From 44151787ff3541b3d7cc9974a49d0f5447c4b0c1 Mon Sep 17 00:00:00 2001
From: Lukas Bentkamp <lukas.bentkamp@ds.mpg.de>
Date: Thu, 2 Jun 2022 17:43:57 +0200
Subject: [PATCH 1/4] Fixing path to fields file
---
TurTLE/PP.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/TurTLE/PP.py b/TurTLE/PP.py
index 4699b52d..657ee8a5 100644
--- a/TurTLE/PP.py
+++ b/TurTLE/PP.py
@@ -782,7 +782,7 @@ class PP(_code):
with h5py.File(os.path.join(self.work_dir, self.simname + '_fields.h5'), 'a') as ff:
ff.require_group('vorticity')
ff.require_group('vorticity/complex')
- checkpoint_file_list = [self.simname + '_checkpoint_{0}.h5'.format(cp)
+ checkpoint_file_list = [os.path.join(self.work_dir, self.simname + '_checkpoint_{0}.h5'.format(cp))
for cp in range(df['checkpoint'][()]+1)]
for cpf_name in checkpoint_file_list:
if os.path.exists(cpf_name):
--
GitLab
From a9f13a42c5aadc758421d42ab3d50217bae4a934 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Fri, 3 Jun 2022 09:24:39 +0200
Subject: [PATCH 2/4] tweaks default filenames/parameter handling
---
TurTLE/DNS.py | 33 ---------------------------------
TurTLE/PP.py | 12 ++----------
TurTLE/TEST.py | 4 ----
TurTLE/_base.py | 45 +++++++++++++++++++++++++++++++++++++++++----
4 files changed, 43 insertions(+), 51 deletions(-)
diff --git a/TurTLE/DNS.py b/TurTLE/DNS.py
index d69af1ea..731cab3c 100644
--- a/TurTLE/DNS.py
+++ b/TurTLE/DNS.py
@@ -131,14 +131,6 @@ class DNS(_code):
self.parameter_description['dky'] = 'Smallest wavenumber in the y direction for a pseudo-spectral run.'
self.parameters['dkz'] = float(1.0)
self.parameter_description['dkz'] = 'Smallest wavenumber in the z direction for a pseudo-spectral run.'
- self.parameters['niter_todo'] = int(8)
- self.parameter_description['niter_todo'] = 'Number of iterations to compute during a single run.'
- self.parameters['niter_stat'] = int(1)
- self.parameter_description['niter_stat'] = 'Interval (in iterations) over which to compute field statistics (i.e. call `do_stats`).'
- self.parameters['niter_out'] = int(8)
- self.parameter_description['niter_out'] = 'Output is performed every `NITER_OUT` iterations.'
- self.parameters['checkpoints_per_file'] = int(1)
- self.parameter_description['checkpoints_per_file'] = 'Number of checkpoints to store in a single checkpoint file. Rule of thumb: files should hold gigabytes of data, rather than megabytes.'
self.parameters['dt'] = float(0.01)
self.parameter_description['dt'] = 'Fixed timestep to use. It is strongly recommended not to change this value in between jobs.'
self.parameters['nu'] = float(0.1)
@@ -238,22 +230,6 @@ class DNS(_code):
self.parameters['nz']//2 + 1).astype(np.float64)*self.parameters['dkz']
kspace['kz'] = np.roll(kspace['kz'], self.parameters['nz']//2+1)
return kspace
- def get_data_file_name(self):
- return os.path.join(self.work_dir, self.simname + '.h5')
- def get_data_file(self):
- return h5py.File(self.get_data_file_name(), 'r')
- def get_particle_file_name(self):
- return os.path.join(self.work_dir, self.simname + '_particles.h5')
- def get_particle_file(self):
- return h5py.File(self.get_particle_file_name(), 'r')
- def get_cache_file_name(self):
- return os.path.join(self.work_dir, self.simname + '_cache.h5')
- def get_cache_file(self):
- return h5py.File(self.get_cache_file_name(), 'r')
- def get_postprocess_file_name(self):
- return self.get_cache_file_name()
- def get_postprocess_file(self):
- return h5py.File(self.get_postprocess_file_name(), 'r')
def compute_statistics(
self,
iter0 = 0,
@@ -878,15 +854,6 @@ class DNS(_code):
opt = self.prepare_launch(args = args)
self.launch_jobs(opt = opt, **kwargs)
return None
- def get_checkpoint_0_fname(self):
- return os.path.join(
- self.work_dir,
- self.simname + '_checkpoint_0.h5')
- def get_checkpoint_fname(self, iteration = 0):
- checkpoint = (iteration // self.parameters['niter_out']) // self.parameters['checkpoints_per_file']
- return os.path.join(
- self.work_dir,
- self.simname + '_checkpoint_{0}.h5'.format(checkpoint))
def generate_tracer_state(
self,
rseed = None,
diff --git a/TurTLE/PP.py b/TurTLE/PP.py
index 657ee8a5..89fe4319 100644
--- a/TurTLE/PP.py
+++ b/TurTLE/PP.py
@@ -152,14 +152,6 @@ class PP(_code):
elif dns_type == 'get_rfields':
pars['TrS2_on'] = int(0)
return pars
- def get_data_file_name(self):
- return os.path.join(self.work_dir, self.simname + '.h5')
- def get_data_file(self):
- return h5py.File(self.get_data_file_name(), 'r')
- def get_particle_file_name(self):
- return os.path.join(self.work_dir, self.simname + '_particles.h5')
- def get_particle_file(self):
- return h5py.File(self.get_particle_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):
@@ -779,10 +771,10 @@ class PP(_code):
last_iteration = df['iteration'][()]
cppf = df['parameters/checkpoints_per_file'][()]
niter_out = df['parameters/niter_out'][()]
- with h5py.File(os.path.join(self.work_dir, self.simname + '_fields.h5'), 'a') as ff:
+ with h5py.File(self.get_fields_fname(), 'a') as ff:
ff.require_group('vorticity')
ff.require_group('vorticity/complex')
- checkpoint_file_list = [os.path.join(self.work_dir, self.simname + '_checkpoint_{0}.h5'.format(cp))
+ checkpoint_file_list = [self.get_checkpoint_fname(checkpoint = cp)
for cp in range(df['checkpoint'][()]+1)]
for cpf_name in checkpoint_file_list:
if os.path.exists(cpf_name):
diff --git a/TurTLE/TEST.py b/TurTLE/TEST.py
index 925f71f6..9ddcfaa0 100644
--- a/TurTLE/TEST.py
+++ b/TurTLE/TEST.py
@@ -176,10 +176,6 @@ class TEST(_code):
self.parameters['nz']//2 + 1).astype(np.float64)*self.parameters['dkz']
kspace['kz'] = np.roll(kspace['kz'], self.parameters['nz']//2+1)
return kspace
- def get_data_file_name(self):
- return os.path.join(self.work_dir, self.simname + '.h5')
- def get_data_file(self):
- return h5py.File(self.get_data_file_name(), 'r')
def write_par(
self,
iter0 = 0,
diff --git a/TurTLE/_base.py b/TurTLE/_base.py
index 2b882dd0..da1c91fc 100644
--- a/TurTLE/_base.py
+++ b/TurTLE/_base.py
@@ -41,11 +41,20 @@ class _base(object):
### simulation parameters
self.parameters = {'nx' : 32,
'ny' : 32,
- 'nz' : 32}
+ 'nz' : 32,
+ 'niter_todo' : int(8),
+ 'niter_stat' : int(1),
+ 'niter_out' : int(8),
+ 'checkpoints_per_file' : int(1),
+ }
self.parameter_description = {
- 'nx' : 'Number of real-space grid nodes in the x direction.',
- 'ny' : 'Number of real-space grid nodes in the y direction.',
- 'nz' : 'Number of real-space grid nodes in the z direction.',
+ 'nx' : 'Number of real-space grid nodes in the x direction (fastest array index in real-space representation).',
+ 'ny' : 'Number of real-space grid nodes in the y direction.',
+ 'nz' : 'Number of real-space grid nodes in the z direction (slowest array index in real-space representation).',
+ 'niter_todo' : 'Number of iterations to compute during a single run.',
+ 'niter_stat' : 'Interval (in iterations) over which to compute field statistics (i.e. call `do_stats`).',
+ 'niter_out' : 'Output is performed every `NITER_OUT` iterations.',
+ 'checkpoints_per_file' : 'Number of checkpoints to store in a single checkpoint file. Rule of thumb: files should hold gigabytes of data, rather than megabytes.',
}
self.string_length = 512
self.work_dir = os.path.realpath(work_dir)
@@ -366,4 +375,32 @@ class _base(object):
help = description,
default = None)
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(self.get_data_file_name(), 'r')
+ def get_particle_file_name(self):
+ return os.path.join(self.work_dir, self.simname + '_particles.h5')
+ def get_particle_file(self):
+ return h5py.File(self.get_particle_file_name(), 'r')
+ def get_cache_file_name(self):
+ return os.path.join(self.work_dir, self.simname + '_cache.h5')
+ def get_cache_file(self):
+ return h5py.File(self.get_cache_file_name(), 'r')
+ def get_postprocess_file_name(self):
+ return self.get_cache_file_name()
+ def get_postprocess_file(self):
+ return h5py.File(self.get_postprocess_file_name(), 'r')
+ def get_checkpoint_0_fname(self):
+ return os.path.join(
+ self.work_dir,
+ self.simname + '_checkpoint_0.h5')
+ def get_checkpoint_fname(self, iteration = 0, checkpoint = None):
+ if type(checkpoint) == type(None):
+ checkpoint = (iteration // self.parameters['niter_out']) // self.parameters['checkpoints_per_file']
+ return os.path.join(
+ self.work_dir,
+ self.simname + '_checkpoint_{0}.h5'.format(checkpoint))
+ def get_fields_fname(self):
+ return os.path.join(self.work_dir, self.simname + '_fields.h5')
--
GitLab
From 17112cd50ff70351c3a206d27572eafbfd8e8d3f Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Fri, 3 Jun 2022 09:47:16 +0200
Subject: [PATCH 3/4] fixes parameter conflict
---
TurTLE/TEST.py | 1 -
TurTLE/test/test_particle_integration.py | 3 ++-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/TurTLE/TEST.py b/TurTLE/TEST.py
index 9ddcfaa0..0b7d8df5 100644
--- a/TurTLE/TEST.py
+++ b/TurTLE/TEST.py
@@ -137,7 +137,6 @@ class TEST(_code):
pars['nxparticles'] = 13
pars['nzparticles'] = 11
pars['dt'] = 0.125
- pars['niter_todo'] = 128
if dns_type == 'phase_shift_test':
pars['random_phase_seed'] = 1
if dns_type in ['dealias_test', 'Gauss_field_test']:
diff --git a/TurTLE/test/test_particle_integration.py b/TurTLE/test/test_particle_integration.py
index 93bb0f4a..def55e5b 100644
--- a/TurTLE/test/test_particle_integration.py
+++ b/TurTLE/test/test_particle_integration.py
@@ -11,7 +11,8 @@ def main():
c.launch([
'test_particle_integration',
'--np', '4',
- '--ntpp', '3'])
+ '--ntpp', '3',
+ '--niter_todo', '128'])
data_file = h5py.File(c.simname + '_particles.h5', 'r')
--
GitLab
From 2c05c5281233f2770a7d3f023e866f7dd5ae9552 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Fri, 3 Jun 2022 10:00:35 +0200
Subject: [PATCH 4/4] cleans up class, adds important documentation point
---
TurTLE/PP.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/TurTLE/PP.py b/TurTLE/PP.py
index 89fe4319..f653f5db 100644
--- a/TurTLE/PP.py
+++ b/TurTLE/PP.py
@@ -153,9 +153,10 @@ class PP(_code):
pars['TrS2_on'] = int(0)
return pars
def get_postprocess_file_name(self):
+ """
+ Reimplemented from `_base` for postprocessing codes.
+ """
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):
"""Run basic postprocessing on raw data.
The energy spectrum :math:`E(t, k)` and the enstrophy spectrum
--
GitLab