From d95e70918f355617a957238a6ca81758cc9f575f Mon Sep 17 00:00:00 2001
From: Chichi Lalescu <chichilalescu@gmail.com>
Date: Fri, 7 Apr 2017 12:47:26 +0200
Subject: [PATCH] not tested --- put particle code in vorticity equation
---
bfps/NSVorticityEquation.py | 60 +++++++++++++++++++++++++++++++++++
setup.py | 62 +------------------------------------
2 files changed, 61 insertions(+), 61 deletions(-)
diff --git a/bfps/NSVorticityEquation.py b/bfps/NSVorticityEquation.py
index aa7ff11e..bac06e02 100644
--- a/bfps/NSVorticityEquation.py
+++ b/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
diff --git a/setup.py b/setup.py
index 8d4ae0f9..21acd263 100644
--- a/setup.py
+++ b/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:
--
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