clearer documentation of time step used in BD clas

salilab · Oct 16, 2017 · 96e914f · 96e914f
1 parent ac477b3
commit 96e914f
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Showing 3 changed files with 16 additions and 9 deletions.
diff --git a/modules/atom/include/BrownianDynamics.h b/modules/atom/include/BrownianDynamics.h
@@ -68,6 +68,10 @@ class SimulationParameters;
     If the skt (stochastic Runge Kutta) flag is true, the simulation is
     altered slightly to apply the SKT scheme.
 
+    _Time step_
+    The time step is always equal precisely to Simulater::get_maximum_time_step() 
+    when using either Simulator::simulate() or Optimizer::optimize()
+
     \see Diffusion
     \see RigidBodyDiffusion
   */
@@ -114,13 +118,13 @@ class IMPATOMEXPORT BrownianDynamics : public Simulator {
   /** Calls do_advance_chunk() to advance ps in chunks
 
    @param sc particles to simulate in this step
-   @param dt maximal step size in femtoseconds
+   @param dt_fs step size in femtoseconds
 
    @return the time step actually simulated (for this class,
-           it is always equal to the inut dt)
+           it is always equal to the input dt_fs)
   */
   virtual double do_step(const ParticleIndexes &sc,
-                         double dt) IMP_OVERRIDE;
+                         double dt_fs) IMP_OVERRIDE;
 
   virtual bool get_is_simulation_particle(ParticleIndex p) const
       IMP_OVERRIDE;

diff --git a/modules/atom/include/BrownianDynamicsTAMD.h b/modules/atom/include/BrownianDynamicsTAMD.h
@@ -62,6 +62,10 @@ class SimulationParameters;
     If the skt (stochastic runge kutta) flag is true, the simulation is
     altered slightly to apply the SKT scheme.
 
+    _Time step_
+    The time step is always equal precisely to Simulater::get_maximum_time_step() 
+    when using either Simulator::simulate() or Optimizer::optimize()
+
     \see Diffusion
     \see RigidBodyDiffusion
   */

diff --git a/modules/atom/src/BrownianDynamics.cpp b/modules/atom/src/BrownianDynamics.cpp
@@ -276,18 +276,17 @@ BrownianDynamics::reset_random_pool()
  */
 double
 BrownianDynamics::do_step
-(const ParticleIndexes &ps, double dt)
+(const ParticleIndexes &ps, double dt_fs)
 {
-  double dtfs(dt);
   double ikT = 1.0 / get_kt();
   get_scoring_function()->evaluate(true);
   //  Ek = 0.0; // DEBUG: monitor kinetic energy
   //  M = 0.0; // DEBUG: monitor kinetic energy
   const unsigned int chunk_size = 5000;
   for (unsigned int b = 0; b < ps.size(); b += chunk_size) {
     IMP_TASK_SHARED(
-        (dtfs, ikT, b), (ps),
-        do_advance_chunk(dtfs, ikT, ps, b,
+        (dt_fs, ikT, b), (ps),
+        do_advance_chunk(dt_fs, ikT, ps, b,
                          std::min<unsigned int>(b + chunk_size, ps.size()));
         , "brownian");
   }
@@ -302,10 +301,10 @@ BrownianDynamics::do_step
   if (srk_) {
     get_scoring_function()->evaluate(true);
     for (unsigned int i = 0; i < ps.size(); ++i) {
-      advance_coordinates_1(ps[i], i, dtfs, ikT);
+      advance_coordinates_1(ps[i], i, dt_fs, ikT);
     }
   }
-  return dt;
+  return dt_fs;
 }
 
 namespace {