Changeset fdd121

Timestamp:

Nov 5, 2017, 1:55:28 AM (8 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

ForceAnnealing_with_BondGraph_continued_betteresults

Children:

d79ef32

Parents:

5b6afad

git-author:

Frederik Heber <frederik.heber@…> (05/24/17 09:55:56)

git-committer:

Frederik Heber <frederik.heber@…> (11/05/17 01:55:28)

Message:

Added damping-factor as another option to ForceAnnealing for proper testing of bond graph change effectiveness.

Files:

• src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) (1 diff)
• src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) (1 diff)
• src/Dynamics/ForceAnnealing.hpp (modified) (1 diff)
• tests/Python/AllActions/options.dat (modified) (1 diff)

src/Actions/MoleculeAction/ForceAnnealingAction.cpp

@@ -94 +94 @@
       true,
       params.steps.get(),
-      params.MaxDistance.get());
+      params.MaxDistance.get(),
+      params.DampingFactor.get());
   // parse forces into next step
   if (!params.forcesfile.get().string().empty()) {

src/Actions/MoleculeAction/ForceAnnealingAction.def

@@ -12 +12 @@
 #include "Parameters/Validators/GenericValidators.hpp"
 #include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/RangeValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (boost::filesystem::path)(unsigned int)(bool)(int)
-#define paramtokens ("forces-file")("steps")("output-every-step")("max-distance")
-#define paramdescriptions ("file containing")("fixed number of optimization steps to be performed")("whether WorldTime should be increased and output written after every step, useful if optimization might hang")("maximum distance to which bond graph is taken into account")
-#define paramdefaults (PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(PARAM_DEFAULT("0"))(PARAM_DEFAULT(0))
-#define paramreferences (forcesfile)(steps)(DoOutput)(MaxDistance)
+#define paramtypes (boost::filesystem::path)(unsigned int)(bool)(int)(double)
+#define paramtokens ("forces-file")("steps")("output-every-step")("max-distance")("damping-factor")
+#define paramdescriptions ("file containing")("fixed number of optimization steps to be performed")("whether WorldTime should be increased and output written after every step, useful if optimization might hang")("maximum distance to which bond graph is taken into account")("damping factor for decreasing the shift with bond graph distance from the causing site")
+#define paramdefaults (PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(PARAM_DEFAULT("0"))(PARAM_DEFAULT(0))(PARAM_DEFAULT(0.5))
+#define paramreferences (forcesfile)(steps)(DoOutput)(MaxDistance)(DampingFactor)
 #define paramvalids \
 (DummyValidator< boost::filesystem::path >()) \
 (NotZeroValidator< unsigned int >()) \
 (DummyValidator<bool>()) \
-(DummyValidator< int >())
+(DummyValidator< int >()) \
+(RangeValidator< double >(0,1))
 
 #define statetypes (std::vector<AtomicInfo>)(std::vector<AtomicInfo>)

src/Dynamics/ForceAnnealing.hpp

@@ -62 +62 @@
       bool _IsAngstroem,
       const size_t _maxSteps,
-      const int _max_distance) :
+      const int _max_distance,
+      const double _damping_factor) :
     AtomicForceManipulator<T>(_atoms, 1., _IsAngstroem),
     maxSteps(_maxSteps),
     max_distance(_max_distance),
-    damping_factor(0.5)
+    damping_factor(_damping_factor)
   {}
   /** Destructor of class ForceAnnealing.

tests/Python/AllActions/options.dat

@@ -49 +49 @@
 count   "12"
 create-micelle  "200"
+damping-factor  "0.5"
 default-molname "molname"
 deltat  "0.01"