add an option to output hdf5 more

frequently than output protobuf file +
little restructuring of Statistics for better
 readability by fragmenting update()
(update() still way too long)

data/npctransport.proto

@@ -139,7 +139,8 @@ message Configuration {
   optional int32 is_multiple_hdf5s=43;  // if true, output new hdf5 every output_statistics_interval_ns, 
                                         // then add a numeric suffix to hdf5 for each dump
                                         // e.g. output_1.pb.hdf5, output_2.pb.hdf5, etc. Default is only once in the end.
-  // n=43
+  optional int32 full_output_statistics_interval_factor=44 [default=1]; // if >1, output full output file every output_statistics_interval_ns*full_output_interval_factor 
+  // n=44
   }
 
 // if you add any parameters you must update automatic_parameters.cpp
@@ -269,7 +270,7 @@ message Assignment {
   optional int32 output_statistics_interval_frames=41 [default=100000]; // update interval of statistics file (including order params) in frames
   optional FloatAssignment temperature_k=42; // simulation temperature
   optional double output_npctransport_version=43; // a version number for npctransport by which to interpret output file that contains this assignment
-  optional int32 is_xyz_hist_stats=44 [default=1]; // whether to use an xyz histogram instead of zr histogram (= whether to project x and y to sqrt(x^2+y^2)
+  optional int32 is_xyz_hist_stats=44 [default=1]; // whether to use an xyz histogram instead of zr histogram (= whether to project x and y to sqrt(x^2+y^2); if so output ot HDF5 file
   optional double xyz_stats_crop_factor=49 [default=0.5]; // percentage of box to crop from each axis for xyz histogram (symmetrically). 
   optional double xyz_stats_voxel_size_a=50 [default=10.0]; // size of voxel in A for xyz histogram
   optional double xyz_stats_max_box_size_a=51 [default=2000.0]; // maximal size of box for xyz stats
@@ -280,7 +281,8 @@ message Assignment {
   optional int32 is_multiple_hdf5s=52;  // if true, output new hdf5 every output_statistics_interval_ns, 
                                         // then add a numeric suffix to hdf5 for each dump
                                         // e.g. output_1.pb.hdf5, output_2.pb.hdf5, etc. Default is only once in the end.
-  // n=52
+    optional int32 full_output_statistics_interval_factor=53 [default=1]; // if >1, output full output file every output_statistics_interval_ns*full_output_interval_factor 
+  // n=53
 }
 
 message Statistics {

include/SimulationData.h

@@ -65,6 +65,7 @@ class IMPNPCTRANSPORTEXPORT SimulationData : public Object {
   Parameter<double> statistics_fraction_;
   Parameter<int> statistics_interval_frames_;
   Parameter<int> output_statistics_interval_frames_;
+  Parameter<int> full_output_statistics_interval_factor_;
   Parameter<int> is_multiple_hdf5s_;
   Parameter<double> time_step_;
   Parameter<double> time_step_wave_factor_;
@@ -90,6 +91,9 @@ class IMPNPCTRANSPORTEXPORT SimulationData : public Object {
   int get_output_statistics_interval_frames() const
   { return output_statistics_interval_frames_; }
 
+  int get_full_output_statistics_interval_factor() const
+  { return full_output_statistics_interval_factor_; }
+
   // if true, hdf5s are generated every get_output_statistics_interval_frames() frames
   bool get_is_multiple_hdf5s()
   {

include/Statistics.h

@@ -228,6 +228,10 @@ class IMPNPCTRANSPORTEXPORT Statistics : public Object {
 
       @note this method is not const cause it may invoke e.g., energy evaluation
             though it does not substantially change anything in the state of the object
+      @note if configuration file full_output_statistics_interval_factor
+            is larger than 1, then full statistics are dumped every N calls
+            to update(), where N is the value of full_output_statistics_interval_factor,
+            and only the HDF5 file is updated at each call.
    */
   void update(const IMP::internal::SimpleTimer &timer,
               unsigned int nf_new = 1);
@@ -284,10 +288,18 @@ class IMPNPCTRANSPORTEXPORT Statistics : public Object {
 
   //! updates pStats with all statistics related to fgs, averaged over
   //! nf_new additional frames
+  //! @param zr_hist a grid on z / (x,y)-radial axis relevant only if not outputting xyz stats to hdf5
   void update_fg_stats( ::npctransport_proto::Statistics* pStats,
                         unsigned int nf_new,
-                        unsigned int zr_hist[4][3],
-                        RMF::HDF5::File hdf5_file);
+                        unsigned int zr_hist[4][3]);
+
+  //! updates pStats with all statistics related to floaters, averaged over
+  //! nf_new additional frames
+  //!
+  //! @return for historical reasons, returns a map of diffusion coefficients for each particle type
+  //! to be used in order params later on
+  std::map<IMP::core::ParticleType, double> update_floater_stats( ::npctransport_proto::Statistics* pStats,
+                        unsigned int nf_new);
 
 
 
@@ -335,6 +347,8 @@ class IMPNPCTRANSPORTEXPORT Statistics : public Object {
   void fill_in_zr_hist(unsigned int zr_hist[4][3],
                        ParticlesTemp ps) const;
 
+  void update_hdf5_statistics(); // output HDF5 statistics
+
 
  public:
   IMP_OBJECT_METHODS(Statistics);

src/SimulationData.cpp

@@ -172,6 +172,7 @@ void SimulationData::initialize(std::string prev_output_file,
   GET_VALUE(range);
   GET_VALUE(statistics_interval_frames);
   GET_VALUE_DEF(output_statistics_interval_frames,10000);
+  GET_VALUE_DEF(full_output_statistics_interval_factor, 1);
   GET_VALUE_DEF(is_multiple_hdf5s, false);
   GET_ASSIGNMENT(statistics_fraction);
   GET_VALUE(time_step);