Merged in bopkth/ipic3d-klm (pull request #3)

Master

CMakeLists.txt

@@ -32,7 +32,7 @@ elseif (${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64") ## Xeon
      set(CMAKE_CXX_COMPILER "icpc")  
    endif()
    #set(CMAKE_CXX_FLAGS "-O3 -openmp -g -xHost -fno-exceptions -vec-report")
-   set(CMAKE_CXX_FLAGS  "-O3 ") # -DPRINTPCL for printing particle subcycles  -DNO_HDF5 to disable output
+   set(CMAKE_CXX_FLAGS  "-O3 -DNO_HDF5  -DPRINTPCL") # -DPRINTPCL for printing particle subcycles  -DNO_HDF5 to disable output
 else()
    set(CMAKE_CXX_FLAGS "-O3")
 endif()
@@ -52,13 +52,13 @@ endif()
 SITE_NAME(myhostname)
 if (${myhostname} MATCHES "(.*)pdc(.*)")
    set(HDF5_INCLUDE_DIRS /opt/cray/hdf5/1.8.7/cray/73/include)
-elseif(${myhostname} MATCHES "localhost")
-   set(CMAKE_CXX_COMPILER mpicc)  
-   set(CMAKE_CXX_FLAGS "-O2")
-   set(CMAKE_PREFIX_PATH /Users/Ivy/Software/install/hdf5-1.8.14/)
-   find_package(HDF5 COMPONENTS HL C )
-else()
-   find_package(HDF5 COMPONENTS HL C )   
+#elseif(${myhostname} MATCHES "localhost")
+#   set(CMAKE_CXX_COMPILER mpicc)  
+#   set(CMAKE_CXX_FLAGS "-O2")
+#   set(CMAKE_PREFIX_PATH /Users/Ivy/Software/install/hdf5-1.8.14/)
+#   find_package(HDF5 COMPONENTS HL C )
+#else()
+#    find_package(HDF5 COMPONENTS HL C )   
 endif()
 
 

inputfiles/testGEM2D_NoHDF5.inp

@@ -0,0 +1,152 @@
+ # Publications that use results from iPIC3D need to properly cite  
+ # 'S. Markidis, G. Lapenta, and Rizwan-uddin. "Multi-scale simulations of 
+ # plasma with iPIC3D." Mathematics and Computers in Simulation 80.7 (2010): 1509-1519.'
+ #
+ #        Copyright 2015 KTH Royal Institute of Technology
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at 
+ #
+ #         http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+
+SaveDirName = data
+RestartDirName = data
+
+# New flags:
+Case              = GEM       # Select the case
+PoissonCorrection = no       # Poisson correction
+WriteMethod       = pvtk
+SimulationName    = testGEM8p  # Simulation name for the output
+
+#  %%%%%%%%%%%%%%%%%%% Magnetic Reconnection %%%%%%%%%%%%%%%%%%
+B0x = 0.0195
+B0y = 0.0
+B0z = 0.0
+delta = 0.5
+
+
+#  %%%%%%%%%%%%%%%%%%% TIME %%%%%%%%%%%%%%%%%%
+dt = 0.15          # dt = time step   
+ncycles = 201    # cycles
+th = 1.0          # th =   decentering parameter
+c = 1.0
+
+#  %%%%%%%%%%%%%%%%%%% SMOOTH %%%%%%%%%%%%%%%%%%
+Smooth = 0.2      # Smoothing value (5-points stencil)
+
+Lx = 20   # Lx = simulation box length - x direction    
+Ly = 10  # Ly = simulation box length - y direction   
+Lz = 10   # Lz = simulation box length - z direction
+nxc = 240  # nxc = number of cells - x direction        
+nyc = 120  # nyc = number of cells - y direction 
+nzc = 1  # nzc = number of cells - z direction 
+
+# %%%%%%%%%%%%%% MPI TOPOLOGY %%%%%%%%%%%%%%
+# number of MPI subdomains in each direction
+XLEN = 6
+YLEN = 3
+ZLEN = 1
+# topology of subdomains in each dimension (1=true, 0=false)
+PERIODICX = 1
+PERIODICY = 0
+PERIODICZ = 1
+
+
+# %%%%%%%%%%%%%% PARTICLES %%%%%%%%%%%%%%%%%
+#    ns = number of species
+#    0 = electrons
+#    1 = protons
+#    ...
+ns = 4
+
+# qom = charge to mass ratio for different species */
+qom = -64.0 1.0 -64 1.0
+
+# Initial density (make sure that plasma is neutral)
+rhoINIT = 1.0 1.0 0.1 0.1
+rhoINJECT = 0.0 0.0 0.0 0.0
+
+# TrackParticleID[species] = 1=true, 0=false --> Assign ID to particles 
+TrackParticleID= 1 1 1 1 
+
+# uth = thermal velocity for different species - Direction X  */
+uth  = 0.045 0.0126 0.045 0.0126
+# vth = thermal velocity for different species - Direction Y */
+vth  = 0.045 0.0126 0.045 0.0126
+# wth = thermal velocity for different species - Direction Z */
+wth  = 0.045 0.0126 0.045 0.0126
+# u0 = drift velocity   - Direction X    */
+u0 = 0.0 0.0 0.0 0.0
+# v0 = drift velocity   - Direction Y    */
+v0 = 0.0 0.0 0.0 0.0
+# w0 = drift velocity   - Direction Z    */
+w0 = 0.0065 -0.0325 0.0 0.0 
+
+# npcelx = number of particles per cell - Direction X 
+npcelx = 3 3 3 3 
+# npcely = number of particles per cell - Direction Y */
+npcely = 3 3 3 3 
+# npcelz = number of particles per cell - Direction Z */
+npcelz = 3 3 3 3 
+
+# &&&&&&&&&&&& boundary conditions &&&&&&&&&&&&&&&
+# PHI Electrostatic Potential     
+# 0,1 = Dirichilet boundary condition      
+# 2   = Neumann boundary condition
+bcPHIfaceXright = 1
+bcPHIfaceXleft  = 1
+bcPHIfaceYright = 1
+bcPHIfaceYleft  = 1
+bcPHIfaceZright = 1
+bcPHIfaceZleft  = 1
+
+#    EM field boundary condition
+#    0 = perfect conductor
+#    1 = magnetic mirror
+
+    bcEMfaceXright = 0
+    bcEMfaceXleft =  0
+    bcEMfaceYright = 0
+    bcEMfaceYleft =  0
+    bcEMfaceZright = 0
+    bcEMfaceZleft =  0
+#    Particles Boundary condition
+#    0 = exit
+#    1 = perfect mirror
+#    2 = riemission
+#    Caveat: if your processor topology is set to be periodic in a direction automatically the boundary condition in that direction will be periodic*/
+    bcPfaceXright = 1
+    bcPfaceXleft =  1
+    bcPfaceYright = 1
+    bcPfaceYleft =  1
+    bcPfaceZright = 1
+    bcPfaceZleft =  1
+
+#  print to video results */
+    verbose = 1
+
+# velocity of the injection from the wall 
+    Vinj= 0.0
+
+# CG solver stopping criterium tolerance 
+   CGtol = 1E-3
+# GMRES solver stopping criterium tolerance 
+   GMREStol = 1E-3
+# mover predictor corrector iteration 
+   NiterMover  = 5
+# Output for field
+   FieldOutputCycle = 5
+   FieldOutputTag   = B+E+Je+Ji
+   MomentsOutputTag = rho+PXX+PXY+PXZ+PYY+PYZ+PZZ
+# Output for particles if 0 it doesnt save particles data
+   ParticlesOutputCycle = 0
+   ParticlesOutputTag = position+velocity+q
+# restart cycle
+   RestartOutputCycle = 0
+   CallFinalize=0

particles/Particles3D.cpp

@@ -647,14 +647,15 @@ void Particles3D::mover_PC_AoS(Field * EMf)
 	{
 	  convertParticlesToAoS();
 
-	  /*
+#ifdef PRINTPCL   
           #pragma omp master
 	  if (vct->getCartesian_rank() == 0) {
 		cout << "***AoS MOVER species " << ns << " *** Max." << NiterMover << " ITERATIONS   ****" << endl;
-	  }*/
-
+	  }
+	  int sum_innter = 0;
+#endif
 	  const_arr4_pfloat fieldForPcls = EMf->get_fieldForPcls();
-	  //int sum_innter = 0;
+
 
 	  const double dto2 = .5 * dt, qdto2mc = qom * dto2 / c;
 	  #pragma omp for schedule(static)
@@ -758,7 +759,7 @@ void Particles3D::mover_PC_AoS(Field * EMf)
 
 		}// end of iteration
 
-		//sum_innter +=innter;
+		sum_innter +=innter;
 
 		// update the final position and velocity
 		if(cap_velocity())
@@ -785,10 +786,12 @@ void Particles3D::mover_PC_AoS(Field * EMf)
 		pcl->set_v(2.0 * vavg - vorig);
 		pcl->set_w(2.0 * wavg - worig);
 	  }// END OF ALL THE PARTICLES
-	  /*
+
+#ifdef PRINTPCL  
 	  if (vct->getCartesian_rank() == 0) {
 		cout << "***AoS MOVER species " << ns << " *** Avg." << (double)sum_innter/((double)getNOP()) << " ITERATIONS   ****" << endl;
-	  }*/
+	  }
+#endif
 	}
 }
 

performances/Timing.cpp

@@ -25,7 +25,7 @@
 
 /**
  * 
- * series of methods for timing and profiling PARSEK 
+ * series of methods for timing and profiling
  * @date Fri Jun 4 2007
  * @author Stefano Markidis, Giovanni Lapenta
  * @version 2.0
@@ -76,17 +76,17 @@ void Timing::stopTiming() {
   if (rank_id == 0) {
     // replace %g with %11.3e?
     printf( "\n\n*** SIMULATION ENDED SUCESSFULLY ***\n"
-            " PARSEK Simulation Time: %g sec (%g hours)\n***\n\n",
+            " Simulation Time: %g sec (%g hours)\n***\n\n",
             texecution, texecution / 3600);
     //cout << endl;
     //cout << endl;
     //cout << "*** SIMULATION ENDED SUCESSFULLY ***" << endl;
-    //cout << " PARSEK Simulation Time: " << texecution << " sec" << " (" << texecution / 3600 << " hours)" << endl;
+    //cout << " Simulation Time: " << texecution << " sec" << " (" << texecution / 3600 << " hours)" << endl;
     //cout << "***" << endl;
     //cout << endl;
   }
   // close the log file
-  // MPE_Finish_log("PARSEK_LOG");
+  // MPE_Finish_log("iPIC3D_LOG");
 }
 
 /** start timing the mover */