From a2b474e05ae5444dc11567f78b548effc136b259 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Mon, 4 Feb 2019 09:44:55 +0100
Subject: [PATCH] checkpoint
---
bfps/DNS.py | 107 +++++++++++++++---------------
bfps/test/test_particle_clouds.py | 66 ++++++++++++++++++
2 files changed, 120 insertions(+), 53 deletions(-)
create mode 100644 bfps/test/test_particle_clouds.py
diff --git a/bfps/DNS.py b/bfps/DNS.py
index c1835062..3aa47fd4 100644
--- a/bfps/DNS.py
+++ b/bfps/DNS.py
@@ -430,9 +430,7 @@ class DNS(_code):
return None
def write_par(
self,
- iter0 = 0,
- particle_ic = None,
- particles_off = False):
+ iter0 = 0):
assert (self.parameters['niter_todo'] % self.parameters['niter_stat'] == 0)
assert (self.parameters['niter_todo'] % self.parameters['niter_out'] == 0)
assert (self.parameters['niter_out'] % self.parameters['niter_stat'] == 0)
@@ -479,7 +477,7 @@ class DNS(_code):
4),
dtype = np.int64)
ofile['checkpoint'] = int(0)
- if (self.dns_type in ['NSVE', 'NSVE_no_output']) or particles_off:
+ if (self.dns_type in ['NSVE', 'NSVE_no_output']):
return None
if type(particle_ic) == type(None):
@@ -995,58 +993,61 @@ class DNS(_code):
particle_file.create_group('tracers0/pressure_gradient')
particle_file.create_group('tracers0/pressure_Hessian')
return None
- def launch_jobs(
+ def generate_initial_condition(
self,
- opt = None,
- particle_initial_condition = None):
- if not os.path.exists(os.path.join(self.work_dir, self.simname + '.h5')):
- # take care of fields' initial condition
- # first, check if initial field exists
- need_field = False
- if not os.path.exists(self.get_checkpoint_0_fname()):
+ opt = None):
+ # take care of fields' initial condition
+ # first, check if initial field exists
+ need_field = False
+ if not os.path.exists(self.get_checkpoint_0_fname()):
+ need_field = True
+ else:
+ f = h5py.File(self.get_checkpoint_0_fname(), 'r')
+ try:
+ dset = f['vorticity/complex/0']
+ need_field = (dset.shape == (self.parameters['ny'],
+ self.parameters['nz'],
+ self.parameters['nx']//2+1,
+ 3))
+ except:
need_field = True
+ f.close()
+ if need_field:
+ f = h5py.File(self.get_checkpoint_0_fname(), 'a')
+ if len(opt.src_simname) > 0:
+ source_cp = 0
+ src_file = 'not_a_file'
+ while True:
+ src_file = os.path.join(
+ os.path.realpath(opt.src_work_dir),
+ opt.src_simname + '_checkpoint_{0}.h5'.format(source_cp))
+ f0 = h5py.File(src_file, 'r')
+ if '{0}'.format(opt.src_iteration) in f0['vorticity/complex'].keys():
+ f0.close()
+ break
+ source_cp += 1
+ self.copy_complex_field(
+ src_file,
+ 'vorticity/complex/{0}'.format(opt.src_iteration),
+ f,
+ 'vorticity/complex/{0}'.format(0))
else:
- f = h5py.File(self.get_checkpoint_0_fname(), 'r')
- try:
- dset = f['vorticity/complex/0']
- need_field = (dset.shape == (self.parameters['ny'],
- self.parameters['nz'],
- self.parameters['nx']//2+1,
- 3))
- except:
- need_field = True
- f.close()
- if need_field:
- f = h5py.File(self.get_checkpoint_0_fname(), 'a')
- if len(opt.src_simname) > 0:
- source_cp = 0
- src_file = 'not_a_file'
- while True:
- src_file = os.path.join(
- os.path.realpath(opt.src_work_dir),
- opt.src_simname + '_checkpoint_{0}.h5'.format(source_cp))
- f0 = h5py.File(src_file, 'r')
- if '{0}'.format(opt.src_iteration) in f0['vorticity/complex'].keys():
- f0.close()
- break
- source_cp += 1
- self.copy_complex_field(
- src_file,
- 'vorticity/complex/{0}'.format(opt.src_iteration),
- f,
- 'vorticity/complex/{0}'.format(0))
- else:
- data = self.generate_vector_field(
- write_to_file = False,
- spectra_slope = 2.0,
- amplitude = 0.05)
- f['vorticity/complex/{0}'.format(0)] = data
- f.close()
- self.write_par(
- particle_ic = None)
- # take care of particles' initial condition
- if self.dns_type in ['NSVEparticles', 'NSVEcomplex_particles', 'NSVEparticles_no_output', 'NSVEp_extra_sampling']:
- self.generate_particle_data(opt = opt)
+ data = self.generate_vector_field(
+ write_to_file = False,
+ spectra_slope = 2.0,
+ amplitude = 0.05)
+ f['vorticity/complex/{0}'.format(0)] = data
+ f.close()
+ # now take care of particles' initial condition
+ if self.dns_type in ['NSVEparticles', 'NSVEcomplex_particles', 'NSVEparticles_no_output', 'NSVEp_extra_sampling']:
+ self.generate_particle_data(opt = opt)
+ return None
+ def launch_jobs(
+ self,
+ opt = None):
+ if not os.path.exists(self.get_data_file_name()):
+ self.generate_initial_condition()
+ self.write_par()
self.run(
nb_processes = opt.nb_processes,
nb_threads_per_process = opt.nb_threads_per_process,
diff --git a/bfps/test/test_particle_clouds.py b/bfps/test/test_particle_clouds.py
new file mode 100644
index 00000000..1a890495
--- /dev/null
+++ b/bfps/test/test_particle_clouds.py
@@ -0,0 +1,66 @@
+#! /usr/bin/env python
+#######################################################################
+# #
+# Copyright 2019 Max Planck Institute #
+# for Dynamics and Self-Organization #
+# #
+# This file is part of bfps. #
+# #
+# bfps is free software: you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published #
+# by the Free Software Foundation, either version 3 of the License, #
+# or (at your option) any later version. #
+# #
+# bfps is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details. #
+# #
+# You should have received a copy of the GNU General Public License #
+# along with bfps. If not, see <http://www.gnu.org/licenses/> #
+# #
+# Contact: Cristian.Lalescu@ds.mpg.de #
+# #
+#######################################################################
+
+
+
+import os
+import numpy as np
+import h5py
+import sys
+
+import bfps
+from bfps import DNS
+
+def main():
+ nclouds = 4
+ nparticles_per_cloud = 3
+ nparticles = nclouds*nparticles_per_cloud
+ niterations = 32
+ c = DNS()
+ ic_file = h5py.File(c.get_checkpoint_0_fname(), 'a')
+ ic_file['tracers0/state/0'] = np.random.random((nclouds, nparticles_per_cloud, 3))
+ ic_file['tracers0/rhs/0'] = np.zeros((2, nclouds, nparticles_per_cloud, 3))
+ ic_file.close()
+ c.launch(
+ ['NSVEparticles',
+ '-n', '32',
+ '--src-simname', 'B32p1e4',
+ '--forcing_type', 'linear',
+ '--src-wd', bfps.lib_dir + '/test',
+ '--src-iteration', '0',
+ '--np', '4',
+ '--ntpp', '1',
+ '--fftw_plan_rigor', 'FFTW_PATIENT',
+ '--niter_todo', '{0}'.format(niterations),
+ '--niter_out', '{0}'.format(niterations),
+ '--niter_stat', '1',
+ '--nparticles', '{0}'.format(nparticles),
+ '--tracers0_integration_steps', '2',
+ '--wd', './'])
+ return None
+
+if __name__ == '__main__':
+ main()
+
--
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