From 3cf8b842a3a049de871edd1a1a657e35a4f0ab9f Mon Sep 17 00:00:00 2001
From: Chris Eldred <celdred@sandia.gov>
Date: Tue, 7 Nov 2023 13:53:24 -0700
Subject: [PATCH] fix 3D velocity diffusion

---
 dynamics/spam/src/models/extrudedmodel.h         |  12 ++++++------
 .../build/vcoords_equal_50_20km.nc               | Bin 8600 -> 0 bytes
 .../mmf_simplified/pam-c/set_pamc_cmakevars.sh   |   4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)
 delete mode 100644 standalone/mmf_simplified/build/vcoords_equal_50_20km.nc

diff --git a/dynamics/spam/src/models/extrudedmodel.h b/dynamics/spam/src/models/extrudedmodel.h
index 57be8e97..95a573a0 100644
--- a/dynamics/spam/src/models/extrudedmodel.h
+++ b/dynamics/spam/src/models/extrudedmodel.h
@@ -1537,7 +1537,7 @@ class ModelTendencies : public ExtrudedTendencies {
     YAKL_SCOPE(primal_geometry, this->primal_geometry);
     YAKL_SCOPE(dual_geometry, this->dual_geometry);
 
-    // *d*d
+    // *d*d = vort
     parallel_for(
         "Velocity diffusion 1",
         SimpleBounds<4>(primal_topology.nl, primal_topology.n_cells_y,
@@ -1607,7 +1607,7 @@ class ModelTendencies : public ExtrudedTendencies {
                                                   i, j, k, n);
           for (int d = 0; d < ndims; ++d) {
             Vtendvar(d, k + pks, j + pjs, i + pis, n) +=
-                velocity_coeff * vdiff(d);
+                velocity_vort_horiz_diffusion_coeff * vdiff(d);
           }
         });
 
@@ -1621,10 +1621,10 @@ class ModelTendencies : public ExtrudedTendencies {
               wdiff, FWvar, primal_geometry, dual_geometry, pis, pjs, pks, i, j,
               k, n);
           Wtendvar(0, k + pks, j + pjs, i + pis, n) +=
-              velocity_coeff * wdiff(0);
+              velocity_vort_vert_diffusion_coeff * wdiff(0);
         });
 
-    // d*d*
+    // d*d* = div
     parallel_for(
         "Velocity diffusion 7",
         SimpleBounds<4>(dual_topology.nl, dual_topology.n_cells_y,
@@ -1679,7 +1679,7 @@ class ModelTendencies : public ExtrudedTendencies {
           compute_D0<1>(vdiff, dens0var, pis, pjs, pks, i, j, k, n);
           for (int d = 0; d < ndims; ++d) {
             Vtendvar(d, pks + k, pjs + j, pis + i, n) -=
-                velocity_coeff * vdiff(0, d);
+                velocity_div_horiz_diffusion_coeff * vdiff(0, d);
           }
         });
 
@@ -1691,7 +1691,7 @@ class ModelTendencies : public ExtrudedTendencies {
           SArray<real, 1, 1, 1> wdiff;
           compute_D0_vert<1>(wdiff, dens0var, pis, pjs, pks, i, j, k, n);
           Wtendvar(0, pks + k, pjs + j, pis + i, n) -=
-              velocity_coeff * wdiff(0);
+              velocity_div_vert_diffusion_coeff * wdiff(0);
         });
 
     yakl::timer_stop("add_velocity_diffusion");
diff --git a/standalone/mmf_simplified/build/vcoords_equal_50_20km.nc b/standalone/mmf_simplified/build/vcoords_equal_50_20km.nc
deleted file mode 100644
index e7e7104d0323c838d47a5a4a6121e332cac19086..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/standalone/mmf_simplified/pam-c/set_pamc_cmakevars.sh b/standalone/mmf_simplified/pam-c/set_pamc_cmakevars.sh
index e9b289a7..6a13aac8 100644
--- a/standalone/mmf_simplified/pam-c/set_pamc_cmakevars.sh
+++ b/standalone/mmf_simplified/pam-c/set_pamc_cmakevars.sh
@@ -1,8 +1,8 @@
 #!/bin/bash
 
 add_cmake_vars="  -DPAMC_MODEL=extrudedmodel "
-add_cmake_vars+=" -DPAMC_HAMIL=man       "
-add_cmake_vars+=" -DPAMC_THERMO=constkappavirpottemp      "
+add_cmake_vars+=" -DPAMC_HAMIL=an       "
+add_cmake_vars+=" -DPAMC_THERMO=idealgaspottemp      "
 add_cmake_vars+=" -DPAMC_IO=serial        "
 
 #ce mce_rho an man