Fix some EMHD stuff

Not all flag names were updated "EMHD"->"EMHDVar", I suspect a merge somewhere regressed that. Also fix some more scripts
AFD-Illinois · Oct 5, 2023 · 26cf7f1 · 26cf7f1
1 parent 802bdb2
commit 26cf7f1
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Showing 5 changed files with 19 additions and 22 deletions.
diff --git a/kharma/emhd/emhd.cpp b/kharma/emhd/emhd.cpp
@@ -128,7 +128,7 @@ std::shared_ptr<KHARMAPackage> Initialize(ParameterInput *pin, std::shared_ptr<P
     // EMHD is supported only with imex driver and implicit evolution,
     // synchronizing primitive variables
     Metadata::AddUserFlag("EMHDVar"); // "EMHD" name now taken by Parthenon for general flag, we want this one specific
-    std::vector<MetadataFlag> emhd_flags = {Metadata::Cell, Metadata::GetUserFlag("Implicit"), Metadata::GetUserFlag("EMHD")};
+    std::vector<MetadataFlag> emhd_flags = {Metadata::Cell, Metadata::GetUserFlag("Implicit"), Metadata::GetUserFlag("EMHDVar")};
 
     auto flags_prim = packages->Get("Driver")->Param<std::vector<MetadataFlag>>("prim_flags");
     flags_prim.insert(flags_prim.end(), emhd_flags.begin(), emhd_flags.end());
@@ -185,8 +185,9 @@ void BlockUtoP(MeshBlockData<Real> *rc, IndexDomain domain, bool coarse)
 {
     auto pmb = rc->GetBlockPointer();
 
+    // Get only relevant cons, but all prims as we need the Lorentz factor
     PackIndexMap prims_map, cons_map;
-    auto U_E = rc->PackVariables(std::vector<MetadataFlag>{Metadata::GetUserFlag("EMHD"), Metadata::Conserved}, cons_map);
+    auto U_E = rc->PackVariables(std::vector<MetadataFlag>{Metadata::GetUserFlag("EMHDVar"), Metadata::Conserved}, cons_map);
     auto P = rc->PackVariables(std::vector<MetadataFlag>{Metadata::GetUserFlag("Primitive")}, prims_map);
     const VarMap m_p(prims_map, false), m_u(cons_map, true);
 
@@ -217,9 +218,10 @@ void BlockPtoU(MeshBlockData<Real> *rc, IndexDomain domain, bool coarse)
 {
     auto pmb = rc->GetBlockPointer();
 
+    // Get only relevant cons, but all prims as we need the Lorentz factor
     PackIndexMap prims_map, cons_map;
-    auto U_E = rc->PackVariables(std::vector<MetadataFlag>{Metadata::GetUserFlag("EMHDVar"), Metadata::Conserved}, cons_map);
-    auto P = rc->PackVariables(std::vector<MetadataFlag>{Metadata::GetUserFlag("Primitive")}, prims_map);
+    auto U_E = rc->PackVariables({Metadata::GetUserFlag("EMHDVar"), Metadata::Conserved}, cons_map);
+    auto P = rc->PackVariables({Metadata::GetUserFlag("Primitive")}, prims_map);
     const VarMap m_p(prims_map, false), m_u(cons_map, true);
 
     const auto& G = pmb->coords;

diff --git a/tests/bz_monopole/run.sh b/tests/bz_monopole/run.sh
@@ -6,13 +6,13 @@ BASE=../..
 exit_code=0
 
 # Full run to test stability to completion
-$BASE/run.sh -i $BASE/pars/bz_monopole.par debug/verbose=1 parthenon/output0/single_precision_output=false >log_bz_monopole_full.txt 2>&1 #|| exit_code=$?
+$BASE/run.sh -i $BASE/pars/tests/bz_monopole.par debug/verbose=1 parthenon/output0/single_precision_output=false >log_bz_monopole_full.txt 2>&1 || exit_code=$?
 
 # At *least* check divB
 pyharm-check-basics bz_monopole.out0.final.phdf || exit_code=$?
 
 # Take 1 step to look for early signs of non-fatal instabilities
-$BASE/run.sh -i $BASE/pars/bz_monopole.par parthenon/time/nlim=1 parthenon/output0/dt=0.0 parthenon/output0/single_precision_output=false >log_bz_monopole_step.txt 2>&1 #|| exit_code=$?
+$BASE/run.sh -i $BASE/pars/tests/bz_monopole.par parthenon/time/nlim=1 parthenon/output0/dt=0.0 parthenon/output0/single_precision_output=false >log_bz_monopole_step.txt 2>&1 #|| exit_code=$?
 
-# Check is for plots only!
+# This just makes plots, it doesn't check anything
 python ./check.py
diff --git a/tests/conducting_atmosphere/run.sh b/tests/conducting_atmosphere/run.sh
@@ -13,7 +13,7 @@ conv_2d() {
     for res in "${RES_LIST[@]}"
     do
         cp conducting_atmosphere_${res}_default/atmosphere_soln_*.txt .
-        $BASE/run.sh -n 1 -i $BASE/pars/conducting_atmosphere.par debug/verbose=1 \
+        $BASE/run.sh -n 1 -i ./conducting_atmosphere.par debug/verbose=1 \
             parthenon/time/tlim=200 parthenon/output0/dt=1000000 \
             parthenon/mesh/nx1=$res parthenon/mesh/nx2=$res parthenon/mesh/nx3=1 \
             parthenon/meshblock/nx1=$res parthenon/meshblock/nx2=$res parthenon/meshblock/nx3=1 \
@@ -35,4 +35,4 @@ conv_2d() {
 }
 
 ALL_RES="64,128,256,512"
-conv_2d emhd2d_weno GRMHD/reconstruction=weno5 "in 2D, WENO5"
+conv_2d emhd2d_weno driver/reconstruction=weno5 "in 2D, WENO5"
diff --git a/tests/emhdshock/check.py b/tests/emhdshock/check.py
@@ -9,7 +9,7 @@
 
 if __name__=='__main__':
 	outputdir = './'
-	kharmadir = '/home/vdhruv2/kharma'
+	kharmadir = '../../'
 	RES = [int(r) for r in sys.argv[1].split(",")]
 
 	CONDUCTION = 1
@@ -25,13 +25,13 @@
 	for r, res in enumerate(RES):
 
 		# load analytic result
-		rho_analytic	 = np.loadtxt(os.path.join(kharmadir, 'kharma/prob/emhd/', 'shock_soln_{}_default'.format(res), 'shock_soln_rho.txt'))
-		u_analytic		 = np.loadtxt(os.path.join(kharmadir, 'kharma/prob/emhd/', 'shock_soln_{}_default'.format(res), 'shock_soln_u.txt'))
-		u1_analytic		 = np.loadtxt(os.path.join(kharmadir, 'kharma/prob/emhd/', 'shock_soln_{}_default'.format(res), 'shock_soln_u1.txt'))
+		rho_analytic	 = np.loadtxt(os.path.join(outputdir, 'shock_soln_{}_default'.format(res), 'shock_soln_rho.txt'))
+		u_analytic		 = np.loadtxt(os.path.join(outputdir, 'shock_soln_{}_default'.format(res), 'shock_soln_u.txt'))
+		u1_analytic		 = np.loadtxt(os.path.join(outputdir, 'shock_soln_{}_default'.format(res), 'shock_soln_u1.txt'))
 		if CONDUCTION:
-			q_analytic   = np.loadtxt(os.path.join(kharmadir, 'kharma/prob/emhd/', 'shock_soln_{}_default'.format(res), 'shock_soln_q.txt'))
-		dP_analytic    = np.loadtxt(os.path.join(kharmadir, 'kharma/prob/emhd/', 'shock_soln_{}_default'.format(res), 'shock_soln_dP.txt'))
-		x_analytic     = np.loadtxt(os.path.join(kharmadir, 'kharma/prob/emhd/', 'shock_soln_{}_default'.format(res), 'shock_soln_xCoords.txt'))
+			q_analytic   = np.loadtxt(os.path.join(outputdir, 'shock_soln_{}_default'.format(res), 'shock_soln_q.txt'))
+		dP_analytic    = np.loadtxt(os.path.join(outputdir, 'shock_soln_{}_default'.format(res), 'shock_soln_dP.txt'))
+		x_analytic     = np.loadtxt(os.path.join(outputdir, 'shock_soln_{}_default'.format(res), 'shock_soln_xCoords.txt'))
 
 		# load code data
 		dfile = h5py.File('emhd_1d_{}_end.h5'.format(res), 'r')

diff --git a/tests/emhdshock/check.sh b/tests/emhdshock/check.sh
@@ -2,16 +2,11 @@
 
 # Run checks against analytic result for specified tests
 
-. /home/vdhruv2/anaconda3/etc/profile.d/conda.sh
-conda activate pyharm
-
 # Very small amplitude by default, preserve double precision
-~/pyHARM/scripts/pyharm-convert --double *.phdf
+pyharm convert --double *.phdf
 
 RES1D="256,512,1024,2048"
 
-conda activate base
-
 fail=0
 
 python3 check.py $RES1D "EMHD shock" emhd1d || fail=1