update

mpp @ 20c09dfd

-Subproject commit 37c2aba31c73fc3f239a9a5a40b43d553f4d8e00
+Subproject commit 20c09dfd1f52ee0593c136ced501b1d54c78d524

src/electrophysiology/assemble/IElphyAssemble.cpp

@@ -8,6 +8,9 @@
 #include "CardiacInterpolation.hpp"
 #include "MCellModel.hpp"
 
+#include <fstream>
+#include <iostream>
+
 IElphyAssemble::IElphyAssemble(ElphyProblem &elphyProblem, int degree, int exactUpTo)
     : INonLinearTimeAssemble(), ICardiacAssemble("ElphyVTK"), problem(elphyProblem), degree(degree),
       disc(elphyProblem.GetMeshes(), degree, exactUpTo < 0 ? 2 * degree : exactUpTo, DomainPart, 1),
@@ -159,12 +162,40 @@ void IElphyAssemble::PlotExcitation() const {
 
 void IElphyAssemble::PlotActivation() const {
   if (problem.UpdateActivationTime == false) return;
-
+  //writeActivationTimeFile();
   auto &plot = mpp::plot("ActivationTime");
   plot.AddData("Activation", *activationTime);
   plot.PlotFile("ActivationTime");
 }
+void IElphyAssemble::writeActivationTimeFile() const {
+  string filename("data/AT.txt");
+  std::fstream file_out;
+  ExchangeBuffer B;
+  for (row r= (*activationTime).rows(); r != (*activationTime).rows_end(); ++r) {
+    if((*activationTime).find_procset(r()) == (*activationTime).procsets_end() || (*activationTime).find_procset(r()).master() == PPM->Proc()) {
+    //if((*activationTime).find_procset(r()).master()==PPM->Proc()) {
+    B.Send(0) << r() << (*activationTime)(r(), 0);
+    }
+  }
+  B.Communicate();
 
+  if (PPM->Master()) {
+    file_out.open(filename, std::ios_base::out);
+    if (!file_out.is_open()) {
+      std::cout << "failed to open " << filename << '\n';
+    } else {
+      for (int i = 0; i < PPM->Size(); i++) {
+        for (row r = (*activationTime).rows(); r != (*activationTime).rows_end(); ++r) {
+          Point p;
+          double actiTime;
+          B.Receive(i) >> p >> actiTime ;
+          file_out << p << " " <<actiTime << endl;
+        }
+      }
+    }
+  }
+
+}
 void IElphyAssemble::PrintActivationTime() const {
   auto &AT = *activationTime;
   if (problem.UpdateActivationTime) {

src/electrophysiology/assemble/IElphyAssemble.hpp

@@ -119,6 +119,8 @@ public:
 
   void PlotActivation() const;
 
+  void writeActivationTimeFile() const;
+
   void PlotPotential(Vector &V, const std::string &varname, int step) const;
 
   Vector &ActivationTime() const;

tools/solving/biventricleThesis.py

@@ -5,7 +5,7 @@ import shutil
 import mpp.python.mppy as mppy
 
 lList = [0,1,2,3]
-lList = [3]
+lList = [0]
 tList = [0,1,2,3]
 #start_dt=0.0001
 start_dt=0.0004
@@ -14,7 +14,7 @@ path='../../../data/biventricleTT/'
 pathToMakeFolders=path #'../'+path
 
 def moveActivationtime(l,j, expPath):
-    shutil.move('../../build/data/vtu/ActivationTime.pvtu', pathToMakeFolders+expPath+'AT_l'+str(l)+'j'+str(j)+'.vtu')
+    shutil.move('../../build/data/vtu/ActivationTime.vtu', pathToMakeFolders+expPath+'AT_l'+str(l)+'j'+str(j)+'.vtu')
     
         
 
@@ -45,7 +45,7 @@ if __name__=="__main__":
     #startExperiment(procs,startconf,pathExperiment,{"ElphyModelName": "TenTusscher"})
     
     pathExperiment="OnCells/SI0004/"
-    startExperiment(procs,startconf,pathExperiment,{"ElphyModelName": "TenTusscher","ElphyModel":"SemiImplicitOnCells"})
+    startExperiment(procs,startconf,pathExperiment,{"ElphyModelName": "TenTusscher","ElphyModel":"SemiImplicitOnCells","ParallelPlotting":0,"Compression":"ascii"})