From f2de08f05aad1bd90b1b90e35cf47781628f9828 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 24 Oct 2020 17:12:13 -0600
Subject: [PATCH 1/9] Add (broken) test with non-uniform metrics over full grid

---
 test/conftest.py        | 52 +++++++++++++++++++++++++++--------------
 test/wavy_metrics_3d.py | 23 ++++++++++++++++++
 2 files changed, 58 insertions(+), 17 deletions(-)

diff --git a/test/conftest.py b/test/conftest.py
index 994bf91..b5f456f 100644
--- a/test/conftest.py
+++ b/test/conftest.py
@@ -196,7 +196,7 @@ def grid_states_generator():
     def grid_states(states_str, grid_sizes_str, dir_str):
         nx, ny, nz = parse_grid_sizes(grid_sizes_str)
         nxhalo, nyhalo, nzhalo = halo_sizes(nx, ny, nz)
-        halo = (nxhalo - nx)/2
+        halo = int((nxhalo - nx)/2)
         states = np.empty(
                     (ref.gas.nvars, nxhalo, nyhalo, nzhalo),
                     dtype=np.float64, order="F")
@@ -286,6 +286,17 @@ def grid_states_generator():
             state_right = ref.gas.conserved(rho_right, vel_right, pressure_right)
 
             set_states_double_hump(state_base, state_left, state_right)
+        elif states_str == "sine":
+            def sin_func(i, n):
+                return np.sin(2*np.pi*(i - halo)/n)
+
+            vel = np.array([1.0, 2.0, 3.0])
+            pressure = 3.2
+            for i in range(nxhalo):
+                for j in range(nyhalo):
+                    for k in range(nzhalo):
+                        rho = sin_func(i, nx)*sin_func(j, ny)*sin_func(k, nz) + 1.1
+                        states[:, i, j, k] = ref.gas.conserved(rho, vel, pressure)
         else:
             raise ValueError("States string {} not supported".format(states_str))
         return states
@@ -298,7 +309,10 @@ def grid_metrics_generator():
     ndim = ref.gas.ndim
 
     def grid_metrics(metric_str, grid_sizes_str, dim):
-        nxhalo, nyhalo, nzhalo = halo_sizes(*parse_grid_sizes(grid_sizes_str))
+        nx, ny, nz = parse_grid_sizes(grid_sizes_str)
+        nxhalo, nyhalo, nzhalo = halo_sizes(nx, ny, nz)
+        halo = int((nxhalo - nx)/2)
+
         if (metric_str == "uniform"):
             metrics = np.full(
                     (ndim, ndim, nxhalo, nyhalo, nzhalo),
@@ -311,6 +325,9 @@ def grid_metrics_generator():
             jacobians = np.full(
                     (nxhalo, nyhalo, nzhalo),
                     1.0, dtype=np.float64, order="F")
+        elif (metric_str == "wavy3d"):
+            metrics = wavy3d.grid_metrics(nx, ny, nz, halo)
+            jacobians = wavy3d.grid_jacobians(nx, ny, nz, halo)
         else:
             raise ValueError("Metric string {} not supported".format(metric_str))
         return metrics, jacobians
@@ -319,21 +336,22 @@ def grid_metrics_generator():
 
 
 @pytest.fixture(scope="session", params=[
-    ("flat", "10x10x10", "x", "uniform"),
-    ("flat", "10x10x10", "y", "uniform"),
-    ("flat", "10x10x10", "z", "uniform"),
-    ("single_jump", "10x10x10", "x", "uniform"),
-    ("single_jump", "10x10x10", "y", "uniform"),
-    ("single_jump", "10x10x10", "z", "uniform"),
-    ("single_jump", "12x14x16", "x", "uniform"),
-    ("single_jump", "12x14x16", "y", "uniform"),
-    ("single_jump", "12x14x16", "z", "uniform"),
-    ("single_jump_varying", "10x10x10", "x", "uniform"),
-    ("single_jump_varying", "10x10x10", "y", "uniform"),
-    ("single_jump_varying", "10x10x10", "z", "uniform"),
-    ("double_hump", "25x25x25", "x", "uniform"),
-    ("double_hump", "25x25x25", "y", "uniform"),
-    ("double_hump", "25x25x25", "z", "uniform"),
+    #("flat", "10x10x10", "x", "uniform"),
+    #("flat", "10x10x10", "y", "uniform"),
+    #("flat", "10x10x10", "z", "uniform"),
+    #("single_jump", "10x10x10", "x", "uniform"),
+    #("single_jump", "10x10x10", "y", "uniform"),
+    #("single_jump", "10x10x10", "z", "uniform"),
+    #("single_jump", "12x14x16", "x", "uniform"),
+    #("single_jump", "12x14x16", "y", "uniform"),
+    #("single_jump", "12x14x16", "z", "uniform"),
+    #("single_jump_varying", "10x10x10", "x", "uniform"),
+    #("single_jump_varying", "10x10x10", "y", "uniform"),
+    #("single_jump_varying", "10x10x10", "z", "uniform"),
+    #("double_hump", "25x25x25", "x", "uniform"),
+    #("double_hump", "25x25x25", "y", "uniform"),
+    #("double_hump", "25x25x25", "z", "uniform"),
+    ("sine", "10x10x10", "x", "wavy3d"),
     # FIXME: add remaining cases
     ])
 def grid_data(request, grid_states_generator, grid_metrics_generator):
diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index 93011a1..3a0d8dc 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -149,3 +149,26 @@ def jacobians(dim):
 
 def metrics(dim):
     return weighted_metrics(dim)*jacobians(dim)[:, None, None]
+
+
+def grid(func, nx, ny, nz, halo):
+    return np.array([[[func(i, j, k)
+                        for i in range(nx + 2*halo)]
+                        for j in range(ny + 2*halo)]
+                        for k in range(nz + 2*halo)],
+                     dtype=np.float64,
+                     order="F")
+
+
+def grid_weighted_metrics(nx, ny, nz, halo):
+    return grid(weighted_metric_mat, nx, ny, nz, halo)
+
+
+def grid_jacobians(nx, ny, nz, halo):
+    return np.reciprocal(grid(inverse_jacobian, nx, ny, nz, halo))
+
+
+def grid_metrics(nx, ny, nz, halo):
+    return ((np.moveaxis(grid_weighted_metrics(nx, ny, nz, halo),
+                [3, 4, 0, 1, 2], [0, 1, 2, 3, 4])
+            *grid_jacobians(nx, ny, nz, halo)[None, None, :, :, :]).copy(order="F"))
-- 
GitLab


From 0a7ea1ad4f32c1d700720d6607becd784261c723 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Mon, 16 Nov 2020 07:56:20 -0700
Subject: [PATCH 2/9] Added new tests for frozen metric computation, still
 missing fluxes

---
 test/data_for_test.py         |  5 ++-
 test/test_flux_derivatives.py |  1 +
 test/test_frozen_metrics.py   | 76 +++++++++++++++++++++++++++++++++++
 test/wavy_metrics_3d.py       |  2 +-
 4 files changed, 81 insertions(+), 3 deletions(-)
 create mode 100644 test/test_frozen_metrics.py

diff --git a/test/data_for_test.py b/test/data_for_test.py
index 2cf9c2f..65050de 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -1,4 +1,4 @@
-__copyright__ = "Copyright (C) 2019-2020 Timothy A. Smith"
+__copyright__ = "Copyright (C) 2019 Timothy A. Smith"
 
 __license__ = """
 Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -76,7 +76,8 @@ class WindowResults:
 
         self.frozen_metrics = pair.frozen_metrics
         self.frozen_jacobian = pair.frozen_jacobian
-        self.combined_frozen_metric = pair.combined_frozen_metrics[self.dir_internal]
+        self.combined_frozen_metrics = pair.combined_frozen_metrics
+        self.combined_frozen_metric = self.combined_frozen_metrics[self.dir_internal]
 
         self.generalized_states_frozen = self.states/self.frozen_jacobian
 
diff --git a/test/test_flux_derivatives.py b/test/test_flux_derivatives.py
index b52c59b..3352740 100644
--- a/test/test_flux_derivatives.py
+++ b/test/test_flux_derivatives.py
@@ -36,6 +36,7 @@ import pytest
 import utilities as u
 
 
+@pytest.mark.skip
 def test_compute_flux_derivatives(queue, grid_results):
     data = grid_results
 
diff --git a/test/test_frozen_metrics.py b/test/test_frozen_metrics.py
new file mode 100644
index 0000000..0c21609
--- /dev/null
+++ b/test/test_frozen_metrics.py
@@ -0,0 +1,76 @@
+__copyright__ = "Copyright (C) 2019 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  # noqa: F401
+import numpy.linalg as la  # noqa: F401
+import pyopencl as cl  # noqa: F401
+import pyopencl.array  # noqa
+import pyopencl.tools  # noqa
+import pyopencl.clrandom  # noqa
+import loopy as lp  # noqa
+
+import sys
+import logging
+
+import pytest
+
+import utilities as u
+
+
+def test_frozen_metrics_generalized_flux(queue, window_results):
+    data = window_results
+
+    prg = u.get_weno_program_with_root_kernel("convert_to_generalized_frozen")
+
+    pair_metrics = np.moveaxis(data.metrics[2:4], 0, -1).copy(order="F")
+    pair_jacobians = data.jacobians[2:4].copy()
+
+    frozen_metrics_dev = u.empty_array_on_device(queue, data.ndim, data.ndim)
+    combined_frozen_metrics_dev = u.empty_array_on_device(queue, data.ndim)
+    generalized_states_frozen_dev = u.empty_array_on_device(queue, data.nvars, 6)
+    generalized_fluxes_frozen_dev = u.empty_array_on_device(queue, data.nvars, 6)
+
+    prg(queue,
+            nvars=data.nvars,
+            ndim=data.ndim,
+            states=data.states,
+            fluxes=data.generalized_fluxes,
+            metrics=pair_metrics,
+            metric_jacobians=pair_jacobians,
+            metrics_frozen=frozen_metrics_dev,
+            combined_frozen_metrics=combined_frozen_metrics_dev,
+            generalized_states_frozen=generalized_states_frozen_dev,
+            generalized_fluxes_frozen=generalized_fluxes_frozen_dev)
+
+    u.compare_arrays(frozen_metrics_dev.get(), data.frozen_metrics)
+    u.compare_arrays(combined_frozen_metrics_dev.get(), data.combined_frozen_metrics)
+    u.compare_arrays(generalized_states_frozen_dev.get(),
+                        data.generalized_states_frozen)
+
+
+# This lets you run 'python test.py test_case(cl._csc)' without pytest.
+if __name__ == "__main__":
+    if len(sys.argv) > 1:
+        logging.basicConfig(level="INFO")
+        exec(sys.argv[1])
+    else:
+        pytest.main([__file__])
diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index 3a0d8dc..69a42fb 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -1,4 +1,4 @@
-__copyright__ = "Copyright (C) 2020 Timothy A. Smith"
+__copyright__ = "Copyright (C) 2019 Timothy A. Smith"
 
 __license__ = """
 Permission is hereby granted, free of charge, to any person obtaining a copy
-- 
GitLab


From 7f6a05cd31adea1eea0c4e4aa89841b1ac1b7e7c Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 21 Nov 2020 21:27:22 -0700
Subject: [PATCH 3/9] Add routine to compute ideal gas fluxes needed for frozen
 metrics

---
 WENO.F90                    | 38 ++++++++++++++++++++++++++++++++++---
 test/data_for_test.py       |  1 +
 test/test_frozen_metrics.py | 20 ++++++++++++++++++-
 3 files changed, 55 insertions(+), 4 deletions(-)

diff --git a/WENO.F90 b/WENO.F90
index 5509694..915d3cb 100644
--- a/WENO.F90
+++ b/WENO.F90
@@ -426,10 +426,39 @@ subroutine lax_wavespeeds(nvars, lambda_pointwise, lambda_roe, wavespeeds)
   end do
 end subroutine
 
+subroutine compute_ideal_gas_fluxes(nvars, ndim, states, fluxes)
+  integer, intent(in) :: nvars, ndim
+  real*8, intent(in) :: states(nvars, -2:3)
+  real*8, intent(out) :: fluxes(nvars, ndim, -2:3)
+
+  integer v, d, k
+  real*8 velocity(ndim)
+  real*8 kinetic_energy, pressure, gm
+
+  gm = 1.4d0
+
+  do k=-2,3
+    kinetic_energy = 0.0d0
+    do v=1,ndim
+      velocity(v) = states(v+1,k)/states(1,k)
+      kinetic_energy = kinetic_energy + 0.5d0*states(1,k)*velocity(v)*velocity(v)
+    end do
+    pressure = (states(ndim+2,k) - kinetic_energy)*(gm - 1.0d0)
+
+    do d=1,ndim
+      do v=1,nvars
+        fluxes(v,d,k) = states(v,k)*velocity(d)
+      end do
+      fluxes(d+1,d,k) = fluxes(d+1,d,k) + pressure
+      fluxes(ndim+2,d,k) = fluxes(ndim+2,d,k) + pressure*velocity(d)
+    end do
+  end do
+end subroutine
+
 subroutine convert_to_generalized_frozen( &
             nvars, ndim, &
             states, &
-            fluxes, &
+            characteristic_fluxes, &
             metrics, &
             metric_jacobians, &
             metrics_frozen, &
@@ -438,7 +467,7 @@ subroutine convert_to_generalized_frozen( &
             generalized_fluxes_frozen)
   integer, intent(in) :: nvars, ndim
   real*8, intent(in) :: states(nvars, -2:3)
-  real*8, intent(in) :: fluxes(nvars, -2:3)
+  real*8, intent(in) :: characteristic_fluxes(nvars, -2:3)
   real*8, intent(in) :: metrics(ndim, ndim, 2)
   real*8, intent(in) :: metric_jacobians(2)
   real*8, intent(out) :: metrics_frozen(ndim, ndim)
@@ -447,10 +476,13 @@ subroutine convert_to_generalized_frozen( &
   real*8, intent(out) :: generalized_fluxes_frozen(nvars, -2:3)
 
   real*8 jacobian_frozen
+  real*8 fluxes(nvars, ndim, -2:3)
 
   integer c, k, v
   integer i, j
 
+  call compute_ideal_gas_fluxes(nvars, ndim, states, fluxes)
+
   do j=1,ndim
     do i=1,ndim
       metrics_frozen(i,j) = 0.0d0
@@ -479,7 +511,7 @@ subroutine convert_to_generalized_frozen( &
       ! FIXME: this is a bug
       ! ... we actually need to recompute the fluxes using frozen metrics
       ! ... but this works when the metric matrix is identity
-      generalized_fluxes_frozen(v,k) = fluxes(v,k)
+      generalized_fluxes_frozen(v,k) = characteristic_fluxes(v,k)
     end do
   end do
 end subroutine
diff --git a/test/data_for_test.py b/test/data_for_test.py
index 65050de..dc4b683 100644
--- a/test/data_for_test.py
+++ b/test/data_for_test.py
@@ -70,6 +70,7 @@ class WindowResults:
 
         self.states = data.states
         self.state_pair = pair.state_pair
+        self.fluxes = data.fluxes
 
         self.metrics = data.metrics
         self.jacobians = data.jacobians
diff --git a/test/test_frozen_metrics.py b/test/test_frozen_metrics.py
index 0c21609..ff8e324 100644
--- a/test/test_frozen_metrics.py
+++ b/test/test_frozen_metrics.py
@@ -36,6 +36,22 @@ import pytest
 import utilities as u
 
 
+def test_compute_ideal_gas_fluxes(queue, window_results):
+    data = window_results
+
+    prg = u.get_weno_program_with_root_kernel("compute_ideal_gas_fluxes")
+
+    fluxes_dev = u.empty_array_on_device(queue, data.nvars, data.ndim, 6)
+
+    prg(queue,
+            nvars=data.nvars,
+            ndim=data.ndim,
+            states=data.states,
+            fluxes=fluxes_dev)
+
+    u.compare_arrays(fluxes_dev.get(), np.moveaxis(data.fluxes, 0, -1))
+
+
 def test_frozen_metrics_generalized_flux(queue, window_results):
     data = window_results
 
@@ -53,7 +69,7 @@ def test_frozen_metrics_generalized_flux(queue, window_results):
             nvars=data.nvars,
             ndim=data.ndim,
             states=data.states,
-            fluxes=data.generalized_fluxes,
+            characteristic_fluxes=data.generalized_fluxes,
             metrics=pair_metrics,
             metric_jacobians=pair_jacobians,
             metrics_frozen=frozen_metrics_dev,
@@ -65,6 +81,8 @@ def test_frozen_metrics_generalized_flux(queue, window_results):
     u.compare_arrays(combined_frozen_metrics_dev.get(), data.combined_frozen_metrics)
     u.compare_arrays(generalized_states_frozen_dev.get(),
                         data.generalized_states_frozen)
+    u.compare_arrays(generalized_fluxes_frozen_dev.get(),
+                        data.generalized_fluxes_frozen)
 
 
 # This lets you run 'python test.py test_case(cl._csc)' without pytest.
-- 
GitLab


From 9291f1c543008fd64dc77ca1649ddb3da5fea10f Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 21 Nov 2020 22:15:20 -0700
Subject: [PATCH 4/9] finish fixing bug in frozen metric computation

---
 WENO.F90                      | 19 ++++++++++---------
 test/conftest.py              | 33 +++++++++++++++++----------------
 test/test_flux_derivatives.py |  1 -
 test/test_frozen_metrics.py   |  1 +
 4 files changed, 28 insertions(+), 26 deletions(-)

diff --git a/WENO.F90 b/WENO.F90
index 915d3cb..453628a 100644
--- a/WENO.F90
+++ b/WENO.F90
@@ -52,7 +52,7 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
       do k=1,nz
           do j=1,ny
               do i=0,nx
-                  call convert_to_generalized_frozen(nvars, ndim, &
+                  call convert_to_generalized_frozen(nvars, ndim, d, &
                       states(:, i-2:i+3, j, k), &
                       fluxes(:, i-2:i+3, j, k), &
                       metrics(:, :, i:i+1, j, k), &
@@ -104,7 +104,7 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
       do k=1,nz
           do i=1,nx
               do j=0,ny
-                  call convert_to_generalized_frozen(nvars, ndim, &
+                  call convert_to_generalized_frozen(nvars, ndim, d, &
                       states(:, i, j-2:j+3, k), &
                       fluxes(:, i, j-2:j+3, k), &
                       metrics(:, :, i, j:j+1, k), &
@@ -157,7 +157,7 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
       do j=1,ny
           do i=1,nx
               do k=0,nz
-                  call convert_to_generalized_frozen(nvars, ndim, &
+                  call convert_to_generalized_frozen(nvars, ndim, d, &
                       states(:, i, j, k-2:k+3), &
                       fluxes(:, i, j, k-2:k+3), &
                       metrics(:, :, i, j, k:k+1), &
@@ -456,7 +456,7 @@ subroutine compute_ideal_gas_fluxes(nvars, ndim, states, fluxes)
 end subroutine
 
 subroutine convert_to_generalized_frozen( &
-            nvars, ndim, &
+            nvars, ndim, d, &
             states, &
             characteristic_fluxes, &
             metrics, &
@@ -465,7 +465,7 @@ subroutine convert_to_generalized_frozen( &
             combined_frozen_metrics, &
             generalized_states_frozen, &
             generalized_fluxes_frozen)
-  integer, intent(in) :: nvars, ndim
+  integer, intent(in) :: nvars, ndim, d
   real*8, intent(in) :: states(nvars, -2:3)
   real*8, intent(in) :: characteristic_fluxes(nvars, -2:3)
   real*8, intent(in) :: metrics(ndim, ndim, 2)
@@ -508,10 +508,11 @@ subroutine convert_to_generalized_frozen( &
 
   do k=-2,3
     do v=1,nvars
-      ! FIXME: this is a bug
-      ! ... we actually need to recompute the fluxes using frozen metrics
-      ! ... but this works when the metric matrix is identity
-      generalized_fluxes_frozen(v,k) = characteristic_fluxes(v,k)
+      generalized_fluxes_frozen(v,k) = 0.0d0
+      do i=1,ndim
+        generalized_fluxes_frozen(v,k) = generalized_fluxes_frozen(v,k) &
+            + metrics_frozen(d,i)*fluxes(v,i,k)
+      end do
     end do
   end do
 end subroutine
diff --git a/test/conftest.py b/test/conftest.py
index b5f456f..db42208 100644
--- a/test/conftest.py
+++ b/test/conftest.py
@@ -336,23 +336,24 @@ def grid_metrics_generator():
 
 
 @pytest.fixture(scope="session", params=[
-    #("flat", "10x10x10", "x", "uniform"),
-    #("flat", "10x10x10", "y", "uniform"),
-    #("flat", "10x10x10", "z", "uniform"),
-    #("single_jump", "10x10x10", "x", "uniform"),
-    #("single_jump", "10x10x10", "y", "uniform"),
-    #("single_jump", "10x10x10", "z", "uniform"),
-    #("single_jump", "12x14x16", "x", "uniform"),
-    #("single_jump", "12x14x16", "y", "uniform"),
-    #("single_jump", "12x14x16", "z", "uniform"),
-    #("single_jump_varying", "10x10x10", "x", "uniform"),
-    #("single_jump_varying", "10x10x10", "y", "uniform"),
-    #("single_jump_varying", "10x10x10", "z", "uniform"),
-    #("double_hump", "25x25x25", "x", "uniform"),
-    #("double_hump", "25x25x25", "y", "uniform"),
-    #("double_hump", "25x25x25", "z", "uniform"),
+    ("flat", "10x10x10", "x", "uniform"),
+    ("flat", "10x10x10", "y", "uniform"),
+    ("flat", "10x10x10", "z", "uniform"),
+    ("single_jump", "10x10x10", "x", "uniform"),
+    ("single_jump", "10x10x10", "y", "uniform"),
+    ("single_jump", "10x10x10", "z", "uniform"),
+    ("single_jump", "12x14x16", "x", "uniform"),
+    ("single_jump", "12x14x16", "y", "uniform"),
+    ("single_jump", "12x14x16", "z", "uniform"),
+    ("single_jump_varying", "10x10x10", "x", "uniform"),
+    ("single_jump_varying", "10x10x10", "y", "uniform"),
+    ("single_jump_varying", "10x10x10", "z", "uniform"),
+    ("double_hump", "25x25x25", "x", "uniform"),
+    ("double_hump", "25x25x25", "y", "uniform"),
+    ("double_hump", "25x25x25", "z", "uniform"),
     ("sine", "10x10x10", "x", "wavy3d"),
-    # FIXME: add remaining cases
+    ("sine", "10x10x10", "y", "wavy3d"),
+    ("sine", "10x10x10", "z", "wavy3d")
     ])
 def grid_data(request, grid_states_generator, grid_metrics_generator):
     states_str = request.param[0]
diff --git a/test/test_flux_derivatives.py b/test/test_flux_derivatives.py
index 3352740..b52c59b 100644
--- a/test/test_flux_derivatives.py
+++ b/test/test_flux_derivatives.py
@@ -36,7 +36,6 @@ import pytest
 import utilities as u
 
 
-@pytest.mark.skip
 def test_compute_flux_derivatives(queue, grid_results):
     data = grid_results
 
diff --git a/test/test_frozen_metrics.py b/test/test_frozen_metrics.py
index ff8e324..e78fcbe 100644
--- a/test/test_frozen_metrics.py
+++ b/test/test_frozen_metrics.py
@@ -68,6 +68,7 @@ def test_frozen_metrics_generalized_flux(queue, window_results):
     prg(queue,
             nvars=data.nvars,
             ndim=data.ndim,
+            d=data.direction,
             states=data.states,
             characteristic_fluxes=data.generalized_fluxes,
             metrics=pair_metrics,
-- 
GitLab


From f0a8ec67d5daac9d2ef52731fb70b6d3ce102c7a Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 21 Nov 2020 22:47:14 -0700
Subject: [PATCH 5/9] fix a flake issue

---
 test/wavy_metrics_3d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index 69a42fb..4a3f601 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -171,4 +171,4 @@ def grid_jacobians(nx, ny, nz, halo):
 def grid_metrics(nx, ny, nz, halo):
     return ((np.moveaxis(grid_weighted_metrics(nx, ny, nz, halo),
                 [3, 4, 0, 1, 2], [0, 1, 2, 3, 4])
-            *grid_jacobians(nx, ny, nz, halo)[None, None, :, :, :]).copy(order="F"))
+           *grid_jacobians(nx, ny, nz, halo)[None, None, :, :, :]).copy(order = "F"))
-- 
GitLab


From b62f0e590650b1e334d22185f582b3f23cea0416 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 21 Nov 2020 22:50:58 -0700
Subject: [PATCH 6/9] guessed wrong about flake's complaint, trying again ...

---
 test/wavy_metrics_3d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/wavy_metrics_3d.py b/test/wavy_metrics_3d.py
index 4a3f601..77a9c29 100644
--- a/test/wavy_metrics_3d.py
+++ b/test/wavy_metrics_3d.py
@@ -171,4 +171,4 @@ def grid_jacobians(nx, ny, nz, halo):
 def grid_metrics(nx, ny, nz, halo):
     return ((np.moveaxis(grid_weighted_metrics(nx, ny, nz, halo),
                 [3, 4, 0, 1, 2], [0, 1, 2, 3, 4])
-           *grid_jacobians(nx, ny, nz, halo)[None, None, :, :, :]).copy(order = "F"))
+           * grid_jacobians(nx, ny, nz, halo)[None, None, :, :, :]).copy(order="F"))
-- 
GitLab


From 71e9280b9d3a3c1b30d75760f533428d46a7a293 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sat, 21 Nov 2020 23:04:07 -0700
Subject: [PATCH 7/9] Remove a useless argument

---
 WENO.F90                    | 5 -----
 test/test_frozen_metrics.py | 1 -
 2 files changed, 6 deletions(-)

diff --git a/WENO.F90 b/WENO.F90
index 453628a..26091ba 100644
--- a/WENO.F90
+++ b/WENO.F90
@@ -54,7 +54,6 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
               do i=0,nx
                   call convert_to_generalized_frozen(nvars, ndim, d, &
                       states(:, i-2:i+3, j, k), &
-                      fluxes(:, i-2:i+3, j, k), &
                       metrics(:, :, i:i+1, j, k), &
                       metric_jacobians(i:i+1, j, k), &
                       metrics_frozen, &
@@ -106,7 +105,6 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
               do j=0,ny
                   call convert_to_generalized_frozen(nvars, ndim, d, &
                       states(:, i, j-2:j+3, k), &
-                      fluxes(:, i, j-2:j+3, k), &
                       metrics(:, :, i, j:j+1, k), &
                       metric_jacobians(i, j:j+1, k), &
                       metrics_frozen, &
@@ -159,7 +157,6 @@ subroutine compute_flux_derivatives(nvars, ndim, nx, ny, nz, d, &
               do k=0,nz
                   call convert_to_generalized_frozen(nvars, ndim, d, &
                       states(:, i, j, k-2:k+3), &
-                      fluxes(:, i, j, k-2:k+3), &
                       metrics(:, :, i, j, k:k+1), &
                       metric_jacobians(i, j, k:k+1), &
                       metrics_frozen, &
@@ -458,7 +455,6 @@ end subroutine
 subroutine convert_to_generalized_frozen( &
             nvars, ndim, d, &
             states, &
-            characteristic_fluxes, &
             metrics, &
             metric_jacobians, &
             metrics_frozen, &
@@ -467,7 +463,6 @@ subroutine convert_to_generalized_frozen( &
             generalized_fluxes_frozen)
   integer, intent(in) :: nvars, ndim, d
   real*8, intent(in) :: states(nvars, -2:3)
-  real*8, intent(in) :: characteristic_fluxes(nvars, -2:3)
   real*8, intent(in) :: metrics(ndim, ndim, 2)
   real*8, intent(in) :: metric_jacobians(2)
   real*8, intent(out) :: metrics_frozen(ndim, ndim)
diff --git a/test/test_frozen_metrics.py b/test/test_frozen_metrics.py
index e78fcbe..cf15153 100644
--- a/test/test_frozen_metrics.py
+++ b/test/test_frozen_metrics.py
@@ -70,7 +70,6 @@ def test_frozen_metrics_generalized_flux(queue, window_results):
             ndim=data.ndim,
             d=data.direction,
             states=data.states,
-            characteristic_fluxes=data.generalized_fluxes,
             metrics=pair_metrics,
             metric_jacobians=pair_jacobians,
             metrics_frozen=frozen_metrics_dev,
-- 
GitLab


From 1bea41cd6e7720d666d630691290d0eb3108e44d Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sun, 22 Nov 2020 09:58:22 -0700
Subject: [PATCH 8/9] clean up README

---
 README.md | 27 +++------------------------
 1 file changed, 3 insertions(+), 24 deletions(-)

diff --git a/README.md b/README.md
index 21420b4..72b75ea 100644
--- a/README.md
+++ b/README.md
@@ -6,15 +6,13 @@ Standalone Fortran WENO code with Loopy transformations.
 
 * The WENO scheme is taken from [1]
 * The Roe matrix implementation follows the internal PlasCom2 documentation
-* Boundary conditions are not really handled correctly at all
+* Boundary conditions are not handled by the main flux derivative kernel
 * A declaration of "real" is not intended to suggest single precision
 * This implementation does not include the severe shock correction proposed
     by [1]
 * Current assumption for metrics is that metrics(i,j) = (\xi_i)_(x_j)
-* It's not immediately obvious, but there might be some wasted work in the
-    frozen generalized flux computation
-* Right now the specific gas constant gamma is implemented as a magic number
-    (1.4) -- this should be generalized
+* Right now an ideal gas formulation is assumed and the specific gas constant
+    gamma is implemented as a magic number (1.4)
 
 ## Fortran dialect wishlist
 
@@ -25,25 +23,6 @@ Standalone Fortran WENO code with Loopy transformations.
   - (e.g. 2:0 instead of 2:0:-1)
 - Scalars with intent(out)
 
-Note: Tag 'nice' references the code at a point where several of these items are used
-
-## Testing plan
-
-Plan to test the following routines directly:
-
-- `compute_flux_derivatives`
-- `convert_to_generalized`
-- `convert_to_generalized_frozen`
-- `convert_from_generalized`
-- `roe_eigensystem`
-- `pointwise_eigenvalues`
-- `lax_wavespeeds`
-- `split_characteristic_fluxes`
-- `weno_flux`
-- `consistent_part`
-- `dissipation_part_pos`
-- `dissipation_part_neg`
-
 ## References
 
 [1] Nonomura, T., Terakado, D., Abe, Y., & Fujii, K. (2015).
-- 
GitLab


From 434a0dd72088d9776f6aa6980277fcc6b4213648 Mon Sep 17 00:00:00 2001
From: "Timothy A. Smith" <2timothy18@gmail.com>
Date: Sun, 22 Nov 2020 09:59:30 -0700
Subject: [PATCH 9/9] cleanup some commented code

---
 WENO.F90 | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/WENO.F90 b/WENO.F90
index 26091ba..fa0d0a4 100644
--- a/WENO.F90
+++ b/WENO.F90
@@ -653,12 +653,10 @@ subroutine weno_weights_pos(nvars, characteristic_fluxes, combined_frozen_metric
   call oscillation_pos(nvars, characteristic_fluxes, IS)
 
   do i=1,nvars
-    sum_alpha(1) = 0.0d0
     do j=1,3
       alpha(j) = C(j)/(IS(i, j) + eps)**p
-      sum_alpha(1) = sum_alpha(1) + alpha(j)
     end do
-    !call sum_array(3, alpha, sum_alpha)
+    call sum_array(3, alpha, sum_alpha)
     do j=1,3
       w(i,j) = alpha(j)/sum_alpha(1)
     end do
-- 
GitLab