Change to Cosmo example

.gitignore

@@ -38,3 +38,4 @@ log*
 *.dSYM
 *.patch
 *.log
+*.err

Examples/Inflation/InflationDiagnostics.hpp → Examples/Cosmo/CosmoDiagnostics.hpp

@@ -3,8 +3,8 @@
  * Please refer to LICENSE in GRChombo's root directory.
  */
 
-#ifndef INFLATIONDIAGNOSTICS_HPP_
-#define INFLATIONDIAGNOSTICS_HPP_
+#ifndef COSMODIAGNOSTICS_HPP_
+#define COSMODIAGNOSTICS_HPP_
 
 #include "CCZ4Geometry.hpp"
 #include "CCZ4Vars.hpp"
@@ -22,7 +22,7 @@
 //! are stored as diagnostics
 
 template <class matter_t>
-class InflationDiagnostics // public MatterConstraints<matter_t>
+class CosmoDiagnostics // public MatterConstraints<matter_t>
 {
   public:
     // Inherit the variable definitions from CCZ4 + matter_t
@@ -45,8 +45,8 @@ class InflationDiagnostics // public MatterConstraints<matter_t>
         }
     };
 
-    //! Constructor of class InflationDiagnostics
-    InflationDiagnostics(const matter_t a_matter, double dx, double G_Newton)
+    //! Constructor of class CosmoDiagnostics
+    CosmoDiagnostics(const matter_t a_matter, double dx, double G_Newton)
         : m_matter(a_matter), m_deriv(dx)
     {
     }
@@ -60,6 +60,6 @@ class InflationDiagnostics // public MatterConstraints<matter_t>
     const FourthOrderDerivatives m_deriv;
 };
 
-#include "InflationDiagnostics.impl.hpp"
+#include "CosmoDiagnostics.impl.hpp"
 
-#endif /* INFLATIONDIAGNOSTICS_HPP_ */
+#endif /* COSMODIAGNOSTICS_HPP_ */

Examples/Inflation/InflationDiagnostics.impl.hpp → Examples/Cosmo/CosmoDiagnostics.impl.hpp

@@ -3,17 +3,17 @@
  * Please refer to LICENSE in GRChombo's root directory.
  */
 
-#if !defined(INFLATIONDIAGNOSTICS_HPP_)
-#error "This file should only be included through InflationDiagnostics.hpp"
+#if !defined(COSMODIAGNOSTICS_HPP_)
+#error "This file should only be included through CosmoDiagnostics.hpp"
 #endif
 
-#ifndef INFLATIONDIAGNOSTICS_IMPL_HPP_
-#define INFLATIONDIAGNOSTICS_IMPL_HPP_
+#ifndef COSMODIAGNOSTICS_IMPL_HPP_
+#define COSMODIAGNOSTICS_IMPL_HPP_
 #include "DimensionDefinitions.hpp"
 
 template <class matter_t>
 template <class data_t>
-void InflationDiagnostics<matter_t>::compute(Cell<data_t> current_cell) const
+void CosmoDiagnostics<matter_t>::compute(Cell<data_t> current_cell) const
 {
     // Load local vars and calculate derivs
     const auto vars = current_cell.template load_vars<Vars>();
@@ -53,4 +53,4 @@ void InflationDiagnostics<matter_t>::compute(Cell<data_t> current_cell) const
     // store_vars(out, current_cell);
 }
 
-#endif /* INFLATIONDIAGNOSTICS_IMPL_HPP_ */
+#endif /* COSMODIAGNOSTICS_IMPL_HPP_ */

Examples/Inflation/InflationLevel.cpp → Examples/Cosmo/CosmoLevel.cpp

@@ -4,7 +4,7 @@
  */
 
 // General includes common to most GR problems
-#include "InflationLevel.hpp"
+#include "CosmoLevel.hpp"
 #include "BoxLoops.hpp"
 #include "NanCheck.hpp"
 #include "PositiveChiAndAlpha.hpp"
@@ -23,9 +23,9 @@
 // Problem specific includes
 #include "AMRReductions.hpp"
 #include "ComputePack.hpp"
+#include "CosmoDiagnostics.hpp"
 #include "CosmoMovingPunctureGauge.hpp"
 #include "GammaCalculator.hpp"
-#include "InflationDiagnostics.hpp"
 #include "InitialK.hpp"
 #include "InitialScalarData.hpp"
 #include "Potential.hpp"
@@ -36,7 +36,7 @@
 #include "CustomExtraction.hpp"
 
 // Things to do at each advance step, after the RK4 is calculated
-void InflationLevel::specificAdvance()
+void CosmoLevel::specificAdvance()
 {
     // Enforce trace free A_ij and positive chi and alpha
     BoxLoops::loop(
@@ -52,11 +52,11 @@ void InflationLevel::specificAdvance()
 }
 
 // Initial data for field and metric variables
-void InflationLevel::initialData()
+void CosmoLevel::initialData()
 {
-    CH_TIME("InflationLevel::initialData");
+    CH_TIME("CosmoLevel::initialData");
     if (m_verbosity)
-        pout() << "InflationLevel::initialData " << m_level << endl;
+        pout() << "CosmoLevel::initialData " << m_level << endl;
 
     // First set everything to zero then initial conditions for scalar field -
     // Set initial condition of inflaton, see details in Potential.hpp and
@@ -82,7 +82,7 @@ void InflationLevel::initialData()
 
 #ifdef CH_USE_HDF5
 // Things to do before outputting a checkpoint file
-void InflationLevel::prePlotLevel()
+void CosmoLevel::prePlotLevel()
 {
     fillAllGhosts();
     Potential potential(m_p.potential_params, m_p.L, m_p.scalar_field_mode);
@@ -91,16 +91,16 @@ void InflationLevel::prePlotLevel()
         MatterConstraints<ScalarFieldWithPotential>(
             scalar_field, m_dx, m_p.G_Newton, c_Ham, Interval(c_Mom, c_Mom)),
         m_state_new, m_state_diagnostics, EXCLUDE_GHOST_CELLS);
-    InflationDiagnostics<ScalarFieldWithPotential> inflation_diagnostics(
+    CosmoDiagnostics<ScalarFieldWithPotential> cosmo_diagnostics(
         scalar_field, m_dx, m_p.G_Newton);
-    BoxLoops::loop(inflation_diagnostics, m_state_new, m_state_diagnostics,
+    BoxLoops::loop(cosmo_diagnostics, m_state_new, m_state_diagnostics,
                    EXCLUDE_GHOST_CELLS);
 }
 #endif
 
 // Things to do in RHS update, at each RK4 step
-void InflationLevel::specificEvalRHS(GRLevelData &a_soln, GRLevelData &a_rhs,
-                                     const double a_time)
+void CosmoLevel::specificEvalRHS(GRLevelData &a_soln, GRLevelData &a_rhs,
+                                 const double a_time)
 {
     // Enforce trace free A_ij and positive chi and alpha
     BoxLoops::loop(
@@ -132,28 +132,28 @@ void InflationLevel::specificEvalRHS(GRLevelData &a_soln, GRLevelData &a_rhs,
 }
 
 // Things to do at ODE update, after soln + rhs
-void InflationLevel::specificUpdateODE(GRLevelData &a_soln,
-                                       const GRLevelData &a_rhs, Real a_dt)
+void CosmoLevel::specificUpdateODE(GRLevelData &a_soln,
+                                   const GRLevelData &a_rhs, Real a_dt)
 {
     // Enforce trace free A_ij
     BoxLoops::loop(TraceARemoval(), a_soln, a_soln, INCLUDE_GHOST_CELLS);
 }
 
-void InflationLevel::preTagCells()
+void CosmoLevel::preTagCells()
 {
     // we don't need any ghosts filled for the fixed grids tagging criterion
     // used here so don't fill any
 }
 
-void InflationLevel::computeTaggingCriterion(
+void CosmoLevel::computeTaggingCriterion(
     FArrayBox &tagging_criterion, const FArrayBox &current_state,
     const FArrayBox &current_state_diagnostics)
 {
     BoxLoops::loop(
         FixedGridsTaggingCriterion(m_dx, m_level, 2.0 * m_p.L, m_p.center),
         current_state, tagging_criterion);
 }
-void InflationLevel::specificPostTimeStep()
+void CosmoLevel::specificPostTimeStep()
 {
     int min_level = 0;
     bool calculate_diagnostics = at_level_timestep_multiple(min_level);
@@ -173,9 +173,9 @@ void InflationLevel::specificPostTimeStep()
                            Interval(c_Mom, c_Mom), c_Ham_abs_sum,
                            Interval(c_Mom_abs_sum, c_Mom_abs_sum)),
                        m_state_new, m_state_diagnostics, EXCLUDE_GHOST_CELLS);
-        InflationDiagnostics<ScalarFieldWithPotential> inflation_diagnostics(
+        CosmoDiagnostics<ScalarFieldWithPotential> cosmo_diagnostics(
             scalar_field, m_dx, m_p.G_Newton);
-        BoxLoops::loop(inflation_diagnostics, m_state_new, m_state_diagnostics,
+        BoxLoops::loop(cosmo_diagnostics, m_state_new, m_state_diagnostics,
                        EXCLUDE_GHOST_CELLS);
 
         if (m_level == min_level)
@@ -227,7 +227,8 @@ void InflationLevel::specificPostTimeStep()
 
             // set up the query and execute it
             std::array<double, CH_SPACEDIM> extr_point = {
-                0., 0., 0.}; // specified point
+                0., m_p.L / 2, m_p.L / 2}; // specified point {x \in [0,L],y \in
+                                           // [0,L], z \in [0,L]}
             CustomExtraction extraction(c_rho, m_p.lineout_num_points, m_p.L,
                                         extr_point, m_dt, m_time);
             extraction.execute_query(&interpolator, m_p.data_path + "lineout");

Examples/Inflation/InflationLevel.hpp → Examples/Cosmo/CosmoLevel.hpp

@@ -23,9 +23,9 @@
    time symmetry assuming conformal flatness). \sa MatterCCZ4(),
    ConstraintsMatter(), ScalarField(), RelaxationChi()
 */
-class InflationLevel : public GRAMRLevel
+class CosmoLevel : public GRAMRLevel
 {
-    friend class DefaultLevelFactory<InflationLevel>;
+    friend class DefaultLevelFactory<CosmoLevel>;
     // Inherit the contructors from GRAMRLevel
     using GRAMRLevel::GRAMRLevel;
 
@@ -66,4 +66,4 @@ class InflationLevel : public GRAMRLevel
     virtual void specificPostTimeStep() override;
 };
 
-#endif /* INFLATIONLEVEL_HPP_ */
+#endif /* COSMOLEVEL_HPP_ */

Examples/Inflation/CustomExtraction.hpp → Examples/Cosmo/CustomExtraction.hpp

@@ -72,11 +72,11 @@ class CustomExtraction
         std::vector<double> interp_z(m_num_points);
 
         // Work out the coordinates
-        // go out along x-axis from m_origin to L/2
+        // go out along x-axis from m_origin to L
         for (int idx = 0; idx < m_num_points; ++idx)
         {
             interp_x[idx] =
-                m_origin[0] + (double(idx) / double(m_num_points) * 0.5 * m_L);
+                m_origin[0] + (double(idx) / double(m_num_points) * m_L);
             interp_y[idx] = m_origin[1];
             interp_z[idx] = m_origin[2];
         }

Examples/Inflation/GNUmakefile → Examples/Cosmo/GNUmakefile

@@ -8,7 +8,7 @@
 
 GRCHOMBO_SOURCE = ../../Source
 
-ebase := Main_Inflation
+ebase := Main_Cosmo
 
 LibNames := AMRTimeDependent AMRTools BoxTools
 

Examples/Inflation/Main_Inflation.cpp → Examples/Cosmo/Main_Cosmo.cpp

@@ -19,7 +19,7 @@
 #include "SimulationParameters.hpp"
 
 // Problem specific includes:
-#include "InflationLevel.hpp"
+#include "CosmoLevel.hpp"
 
 // Chombo namespace
 #include "UsingNamespace.H"
@@ -39,8 +39,8 @@ int runGRChombo(int argc, char *argv[])
     // (To simulate a different problem, define a new child of AMRLevel
     // and an associated LevelFactory)
     CosmoAMR cosmo_amr;
-    DefaultLevelFactory<InflationLevel> scalar_field_level_fact(cosmo_amr,
-                                                                sim_params);
+    DefaultLevelFactory<CosmoLevel> scalar_field_level_fact(cosmo_amr,
+                                                            sim_params);
     setupAMRObject(cosmo_amr, scalar_field_level_fact);
 
     // call this after amr object setup so grids known

Examples/Inflation/Potential.hpp → Examples/Cosmo/Potential.hpp

@@ -42,7 +42,7 @@ class Potential
 
         // The potential gradient at phi
         // m^2 phi
-        dVdphi = pow(m_params.scalar_mass, 2.0) * vars.phi;
+        dVdphi = pow(mass, 2.0) * vars.phi;
     }
 };
 

Examples/Inflation/params.txt → Examples/Cosmo/params.txt

@@ -8,17 +8,17 @@ verbosity = 0
 
 # location / naming of output files
 # output_path = "" # Main path for all files. Must exist!
-chk_prefix = Inflation_
-plot_prefix = Inflationp_
-# restart_file = Inflation_000000.3d.hdf5
+chk_prefix = Cosmo_
+plot_prefix = Cosmop_
+# restart_file = Cosmo_000000.3d.hdf5
 
 # HDF5files are written every dt = L/N*dt_multiplier*checkpoint_interval
-checkpoint_interval = 500
+checkpoint_interval = 1000
 # set to 0 to turn off plot files (except at t=0 and t=stop_time)
 # set to -1 to never ever print plotfiles
-plot_interval = 100
-num_plot_vars = 5
-plot_vars = chi phi rho_scaled S_scaled K_scaled
+plot_interval = 500
+num_plot_vars = 7
+plot_vars = chi phi rho_scaled S_scaled K_scaled Ham Mom
 
 # subpaths - specific directories for hdf5, pout, extraction data
 # (these are created at runtime)
@@ -50,7 +50,7 @@ scalar_mass = 1.0
 scalar_field_mode = 1.0
 
 # lineout params
-lineout_num_points = 20
+lineout_num_points = 10
 
 #################################################
 # Grid parameters
@@ -130,7 +130,7 @@ extrapolating_vars = phi Pi
 
 # dt will be dx*dt_multiplier on each grid level
 dt_multiplier = 0.5
-stop_time = 100.0
+stop_time = 100.
 # max_steps = 4
 
 # Spatial derivative order (only affects CCZ4 RHS)