not tested --- put particle code in vorticity equation

bfps/NSVorticityEquation.py

@@ -117,6 +117,50 @@ class NSVorticityEquation(_fluid_particle_base):
                 //endcpp
                 """
         return None
+    def add_particles(
+            self,
+            integration_steps = 2,
+            neighbours = 1,
+            smoothness = 1):
+        assert(integration_steps > 0 and integration_steps < 6)
+        self.parameters['tracers0_integration_steps'] = int(integration_steps)
+        self.parameters['tracers0_neighbours'] = int(neighbours)
+        self.parameters['tracers0_smoothness'] = int(smoothness)
+        self.parameters['tracers0_interpolator'] = 'spline'
+        self.particle_includes += """
+                #include "particles_system_builder.hpp"
+                #include "particles_output_hdf5.hpp"
+                """
+        ## initialize
+        self.particle_start += """
+            std::unique_ptr<abstract_particles_system<double>> ps = particles_system_builder(
+                    fs->cvorticity,             // (field object)
+                    fs->kk,                     // (kspace object, contains dkx, dky, dkz)
+                    tracers0_integration_steps, // to check coherency between parameters and hdf input file (nb rhs)
+                    nparticles,                 // to check coherency between parameters and hdf input file
+                    fname,                      // particles input filename
+                    "tracers0",                 // dataset name for initial input
+                    tracers0_neighbours,        // parameter (interpolation no neighbours)
+                    tracers0_smoothness,        // parameter
+                    MPI_COMM_WORLD);
+            particles_output_hdf5<double,3,3> particles_output_writer_mpi(MPI_COMM_WORLD, simname, nparticles);
+                    """
+        self.particle_loop += """
+                fs->compute_velocity(fs->cvorticity);
+                fs->cvelocity->ift();
+                ps->completeLoop(dt);
+                """
+        output_particles = """
+                particles_output_writer_mpi.save(ps->getParticlesPositions(),
+                                                 ps->getParticlesCurrentRhs(),
+                                                 ps->getParticlesIndexes(),
+                                                 ps->getLocalNbParticles(),
+                                                 iteration);
+                           """
+        self.fluid_output += output_particles
+        self.particle_end += 'ps.realease();\n'
+
+        return None
     def create_stat_output(
             self,
             dset_name,
@@ -517,6 +561,16 @@ class NSVorticityEquation(_fluid_particle_base):
                dest = 'dtfactor',
                default = 0.5,
                help = 'dt is computed as DTFACTOR / N')
+        parser.add_argument(
+                '--neighbours',
+                type = int,
+                dest = 'neighbours',
+                default = 1)
+        parser.add_argument(
+                '--smoothness',
+                type = int,
+                dest = 'smoothness',
+                default = 1)
         return None
     def prepare_launch(
             self,
@@ -566,6 +620,12 @@ class NSVorticityEquation(_fluid_particle_base):
             **kwargs):
         opt = self.prepare_launch(args = args)
         self.fill_up_fluid_code()
+        if opt.nparticles > 0:
+            self.name += '-particles'
+            self.add_particles(
+                integration_steps = 4,
+                neighbours = opt.neighbours,
+                smoothness = opt.smoothness)
         self.finalize_code()
         self.launch_jobs(opt = opt)
         return None

setup.py

@@ -133,67 +133,6 @@ libraries = ['fftw3_mpi',
              'fftw3f']
 libraries += extra_libraries
 
-
-
-def compile_bfps_library(
-        use_timingoutput = False,
-        extra_compile_args = None):
-    """
-        use_timingoutput sets the USE_TIMINGOUTPUT definition,
-        thus scope timers are being output.
-    """
-    if not os.path.isdir('obj'):
-        os.makedirs('obj')
-        need_to_compile = True
-    if not os.path.isfile('bfps/libbfps.a'):
-        need_to_compile = True
-    else:
-        ofile = 'bfps/libbfps.a'
-        libtime = datetime.datetime.fromtimestamp(os.path.getctime(ofile))
-        latest = libtime
-        for fname in header_list:
-            latest = max(latest,
-                         datetime.datetime.fromtimestamp(os.path.getctime('bfps/' + fname)))
-        need_to_compile = (latest > libtime)
-    if use_timingoutput:
-        extra_compile_args += ['-DUSE_TIMINGOUTPUT']
-    for fname in src_file_list:
-        ifile = 'bfps/cpp/' + fname + '.cpp'
-        ofile = 'obj/' + fname + '.o'
-        if not os.path.exists(ofile):
-            need_to_compile_file = True
-        else:
-            need_to_compile_file = (need_to_compile or
-                                    (datetime.datetime.fromtimestamp(os.path.getctime(ofile)) <
-                                     datetime.datetime.fromtimestamp(os.path.getctime(ifile))))
-        if need_to_compile_file:
-            command_strings = [compiler, '-c']
-            command_strings += ['bfps/cpp/' + fname + '.cpp']
-            command_strings += ['-o', 'obj/' + fname + '.o']
-            command_strings += extra_compile_args
-            command_strings += ['-I' + idir for idir in include_dirs]
-            command_strings.append('-Ibfps/cpp/')
-            print(' '.join(command_strings))
-            subprocess.check_call(command_strings)
-    command_strings = ['ar', 'rvs', 'bfps/libbfps.a']
-    command_strings += ['obj/' + fname + '.o' for fname in src_file_list]
-    print(' '.join(command_strings))
-    subprocess.check_call(command_strings)
-
-    ### save compiling information
-    pickle.dump(
-            {'include_dirs' : include_dirs,
-             'library_dirs' : library_dirs,
-             'compiler'     : compiler,
-             'extra_compile_args' : extra_compile_args,
-             'libraries' : libraries,
-             'install_date' : now,
-             'VERSION' : VERSION,
-             'git_revision' : git_revision},
-            open('bfps/install_info.pickle', 'wb'),
-            protocol = 2)
-    return None
-
 import distutils.cmd
 
 class CompileLibCommand(distutils.cmd.Command):
@@ -222,6 +161,7 @@ class CompileLibCommand(distutils.cmd.Command):
                              datetime.datetime.fromtimestamp(os.path.getctime('bfps/' + fname)))
             need_to_compile = (latest > libtime)
         eca = extra_compile_args
+        eca += ['-fPIC']
         if self.timing_output:
             eca += ['-DUSE_TIMINGOUTPUT']
         for fname in src_file_list: