From 944afb1d206be4967ae98c5fe411e7ff71796eb5 Mon Sep 17 00:00:00 2001
From: rockfool <rockfool10@gmail.com>
Date: Wed, 1 Apr 2020 17:06:44 -0400
Subject: [PATCH 1/6] fix a bug in timer reset

---
 include/openmc/capi.h | 1 +
 openmc/lib/core.py    | 3 +++
 src/finalize.cpp      | 6 ++++++
 3 files changed, 10 insertions(+)

diff --git a/include/openmc/capi.h b/include/openmc/capi.h
index 0c0f18bae..11c90ff3a 100644
--- a/include/openmc/capi.h
+++ b/include/openmc/capi.h
@@ -86,6 +86,7 @@ extern "C" {
   int openmc_id_map(const void* slice, int32_t* data_out);
   int openmc_property_map(const void* slice, double* data_out);
   int openmc_reset();
+  int openmc_reset_timers();
   int openmc_run();
   void openmc_set_seed(int64_t new_seed);
   int openmc_simulation_finalize();
diff --git a/openmc/lib/core.py b/openmc/lib/core.py
index 6a2a7cdea..61b8a6ed6 100644
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -63,6 +63,8 @@ _dll.openmc_run.restype = c_int
 _dll.openmc_run.errcheck = _error_handler
 _dll.openmc_reset.restype = c_int
 _dll.openmc_reset.errcheck = _error_handler
+_dll.openmc_reset_timers.restype = c_int
+_dll.openmc_reset_timers.errcheck = _error_handler
 _run_linsolver_argtypes = [_array_1d_dble, _array_1d_dble, _array_1d_dble,
                            c_double]
 _dll.openmc_run_linsolver.argtypes = _run_linsolver_argtypes
@@ -305,6 +307,7 @@ def plot_geometry():
 def reset():
     """Reset tallies and timers."""
     _dll.openmc_reset()
+    _dll.openmc_reset_timers()
 
 
 def run():
diff --git a/src/finalize.cpp b/src/finalize.cpp
index 74f02cc64..b5d5eb038 100644
--- a/src/finalize.cpp
+++ b/src/finalize.cpp
@@ -165,6 +165,12 @@ int openmc_reset()
   return 0;
 }
 
+int openmc_reset_timers()
+{
+  reset_timers();
+  return 0;
+}
+
 int openmc_hard_reset()
 {
   // Reset all tallies and timers

From e645acdfa1e44e0fac47531456125d1c7be75587 Mon Sep 17 00:00:00 2001
From: rockfool <rockfool10@gmail.com>
Date: Wed, 1 Apr 2020 23:03:02 -0400
Subject: [PATCH 2/6] add timer restart for C API

---
 include/openmc/capi.h  |  1 +
 include/openmc/timer.h |  2 ++
 openmc/lib/core.py     |  3 +++
 src/finalize.cpp       |  6 ++++++
 src/timer.cpp          | 22 ++++++++++++++++++++++
 5 files changed, 34 insertions(+)

diff --git a/include/openmc/capi.h b/include/openmc/capi.h
index 11c90ff3a..a2bab1e2c 100644
--- a/include/openmc/capi.h
+++ b/include/openmc/capi.h
@@ -87,6 +87,7 @@ extern "C" {
   int openmc_property_map(const void* slice, double* data_out);
   int openmc_reset();
   int openmc_reset_timers();
+  int openmc_restart_timers();
   int openmc_run();
   void openmc_set_seed(int64_t new_seed);
   int openmc_simulation_finalize();
diff --git a/include/openmc/timer.h b/include/openmc/timer.h
index cc20751a8..0ebbe0e8d 100644
--- a/include/openmc/timer.h
+++ b/include/openmc/timer.h
@@ -69,6 +69,8 @@ private:
 
 void reset_timers();
 
+void restart_timers();
+
 } // namespace openmc
 
 #endif // OPENMC_TIMER_H
diff --git a/openmc/lib/core.py b/openmc/lib/core.py
index 61b8a6ed6..a30341ed5 100644
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -65,6 +65,8 @@ _dll.openmc_reset.restype = c_int
 _dll.openmc_reset.errcheck = _error_handler
 _dll.openmc_reset_timers.restype = c_int
 _dll.openmc_reset_timers.errcheck = _error_handler
+_dll.openmc_restart_timers.restype = c_int
+_dll.openmc_restart_timers.errcheck = _error_handler
 _run_linsolver_argtypes = [_array_1d_dble, _array_1d_dble, _array_1d_dble,
                            c_double]
 _dll.openmc_run_linsolver.argtypes = _run_linsolver_argtypes
@@ -308,6 +310,7 @@ def reset():
     """Reset tallies and timers."""
     _dll.openmc_reset()
     _dll.openmc_reset_timers()
+    _dll.openmc_restart_timers()
 
 
 def run():
diff --git a/src/finalize.cpp b/src/finalize.cpp
index b5d5eb038..7d80b9fdf 100644
--- a/src/finalize.cpp
+++ b/src/finalize.cpp
@@ -171,6 +171,12 @@ int openmc_reset_timers()
   return 0;
 }
 
+int openmc_restart_timers()
+{
+  restart_timers();
+  return 0;
+}
+
 int openmc_hard_reset()
 {
   // Reset all tallies and timers
diff --git a/src/timer.cpp b/src/timer.cpp
index fdb10f0f2..449e2dce0 100644
--- a/src/timer.cpp
+++ b/src/timer.cpp
@@ -87,4 +87,26 @@ void reset_timers()
   simulation::time_event_death.reset();
 }
 
+void restart_timers()
+{
+  simulation::time_active.restart();
+  simulation::time_bank.restart();
+  simulation::time_bank_sample.restart();
+  simulation::time_bank_sendrecv.restart();
+  simulation::time_finalize.restart();
+  simulation::time_inactive.restart();
+  simulation::time_initialize.restart();
+  simulation::time_read_xs.restart();
+  simulation::time_sample_source.restart();
+  simulation::time_tallies.restart();
+  simulation::time_total.restart();
+  simulation::time_transport.restart();
+  simulation::time_event_init.restart();
+  simulation::time_event_calculate_xs.restart();
+  simulation::time_event_advance_particle.restart();
+  simulation::time_event_surface_crossing.restart();
+  simulation::time_event_collision.restart();
+  simulation::time_event_death.restart();
+}
+
 } // namespace openmc

From 65802068683f1f2b8ca4b6ca19399af815b5a962 Mon Sep 17 00:00:00 2001
From: rockfool <rockfool10@gmail.com>
Date: Wed, 1 Apr 2020 23:06:54 -0400
Subject: [PATCH 3/6] fix a bug in timer.cpp

---
 src/timer.cpp | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/timer.cpp b/src/timer.cpp
index 449e2dce0..71b85e33f 100644
--- a/src/timer.cpp
+++ b/src/timer.cpp
@@ -89,24 +89,24 @@ void reset_timers()
 
 void restart_timers()
 {
-  simulation::time_active.restart();
-  simulation::time_bank.restart();
-  simulation::time_bank_sample.restart();
-  simulation::time_bank_sendrecv.restart();
-  simulation::time_finalize.restart();
-  simulation::time_inactive.restart();
-  simulation::time_initialize.restart();
-  simulation::time_read_xs.restart();
-  simulation::time_sample_source.restart();
-  simulation::time_tallies.restart();
-  simulation::time_total.restart();
-  simulation::time_transport.restart();
-  simulation::time_event_init.restart();
-  simulation::time_event_calculate_xs.restart();
-  simulation::time_event_advance_particle.restart();
-  simulation::time_event_surface_crossing.restart();
-  simulation::time_event_collision.restart();
-  simulation::time_event_death.restart();
+  simulation::time_active.start();
+  simulation::time_bank.start();
+  simulation::time_bank_sample.start();
+  simulation::time_bank_sendrecv.start();
+  simulation::time_finalize.start();
+  simulation::time_inactive.start();
+  simulation::time_initialize.start();
+  simulation::time_read_xs.start();
+  simulation::time_sample_source.start();
+  simulation::time_tallies.start();
+  simulation::time_total.start();
+  simulation::time_transport.start();
+  simulation::time_event_init.start();
+  simulation::time_event_calculate_xs.start();
+  simulation::time_event_advance_particle.start();
+  simulation::time_event_surface_crossing.start();
+  simulation::time_event_collision.start();
+  simulation::time_event_death.start();
 }
 
 } // namespace openmc

From 296dc72b3b05f560424a1df52e324a406c9aeb9f Mon Sep 17 00:00:00 2001
From: rockfool <rockfool10@gmail.com>
Date: Fri, 3 Apr 2020 13:38:39 -0400
Subject: [PATCH 4/6] fix a bug in total timer

---
 openmc/deplete/operator.py |  1 +
 openmc/lib/core.py         |  6 +++++-
 src/timer.cpp              | 17 -----------------
 3 files changed, 6 insertions(+), 18 deletions(-)

diff --git a/openmc/deplete/operator.py b/openmc/deplete/operator.py
index 8eb033783..646a869e1 100644
--- a/openmc/deplete/operator.py
+++ b/openmc/deplete/operator.py
@@ -274,6 +274,7 @@ class Operator(TransportOperator):
         # Run OpenMC
         openmc.lib.reset()
         openmc.lib.run()
+        openmc.lib.reset_timers()
 
         # Extract results
         op_result = self._unpack_tallies_and_normalize(power)
diff --git a/openmc/lib/core.py b/openmc/lib/core.py
index a30341ed5..e2e5e73a9 100644
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -307,8 +307,12 @@ def plot_geometry():
 
 
 def reset():
-    """Reset tallies and timers."""
+    """Reset tallies but keep timers."""
     _dll.openmc_reset()
+
+
+def reset_timers():
+    """Reset timers and restart for next batch."""
     _dll.openmc_reset_timers()
     _dll.openmc_restart_timers()
 
diff --git a/src/timer.cpp b/src/timer.cpp
index 71b85e33f..454f77003 100644
--- a/src/timer.cpp
+++ b/src/timer.cpp
@@ -89,24 +89,7 @@ void reset_timers()
 
 void restart_timers()
 {
-  simulation::time_active.start();
-  simulation::time_bank.start();
-  simulation::time_bank_sample.start();
-  simulation::time_bank_sendrecv.start();
-  simulation::time_finalize.start();
-  simulation::time_inactive.start();
-  simulation::time_initialize.start();
-  simulation::time_read_xs.start();
-  simulation::time_sample_source.start();
-  simulation::time_tallies.start();
   simulation::time_total.start();
-  simulation::time_transport.start();
-  simulation::time_event_init.start();
-  simulation::time_event_calculate_xs.start();
-  simulation::time_event_advance_particle.start();
-  simulation::time_event_surface_crossing.start();
-  simulation::time_event_collision.start();
-  simulation::time_event_death.start();
 }
 
 } // namespace openmc

From 6d55a720f7309b7d317b9eec9fa4abad4a02668a Mon Sep 17 00:00:00 2001
From: rockfool <rockfool10@gmail.com>
Date: Mon, 6 Apr 2020 22:51:30 -0400
Subject: [PATCH 5/6] fix docstring for reset

---
 openmc/lib/core.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openmc/lib/core.py b/openmc/lib/core.py
index e2e5e73a9..8540f832b 100644
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -307,7 +307,7 @@ def plot_geometry():
 
 
 def reset():
-    """Reset tallies but keep timers."""
+    """Reset tally results"""
     _dll.openmc_reset()
 
 

From dd283875a8f8a6bd28ac376cb31ab7f662a39c73 Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Tue, 7 Apr 2020 13:49:10 -0500
Subject: [PATCH 6/6] Remove restart_timers and have openmc_init/run start/stop
 total timer

---
 include/openmc/capi.h  |  1 -
 include/openmc/timer.h |  2 --
 openmc/lib/core.py     |  5 +----
 src/finalize.cpp       |  6 ------
 src/initialize.cpp     |  1 +
 src/simulation.cpp     | 10 ++++++----
 src/timer.cpp          |  5 -----
 7 files changed, 8 insertions(+), 22 deletions(-)

diff --git a/include/openmc/capi.h b/include/openmc/capi.h
index a2bab1e2c..11c90ff3a 100644
--- a/include/openmc/capi.h
+++ b/include/openmc/capi.h
@@ -87,7 +87,6 @@ extern "C" {
   int openmc_property_map(const void* slice, double* data_out);
   int openmc_reset();
   int openmc_reset_timers();
-  int openmc_restart_timers();
   int openmc_run();
   void openmc_set_seed(int64_t new_seed);
   int openmc_simulation_finalize();
diff --git a/include/openmc/timer.h b/include/openmc/timer.h
index 0ebbe0e8d..cc20751a8 100644
--- a/include/openmc/timer.h
+++ b/include/openmc/timer.h
@@ -69,8 +69,6 @@ private:
 
 void reset_timers();
 
-void restart_timers();
-
 } // namespace openmc
 
 #endif // OPENMC_TIMER_H
diff --git a/openmc/lib/core.py b/openmc/lib/core.py
index 8540f832b..b9deed6b1 100644
--- a/openmc/lib/core.py
+++ b/openmc/lib/core.py
@@ -65,8 +65,6 @@ _dll.openmc_reset.restype = c_int
 _dll.openmc_reset.errcheck = _error_handler
 _dll.openmc_reset_timers.restype = c_int
 _dll.openmc_reset_timers.errcheck = _error_handler
-_dll.openmc_restart_timers.restype = c_int
-_dll.openmc_restart_timers.errcheck = _error_handler
 _run_linsolver_argtypes = [_array_1d_dble, _array_1d_dble, _array_1d_dble,
                            c_double]
 _dll.openmc_run_linsolver.argtypes = _run_linsolver_argtypes
@@ -312,9 +310,8 @@ def reset():
 
 
 def reset_timers():
-    """Reset timers and restart for next batch."""
+    """Reset timers."""
     _dll.openmc_reset_timers()
-    _dll.openmc_restart_timers()
 
 
 def run():
diff --git a/src/finalize.cpp b/src/finalize.cpp
index 7d80b9fdf..b5d5eb038 100644
--- a/src/finalize.cpp
+++ b/src/finalize.cpp
@@ -171,12 +171,6 @@ int openmc_reset_timers()
   return 0;
 }
 
-int openmc_restart_timers()
-{
-  restart_timers();
-  return 0;
-}
-
 int openmc_hard_reset()
 {
   // Reset all tallies and timers
diff --git a/src/initialize.cpp b/src/initialize.cpp
index 10d86ee80..3c2cc03ac 100644
--- a/src/initialize.cpp
+++ b/src/initialize.cpp
@@ -78,6 +78,7 @@ int openmc_init(int argc, char* argv[], const void* intracomm)
 
   // Stop initialization timer
   simulation::time_initialize.stop();
+  simulation::time_total.stop();
 
   return 0;
 }
diff --git a/src/simulation.cpp b/src/simulation.cpp
index 64a7d0e80..0a234e53f 100644
--- a/src/simulation.cpp
+++ b/src/simulation.cpp
@@ -47,6 +47,7 @@
 
 int openmc_run()
 {
+  openmc::simulation::time_total.start();
   openmc_simulation_init();
 
   int err = 0;
@@ -56,6 +57,7 @@ int openmc_run()
   }
 
   openmc_simulation_finalize();
+  openmc::simulation::time_total.stop();
   return err;
 }
 
@@ -422,8 +424,8 @@ void finalize_generation()
   }
   global_tally_leakage = 0.0;
 
-  if (settings::run_mode == RunMode::EIGENVALUE) {	
-    // If using shared memory, stable sort the fission bank (by parent IDs) 
+  if (settings::run_mode == RunMode::EIGENVALUE) {
+    // If using shared memory, stable sort the fission bank (by parent IDs)
     // so as to allow for reproducibility regardless of which order particles
     // are run in.
     sort_fission_bank();
@@ -525,7 +527,7 @@ void initialize_history_partial(Particle* p)
     p->flux_derivs_.resize(model::tally_derivs.size(), 0.0);
     std::fill(p->flux_derivs_.begin(), p->flux_derivs_.end(), 0.0);
   }
-  
+
   // Allocate space for tally filter matches
   p->filter_matches_.resize(model::tally_filters.size());
 }
@@ -669,7 +671,7 @@ void transport_event_based()
         process_collision_events();
       }
     }
-    
+
     // Execute death event for all particles
     process_death_events(n_particles);
 
diff --git a/src/timer.cpp b/src/timer.cpp
index 454f77003..fdb10f0f2 100644
--- a/src/timer.cpp
+++ b/src/timer.cpp
@@ -87,9 +87,4 @@ void reset_timers()
   simulation::time_event_death.reset();
 }
 
-void restart_timers()
-{
-  simulation::time_total.start();
-}
-
 } // namespace openmc