Merge branch '344-probe-output' into 'master'

Resolve "Probe Output"

Closes #344

See merge request OPAL/src!161

src/Algorithms/ParallelCyclotronTracker.h

@@ -28,6 +28,7 @@
 #include "Steppers/Steppers.h"
 
 class DataSink;
+class PluginElement;
 
 template <class T, unsigned Dim>
 class PartBunchBase;
@@ -213,6 +214,8 @@ private:
     beamline_list FieldDimensions;
     std::list<Component *> myElements;
     Beamline *itsBeamline;
+    std::vector<PluginElement*> pluginElements_m;
+    std::vector<CavityCrossData> cavCrossDatas_m;
 
     DataSink *itsDataSink;
 
@@ -256,7 +259,7 @@ private:
 
     // for each bunch we have a path length
     double pathLength_m;
-
+    // Multi time step tracker
     void MtsTracker();
 
     void GenericTracker();
@@ -401,7 +404,6 @@ private:
     // Apply effects of RF Gap Crossings.
     // Unit assumptions: [itsBunch_m->R] = m, [itsBunch_m->P] = 1, [h] = s, [c] = m/s, [itsBunch_m->getT()] = s
     bool push(double h);
-
     // Kick particles for time h
     // The fields itsBunch_m->Bf, itsBunch_m->Ef are used to calculate the forces
     bool kick(double h);
@@ -413,7 +415,7 @@ private:
     // apply the plugin elements: probe, collimator, stripper, septum
     bool applyPluginElements(const double dt);
 
-    // destroy particles if they are marked as Bin=-1 in the plugin elements or out of global apeture
+    // destroy particles if they are marked as Bin=-1 in the plugin elements or out of global aperture
     bool deleteParticle(bool = false);
 
     void initTrackOrbitFile();
@@ -456,7 +458,11 @@ private:
 
     stepper::INTEGRATOR stepper_m;
 
-    void update_m(double& t, const double& dt, const bool& dumpEachTurn);
+    /// Check if turn done
+    bool isTurnDone();
+
+    /// Update time and path length, write to output files
+    void update_m(double& t, const double& dt, const bool& finishedTurn);
 
     /*!
      * @returns the time t [ns], time step dt [ns] and the azimuth angle [rad]
@@ -468,13 +474,13 @@ private:
                             dvector_t& Tdeltz,
                             ivector_t& TturnNumber);
 
-    void seoMode_m(double& t, const double dt, bool& dumpEachTurn,
+    void seoMode_m(double& t, const double dt, bool& finishedTurn,
                    dvector_t& Ttime, dvector_t& Tdeltr,
                    dvector_t& Tdeltz, ivector_t& TturnNumber);
 
-    void singleMode_m(double& t, const double dt, bool& dumpEachTurn, double& oldReferenceTheta);
+    void singleMode_m(double& t, const double dt, bool& finishedTurn, double& oldReferenceTheta);
 
-    void bunchMode_m(double& t, const double dt, bool& dumpEachTurn);
+    void bunchMode_m(double& t, const double dt, bool& finishedTurn);
 
     void gapCrossKick_m(size_t i, double t, double dt,
                         const Vector_t& Rold, const Vector_t& Pold);
@@ -490,7 +496,7 @@ private:
                                     const Vector_t& R,
                                     const Vector_t& P,
                                     const double& temp_meanTheta,
-                                    bool& dumpEachTurn);
+                                    bool& finishedTurn);
 
     void computeSpaceChargeFields_m();
 
@@ -520,7 +526,7 @@ private:
     void updateAzimuthAndRadius();
 
     /** multi-bunch mode: set the path length of each bunch in case of restart mode
-     * 
+     *
      * At creation of DataSink the lines are rewinded properly --> the last entry of
      * the path length is therefore the initial path length at restart.
      * @pre In order to work properly in restart mode, the lines in the multi-bunch

src/Classic/AbsBeamline/PluginElement.cpp

@@ -71,7 +71,7 @@ void PluginElement::setOutputFN(std::string fn) {
     filename_m = fn;
 }
 
-std::string PluginElement::getOutputFN() {
+std::string PluginElement::getOutputFN() const {
     if (filename_m == std::string(""))
         return getName();
     else
@@ -227,4 +227,16 @@ int PluginElement::checkPoint(const double &x, const double &y) const {
         }
     }
     return (cn & 1);  // 0 if even (out), and 1 if odd (in)
+}
+
+void PluginElement::save() {
+    Options::OPENMODE mode = Options::openMode;
+    if (numPassages_m > 0) {
+        Options::openMode = Options::APPEND;
+    }
+    lossDs_m->save();
+    if (numPassages_m > 0) {
+        Options::openMode = mode;
+    }
+    numPassages_m++;
 }
\ No newline at end of file

src/Classic/AbsBeamline/PluginElement.h

@@ -50,7 +50,7 @@ public:
     /// Set output filename
     void setOutputFN(std::string fn);
     /// Get output filename
-    std::string getOutputFN();
+    std::string getOutputFN() const;
 
     /// Set dimensions and consistency checks
     void setDimensions(double xstart, double xend, double ystart, double yend);
@@ -65,6 +65,8 @@ public:
     bool check(PartBunchBase<double, 3> *bunch, const int turnnumber, const double t, const double tstep);
     /// Checks if coordinate is within element
     int  checkPoint(const double & x, const double & y) const;
+    /// Save output
+    void save();
 
 protected:
     /// Sets geometry geom_m with element width dist
@@ -111,6 +113,7 @@ protected:
     double A_m, B_m, R_m, C_m; ///< Geometric lengths used in calculations
 
     std::unique_ptr<LossDataSink> lossDs_m;   ///< Pointer to Loss instance
+    int numPassages_m = 0; ///< Number of turns (number of times save() method is called)
 };
 
 #endif // CLASSIC_PluginElement_HH

src/Classic/Structure/LossDataSink.cpp

@@ -121,8 +121,6 @@ SetStatistics::SetStatistics():
     fac_m(0.0)
     { }
 
-extern Inform *gmsg;
-
 LossDataSink::LossDataSink(std::string elem, bool hdf5Save, ElementBase::ElementType type):
     h5hut_mode_m(hdf5Save),
     H5file_m(0),
@@ -278,11 +276,11 @@ void LossDataSink::save(unsigned int numSets) {
         fn_m = element_m + std::string(".loss");
         INFOMSG(level2 << "Save " << fn_m << endl);
         if (Options::openMode == Options::WRITE || !fs::exists(fn_m)) {
-            appendASCII();
-        } else {
             openASCII();
+            writeHeaderASCII();
+        } else {
+            appendASCII();
         }
-        writeHeaderASCII();
         saveASCII();
         closeASCII();
     }
@@ -329,10 +327,6 @@ bool LossDataSink::hasTimeAttribute() {
     return tLoc > 0;
 }
 
-
-
-
-
 void LossDataSink::saveH5(unsigned int setIdx) {
     size_t startIdx = 0;
     size_t nLoc = x_m.size();
@@ -390,36 +384,27 @@ void LossDataSink::saveASCII() {
       ASCII output
     */
     int tag = Ippl::Comm->next_tag(IPPL_APP_TAG3, IPPL_APP_CYCLE);
+    bool hasTime = hasTimeAttribute(); // reduce needed for the case when node 0 has no particles
     if(Ippl::Comm->myNode() == 0) {
         const unsigned partCount = x_m.size();
 
-        if (time_m.size() != 0) {
-            for(unsigned i = 0; i < partCount; i++) {
-                os_m << element_m   << "   ";
-                os_m << x_m[i] << "   ";
-                os_m << y_m[i] << "   ";
-                os_m << z_m[i] << "   ";
-                os_m << px_m[i] << "   ";
-                os_m << py_m[i] << "   ";
-                os_m << pz_m[i] << "   ";
-                os_m << id_m[i]   << "   ";
+        for(unsigned i = 0; i < partCount; i++) {
+            os_m << element_m   << "   ";
+            os_m << x_m[i] << "   ";
+            os_m << y_m[i] << "   ";
+            os_m << z_m[i] << "   ";
+            os_m << px_m[i] << "   ";
+            os_m << py_m[i] << "   ";
+            os_m << pz_m[i] << "   ";
+            os_m << id_m[i]   << "   ";
+            if (hasTime) {
                 os_m << turn_m[i] << "   ";
                 os_m << bunchNum_m[i] << "   ";
-                os_m << time_m[i] << " " << std::endl;
-            }
-        }
-        else {
-            for(unsigned i = 0; i < partCount; i++) {
-                os_m << element_m   << "   ";
-                os_m << x_m[i] << "   ";
-                os_m << y_m[i] << "   ";
-                os_m << z_m[i] << "   ";
-                os_m << px_m[i] << "   ";
-                os_m << py_m[i] << "   ";
-                os_m << pz_m[i] << "   ";
-                os_m << id_m[i]   << "   " << std::endl;
+                os_m << time_m[i];
             }
+            os_m << std::endl;
         }
+
         int notReceived =  Ippl::getNodes() - 1;
         while(notReceived > 0) {
             unsigned dataBlocks = 0;
@@ -430,51 +415,36 @@ void LossDataSink::saveASCII() {
             }
             notReceived--;
             rmsg->get(&dataBlocks);
-            if (time_m.size() != 0) {
-                for(unsigned i = 0; i < dataBlocks; i++) {
-                    long id, turn;
-                    double rx, ry, rz, px, py, pz, time;
-                    rmsg->get(&id);
-                    rmsg->get(&rx);
-                    rmsg->get(&ry);
-                    rmsg->get(&rz);
-                    rmsg->get(&px);
-                    rmsg->get(&py);
-                    rmsg->get(&pz);
+            for(unsigned i = 0; i < dataBlocks; i++) {
+                long id;
+                size_t bunchNum, turn;
+                double rx, ry, rz, px, py, pz, time;
+                rmsg->get(&id);
+                rmsg->get(&rx);
+                rmsg->get(&ry);
+                rmsg->get(&rz);
+                rmsg->get(&px);
+                rmsg->get(&py);
+                rmsg->get(&pz);
+                if (hasTime) {
                     rmsg->get(&turn);
+                    rmsg->get(&bunchNum);
                     rmsg->get(&time);
-                    os_m << element_m << "   ";
-                    os_m << rx << "   ";
-                    os_m << ry << "   ";
-                    os_m << rz << "   ";
-                    os_m << px << "   ";
-                    os_m << py << "   ";
-                    os_m << pz << "   ";
-                    os_m << id << "   ";
-                    os_m << turn << "   ";
-                    os_m << time << std::endl;
                 }
-            }
-            else {
-                for(unsigned i = 0; i < dataBlocks; i++) {
-                    long id;
-                    double rx, ry, rz, px, py, pz;
-                    rmsg->get(&id);
-                    rmsg->get(&rx);
-                    rmsg->get(&ry);
-                    rmsg->get(&rz);
-                    rmsg->get(&px);
-                    rmsg->get(&py);
-                    rmsg->get(&pz);
-                    os_m << element_m << "   ";
-                    os_m << rx << "   ";
-                    os_m << ry << "   ";
-                    os_m << rz << "   ";
-                    os_m << px << "   ";
-                    os_m << py << "   ";
-                    os_m << pz << "   ";
-                    os_m << id << " " << std::endl;
+                os_m << element_m << "   ";
+                os_m << rx << "   ";
+                os_m << ry << "   ";
+                os_m << rz << "   ";
+                os_m << px << "   ";
+                os_m << py << "   ";
+                os_m << pz << "   ";
+                os_m << id << "   ";
+                if (hasTime) {
+                    os_m << turn << "   ";
+                    os_m << bunchNum << "   ";
+                    os_m << time;
                 }
+                os_m << std::endl;
             }
             delete rmsg;
         }
@@ -482,31 +452,20 @@ void LossDataSink::saveASCII() {
         Message *smsg = new Message();
         const unsigned msgsize = x_m.size();
         smsg->put(msgsize);
-        if (time_m.size() != 0) {
-            for(unsigned i = 0; i < msgsize; i++) {
-                smsg->put(id_m[i]);
-                smsg->put(x_m[i]);
-                smsg->put(y_m[i]);
-                smsg->put(z_m[i]);
-                smsg->put(px_m[i]);
-                smsg->put(py_m[i]);
-                smsg->put(pz_m[i]);
+        for(unsigned i = 0; i < msgsize; i++) {
+            smsg->put(id_m[i]);
+            smsg->put(x_m[i]);
+            smsg->put(y_m[i]);
+            smsg->put(z_m[i]);
+            smsg->put(px_m[i]);
+            smsg->put(py_m[i]);
+            smsg->put(pz_m[i]);
+            if (hasTime) {
                 smsg->put(turn_m[i]);
                 smsg->put(bunchNum_m[i]);
                 smsg->put(time_m[i]);
             }
         }
-        else {
-            for(unsigned i = 0; i < msgsize; i++) {
-                smsg->put(id_m[i]);
-                smsg->put(x_m[i]);
-                smsg->put(y_m[i]);
-                smsg->put(z_m[i]);
-                smsg->put(px_m[i]);
-                smsg->put(py_m[i]);
-                smsg->put(pz_m[i]);
-            }
-        }
         bool res = Ippl::Comm->send(smsg, 0, tag);
         if(! res)
             ERRORMSG("LossDataSink Ippl::Comm->send(smsg, 0, tag) failed " << endl;);

src/Classic/Structure/LossDataSink.h

@@ -86,8 +86,6 @@ class LossDataSink {
 
     std::set<SetStatistics> computeStatistics(unsigned int numSets);
 
-    // static void writeStatistics();
-
 private:
     void openASCII() {
         if(Ippl::myNode() == 0) {
@@ -106,7 +104,7 @@ private:
         if(Ippl::myNode() == 0) {
             os_m << "# Element " << element_m << " x (mm),  y (mm),  z (mm),  px ( ),  py ( ),  pz ( ), id";
             if (time_m.size() != 0) {
-                os_m << ",  turn,  time (ns) ";
+                os_m << ",  turn, bunchNumber, time (ns) ";
             }
             os_m << std::endl;
         }