)*sin_z(zeta))/(Lz*Lx)
     arr[2,2] = dx*dy*(Lprod - blue_z(xi, eta, zeta))/Lprod
 
     return arr
-- 
GitLab


From 268e99feaded700bb204a5211ff02548156b8b1b Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 17:21:05 -0700
Subject: [PATCH 08/18] fix some interpreter complaints

---
 test/wavy_metrics_3d.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index 6aca999..adfdf0c 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -24,7 +24,7 @@ THE SOFTWARE.
 # T. Nonomura, et al., Comput. Fluids 107 (2015) 242-255
 
 import numpy as np
-import numpy.pi as pi
+from numpy import pi
 
 # grid parameters
 Lx = 4
@@ -64,13 +64,13 @@ def sin_z(zeta):
 
 
 def blue_x(xi, eta, zeta):
-    return 16*(pi^2)*Lx*dz*dy*cos_y(eta)*cos_z(zeta)*sin_x(xi)^2
+    return 16*(pi**2)*Lx*dz*dy*cos_y(eta)*cos_z(zeta)*sin_x(xi)**2
 
 def blue_y(xi, eta, zeta):
-    return 16*(pi^2)*Ly*dx*dz*cos_z(zeta)*cos_x(xi)*sin_y(eta)^2
+    return 16*(pi**2)*Ly*dx*dz*cos_z(zeta)*cos_x(xi)*sin_y(eta)**2
 
 def blue_z(xi, eta, zeta):
-    return 16*(pi^2)*Lz*dx*dy*cos_y(eta)*cos_x(xi)*sin_z(zeta)^2
+    return 16*(pi**2)*Lz*dx*dy*cos_y(eta)*cos_x(xi)*sin_z(zeta)**2
 
 
 def coords_from_indices(j, k, l):
@@ -111,7 +111,7 @@ def inverse_jacobian(j, k, l):
             - blue_x(xi, eta, zeta)
             - blue_y(xi, eta, zeta)
             - blue_z(xi, eta, zeta)
-            +16*(pi^3)*dx*dy*dz*sin_x(2*xi)*sin_y(2*eta)*sin_z(2*zeta)
+            +16*(pi**3)*dx*dy*dz*sin_x(2*xi)*sin_y(2*eta)*sin_z(2*zeta)
             )/Lprod
 
 
-- 
GitLab


From 8ea794a7d2d7e64ae118a6cb921289d06b1cedeb Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 22:22:19 -0700
Subject: [PATCH 09/18] uncomment tests and add xfail marks

---
 test/data_for_test.py        | 36 ++++++++++++++++++------------------
 test/test_flux_window_ops.py |  4 ++++
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/test/data_for_test.py b/test/data_for_test.py
index 1711bfd..99feb03 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -87,24 +87,24 @@ def metrics_generator():
     ("sine", "x", "wavy3d"),
     ("sine", "y", "wavy3d"),
     ("sine", "z", "wavy3d"),
-    #("sine", "x", "uniform"),
-    #("sine", "y", "uniform"),
-    #("sine", "z", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
-    #("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
-    #("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
-    #("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
-    #("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
-    #("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
-    #("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
+    ("sine", "x", "uniform"),
+    ("sine", "y", "uniform"),
+    ("sine", "z", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
+    ("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
+    ("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
+    ("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
+    ("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
+    ("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
+    ("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
     ])
 def window_data(request, states_generator, metrics_generator):
     states_str = request.param[0]
diff --git a/test/test_flux_window_ops.py b/test/test_flux_window_ops.py
index 4bdb27e..4e72a85 100644
--- a/test/test_flux_window_ops.py
+++ b/test/test_flux_window_ops.py
@@ -98,6 +98,8 @@ def window_results(queue, window_data):
 
 def test_pointwise_eigenvalues(queue, window_results):
     data = window_results
+    if not np.array_equal(data.metrics[0], data.metrics[1]):
+        pytest.xfail("expect failure with non-uniform metrics")
 
     prg = u.get_weno_program_with_root_kernel("pointwise_eigenvalues")
 
@@ -111,6 +113,8 @@ def test_pointwise_eigenvalues(queue, window_results):
 
 def test_flux_splitting(queue, window_results):
     data = window_results
+    if not np.array_equal(data.metrics[0], data.metrics[1]):
+        pytest.xfail("expect failure with non-uniform metrics")
 
     prg = u.get_weno_program_with_root_kernel("split_characteristic_fluxes")
 
-- 
GitLab


From d4ce757bbb7f0c8cf9f7bdabd24c2655b4a42331 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 22:31:56 -0700
Subject: [PATCH 10/18] mark weno weights tests xfail for wavy metric tests

---
 test/test_flux_window_ops.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/test_flux_window_ops.py b/test/test_flux_window_ops.py
index 4e72a85..f1d1a7e 100644
--- a/test/test_flux_window_ops.py
+++ b/test/test_flux_window_ops.py
@@ -203,6 +203,8 @@ def test_dissipation_part_neg(queue, window_results):
 @pytest.mark.slow
 def test_weno_weights_pos(queue, window_results):
     data = window_results
+    if not np.array_equal(data.metrics[0], data.metrics[1]):
+        pytest.xfail("expect failure with non-uniform metrics")
 
     prg = u.get_weno_program_with_root_kernel("weno_weights_pos")
 
@@ -222,6 +224,8 @@ def test_weno_weights_pos(queue, window_results):
 @pytest.mark.slow
 def test_weno_weights_neg(queue, window_results):
     data = window_results
+    if not np.array_equal(data.metrics[0], data.metrics[1]):
+        pytest.xfail("expect failure with non-uniform metrics")
 
     prg = u.get_weno_program_with_root_kernel("weno_weights_neg")
 
-- 
GitLab


From c322d2dfc89239b9ae77350dd062c85fa64701fb Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 22:43:15 -0700
Subject: [PATCH 11/18] remove xfail label for pointwise eigenvalue test

---
 test/test_flux_window_ops.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/test/test_flux_window_ops.py b/test/test_flux_window_ops.py
index f1d1a7e..08885cd 100644
--- a/test/test_flux_window_ops.py
+++ b/test/test_flux_window_ops.py
@@ -98,8 +98,6 @@ def window_results(queue, window_data):
 
 def test_pointwise_eigenvalues(queue, window_results):
     data = window_results
-    if not np.array_equal(data.metrics[0], data.metrics[1]):
-        pytest.xfail("expect failure with non-uniform metrics")
 
     prg = u.get_weno_program_with_root_kernel("pointwise_eigenvalues")
 
-- 
GitLab


From a96678960706b43784cf292f5afc8aa3dd403a0a Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 22:44:22 -0700
Subject: [PATCH 12/18] comment out uniform metric tests for now

---
 test/data_for_test.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/test/data_for_test.py b/test/data_for_test.py
index 99feb03..1711bfd 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -87,24 +87,24 @@ def metrics_generator():
     ("sine", "x", "wavy3d"),
     ("sine", "y", "wavy3d"),
     ("sine", "z", "wavy3d"),
-    ("sine", "x", "uniform"),
-    ("sine", "y", "uniform"),
-    ("sine", "z", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
-    ("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
-    ("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
-    ("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
-    ("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
-    ("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
-    ("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
+    #("sine", "x", "uniform"),
+    #("sine", "y", "uniform"),
+    #("sine", "z", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
+    #("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
+    #("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
+    #("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
+    #("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
+    #("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
+    #("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
     ])
 def window_data(request, states_generator, metrics_generator):
     states_str = request.param[0]
-- 
GitLab


From 0d4ed4d7054949da2b4701648c0a88a780d90b3e Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 23:28:53 -0700
Subject: [PATCH 13/18] pass metrics to pointwise eigenvalues

---
 WENO.F90                     | 22 +++++++++++++++-------
 test/test_flux_window_ops.py |  6 ++++--
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/WENO.F90 b/WENO.F90
index 5a7a6f4..80780a4 100644
--- a/WENO.F90
+++ b/WENO.F90
@@ -61,7 +61,8 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
                                            generalized_states_frozen, &
                                            generalized_fluxes_frozen)
 
-        call pointwise_eigenvalues(nvars, 1, states(:, i-2:i+3, j, k), lambda_pointwise)
+        call pointwise_eigenvalues(nvars, ndim, 1, states(:, i-2:i+3, j, k), &
+                                    metrics(:, :, i-2:i+3, j, k), lambda_pointwise)
         call roe_eigensystem(nvars, ndim, 1, states(:, i:i+1, j, k), &
                               metrics_frozen, R, R_inv, lambda_roe)
 
@@ -111,7 +112,8 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
                                            generalized_states_frozen, &
                                            generalized_fluxes_frozen)
 
-        call pointwise_eigenvalues(nvars, 2, states(:, i, j-2:j+3, k), lambda_pointwise)
+        call pointwise_eigenvalues(nvars, ndim, 2, states(:, i, j-2:j+3, k), &
+                                    metrics(:, :, i, j-2:j+3, k), lambda_pointwise)
         call roe_eigensystem(nvars, ndim, 2, states(:, i, j:j+1, k), &
                               metrics_frozen, R, R_inv, lambda_roe)
 
@@ -162,7 +164,8 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
                                            generalized_states_frozen, &
                                            generalized_fluxes_frozen)
 
-        call pointwise_eigenvalues(nvars, 3, states(:, i, j, k-2:k+3), lambda_pointwise)
+        call pointwise_eigenvalues(nvars, ndim, 3, states(:, i, j, k-2:k+3), &
+                                    metrics(:, :, i, j, k-2:k+3), lambda_pointwise)
         call roe_eigensystem(nvars, ndim, 3, states(:, i, j, k:k+1), &
                               metrics_frozen, R, R_inv, lambda_roe)
 
@@ -199,32 +202,37 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
   !$loopy end tagged: flux_z_diff
 end subroutine
 
-subroutine pointwise_eigenvalues(nvars, d, states, lambda_pointwise)
+subroutine pointwise_eigenvalues(nvars, ndim, d, states, metrics, lambda_pointwise)
   implicit none
 
   integer, intent(in) :: nvars
+  integer, intent(in) :: ndim
   integer, intent(in) :: d
   real*8, intent(in) :: states(nvars, -2:3)
+  real*8, intent(in) :: metrics(ndim, ndim, -2:3)
   real*8, intent(out) :: lambda_pointwise(nvars, -2:3)
 
-  real*8 u(3), c, p, rho, ke
+  real*8 u(3), c, p, rho, ke, metric_norm
   integer v, k, i
 
   do k=-2,3
     rho = states(1,k)
     ke = 0.0d0
+    metric_norm = 0.0d0
     do i=1,3
       u(i) = states(i+1,k)/rho
       ke = ke + u(i)**2
+      metric_norm = metric_norm + metrics(d,i,k)**2
     end do
+    metric_norm = sqrt(metric_norm)
     p = (1.4d0 - 1)*(states(nvars,k) - 0.5d0*rho*ke)
     c = sqrt(1.4d0*p/rho)
 
     do v=1,nvars-2
       lambda_pointwise(v,k) = u(d)
     end do
-    lambda_pointwise(nvars-1,k) = u(d) + c
-    lambda_pointwise(nvars,k) = u(d) - c
+    lambda_pointwise(nvars-1,k) = u(d) + c*metric_norm
+    lambda_pointwise(nvars,k) = u(d) - c*metric_norm
   end do
 end subroutine
 
diff --git a/test/test_flux_window_ops.py b/test/test_flux_window_ops.py
index 08885cd..702c9fc 100644
--- a/test/test_flux_window_ops.py
+++ b/test/test_flux_window_ops.py
@@ -101,10 +101,12 @@ def test_pointwise_eigenvalues(queue, window_results):
 
     prg = u.get_weno_program_with_root_kernel("pointwise_eigenvalues")
 
+    metric_arg = np.moveaxis(data.metrics, 0, -1).copy(order="F")
     lam_dev = u.empty_array_on_device(queue, data.nvars, 6)
 
-    prg(queue, nvars=data.nvars, d=data.direction,
-            states=data.states, lambda_pointwise=lam_dev)
+    prg(queue, nvars=data.nvars, ndim=data.ndim, d=data.direction,
+            states=data.states, metrics=metric_arg,
+            lambda_pointwise=lam_dev)
 
     u.compare_arrays(lam_dev.get(), data.lam_pointwise)
 
-- 
GitLab


From d54ed60aa61a8ecdf5d8e6b5cbc50c05aebabfd2 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 23:30:16 -0700
Subject: [PATCH 14/18] reactivate uniform metric tests

---
 test/data_for_test.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/test/data_for_test.py b/test/data_for_test.py
index 1711bfd..99feb03 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -87,24 +87,24 @@ def metrics_generator():
     ("sine", "x", "wavy3d"),
     ("sine", "y", "wavy3d"),
     ("sine", "z", "wavy3d"),
-    #("sine", "x", "uniform"),
-    #("sine", "y", "uniform"),
-    #("sine", "z", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
-    #("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
-    #("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
-    #("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
-    #("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
-    #("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
-    #("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
+    ("sine", "x", "uniform"),
+    ("sine", "y", "uniform"),
+    ("sine", "z", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
+    ("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
+    ("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
+    ("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
+    ("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
+    ("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
+    ("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
     ])
 def window_data(request, states_generator, metrics_generator):
     states_str = request.param[0]
-- 
GitLab


From de9240f4feda0b9d3301625b886e687e528fa8fc Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 23:38:10 -0700
Subject: [PATCH 15/18] comment out uniform metric tests for now

---
 test/data_for_test.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/test/data_for_test.py b/test/data_for_test.py
index 99feb03..1711bfd 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -87,24 +87,24 @@ def metrics_generator():
     ("sine", "x", "wavy3d"),
     ("sine", "y", "wavy3d"),
     ("sine", "z", "wavy3d"),
-    ("sine", "x", "uniform"),
-    ("sine", "y", "uniform"),
-    ("sine", "z", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
-    ("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
-    ("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
-    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
-    ("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
-    ("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
-    ("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
-    ("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
-    ("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
-    ("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
+    #("sine", "x", "uniform"),
+    #("sine", "y", "uniform"),
+    #("sine", "z", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
+    #("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
+    #("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
+    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
+    #("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
+    #("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
+    #("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
+    #("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
+    #("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
+    #("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
     ])
 def window_data(request, states_generator, metrics_generator):
     states_str = request.param[0]
-- 
GitLab


From b1052ac37e79be192907138ea761a97c7dadca08 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Fri, 6 Mar 2020 23:40:05 -0700
Subject: [PATCH 16/18] take away xfail mark on flux splitting test

---
 test/test_flux_window_ops.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/test/test_flux_window_ops.py b/test/test_flux_window_ops.py
index 702c9fc..bd4ca4e 100644
--- a/test/test_flux_window_ops.py
+++ b/test/test_flux_window_ops.py
@@ -113,8 +113,6 @@ def test_pointwise_eigenvalues(queue, window_results):
 
 def test_flux_splitting(queue, window_results):
     data = window_results
-    if not np.array_equal(data.metrics[0], data.metrics[1]):
-        pytest.xfail("expect failure with non-uniform metrics")
 
     prg = u.get_weno_program_with_root_kernel("split_characteristic_fluxes")
 
-- 
GitLab


From 100bd009f2972e29c471aed5b93da49a80d5f5c1 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 7 Mar 2020 07:49:21 -0700
Subject: [PATCH 17/18] fix bug where test fixture was not passing correct
 generalized states to flux splitting

---
 test/test_flux_window_ops.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/test/test_flux_window_ops.py b/test/test_flux_window_ops.py
index bd4ca4e..8c22c13 100644
--- a/test/test_flux_window_ops.py
+++ b/test/test_flux_window_ops.py
@@ -58,6 +58,8 @@ class WindowResults:
         self.frozen_jacobian = pair.frozen_jacobian
         self.combined_frozen_metric = pair.combined_frozen_metrics[self.dir_internal]
 
+        self.generalized_states_frozen = self.states/self.frozen_jacobian
+
         self.generalized_fluxes = data.generalized_fluxes
         self.generalized_fluxes_frozen = np.array([np.dot(flux, self.frozen_metrics)
                 for flux in data.fluxes])[:,:,self.dir_internal].T.copy(order="F")
@@ -120,7 +122,7 @@ def test_flux_splitting(queue, window_results):
     fluxes_neg_dev = u.empty_array_on_device(queue, data.nvars, 6)
 
     prg(queue, nvars=data.nvars,
-            generalized_states_frozen=data.states,
+            generalized_states_frozen=data.generalized_states_frozen,
             generalized_fluxes_frozen=data.generalized_fluxes_frozen,
             R_inv=data.R_inv,
             wavespeeds=data.wavespeeds,
-- 
GitLab


From 1706874a7c2383dec4e1dc32475b0714cfeaed6d Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 7 Mar 2020 07:49:58 -0700
Subject: [PATCH 18/18] reactivate uniform metric tests

---
 test/data_for_test.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/test/data_for_test.py b/test/data_for_test.py
index 1711bfd..99feb03 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -87,24 +87,24 @@ def metrics_generator():
     ("sine", "x", "wavy3d"),
     ("sine", "y", "wavy3d"),
     ("sine", "z", "wavy3d"),
-    #("sine", "x", "uniform"),
-    #("sine", "y", "uniform"),
-    #("sine", "z", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
-    #("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
-    #("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
-    #("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
-    #("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
-    #("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
-    #("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
-    #("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
-    #("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
-    #("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
+    ("sine", "x", "uniform"),
+    ("sine", "y", "uniform"),
+    ("sine", "z", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "x", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "y", "uniform"),
+    ("1 1 1 1 5.5,1 1 1 1 5.5", "z", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "x", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "y", "uniform"),
+    ("2 4 4 4 20,1 1 1 1 5.5", "z", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "x", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "y", "uniform"),
+    ("1 -1 -1 -1 5.5,2 -4 -4 -4 20", "z", "uniform"),
+    ("2 4 8 12 64,1 1 2 3 11", "x", "uniform"),
+    ("2 8 12 4 64,1 2 3 1 11", "y", "uniform"),
+    ("2 12 4 8 64,1 3 1 2 11", "z", "uniform"),
+    ("1 -1 -2 -3 11,2 -4 -8 -12 64", "x", "uniform"),
+    ("1 -2 -3 -1 11,2 -8 -12 -4 64", "y", "uniform"),
+    ("1 -3 -1 -2 11,2 -12 -4 -8 64", "z", "uniform")
     ])
 def window_data(request, states_generator, metrics_generator):
     states_str = request.param[0]
-- 
GitLab