Merge pull request #294 from hklion/bc_prefix

add bc. prefix to bc options, and make zlo/zhi optional
seahorce-scidac · Nov 13, 2024 · a9f970b · a9f970b
2 parents 2558f41 + daec721
commit a9f970b
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Showing 25 changed files with 59 additions and 151 deletions.
diff --git a/Exec/Advection/inputs b/Exec/Advection/inputs
@@ -12,12 +12,7 @@ geometry.prob_hi     =  41000. 41000.       0.
 
 amr.n_cell           = 81     81      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Exec/Advection/inputs_ml b/Exec/Advection/inputs_ml
@@ -12,12 +12,7 @@ geometry.prob_hi     =  40000. 40000.       0.
 
 amr.n_cell           = 80     80      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 100.0 # Timestep size (seconds)

diff --git a/Exec/Channel_Test/inputs b/Exec/Channel_Test/inputs
@@ -14,11 +14,8 @@ amr.n_cell           =  20     60      50
 
 geometry.is_periodic = 1 0 0
 
-ylo.type = "SlipWall"
-yhi.type = "SlipWall"
-
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
+bc.ylo.type = "SlipWall"
+bc.yhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 400.0 # Timestep size (seconds)

diff --git a/Exec/Channel_Test/inputs_orlanski b/Exec/Channel_Test/inputs_orlanski
@@ -14,22 +14,16 @@ amr.n_cell           =   20     60      50
 
 geometry.is_periodic = 0 0 0
 
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
-
 remora.boundary_per_variable = 1
-temp.type   =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
-salt.type   =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
-scalar.type =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
-u.type      =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
-v.type      =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
-ubar.type   =  outflow outflow outflow outflow
-vbar.type   =  outflow outflow outflow outflow
-zeta.type   =  outflow outflow outflow outflow
-tke.type    =  outflow outflow outflow outflow
+bc.temp.type   =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
+bc.salt.type   =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
+bc.scalar.type =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
+bc.u.type      =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
+bc.v.type      =  orlanski_rad orlanski_rad orlanski_rad orlanski_rad
+bc.ubar.type   =  outflow outflow outflow outflow
+bc.vbar.type   =  outflow outflow outflow outflow
+bc.zeta.type   =  outflow outflow outflow outflow
+bc.tke.type    =  outflow outflow outflow outflow
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 400.0 # Timestep size (seconds)

diff --git a/Exec/DoubleGyre/inputs b/Exec/DoubleGyre/inputs
@@ -13,14 +13,11 @@ amr.n_cell           =  54     108      4
 
 geometry.is_periodic = 0 0 0
 
-xlo.type = "SlipWall"
-xhi.type = "SlipWall"
+bc.xlo.type = "SlipWall"
+bc.xhi.type = "SlipWall"
 
-ylo.type = "SlipWall"
-yhi.type = "SlipWall"
-
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
+bc.ylo.type = "SlipWall"
+bc.yhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 3600.0 # Timestep size (seconds)

diff --git a/Exec/DoublyPeriodic/inputs b/Exec/DoublyPeriodic/inputs
@@ -12,12 +12,7 @@ geometry.prob_hi     =  41000. 80000.       0.
 
 amr.n_cell           =  41     80      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Exec/IdealMiniGrid/inputs b/Exec/IdealMiniGrid/inputs
@@ -13,13 +13,11 @@ geometry.prob_hi     =   320000.  320000.       0.
 amr.n_cell           =  10 16 20
 
 geometry.is_periodic = 0 0 0
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
-xlo.type = "clamped"
-xhi.type = "clamped"
-ylo.type = "clamped"
-yhi.type = "clamped"
+bc.xlo.type = "clamped"
+bc.xhi.type = "clamped"
+bc.ylo.type = "clamped"
+bc.yhi.type = "clamped"
 
 # TIME STEP CONTROL
 remora.fixed_dt            = 200.0 # Timestep size (seconds)

diff --git a/Exec/IdealMiniGrid/inputs_cf_orlanski b/Exec/IdealMiniGrid/inputs_cf_orlanski
@@ -13,20 +13,18 @@ geometry.prob_hi     =   320000.  320000.       0.
 amr.n_cell           =  10 16 20
 
 geometry.is_periodic = 0 0 0
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 remora.boundary_per_variable = 1
-##             WEST              SOUTH             EAST              NORTH
-temp.type   =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
-salt.type   =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
-scalar.type =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
-u.type      =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
-v.type      =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
-ubar.type   =  flather           flather           flather          flather
-vbar.type   =  flather           flather           flather          flather
-zeta.type   =  chapman           chapman           chapman          chapman
-tke.type    =  outflow           outflow           outflow          outflow
+##                WEST              SOUTH             EAST              NORTH
+bc.temp.type   =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
+bc.salt.type   =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
+bc.scalar.type =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
+bc.u.type      =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
+bc.v.type      =  orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg orlanski_rad_nudg
+bc.ubar.type   =  flather           flather           flather          flather
+bc.vbar.type   =  flather           flather           flather          flather
+bc.zeta.type   =  chapman           chapman           chapman          chapman
+bc.tke.type    =  outflow           outflow           outflow          outflow
 
 # TIME STEP CONTROL
 remora.fixed_dt            = 200.0 # Timestep size (seconds)

diff --git a/Exec/IdealMiniGrid/inputs_chapman_flather b/Exec/IdealMiniGrid/inputs_chapman_flather
@@ -13,20 +13,18 @@ geometry.prob_hi     =   320000.  320000.       0.
 amr.n_cell           =  10 16 20
 
 geometry.is_periodic = 0 0 0
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 remora.boundary_per_variable = 1
 ##             WEST     SOUTH    EAST     NORTH
-temp.type   =  clamped  clamped  clamped  clamped
-salt.type   =  clamped  clamped  clamped  clamped
-scalar.type =  clamped  clamped  clamped  clamped
-u.type      =  clamped  clamped  clamped  clamped
-v.type      =  clamped  clamped  clamped  clamped
-ubar.type   =  flather  flather  flather  flather
-vbar.type   =  flather  flather  flather  flather
-zeta.type   =  chapman  chapman  chapman  chapman
-tke.type    =  outflow  outflow  outflow  outflow
+bc.temp.type   =  clamped  clamped  clamped  clamped
+bc.salt.type   =  clamped  clamped  clamped  clamped
+bc.scalar.type =  clamped  clamped  clamped  clamped
+bc.u.type      =  clamped  clamped  clamped  clamped
+bc.v.type      =  clamped  clamped  clamped  clamped
+bc.ubar.type   =  flather  flather  flather  flather
+bc.vbar.type   =  flather  flather  flather  flather
+bc.zeta.type   =  chapman  chapman  chapman  chapman
+bc.tke.type    =  outflow  outflow  outflow  outflow
 
 # TIME STEP CONTROL
 remora.fixed_dt            = 200.0 # Timestep size (seconds)

diff --git a/Exec/ParticlesOverSeaMount/inputs b/Exec/ParticlesOverSeaMount/inputs
@@ -13,12 +13,7 @@ geometry.prob_hi     =  41000. 80000.       0.
 
 amr.n_cell           =  41     80      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Exec/ParticlesOverSeaMount/inputs_ml b/Exec/ParticlesOverSeaMount/inputs_ml
@@ -13,12 +13,7 @@ geometry.prob_hi     =  41000. 80000.       0.
 
 amr.n_cell           =  41     80      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Exec/Seamount/inputs b/Exec/Seamount/inputs
@@ -13,12 +13,7 @@ geometry.prob_hi     =   320000.  320000.       0.
 
 amr.n_cell           =  49   48   13
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 60.0 # Timestep size (seconds)

diff --git a/Exec/Upwelling/inputs b/Exec/Upwelling/inputs
@@ -13,11 +13,8 @@ amr.n_cell           =  41     80      16
 
 geometry.is_periodic = 1 0 0
 
-ylo.type = "SlipWall"
-yhi.type = "SlipWall"
-
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
+bc.ylo.type = "SlipWall"
+bc.yhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Exec/Upwelling/inputs_gls b/Exec/Upwelling/inputs_gls
@@ -13,11 +13,8 @@ amr.n_cell           =  41     80      16
 
 geometry.is_periodic = 1 0 0
 
-ylo.type = "SlipWall"
-yhi.type = "SlipWall"
-
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
+bc.ylo.type = "SlipWall"
+bc.yhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Exec/Upwelling_ML/inputs b/Exec/Upwelling_ML/inputs
@@ -14,12 +14,6 @@ amr.n_cell           =  41     80      16
 
 geometry.is_periodic = 1 1 0
 
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
-
 # TIME STEP CONTROL
 remora.fixed_dt       = 5 # Timestep size (seconds)
 

diff --git a/Source/Initialization/REMORA_init_bcs.cpp b/Source/Initialization/REMORA_init_bcs.cpp
@@ -93,6 +93,9 @@ void REMORA::init_bcs ()
         }
         else if (bc_type_string == "periodic")
         {
+            if (!geom[0].isPeriodic(ori.coordDir())) {
+                amrex::Abort("Periodic boundary specified in a non-periodic direction");
+            }
             phys_bc_type[bcvar_type][ori] = REMORA_BC::periodic;
             domain_bc_type[ori] = "Periodic";
         }
@@ -121,8 +124,10 @@ void REMORA::init_bcs ()
 
     auto f_by_side = [this, &f_set_var_bc] (std::string const& bcid, Orientation ori)
     {
-        ParmParse pp(bcid);
+        ParmParse pp("bc."+bcid);
         std::string bc_type_in = "null";
+        // Default z directions to slipwall
+        if (bcid=="zlo" or bcid=="zhi") bc_type_in = "slipwall";
         pp.query("type", bc_type_in);
         std::string bc_type = amrex::toLower(bc_type_in);
 
@@ -135,7 +140,7 @@ void REMORA::init_bcs ()
     {
         amrex::Vector<Orientation> orientations = {Orientation(Direction::x,Orientation::low), Orientation(Direction::y,Orientation::high),Orientation(Direction::x,Orientation::high),Orientation(Direction::y,Orientation::low)}; // west, south, east, north [matches ROMS]
         std::vector<std::string> bc_types = {"null","null","null","null"};
-        ParmParse pp(varname);
+        ParmParse pp("bc."+varname);
         std::string bc_type_in = "null";
         // default zvel to outflow
         if (bcvar_type == BCVars::zvel_bc) {

diff --git a/Tests/test_files/Advection/Advection.i b/Tests/test_files/Advection/Advection.i
@@ -12,12 +12,7 @@ geometry.prob_hi     =  41000. 41000.       0.
 
 amr.n_cell           = 81     81      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Tests/test_files/Advection_ML/Advection_ML.i b/Tests/test_files/Advection_ML/Advection_ML.i
@@ -12,12 +12,7 @@ geometry.prob_hi     =  40000. 40000.       0.
 
 amr.n_cell           = 80     80      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 100.0 # Timestep size (seconds)

diff --git a/Tests/test_files/Channel_Test/Channel_Test.i b/Tests/test_files/Channel_Test/Channel_Test.i
@@ -14,11 +14,8 @@ amr.n_cell           =  20     60      50
 
 geometry.is_periodic = 1 0 0
 
-ylo.type = "SlipWall"
-yhi.type = "SlipWall"
-
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
+bc.ylo.type = "SlipWall"
+bc.yhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 400.0 # Timestep size (seconds)

diff --git a/Tests/test_files/DoubleGyre/DoubleGyre.i b/Tests/test_files/DoubleGyre/DoubleGyre.i
@@ -11,14 +11,11 @@ amr.n_cell           =  54     108      4
 
 geometry.is_periodic = 0 0 0
 
-xlo.type = "SlipWall"
-xhi.type = "SlipWall"
+bc.xlo.type = "SlipWall"
+bc.xhi.type = "SlipWall"
 
-ylo.type = "SlipWall"
-yhi.type = "SlipWall"
-
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
+bc.ylo.type = "SlipWall"
+bc.yhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 3600.0 # Timestep size (seconds)

diff --git a/Tests/test_files/DoublyPeriodic/DoublyPeriodic.i b/Tests/test_files/DoublyPeriodic/DoublyPeriodic.i
@@ -12,12 +12,7 @@ geometry.prob_hi     =  41000. 80000.       0.
 
 amr.n_cell           =  41     80      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i b/Tests/test_files/DoublyPeriodic_bathy/DoublyPeriodic_bathy.i
@@ -12,12 +12,7 @@ geometry.prob_hi     =  41000. 80000.       0.
 
 amr.n_cell           =  41     80      16
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 300.0 # Timestep size (seconds)

diff --git a/Tests/test_files/Seamount/Seamount.i b/Tests/test_files/Seamount/Seamount.i
@@ -13,12 +13,7 @@ geometry.prob_hi     =   320000.  320000.       0.
 
 amr.n_cell           =  49   48   13
 
-# periodic in x to match WRF setup
 geometry.is_periodic = 1 1 0
-#ylo.type = "SlipWall"
-#yhi.type = "SlipWall"
-zlo.type = "SlipWall"
-zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
 remora.fixed_dt       = 60.0 # Timestep size (seconds)