Merge branch 'feature/executable' into develop

bfps/Launcher.py

+import os
+
+import sys
+import numpy as np
+import bfps
+
+class Launcher:
+    def __init__(
+            self,
+            data_dir = './'):
+        self.parser = bfps.get_parser(
+                bfps.NavierStokes,
+                work_dir = os.path.realpath(data_dir))
+        self.parser.add_argument(
+                '--QR-stats',
+                action = 'store_true',
+                dest = 'QR_stats')
+        self.parser.add_argument(
+                '--kMeta',
+                type = float,
+                dest = 'kMeta',
+                default = 2.0)
+        self.parser.add_argument(
+                '--dtfactor',
+                type = float,
+                dest = 'dtfactor',
+                default = 0.5,
+                help = 'dt is computed as DTFACTOR / N')
+        self.parser.add_argument(
+                '--environment',
+                type = str,
+                dest = 'environment',
+                default = '')
+        self.parser.add_argument(
+                '--src-simname',
+                type = str,
+                dest = 'src_simname',
+                default = '')
+        self.parser.add_argument(
+                '--src-iteration',
+                type = int,
+                dest = 'src_iteration',
+                default = 0)
+        self.data_dir = data_dir
+        self.base_class = bfps.NavierStokes
+        return None
+    def __call__(
+            self,
+            args = None):
+        opt = self.parser.parse_args(args)
+        if opt.environment != '':
+            bfps.host_info['environment'] = opt.environment
+        opt.nx = opt.n
+        opt.ny = opt.n
+        opt.nz = opt.n
+        opt.work_dir = os.path.join(
+                os.path.realpath(opt.work_dir),
+                'N{0:0>4}'.format(opt.n))
+        c = self.base_class(
+                fluid_precision = opt.precision,
+                simname = opt.simname,
+                QR_stats_on = opt.QR_stats)
+        c.pars_from_namespace(opt)
+        # with the default Lundgren forcing, I can estimate the dissipation
+        # with nondefault forcing, figure out the amplitude for this viscosity
+        # yourself
+        c.parameters['nu'] = (opt.kMeta * 2 / opt.n)**(4./3)
+        c.parameters['dt'] = (opt.dtfactor / opt.n)
+        if ((c.parameters['niter_todo'] % c.parameters['niter_out']) != 0):
+            c.parameters['niter_out'] = c.parameters['niter_todo']
+        if c.QR_stats_on:
+            # max_Q_estimate and max_R_estimate are just used for the 2D pdf
+            # therefore I just want them to be small multiples of mean trS2
+            # I'm already estimating the dissipation with kMeta...
+            meantrS2 = (opt.n//2 / opt.kMeta)**4 * c.parameters['nu']**2
+            c.parameters['max_Q_estimate'] = meantrS2
+            c.parameters['max_R_estimate'] = .4*meantrS2**1.5
+        c.fill_up_fluid_code()
+        c.finalize_code()
+        c.write_src()
+        c.set_host_info(bfps.host_info)
+        if opt.run:
+            if not os.path.exists(os.path.join(c.work_dir, c.simname + '.h5')):
+                c.write_par()
+                if c.parameters['nparticles'] > 0:
+                    if opt.particle_rand_seed != 0:
+                        rseed = opt.particle_rand_seed
+                    else:
+                        rseed = None
+                    data = c.generate_tracer_state(species = 0, rseed = rseed)
+                    for s in range(1, c.particle_species):
+                        c.generate_tracer_state(species = s, data = data)
+                init_condition_file = os.path.join(
+                        c.work_dir,
+                        c.simname + '_cvorticity_i{0:0>5x}'.format(0))
+                if not os.path.exists(init_condition_file):
+                    if len(opt.src_simname) > 0:
+                        src_file = os.path.join(
+                                c.work_dir,
+                                opt.src_simname + '_cvorticity_i{0:0>5x}'.format(opt.src_iteration))
+                        os.symlink(src_file, init_condition_file)
+                    else:
+                       c.generate_vector_field(
+                               write_to_file = True,
+                               spectra_slope = 2.0,
+                               amplitude = 0.25)
+            c.run(ncpu = opt.ncpu,
+                  njobs = opt.njobs)
+        return c
+
+

bfps/NavierStokes.py

@@ -579,10 +579,14 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
         self.particle_stat_src += '}\n'
         self.particle_species += nspecies
         return None
+    def get_data_file_name(self):
+        return os.path.join(self.work_dir, self.simname + '.h5')
     def get_data_file(self):
-        return h5py.File(os.path.join(self.work_dir, self.simname + '.h5'), 'r')
+        return h5py.File(self.get_data_file_name(), 'r')
     def get_postprocess_file_name(self):
         return os.path.join(self.work_dir, self.simname + '_postprocess.h5')
+    def get_postprocess_file(self):
+        return h5py.File(self.get_postprocess_file_name(), 'r')
     def compute_statistics(self, iter0 = 0, iter1 = None):
         if len(list(self.statistics.keys())) > 0:
             return None

bfps/__init__.py

@@ -25,7 +25,7 @@
 
 
 import os
-import subprocess
+import sys
 import pickle
 
 import pkg_resources
@@ -43,6 +43,11 @@ install_info = pickle.load(
                           'install_info.pickle'),
              'rb'))
 
+homefolder = os.path.expanduser('~')
+bfpsfolder = os.path.join(homefolder, '.config/', 'bfps')
+sys.path.append(bfpsfolder)
+from host_information import host_info
+
 from .code import code
 from .fluid_converter import fluid_converter
 from .fluid_resize import fluid_resize

bfps/__main__.py

+import sys
+from .Launcher import Launcher
+
+def main():
+    l = Launcher()
+    l(sys.argv[1:] + ['--run'])
+    return None
+
+if __name__ == '__main__':
+    main()
+

bfps/fluid_base.py

@@ -71,9 +71,9 @@ class fluid_particle_base(bfps.code):
         self.parameters['nparticles'] = 0
         self.parameters['dt'] = 0.01
         self.parameters['nu'] = 0.1
-        self.parameters['famplitude'] = 1.0
         self.parameters['fmode'] = 1
-        self.parameters['fk0'] = 0.0
+        self.parameters['famplitude'] = 0.5
+        self.parameters['fk0'] = 1.5
         self.parameters['fk1'] = 3.0
         self.parameters['forcing_type'] = 'linear'
         self.parameters['histogram_bins'] = 256

setup.py

@@ -44,6 +44,13 @@ if not os.path.exists(os.path.join(bfpsfolder, 'machine_settings.py')):
     if not os.path.isdir(bfpsfolder):
         os.mkdir(bfpsfolder)
     shutil.copyfile('./machine_settings_py.py', os.path.join(bfpsfolder, 'machine_settings.py'))
+# check if .config/bfps/host_information.py file exists, create it if not
+if not os.path.exists(os.path.join(bfpsfolder, 'host_information.py')):
+    if not os.path.isdir(bfpsfolder):
+        os.mkdir(bfpsfolder)
+    open(os.path.join(bfpsfolder, 'host_information.py'),
+         'w').write('host_info = {\'type\' : \'none\'}\n')
+    shutil.copyfile('./machine_settings_py.py', os.path.join(bfpsfolder, 'machine_settings.py'))
 sys.path.append(bfpsfolder)
 # import stuff required for compilation of static library
 from machine_settings import include_dirs, library_dirs, extra_compile_args, extra_libraries
@@ -190,6 +197,10 @@ setup(
         cmdclass={'build' : CustomBuild},
         package_data = {'bfps': header_list + ['libbfps.a',
                                                'install_info.pickle']},
+        entry_points = {
+            'console_scripts': [
+                'bfps = bfps.__main__:main'],
+            },
         version = VERSION,
 ########################################################################
 # useless stuff folows