initial condition --> initial conditions

src/pks/energy/energy_surface_ice.cc

@@ -109,7 +109,7 @@ EnergySurfaceIce::Initialize()
 {
   // -- set the cell initial condition if it is taken from the subsurface
   if (!S_->GetRecord(key_, tag_next_).initialized()) {
-    if (!plist_->isSublist("initial condition")) {
+    if (!plist_->isSublist("initial conditions")) {
       Errors::Message message;
       message << name_ << " has no initial condition parameter list.";
       Exceptions::amanzi_throw(message);
@@ -122,7 +122,7 @@ EnergySurfaceIce::Initialize()
   // Set the cell initial condition if it is taken from the subsurface
   if (!S_->GetRecord(key_, tag_next_).initialized()) {
     // TODO: make this go away!  This should be in an MPC?
-    Teuchos::ParameterList& ic_plist = plist_->sublist("initial condition");
+    Teuchos::ParameterList& ic_plist = plist_->sublist("initial conditions");
     if (ic_plist.get<bool>("initialize surface temperature from subsurface", false)) {
       Teuchos::RCP<CompositeVector> surf_temp_cv =
         S_->GetPtrW<CompositeVector>(key_, tag_next_, name_);

src/pks/energy/energy_three_phase.cc

@@ -45,9 +45,9 @@ void
 ThreePhase::Initialize()
 {
   // INTERFROST comparison needs some very specialized ICs
-  if (plist_->sublist("initial condition").isParameter("interfrost initial condition")) {
+  if (plist_->sublist("initial conditions").isParameter("interfrost initial condition")) {
     AMANZI_ASSERT(
-      plist_->sublist("initial condition").get<std::string>("interfrost initial condition") ==
+      plist_->sublist("initial conditions").get<std::string>("interfrost initial condition") ==
       "TH3");
     Teuchos::RCP<CompositeVector> temp = S_->GetPtrW<CompositeVector>(key_, tag_next_, name_);
     double r_sq = std::pow(0.5099, 2);
@@ -67,7 +67,7 @@ ThreePhase::Initialize()
     S_->GetRecordW(key_, tag_next_, name_).set_initialized();
 
     // additionally call Initalize() to get faces from cell values
-    S_->GetRecordW(key_, tag_next_, name_).Initialize(plist_->sublist("initial condition"));
+    S_->GetRecordW(key_, tag_next_, name_).Initialize(plist_->sublist("initial conditions"));
   }
 
   EnergyBase::Initialize();

src/pks/flow/overland_pressure_pk.cc

@@ -428,7 +428,7 @@ OverlandPressureFlow::Initialize()
 
   // initial condition is tricky
   if (!S_->GetRecord(key_, tag_next_).initialized()) {
-    if (!plist_->isSublist("initial condition")) {
+    if (!plist_->isSublist("initial conditions")) {
       Errors::Message message;
       message << name_ << " has no initial condition parameter list.";
       Exceptions::amanzi_throw(message);
@@ -443,7 +443,7 @@ OverlandPressureFlow::Initialize()
     // There is a function to do this already in that MPC.
     //
     // set the cell initial condition if it is taken from the subsurface
-    Teuchos::ParameterList ic_plist = plist_->sublist("initial condition");
+    Teuchos::ParameterList ic_plist = plist_->sublist("initial conditions");
     if (ic_plist.get<bool>("initialize surface head from subsurface", false)) {
       Epetra_MultiVector& pres = *pres_cv->ViewComponent("cell", false);
 

src/pks/flow/richards_pk.cc

@@ -578,10 +578,10 @@ void
 Richards::InitializeHydrostatic_(const Tag& tag)
 {
   // constant head over the surface
-  if (plist_->sublist("initial condition").isParameter("hydrostatic head [m]")) {
-    double head_wt = plist_->sublist("initial condition").get<double>("hydrostatic head [m]");
+  if (plist_->sublist("initial conditions").isParameter("hydrostatic head [m]")) {
+    double head_wt = plist_->sublist("initial conditions").get<double>("hydrostatic head [m]");
     double rho =
-      plist_->sublist("initial condition").get<double>("hydrostatic water density [kg m^-3]");
+      plist_->sublist("initial conditions").get<double>("hydrostatic water density [kg m^-3]");
     int ncols = mesh_->columns.num_columns_owned;
 
     const auto& gvec = S_->Get<AmanziGeometry::Point>("gravity", Tags::DEFAULT);
@@ -653,10 +653,10 @@ Richards::InitializeHydrostatic_(const Tag& tag)
   }
 
   // constant head datum
-  if (plist_->sublist("initial condition").isParameter("hydrostatic water level [m]")) {
-    double z_wt = plist_->sublist("initial condition").get<double>("hydrostatic water level [m]");
+  if (plist_->sublist("initial conditions").isParameter("hydrostatic water level [m]")) {
+    double z_wt = plist_->sublist("initial conditions").get<double>("hydrostatic water level [m]");
     double rho =
-      plist_->sublist("initial condition").get<double>("hydrostatic water density [kg m^-3]");
+      plist_->sublist("initial conditions").get<double>("hydrostatic water density [kg m^-3]");
 
     int z_index = mesh_->getSpaceDimension() - 1;
     const auto& gravity = S_->Get<AmanziGeometry::Point>("gravity", Tags::DEFAULT);

src/pks/surface_balance/CLM/surface_balance_CLM.cc

@@ -281,7 +281,7 @@ void
 SurfaceBalanceCLM::InitializeCLM_(const Tag& tag)
 {
   // Initialize the CLM instance
-  Teuchos::ParameterList& ic_list = plist_->sublist("initial condition");
+  Teuchos::ParameterList& ic_list = plist_->sublist("initial conditions");
   double snow_depth = ic_list.get<double>("initial snow depth [m]");
   double temp = ic_list.get<double>("initial temperature [K]");
   double year = ic_list.get<double>("initial time [yr]");

src/pks/surface_balance/surface_balance_implicit_subgrid.cc

@@ -91,7 +91,7 @@ ImplicitSubgrid::Initialize()
   SurfaceBalanceBase::Initialize();
 
   // initialize snow density, age
-  Teuchos::ParameterList& ic_list = plist_->sublist("initial condition");
+  Teuchos::ParameterList& ic_list = plist_->sublist("initial conditions");
 
   if (!S_->GetRecord(snow_dens_key_, tag_next_).initialized()) {
     if (ic_list.isParameter("restart file")) {

src/pks/test_pks/divgrad_test/divgrad_test.cc

@@ -79,15 +79,15 @@ void
 DivGradTest::initialize(const Teuchos::Ptr<State>& S)
 {
   // Check for PK-specific initialization
-  if (!plist_->isSublist("initial condition")) {
+  if (!plist_->isSublist("initial conditions")) {
     std::stringstream messagestream;
     messagestream << name_ << " has no initial condition parameter list.";
     Errors::Message message(messagestream.str());
     Exceptions::amanzi_throw(message);
   }
 
   // make sure the initial condition doesn't set faces in another way
-  Teuchos::ParameterList ic_plist = plist_->sublist("initial condition");
+  Teuchos::ParameterList ic_plist = plist_->sublist("initial conditions");
   ic_plist.set("initialize faces from cells", false);
 
   // initialize primary variable from the ic_plist condition

tools/input_converters/xml-1.5-master.py

@@ -16,7 +16,7 @@
 from amanzi_xml.utils import io as aio
 from amanzi_xml.utils import errors as aerrors
 from amanzi_xml.common import parameter, parameter_list
-
+import fix_chemistry_ts_control
 
 def enforceDtHistory(xml):
     """Find and revert the timestep from file option, moving it to the cycle driver list."""
@@ -275,13 +275,22 @@ def fixTransportPKs(xml):
             pk_type.setValue("transport ATS")
             print("fixing transport pk")
             fixTransportPK(pk, evals_list)
-
+
+def initialConditionsList(xml):
+    for pk in xml.sublist("PKs"):
+        if pk.isElement("initial condition"):
+            pk.sublist("initial condition").setName("initial conditions")
+
 
 def update(xml):
     #enforceDtHistory(xml)
     timeStep(xml)
     tensorPerm(xml)
+    initialConditionsList(xml)
     fixTransportPKs(xml)
+
+    # this fixes chemistry
+    fix_chemistry_ts_control.fixAll(xml)
 
 
 if __name__ == "__main__":

tools/utils/plot_lines.py

@@ -0,0 +1,48 @@
+import numpy as np
+from matplotlib import pyplot as plt
+import matplotlib.collections
+
+def plotLines(x, y, t, ax=None, colorbar=True, colorbar_ticks=True, colorbar_label=None, t_min=None, t_max=None, **kwargs):
+    """Plots lines by color."""
+
+    # create an axis if none
+    if ax is None:
+        fig, ax = plt.subplots()
+    else:
+        fig = ax.get_figure()
+
+    # set bounds
+    if t_min is None:
+        t_min = t[0]
+    if t_max is None:
+        t_max = t[-1]
+
+    # plot the lines
+    segments = [np.column_stack((x,y)) for (x,y) in zip(x,y)]
+    lc = matplotlib.collections.LineCollection(segments, **kwargs)
+    c = (t - t_min) / (t_max - t_min)
+    lc.set_array(c)
+
+    # add to axis
+    ax.add_collection(lc)
+    ax.autoscale()
+
+    if colorbar:
+        # create the colorbar
+        axcb = fig.colorbar(lc)
+
+        # label it
+        if colorbar_label is not None:
+            axcb.set_label(colorbar_label)
+
+        # transform ticks from [0,1] to [times[0], times[-1]]
+        if colorbar_ticks:
+            xticks = axcb.get_ticks()
+            new_ticks = [t * (t_max - t_min) + t_min for t in xticks]
+            axcb.set_ticklabels([str(np.round(t, 2)) for t in new_ticks])
+        else:
+            axcb.set_ticks(list())
+    else:
+        axcb = None
+    return ax, axcb
+