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Commit 10fcb49b authored by Cristian Lalescu's avatar Cristian Lalescu
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Merge branch 'develop' into feature/collisions

parents afea23ca ab9ad5bb
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CMakeLists.txt
View file @ 10fcb49b
......@@ -3,20 +3,20 @@
# Copyright 2019 Max Planck Institute #
# for Dynamics and Self-Organization #
# #
# This file is part of bfps. #
# This file is part of TurTLE. #
# #
# bfps is free software: you can redistribute it and/or modify #
# TurTLE 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, #
# TurTLE 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/> #
# along with TurTLE. If not, see <http://www.gnu.org/licenses/> #
# #
# Contact: Cristian.Lalescu@ds.mpg.de #
# #
......@@ -272,6 +272,7 @@ set(cpp_for_lib
${PROJECT_SOURCE_DIR}/cpp/full_code/symmetrize_test.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/field_output_test.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/get_rfields.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/write_rpressure.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/bandpass_stats.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/field_single_to_double.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/resize.cpp
......@@ -300,6 +301,7 @@ set(cpp_for_lib
${PROJECT_SOURCE_DIR}/cpp/full_code/test_interpolation.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEparticles.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEcomplex_particles.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE_Stokes_particles.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEp_extra_sampling.cpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_inner_computer.cpp
${PROJECT_SOURCE_DIR}/cpp/full_code/ornstein_uhlenbeck_process.cpp
......@@ -320,6 +322,7 @@ set(hpp_for_lib
${PROJECT_SOURCE_DIR}/cpp/full_code/symmetrize_test.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/field_output_test.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/get_rfields.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/write_rpressure.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/bandpass_stats.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/field_single_to_double.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/resize.hpp
......@@ -348,14 +351,16 @@ set(hpp_for_lib
${PROJECT_SOURCE_DIR}/cpp/full_code/test_interpolation.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEparticles.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEcomplex_particles.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE_Stokes_particles.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEp_extra_sampling.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_inner_computer.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_inner_computer_2nd_order.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_inner_computer_empty.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particles_input.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particles_output.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particles_system.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/abstract_particles_system_with_p2p.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/alltoall_exchanger.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/env_utils.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/lock_free_bool_array.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/p2p_computer_empty.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/p2p_computer.hpp
......@@ -368,7 +373,6 @@ set(hpp_for_lib
${PROJECT_SOURCE_DIR}/cpp/particles/particles_distr_mpi.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_field_computer.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_generic_interp.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_inner_computer_empty.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_input_hdf5.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_output_hdf5.hpp
${PROJECT_SOURCE_DIR}/cpp/particles/particles_output_mpiio.hpp
......@@ -382,6 +386,7 @@ set(hpp_for_lib
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVE_no_output.hpp
${PROJECT_SOURCE_DIR}/cpp/full_code/NSVEparticles_no_output.hpp
${PROJECT_SOURCE_DIR}/cpp/base.hpp
${PROJECT_SOURCE_DIR}/cpp/env_utils.hpp
${PROJECT_SOURCE_DIR}/cpp/fftw_interface.hpp
${PROJECT_SOURCE_DIR}/cpp/bfps_timer.hpp
${PROJECT_SOURCE_DIR}/cpp/omputils.hpp
......@@ -408,6 +413,13 @@ configure_file(${PROJECT_SOURCE_DIR}/cmake/TurTLEConfig.cmake.in ${PROJECT_BINAR
install(FILES "${PROJECT_BINARY_DIR}/TurTLEConfig.cmake" DESTINATION lib/)
export(TARGETS TurTLE FILE "${PROJECT_BINARY_DIR}/TurTLELibraryDepends.cmake")
install(EXPORT TURTLE_EXPORT DESTINATION lib/)
if(EXISTS "${PROJECT_BINARY_DIR}/bash_setup_for_TurTLE.sh")
install(
FILES "${PROJECT_BINARY_DIR}/bash_setup_for_TurTLE.sh"
PERMISSIONS OWNER_READ GROUP_READ WORLD_READ
DESTINATION "lib/"
)
endif()
#####################################################################################
......@@ -420,3 +432,70 @@ else()
install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E copy ${PROJECT_SOURCE_DIR}/pc_host_info.py ${PROJECT_BINARY_DIR}/python/TurTLE/host_info.py)")
endif()
install(CODE "execute_process(COMMAND python3 ${PROJECT_SOURCE_DIR}/setup.py install --force --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/python/)")
#####################################################################################
## Add tests
include(CTest)
set(TEST_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/test_runs/")
enable_testing()
if (BUILD_TESTING)
file(MAKE_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
### basic functionality
add_test(
NAME test_fftw
COMMAND turtle.test_fftw
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_Parseval
COMMAND turtle.test_Parseval
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
### compare DNS output to stored results
add_test(
NAME test_NSVEparticles
COMMAND turtle.test_NSVEparticles --ntpp 2
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
### simple runs of post-processing tools
add_test(
NAME test_pp_single_to_double
COMMAND turtle PP field_single_to_double --simname dns_nsveparticles --iter0 32 --iter1 32
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_pp_get_rfields
COMMAND turtle PP get_rfields --simname dns_nsveparticles --iter0 0 --iter1 64
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_pp_write_rpressure
COMMAND turtle PP write_rpressure --simname dns_nsveparticles --iter0 0 --iter1 64
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_pp_joint_acc_vel_stats
COMMAND turtle PP joint_acc_vel_stats --simname dns_nsveparticles --iter0 0 --iter1 64
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_pp_resize
COMMAND turtle PP resize --simname dns_nsveparticles --new_nx 96 --new_ny 96 --new_nz 96 --new_simname dns_nsveparticles_resized
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
### simple runs of different DNS
add_test(
NAME test_NSVEp_extra_sampling
COMMAND turtle DNS NSVEp_extra_sampling -n 32 --src-simname dns_nsveparticles --src-iteration 32 --simname dns_nsvep_extra_sampling --nparticles 1000
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_NSVEcomplex_particles
COMMAND turtle DNS NSVEcomplex_particles -n 32 --src-simname dns_nsveparticles --src-iteration 32 --simname dns_nsvecomplex_particles --nparticles 1000
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_static_field
COMMAND turtle DNS static_field --simname dns_static_field --nparticles 10000
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_kraichnan_field
COMMAND turtle DNS kraichnan_field --simname dns_kraichnan_field --dtfactor 0.05 --nparticles 10000 --ntpp 2
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
add_test(
NAME test_NSVE_Stokes_particles
COMMAND turtle DNS NSVE_Stokes_particles -n 32 --src-simname dns_nsveparticles --src-iteration 32 --simname dns_nsve_tokes_particles --nparticles 10000
WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
endif(BUILD_TESTING)
TurTLE/DNS.py
View file @ 10fcb49b
......@@ -439,7 +439,14 @@ class DNS(_code):
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)
if self.dns_type in ['NSVEparticles_no_output', 'NSVEcomplex_particles', 'NSVEparticles', 'static_field', 'static_field_with_ghost_collisions', 'kraichnan_field']:
if self.dns_type in [
'NSVEparticles_no_output',
'NSVEcomplex_particles',
'NSVE_Stokes_particles',
'NSVEparticles',
'static_field',
'static_field_with_ghost_collisions',
'kraichnan_field']:
assert (self.parameters['niter_todo'] % self.parameters['niter_part'] == 0)
assert (self.parameters['niter_out'] % self.parameters['niter_part'] == 0)
_code.write_par(self, iter0 = iter0)
......@@ -654,40 +661,45 @@ class DNS(_code):
'NSVEparticles',
help = 'plain Navier-Stokes vorticity formulation, with basic fluid tracers')
parser_NSVE_Stokes_particles = subparsers.add_parser(
'NSVE_Stokes_particles',
help = 'plain Navier-Stokes vorticity formulation, with passive Stokes drag particles')
parser_NSVEp2p = subparsers.add_parser(
'NSVEcomplex_particles',
help = 'plain Navier-Stokes vorticity formulation, with oriented active particles')
parser_NSVEp_extra = subparsers.add_parser(
'NSVEp_extra_sampling',
help = 'plain Navier-Stokes vorticity formulation, with basic fluid tracers, that sample velocity gradient, as well as pressure and its derivatives.')
for parser in [
for pp in [
'NSVE',
'NSVE_no_output',
'NSVEparticles_no_output',
'NSVEp2',
'NSVEp2p',
'NSVE_Stokes_particles',
'NSVEp_extra',
'static_field',
'static_field_with_ghost_collisions',
'kraichnan_field']:
eval('self.simulation_parser_arguments({0})'.format('parser_' + parser))
eval('self.job_parser_arguments({0})'.format('parser_' + parser))
eval('self.parameters_to_parser_arguments({0})'.format('parser_' + parser))
eval('self.simulation_parser_arguments({0})'.format('parser_' + pp))
eval('self.job_parser_arguments({0})'.format('parser_' + pp))
eval('self.parameters_to_parser_arguments({0})'.format('parser_' + pp))
eval('self.parameters_to_parser_arguments('
'parser_{0},'
'self.generate_extra_parameters(\'{0}\'))'.format(parser))
for parser in [
'self.generate_extra_parameters(\'{0}\'))'.format(pp))
for pp in [
'NSVEparticles_no_output',
'NSVEp2',
'NSVEp2p',
'NSVE_Stokes_particles',
'NSVEp_extra',
'static_field',
'kraichnan_field']:
eval('self.particle_parser_arguments({0})'.format('parser_' + parser))
eval('self.particle_parser_arguments({0})'.format('parser_' + pp))
eval('self.parameters_to_parser_arguments('
'parser_{0},'
'self.NSVEp_extra_parameters)'.format(parser))
'self.NSVEp_extra_parameters)'.format(pp))
return None
def generate_extra_parameters(
self,
......@@ -698,7 +710,11 @@ class DNS(_code):
pars['field_random_seed'] = int(1)
pars['spectrum_slope'] = float(-5./3)
pars['spectrum_k_cutoff'] = float(16)
pars['spectrum_coefficient'] = float(1)
pars['spectrum_coefficient'] = float(0.1)
if dns_type == 'NSVE_Stokes_particles':
pars['initial_field_amplitude'] = float(0.0)
pars['initial_particle_vel'] = float(0.05)
pars['drag_coefficient'] = float(0.1)
return pars
def prepare_launch(
self,
......@@ -737,6 +753,7 @@ class DNS(_code):
if self.dns_type in [
'NSVEparticles',
'NSVEcomplex_particles',
'NSVE_Stokes_particles',
'NSVEparticles_no_output',
'NSVEp_extra_sampling',
'static_field',
......@@ -812,7 +829,15 @@ class DNS(_code):
# hardcoded FFTW complex representation size
field_size = 3*(opt.nx+2)*opt.ny*opt.nz*self.fluid_dtype.itemsize
checkpoint_size = field_size
if self.dns_type in ['static_field', 'NSVEparticles', 'NSVEcomplex_particles', 'NSVEparticles_no_output', 'NSVEp_extra_sampling', 'static_field_with_ghost_collisions', 'kraichnan_field']:
if self.dns_type in [
'kraichnan_field',
'static_field',
'static_field_with_ghost_collisions',
'NSVEparticles',
'NSVEcomplex_particles',
'NSVE_Stokes_particles',
'NSVEparticles_no_output',
'NSVEp_extra_sampling']:
rhs_size = self.parameters['tracers0_integration_steps']
if type(opt.tracers0_integration_steps) != type(None):
rhs_size = opt.tracers0_integration_steps
......@@ -852,7 +877,9 @@ class DNS(_code):
integration_steps = self.NSVEp_extra_parameters['tracers0_integration_steps']
if 'tracers{0}_integration_steps'.format(species) in self.parameters.keys():
integration_steps = self.parameters['tracers{0}_integration_steps'.format(species)]
if self.dns_type == 'NSVEcomplex_particles' and species == 0:
if self.dns_type in [
'NSVEcomplex_particles',
'NSVE_Stokes_particles'] and species == 0:
ncomponents = 6
with h5py.File(self.get_checkpoint_0_fname(), 'a') as data_file:
nn = self.parameters['nparticles']
......@@ -884,12 +911,18 @@ class DNS(_code):
if nn > batch_size:
dset[cc*batch_size:(cc+1)*batch_size, :3] = get_random_phases(batch_size)
if dset.shape[1] == 6:
dset[cc*batch_size:(cc+1)*batch_size, 3:] = get_random_versors(batch_size)
if self.dns_type == 'NSVE_Stokes_particles':
dset[cc*batch_size:(cc+1)*batch_size, 3:] = self.parameters['initial_particle_vel']*get_random_versors(batch_size)
else:
dset[cc*batch_size:(cc+1)*batch_size, 3:] = get_random_versors(batch_size)
nn -= batch_size
else:
dset[cc*batch_size:cc*batch_size+nn, :3] = get_random_phases(nn)
if dset.shape[1] == 6:
dset[cc*batch_size:cc*batch_size+nn, 3:] = get_random_versors(nn)
if self.dns_type == 'NSVE_Stokes_particles':
dset[cc*batch_size:cc*batch_size+nn, 3:] = self.parameters['initial_particle_vel']*get_random_versors(nn)
else:
dset[cc*batch_size:cc*batch_size+nn, 3:] = get_random_versors(nn)
nn = 0
cc += 1
except Exception as e:
......@@ -1036,6 +1069,8 @@ class DNS(_code):
if self.dns_type in ['NSVEcomplex_particles']:
particle_file.create_group('tracers0/orientation')
particle_file.create_group('tracers0/velocity_gradient')
if self.dns_type in ['NSVE_Stokes_particles']:
particle_file.create_group('tracers0/momentum')
if self.dns_type in ['NSVEp_extra_sampling']:
particle_file.create_group('tracers0/velocity_gradient')
particle_file.create_group('tracers0/pressure')
......@@ -1049,6 +1084,16 @@ class DNS(_code):
# first, check if initial field exists
need_field = False
if self.check_current_vorticity_exists:
need_field = True
if self.dns_type in [
'NSVE',
'NSVE_no_output',
'static_field',
'NSVEparticles',
'NSVEcomplex_particles',
'NSVE_Stokes_particles',
'NSVEparticles_no_output',
'NSVEp_extra_sampling']:
if not os.path.exists(self.get_checkpoint_0_fname()):
need_field = True
else:
......@@ -1082,10 +1127,16 @@ class DNS(_code):
f,
'vorticity/complex/{0}'.format(0))
else:
data = self.generate_vector_field(
if self.dns_type == 'NSVE_Stokes_particles':
data = self.generate_vector_field(
write_to_file = False,
spectra_slope = 2.0,
amplitude = self.parameters['initial_field_amplitude'])
else:
data = self.generate_vector_field(
write_to_file = False,
spectra_slope = 2.0,
amplitude = 0.05)
amplitude = 0.05)
f['vorticity/complex/{0}'.format(0)] = data
f.close()
if self.dns_type == 'kraichnan_field':
......@@ -1100,6 +1151,7 @@ class DNS(_code):
'static_field_with_ghost_collisions',
'NSVEparticles',
'NSVEcomplex_particles',
'NSVE_Stokes_particles',
'NSVEparticles_no_output',
'NSVEp_extra_sampling']:
self.generate_particle_data(opt = opt)
......
TurTLE/PP.py
View file @ 10fcb49b
......@@ -145,6 +145,8 @@ class PP(_code):
pars['filter_type'] = 'Gauss'
pars['max_velocity_estimate'] = float(10)
pars['histogram_bins'] = int(129)
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')
......@@ -447,13 +449,17 @@ class PP(_code):
parser_resize = subparsers.add_parser(
'resize',
help = 'get joint acceleration and velocity statistics')
parser_write_rpressure = subparsers.add_parser(
'write_rpressure',
help = 'write real pressure field to binary')
for pp_type in [
'resize',
'joint_acc_vel_stats',
'bandpass_stats',
'get_rfields',
'field_single_to_double',
'native_binary_to_hdf5']:
'native_binary_to_hdf5',
'write_rpressure']:
eval('self.simulation_parser_arguments(parser_' + pp_type + ')')
eval('self.job_parser_arguments(parser_' + pp_type + ')')
eval('self.parameters_to_parser_arguments(parser_' + pp_type + ')')
......@@ -805,15 +811,21 @@ 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 = glob.glob(self.simname + '_checkpoint_*.h5')
checkpoint_file_list = [self.simname + '_checkpoint_{0}.h5'.format(cp)
for cp in range(df['checkpoint'][()]+1)]
for cpf_name in checkpoint_file_list:
cpf = h5py.File(cpf_name, 'r')
for iter_name in cpf['vorticity/complex'].keys():
if iter_name not in ff['vorticity/complex'].keys():
ff['vorticity/complex/' + iter_name] = h5py.ExternalLink(
cpf_name,
'vorticity/complex/' + iter_name)
cpf.close()
if os.path.exists(cpf_name):
cpf = h5py.File(cpf_name, 'r')
if 'vorticity' not in cpf.keys():
print('file ', cpf_name, ' does not have vorticity group')
continue
else:
for iter_name in cpf['vorticity/complex'].keys():
if iter_name not in ff['vorticity/complex'].keys():
ff['vorticity/complex/' + iter_name] = h5py.ExternalLink(
cpf_name,
'vorticity/complex/' + iter_name)
cpf.close()
return None
def launch_jobs(
self,
......
TurTLE/TEST.py
View file @ 10fcb49b
......@@ -188,6 +188,7 @@ class TEST(_code):
scal_rspace_stats = []
if self.dns_type in ['Gauss_field_test']:
vec_spectra_stats.append('velocity')
vec_spectra_stats.append('k*velocity')
vec4_rspace_stats.append('velocity')
tens_rspace_stats.append('velocity_gradient')
scal_rspace_stats.append('velocity_divergence')
......@@ -377,6 +378,7 @@ class TEST(_code):
eval('self.simulation_parser_arguments(parser_' + parser + ')')
eval('self.job_parser_arguments(parser_' + parser + ')')
eval('self.parameters_to_parser_arguments(parser_' + parser + ')')
eval('self.parameters_to_parser_arguments(parser_' + parser + ', self.generate_extra_parameters(dns_type = \'' + parser + '\'))')
return None
def prepare_launch(
self,
......
TurTLE/_code.py
View file @ 10fcb49b
......@@ -4,18 +4,18 @@
# #
# This file is part of bfps. #
# #
# TurTLE is free software: you can redistribute it and/or modify #
# TurTLE 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. #
# #
# TurTLE is distributed in the hope that it will be useful, #
# TurTLE 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 TurTLE. If not, see <http://www.gnu.org/licenses/> #
# along with TurTLE. If not, see <http://www.gnu.org/licenses/> #
# #
# Contact: Cristian.Lalescu@ds.mpg.de #
# #
......@@ -678,9 +678,9 @@ class _code(_base):
script_file.write('#SBATCH -o ' + out_file + '\n')
# set up environment
script_file.write('#SBATCH --get-user-env\n')
script_file.write('#SBATCH --partition={0}\n'.format(
self.host_info['environment']))
if self.host_info['explicit_slurm_environment']:
script_file.write('#SBATCH --partition={0}\n'.format(
self.host_info['environment']))
if 'account' in self.host_info.keys():
script_file.write('#SBATCH --account={0}\n'.format(
self.host_info['account']))
......@@ -717,14 +717,19 @@ class _code(_base):
script_file.write('#SBATCH --mail-type=none\n')
script_file.write('#SBATCH --time={0}:{1:0>2d}:00\n'.format(hours, minutes))
if 'extra_slurm_lines' in self.host_info.keys():
for line in self.host_info['extra_slurm_lines']:
script_file.write(line + '\n')
## following cleans up environment for job.
## put these in the 'extra_slurm_lines' list if you need them
## make sure that "~/.config/TurTLE/bashrc" exists and builds desired job environment
script_file.write('#SBATCH --export=NONE\n')
script_file.write('#SBATCH --get-user-env\n')
script_file.write('source ~/.config/TurTLE/bashrc\n')
#script_file.write('#SBATCH --export=NONE\n')
#script_file.write('#SBATCH --get-user-env\n')
#script_file.write('export OMP_PLACES=cores\n') # or threads, as appropriate
# also look up OMP_PROC_BIND and SLURM_HINT
#script_file.write('source ~/.config/TurTLE/bashrc\n')
if nb_threads_per_process > 1:
script_file.write('export OMP_NUM_THREADS={0}\n'.format(nb_threads_per_process))
script_file.write('export OMP_PLACES=cores\n')
script_file.write('export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}\n')
script_file.write('echo "Start time is `date`"\n')
script_file.write('cd ' + self.work_dir + '\n')
......
TurTLE/test/test_Gaussian_field.py
View file @ 10fcb49b
......@@ -5,7 +5,7 @@ from scipy import trapz
from scipy.stats import norm
from scipy.integrate import quad
import h5py
import sys
import sys, os
import time
import TurTLE
......@@ -17,24 +17,28 @@ except:
plt = None
def main():
c = TEST()
# size of grid
n = 256
n = 1024
slope = -5./3.
k_cutoff = 30.
k_cutoff = 64.
func = lambda k, k_c=k_cutoff, s=slope : k**s*np.exp(-k/k_c)
total_energy = quad(func, 1, k_cutoff*4)[0]
total_energy = quad(func, 0.6, k_cutoff*8)[0]
coeff = 1./total_energy
bin_no = 100
rseed = int(time.time())
simname = 'Gaussianity_test'
c.launch(
if not os.path.exists(simname+'.h5'):
c = TEST()
opt = c.launch(
['Gauss_field_test',
'--nx', str(n),
'--ny', str(n),
'--nz', str(n),
'--simname', 'Gaussianity_test',
'--simname', simname,
'--np', '4',
'--environment', 'short',
'--minutes', '60',
'--ntpp', '1',
'--wd', './',
'--histogram_bins', str(bin_no),
......@@ -44,7 +48,7 @@ def main():
'--spectrum_coefficient', str(coeff),
'--field_random_seed', str(rseed)] +
sys.argv[1:])
plot_stuff(c.simname, total_energy = total_energy)
plot_stuff(simname, total_energy = total_energy)
return None
def plot_stuff(simname, total_energy = 1.):
......@@ -82,6 +86,7 @@ def plot_stuff(simname, total_energy = 1.):
f_vel = hist_vel / np.sum(hist_vel, axis=0, keepdims=True).astype(float) / velbinsize
print('Energy analytically: {}'.format(total_energy))
print(np.sum(energy*np.arange(len(energy))**2))
print('Energy sum: {}'.format(np.sum(energy*df['kspace/dk'][()])))
print('Moment sum: {}'.format(df['statistics/moments/velocity'][0,2,3]/2))
print('Velocity variances: {}'.format(trapz(vel[:,None]**2*f_vel, vel[:,None], axis=0)))
......@@ -101,6 +106,17 @@ def plot_stuff(simname, total_energy = 1.):
df['statistics/moments/velocity_divergence'][0, 2]))
print('Gradient second moment is: {0}'.format(
df['statistics/moments/velocity_gradient'][0, 2].mean()))
print('----------- k2-premultiplied spectrum -----------')
k2func = lambda k, k_c=k_cutoff, s=slope : k**(2+s)*np.exp(-k/k_c)
k2sum_analytic = quad(k2func, 0, k_cutoff*20)[0]
print('Analytically: {}'.format(k2sum_analytic))
k2spec_trace = (
df['statistics/spectra/k*velocity_k*velocity'][..., 0, 0]
+ df['statistics/spectra/k*velocity_k*velocity'][..., 1, 1]
+ df['statistics/spectra/k*velocity_k*velocity'][..., 2, 2])
print('Energy sum: {}'.format(np.sum(k2spec_trace*df['kspace/dk'][()])/2./coeff))
df.close()
return None
......
TurTLE/test/test_particle_clouds.py
View file @ 10fcb49b
......@@ -33,22 +33,22 @@ import sys
import TurTLE
from TurTLE import DNS
def main():
def basic_test():
nclouds = 10
nparticles_per_cloud = 1000
nparticles = nclouds*nparticles_per_cloud
niterations = 32
c = DNS()
c.dns_type = 'NSVEparticles'
c.parameters['nparticles'] = nparticles
c.parameters['tracers1_integration_steps'] = 4
c.generate_tracer_state(rseed = 2, species = 1)
del c.parameters['nparticles']
del c.parameters['tracers1_integration_steps']
c.simname = 'basic_cloud_test'
f0 = h5py.File(
os.path.join(
os.path.join(TurTLE.lib_dir, 'test'),
'B32p1e4_checkpoint_0.h5'),
'r')
ic_file = h5py.File(c.get_checkpoint_0_fname(), 'a')
ic_file['tracers0/state/0'] = ic_file['tracers1/state/0'][...].reshape(nclouds, nparticles_per_cloud, 3)
ic_file['tracers0/rhs/0'] = ic_file['tracers1/rhs/0'][...].reshape(4, nclouds, nparticles_per_cloud, 3)
ic_file['tracers0/state/0'] = f0['tracers0/state/0'][...].reshape(nclouds, nparticles_per_cloud, 3)
ic_file['tracers0/rhs/0'] = f0['tracers0/rhs/0'][...].reshape(4, nclouds, nparticles_per_cloud, 3)
ic_file.close()
c.launch(
['NSVEparticles',
......@@ -57,12 +57,14 @@ def main():
'--forcing_type', 'linear',
'--src-wd', TurTLE.lib_dir + '/test',
'--src-iteration', '0',
'--simname', c.simname,
'--np', '4',
'--ntpp', '1',
'--fftw_plan_rigor', 'FFTW_PATIENT',
'--niter_todo', '{0}'.format(niterations),
'--niter_out', '{0}'.format(niterations),
'--niter_stat', '1',
'--checkpoints_per_file', '{0}'.format(3),
'--nparticles', '{0}'.format(nparticles),
'--njobs', '2',
'--wd', './'])
......@@ -79,6 +81,7 @@ def main():
x0 = f0['tracers0/state/{0}'.format(iteration)][...]
x1 = f1