Merge pull request #416 from kirichoi/start_time

Proposed solution to Issue #411
sys-bio · Sep 30, 2017 · e8b5b72 · e8b5b72
2 parents 1554ef3 + 300de2d
commit e8b5b72
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Showing 2 changed files with 18 additions and 12 deletions.
diff --git a/source/rrRoadRunner.cpp b/source/rrRoadRunner.cpp
@@ -989,8 +989,10 @@ bool RoadRunner::clearModel()
 
 void RoadRunner::reset()
 {
-    uint opt = rr::Config::getInt(rr::Config::MODEL_RESET);
-    reset(opt);
+    uint opt1 = rr::Config::getInt(rr::Config::MODEL_RESET);
+    reset(opt1);
+    uint opt2 = rr::SelectionRecord::DEPENDENT_INITIAL_GLOBAL_PARAMETER;
+    reset(opt2);
 }
 
 void RoadRunner::reset(int options)
@@ -1332,8 +1334,8 @@ const DoubleMatrix* RoadRunner::simulate(const Dictionary* dict)
 
     applySimulateOptions();
 
-    const double timeEnd = self.simulateOpt.duration + self.simulateOpt.start;
-    const double timeStart = self.simulateOpt.start;
+    const double timeEnd = self.simulateOpt.duration;
+    const double timeStart = 0;
 
     // evalute the model with its current state
     self.model->getStateVectorRate(timeStart, 0, 0);
@@ -1563,6 +1565,12 @@ const DoubleMatrix* RoadRunner::simulate(const Dictionary* dict)
 
     Log(Logger::LOG_DEBUG) << "Simulation done..";
 
+    for (int i = 0; i < self.simulationResult.numRows(); i++) {
+        self.simulationResult[i][getTimeRowIndex()] = self.simulationResult[i][getTimeRowIndex()] + self.simulateOpt.start;
+    }
+
+    Log(Logger::LOG_DEBUG) << "Added delta T.";
+
     return &self.simulationResult;
 }
 
@@ -4049,10 +4057,9 @@ void RoadRunner::applySimulateOptions()
 {
     get_self();
 
-    if (self.simulateOpt.duration < 0 || self.simulateOpt.start < 0
-            || self.simulateOpt.steps < 0 )
+    if (self.simulateOpt.duration < 0  || self.simulateOpt.steps < 0 )
     {
-        throw std::invalid_argument("duration, startTime and steps must be non-negative");
+        throw std::invalid_argument("duration and steps must be non-negative");
     }
 
     // This one creates the list of what we will look at in the result

diff --git a/wrappers/C/Testing/Suite_TestModel.cpp b/wrappers/C/Testing/Suite_TestModel.cpp
@@ -1159,9 +1159,9 @@ SUITE(TEST_MODEL)
         clog << endl << "  simulate with " << opt.start << ", " << opt.duration << ", " << opt.steps << "\n";
         const DoubleMatrix *rk4 = rri->simulate(&opt);
 
-        for (int i = 0; i < cvode[-1].size(); i++)
+        for (int k = 0; k < cvode->CSize(); k++)
         {
-            CHECK_CLOSE(*cvode[-1][i], *rk4[-1][i], 1e-6);
+            CHECK_CLOSE((*cvode)(cvode->RSize() - 1, k), (*rk4)(rk4->RSize() - 1, k), 1e-6);
         }
     }
 
@@ -1191,9 +1191,8 @@ SUITE(TEST_MODEL)
         clog << endl << "  simulate with " << opt.start << ", " << opt.duration << ", " << opt.steps << "\n";
         const DoubleMatrix *rk45 = rri->simulate(&opt);
 
-        for (int i = 0; i < cvode[-1].size(); i++)
-        {
-            CHECK_CLOSE(*cvode[-1][i], *rk45[-1][i], 1e-6);
+        for (int k = 0; k < cvode->CSize(); k++){
+            CHECK_CLOSE((*cvode)(cvode->RSize() - 1, k), (*rk45)(rk45->RSize() - 1, k), 1e-6);
         }
     }