Updates TimeStepManager (#273)

* updates coordinator to match changes in TSM * adds scripts, makes plist names consistent (e.g. all others use timestep) * minor fixes for converter, better comments to show what is going on in BDF, tweaks to test_manager to write out failed tests * changes all time step --> timestep, revisions on timestep control for putting responsibility for recovering from event-based dt reductions on TimestepController * changes to BDF API to allow it to be constructed in setup, not in init, and to alloc less memory * time step --> timestep * moves ats-regression-tests pointer
amanzi · Oct 18, 2024 · 5cdea9a · 5cdea9a
1 parent 3e0d817
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diff --git a/docs/documentation/source/developer/NOTES.md b/docs/documentation/source/developer/NOTES.md
@@ -7,7 +7,7 @@ guidelines when using these levels in your code:
 
 - `Teuchos::VERB_NONE` Really, don't ever use this.  Don't do output at all.
 
-- `Teuchos::VERB_LOW` Should be used by time step-level work only.  It
+- `Teuchos::VERB_LOW` Should be used by timestep-level work only.  It
   should print a message saying "start a timestep" and the result of
   that timestep (success/fail).  So really almost exclusively in a
   PK's AdvanceStep() and ValidStep() methods, if they exist.

diff --git a/docs/tutorial/session5-sampling/test7-v_fwd.xml b/docs/tutorial/session5-sampling/test7-v_fwd.xml
@@ -129,7 +129,7 @@
           <Parameter name="primary variable" type="string" value="precipitation_snow" />
           <Parameter name="conserved quantity key" type="string" value="precipitation_snow" />
           <Parameter name="domain name" type="string" value="surface" />
-          <Parameter name="initial time step" type="double" value="86400.0" />
+          <Parameter name="initial timestep" type="double" value="86400.0" />
           <Parameter name="upwind conductivity method" type="string" value="upwind by potential difference" />
           <ParameterList name="precipitation function" type="ParameterList">
             <ParameterList name="function-tabular" type="ParameterList">
@@ -164,10 +164,10 @@
             <ParameterList name="timestep controller smarter parameters" type="ParameterList">
               <Parameter name="max iterations" type="int" value="18" />
               <Parameter name="min iterations" type="int" value="10" />
-              <Parameter name="time step reduction factor" type="double" value="0.25" />
-              <Parameter name="time step increase factor" type="double" value="1.5" />
-              <Parameter name="max time step" type="double" value="100000000.0" />
-              <Parameter name="min time step" type="double" value="1e-10" />
+              <Parameter name="timestep reduction factor" type="double" value="0.25" />
+              <Parameter name="timestep increase factor" type="double" value="1.5" />
+              <Parameter name="max timestep" type="double" value="100000000.0" />
+              <Parameter name="min timestep" type="double" value="1e-10" />
               <Parameter name="growth wait after fail" type="int" value="2" />
               <Parameter name="count before increasing increase factor" type="int" value="2" />
             </ParameterList>
@@ -250,10 +250,10 @@
             <ParameterList name="timestep controller smarter parameters" type="ParameterList">
               <Parameter name="max iterations" type="int" value="18" />
               <Parameter name="min iterations" type="int" value="10" />
-              <Parameter name="time step reduction factor" type="double" value="0.5" />
-              <Parameter name="time step increase factor" type="double" value="1.5" />
-              <Parameter name="max time step" type="double" value="100000000.0" />
-              <Parameter name="min time step" type="double" value="1e-10" />
+              <Parameter name="timestep reduction factor" type="double" value="0.5" />
+              <Parameter name="timestep increase factor" type="double" value="1.5" />
+              <Parameter name="max timestep" type="double" value="100000000.0" />
+              <Parameter name="min timestep" type="double" value="1e-10" />
               <Parameter name="growth wait after fail" type="int" value="2" />
               <Parameter name="count before increasing increase factor" type="int" value="2" />
             </ParameterList>
@@ -270,8 +270,8 @@
               <Parameter name="primary variable" type="string" value="snow_depth" />
               <Parameter name="conserved quantity key" type="string" value="snow_depth" />
               <Parameter name="domain name" type="string" value="surface" />
-              <Parameter name="initial time step" type="double" value="86400.0" />
-              <Parameter name="max time step" type="double" value="86400.0" />
+              <Parameter name="initial timestep" type="double" value="86400.0" />
+              <Parameter name="max timestep" type="double" value="86400.0" />
               <Parameter name="snow-ground transitional depth" type="double" value="0.05" />
               <Parameter name="wind speed reference height [m]" type="double" value="2.0" />
               <ParameterList name="VerboseObject" type="ParameterList">
@@ -360,9 +360,9 @@
                   <Parameter name="source term" type="bool" value="true" />
                   <Parameter name="clobber surface rel perm" type="bool" value="true" />
                   <Parameter name="limit correction to pressure change [Pa]" type="double" value="400000.0" />
-                  <Parameter name="max valid change in saturation in a time step [-]" type="double" value="0.1" />
-                  <Parameter name="max valid change in ice saturation in a time step [-]" type="double" value="0.1" />
-                  <Parameter name="initial time step" type="double" value="86400.0" />
+                  <Parameter name="max valid change in saturation in a timestep [-]" type="double" value="0.1" />
+                  <Parameter name="max valid change in ice saturation in a timestep [-]" type="double" value="0.1" />
+                  <Parameter name="initial timestep" type="double" value="86400.0" />
                   <Parameter name="relative permeability method" type="string" value="upwind with Darcy flux" />
                   <Parameter name="permeability rescaling" type="double" value="10000000.0" />
                   <Parameter name="debug cells" type="Array(int)" value="{3423}" />
@@ -440,7 +440,7 @@
                   <Parameter name="primary variable" type="string" value="surface-pressure" />
                   <Parameter name="domain name" type="string" value="surface" />
                   <Parameter name="source term" type="bool" value="true" />
-                  <Parameter name="initial time step" type="double" value="86400.0" />
+                  <Parameter name="initial timestep" type="double" value="86400.0" />
                   <ParameterList name="VerboseObject" type="ParameterList">
                     <Parameter name="Verbosity Level" type="string" value="high" />
                   </ParameterList>
@@ -486,7 +486,7 @@
                   <Parameter name="source term" type="bool" value="false" />
                   <Parameter name="supress advective terms in preconditioner" type="bool" value="true" />
                   <Parameter name="limit correction to temperature change [K]" type="double" value="1.0" />
-                  <Parameter name="initial time step" type="double" value="86400.0" />
+                  <Parameter name="initial timestep" type="double" value="86400.0" />
                   <Parameter name="debug cells" type="Array(int)" value="{3423}" />
                   <ParameterList name="VerboseObject" type="ParameterList">
                     <Parameter name="Verbosity Level" type="string" value="high" />
@@ -573,7 +573,7 @@
                   <Parameter name="flux key" type="string" value="surface-mass_flux" />
                   <Parameter name="supress advective terms in preconditioner" type="bool" value="false" />
                   <Parameter name="upwind conductivity method" type="string" value="arithmetic mean" />
-                  <Parameter name="initial time step" type="double" value="86400.0" />
+                  <Parameter name="initial timestep" type="double" value="86400.0" />
                   <ParameterList name="VerboseObject" type="ParameterList">
                     <Parameter name="Verbosity Level" type="string" value="high" />
                   </ParameterList>

diff --git a/src/constitutive_relations/eos/vapor_pressure_water.cc b/src/constitutive_relations/eos/vapor_pressure_water.cc
@@ -35,7 +35,7 @@ VaporPressureWater::SaturatedVaporPressure(double T)
 {
   if (T < 100. || T > 373.0) {
     std::cout << "Invalid temperature, T = " << T << std::endl;
-    Exceptions::amanzi_throw(Errors::CutTimeStep());
+    Exceptions::amanzi_throw(Errors::CutTimestep());
   }
   return 100.0 * exp(ka0_ + ka_ / T + (kb_ + kc_ * T) * T + kd_ * log(T));
 };
@@ -45,7 +45,7 @@ VaporPressureWater::DSaturatedVaporPressureDT(double T)
 {
   if (T < 100. || T > 373.0) {
     std::cout << "Invalid temperature, T = " << T << std::endl;
-    Errors::Message m("Cut time step");
+    Errors::Message m("Cut timestep");
     Exceptions::amanzi_throw(m);
   }
   return SaturatedVaporPressure(T) * (-ka_ / (T * T) + kb_ + 2.0 * kc_ * T + kd_ / T);

diff --git a/src/constitutive_relations/eos/viscosity_water.cc b/src/constitutive_relations/eos/viscosity_water.cc
@@ -49,7 +49,7 @@ ViscosityWater::Viscosity(double T)
 
   if (visc < 1.e-16) {
     std::cout << "Invalid temperature, T = " << T << std::endl;
-    Exceptions::amanzi_throw(Errors::CutTimeStep());
+    Exceptions::amanzi_throw(Errors::CutTimestep());
   }
   return visc;
 };

diff --git a/src/executables/ats_driver.cc b/src/executables/ats_driver.cc
@@ -162,7 +162,7 @@ ATSDriver::cycle_driver()
       } // while not finished
 
 #if !DEBUG_MODE
-    } catch (Errors::TimeStepCrash& e) {
+    } catch (Errors::TimestepCrash& e) {
       // write one more vis for help debugging
       S_->advance_cycle(Amanzi::Tags::NEXT);
       visualize(true); // force vis

diff --git a/src/executables/ats_driver.hh b/src/executables/ats_driver.hh
@@ -73,7 +73,7 @@ simulation, including starting and ending times and restart options.
 Note: Either `"end cycle`" or `"end time`" are required, and if
 both are present, the simulation will stop with whichever arrives
 first.  An `"end cycle`" is commonly used to ensure that, in the case
-of a time step crash, we do not continue on forever spewing output.
+of a timestep crash, we do not continue on forever spewing output.
 
 Example:
 

diff --git a/src/executables/coordinator.cc b/src/executables/coordinator.cc
@@ -251,17 +251,17 @@ Coordinator::Coordinator(const Teuchos::RCP<Teuchos::ParameterList>& plist,
       }
     }
 
-    // create the time step manager, register assorted timestep control events
-    tsm_ = Teuchos::rcp(new Amanzi::TimeStepManager());
-    checkpoint_->RegisterWithTimeStepManager(tsm_.ptr());
-    for (const auto& obs : observations_) obs->RegisterWithTimeStepManager(tsm_.ptr());
-    for (const auto& vis : visualization_) vis->RegisterWithTimeStepManager(tsm_.ptr());
+    // create the timestep manager, register assorted timestep control events
+    tsm_ = Teuchos::rcp(new Amanzi::Utils::TimeStepManager(coordinator_list_->sublist("timestep manager")));
+    checkpoint_->RegisterWithTimeStepManager(*tsm_);
+    for (const auto& obs : observations_) obs->RegisterWithTimeStepManager(*tsm_);
+    for (const auto& vis : visualization_) vis->RegisterWithTimeStepManager(*tsm_);
     tsm_->RegisterTimeEvent(t1_);
 
     if (coordinator_list_->isSublist("required times")) {
       Teuchos::ParameterList& sublist = coordinator_list_->sublist("required times");
-      Amanzi::IOEvent pause_times(sublist);
-      pause_times.RegisterWithTimeStepManager(tsm_.ptr());
+      Amanzi::Utils::IOEvent pause_times(sublist);
+      pause_times.RegisterWithTimeStepManager(*tsm_);
     }
   }
   if (vo_->os_OK(Teuchos::VERB_LOW)) {
@@ -502,8 +502,8 @@ Coordinator::initializeFromPlist_()
   }
   t1_ = units.ConvertTime(t1_, t1_units, "s", success);
 
-  max_dt_ = coordinator_list_->get<double>("max time step size [s]", 1.0e99);
-  min_dt_ = coordinator_list_->get<double>("min time step size [s]", 1.0e-12);
+  max_dt_ = coordinator_list_->get<double>("max timestep size [s]", 1.0e99);
+  min_dt_ = coordinator_list_->get<double>("min timestep size [s]", 1.0e-12);
   cycle0_ = coordinator_list_->get<int>("start cycle", -1);
   cycle1_ = coordinator_list_->get<int>("end cycle", -1);
   duration_ = coordinator_list_->get<double>("wallclock duration [hrs]", -1.0);
@@ -554,7 +554,6 @@ Coordinator::advance()
   double t_new = S_->get_time(Amanzi::Tags::NEXT);
 
   bool fail = pk_->AdvanceStep(t_old, t_new, false);
-  if (!fail) fail |= !pk_->ValidStep();
 
   // write state post-advance, if extreme
   WriteStateStatistics(*S_, *vo_, Teuchos::VERB_EXTREME);

diff --git a/src/executables/coordinator.hh b/src/executables/coordinator.hh
@@ -23,7 +23,9 @@
 #include "VerboseObject.hh"
 
 namespace Amanzi {
+namespace Utils {
 class TimeStepManager;
+} // namespace Utils
 class Visualization;
 class Checkpoint;
 class State;
@@ -66,8 +68,8 @@ class Coordinator {
   Teuchos::RCP<Amanzi::State> S_;
   Teuchos::RCP<Amanzi::TreeVector> soln_;
 
-  // time step manager
-  Teuchos::RCP<Amanzi::TimeStepManager> tsm_;
+  // timestep manager
+  Teuchos::RCP<Amanzi::Utils::TimeStepManager> tsm_;
 
   // misc setup information
   Teuchos::RCP<Teuchos::ParameterList> plist_;

diff --git a/src/executables/test/executable_coupled_water1.xml b/src/executables/test/executable_coupled_water1.xml
@@ -109,12 +109,13 @@
           </ParameterList>
         </ParameterList>
         <ParameterList name="timestep controller smarter parameters" type="ParameterList">
+          <Parameter name="initial timestep [s]" type="double" value="1" />
           <Parameter name="max iterations" type="int" value="18" />
           <Parameter name="min iterations" type="int" value="10" />
-          <Parameter name="time step reduction factor" type="double" value="0.5" />
-          <Parameter name="time step increase factor" type="double" value="1.25" />
-          <Parameter name="max time step" type="double" value="600" />
-          <Parameter name="min time step" type="double" value="1e-10" />
+          <Parameter name="timestep reduction factor" type="double" value="0.5" />
+          <Parameter name="timestep increase factor" type="double" value="1.25" />
+          <Parameter name="max timestep" type="double" value="600" />
+          <Parameter name="min timestep" type="double" value="1e-10" />
           <Parameter name="growth wait after fail" type="int" value="2" />
           <Parameter name="count before increasing increase factor" type="int" value="2" />
         </ParameterList>
@@ -127,7 +128,7 @@
       <Parameter name="primary variable key" type="string" value="pressure" />
       <Parameter name="relative permeability method" type="string" value="upwind with Darcy flux" />
       <Parameter name="permeability rescaling" type="double" value="10000000" />
-      <Parameter name="max valid change in saturation in a time step [-]" type="double" value="0.1" />
+      <Parameter name="max valid change in saturation in a timestep [-]" type="double" value="0.1" />
       <Parameter name="debug cells" type="Array(int)" value="{0}" />
       <ParameterList name="verbose object" type="ParameterList">
         <Parameter name="verbosity level" type="string" value="high" />

diff --git a/src/executables/test/executable_coupled_water2.xml b/src/executables/test/executable_coupled_water2.xml
@@ -109,12 +109,13 @@
           </ParameterList>
         </ParameterList>
         <ParameterList name="timestep controller smarter parameters" type="ParameterList">
+          <Parameter name="initial timestep [s]" type="double" value="1" />
           <Parameter name="max iterations" type="int" value="18" />
           <Parameter name="min iterations" type="int" value="10" />
-          <Parameter name="time step reduction factor" type="double" value="0.5" />
-          <Parameter name="time step increase factor" type="double" value="1.25" />
-          <Parameter name="max time step" type="double" value="600" />
-          <Parameter name="min time step" type="double" value="1e-10" />
+          <Parameter name="timestep reduction factor" type="double" value="0.5" />
+          <Parameter name="timestep increase factor" type="double" value="1.25" />
+          <Parameter name="max timestep" type="double" value="600" />
+          <Parameter name="min timestep" type="double" value="1e-10" />
           <Parameter name="growth wait after fail" type="int" value="2" />
           <Parameter name="count before increasing increase factor" type="int" value="2" />
         </ParameterList>
@@ -127,7 +128,7 @@
       <Parameter name="primary variable key" type="string" value="pressure" />
       <Parameter name="relative permeability method" type="string" value="upwind with Darcy flux" />
       <Parameter name="permeability rescaling" type="double" value="10000000" />
-      <Parameter name="max valid change in saturation in a time step [-]" type="double" value="0.1" />
+      <Parameter name="max valid change in saturation in a timestep [-]" type="double" value="0.1" />
       <Parameter name="debug cells" type="Array(int)" value="{0}" />
       <ParameterList name="verbose object" type="ParameterList">
         <Parameter name="verbosity level" type="string" value="high" />

diff --git a/src/executables/test/executable_coupled_water3.xml b/src/executables/test/executable_coupled_water3.xml
@@ -109,12 +109,13 @@
           </ParameterList>
         </ParameterList>
         <ParameterList name="timestep controller smarter parameters" type="ParameterList">
+          <Parameter name="initial timestep [s]" type="double" value="1" />
           <Parameter name="max iterations" type="int" value="18" />
           <Parameter name="min iterations" type="int" value="10" />
-          <Parameter name="time step reduction factor" type="double" value="0.5" />
-          <Parameter name="time step increase factor" type="double" value="1.25" />
-          <Parameter name="max time step" type="double" value="600" />
-          <Parameter name="min time step" type="double" value="1e-10" />
+          <Parameter name="timestep reduction factor" type="double" value="0.5" />
+          <Parameter name="timestep increase factor" type="double" value="1.25" />
+          <Parameter name="max timestep" type="double" value="600" />
+          <Parameter name="min timestep" type="double" value="1e-10" />
           <Parameter name="growth wait after fail" type="int" value="2" />
           <Parameter name="count before increasing increase factor" type="int" value="2" />
         </ParameterList>
@@ -127,7 +128,7 @@
       <Parameter name="primary variable key" type="string" value="pressure" />
       <Parameter name="relative permeability method" type="string" value="upwind with Darcy flux" />
       <Parameter name="permeability rescaling" type="double" value="10000000" />
-      <Parameter name="max valid change in saturation in a time step [-]" type="double" value="0.1" />
+      <Parameter name="max valid change in saturation in a timestep [-]" type="double" value="0.1" />
       <Parameter name="debug cells" type="Array(int)" value="{0}" />
       <ParameterList name="verbose object" type="ParameterList">
         <Parameter name="verbosity level" type="string" value="high" />

diff --git a/src/pks/biogeochemistry/bgc_simple/PFT.hh b/src/pks/biogeochemistry/bgc_simple/PFT.hh
@@ -92,13 +92,13 @@ class PFT {
   double Jmax25;             //umol electron/m2 leaf/s
   double GDDleafon;          //growing degree days for leaf on
   double GDD;                //growing degree days
-  double mResp;              //maintanence respiration, kg C/grid cell /time step
-  double gResp;              //maintanence respiration, kg C/grid cell /time step
+  double mResp;              //maintanence respiration, kg C/grid cell /timestep
+  double gResp;              //maintanence respiration, kg C/grid cell /timestep
   double GDDbase;            //growing degree days base temperature
   double annNPP;
-  double GPP;          //gross primary proeduction; kg C/grid cell /time step
-  double NPP;          //net primary proeduction; kg C/grid cell/time step
-  double ET;           //Transpiration; kg water/time step/grid cell
+  double GPP;          //gross primary proeduction; kg C/grid cell /timestep
+  double NPP;          //net primary proeduction; kg C/grid cell/timestep
+  double ET;           //Transpiration; kg water/timestep/grid cell
   int leafstatus;      //1=off; 2==on
   bool evergreen;      //1=yes; 0=no
   double LUE;          //light use efficiency

diff --git a/src/pks/biogeochemistry/bgc_simple/bgc_simple.cc b/src/pks/biogeochemistry/bgc_simple/bgc_simple.cc
@@ -52,7 +52,7 @@ BGCSimple::BGCSimple(Teuchos::ParameterList& pk_tree,
     Keys::readKey(*plist_, domain_surf_, "total leaf area index", "total_leaf_area_index");
 
   // initial timestep
-  dt_ = plist_->get<double>("initial time step", 1.);
+  dt_ = plist_->get<double>("initial timestep", 1.);
 
   // Create the additional, non-managed data structures
   num_pools_ = plist_->get<int>("number of carbon pools", 7);

diff --git a/src/pks/biogeochemistry/bgc_simple/bgc_simple.hh b/src/pks/biogeochemistry/bgc_simple/bgc_simple.hh
@@ -36,7 +36,7 @@ that build_columns in the subsurface Mesh_ spec has been supplied.
 .. _bgc-simple-spec:
 .. admonition:: bgc-simple-spec
 
-  * `"initial time step`" ``[double]`` **1.0** Initial time step size `[s]`
+  * `"initial timestep`" ``[double]`` **1.0** Initial timestep size `[s]`
 
   * `"number of carbon pools`" ``[int]`` **7** Unclear whether this can actually change?