diff --git a/CMakeLists.txt b/CMakeLists.txt index da1d4bd2924c017dd82018265cd1f04d04a8d97e..627474c66f465e29bec62d833e44f9bda35c1a72 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -489,13 +489,6 @@ LIST(APPEND source_files ${hpp_for_lib} ${cpp_for_lib}) add_library(TurTLE ${source_files}) -# TODO: we should be using the bit below, but we need to fix everything else about TURTLE_LIBS before we can do that -#target_link_libraries(TurTLE PUBLIC OpenMP::OpenMP_CXX) - -set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") -set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}") -list(APPEND TURTLE_LIBS "${OpenMP_CXX_LIB_NAMES}") - target_link_libraries(TurTLE ${TURTLE_LIBS}) target_compile_options(TurTLE PRIVATE $<$<CONFIG:DEBUG>:-O1>) diff --git a/TurTLE/DNS.py b/TurTLE/DNS.py index de8b7ff17bc251801093b8e04a6cc4f8f6f4a567..d2f7dba660f04bd6082ea87594b020892cbbe04d 100644 --- a/TurTLE/DNS.py +++ b/TurTLE/DNS.py @@ -344,13 +344,17 @@ class DNS(_code): if k in pp_file.keys(): self.statistics[k] = pp_file[k][...] # sanity check --- Parseval theorem check - test_energy = (np.max(np.abs( + energy_error = np.max(np.abs( self.statistics['renergy(t)'] - - self.statistics['energy(t)']) / self.statistics['energy(t)']) < 1e-5) - test_enstrophy = (np.max(np.abs( + self.statistics['energy(t)']) / self.statistics['energy(t)']) + test_energy = (energy_error < 1e-5) + enstrophy_error = np.max(np.abs( self.statistics['renstrophy(t)'] - - self.statistics['enstrophy(t)']) / self.statistics['enstrophy(t)']) < 1e-5) + self.statistics['enstrophy(t)']) / self.statistics['enstrophy(t)']) + test_enstrophy = (enstrophy_error < 1e-5) if strict_Parseval_check: + #print('energy error', energy_error) + #print('enstrophy error', enstrophy_error) assert(test_energy) assert(test_enstrophy) else: @@ -383,7 +387,7 @@ class DNS(_code): Further computation of statistics based on the contents of ``simname_cache.h5``. Standard quantities are as follows - (consistent with [Ishihara]_): + (consistent with [ishihara2007jfm]_): .. math:: @@ -399,13 +403,6 @@ class DNS(_code): Re = \\frac{U_{\\textrm{int}} L_{\\textrm{int}}}{\\nu}, \\hskip .5cm R_{\\lambda} = \\frac{U_{\\textrm{int}} \\lambda}{\\nu} - - .. [Ishihara] T. Ishihara et al, - *Small-scale statistics in high-resolution direct numerical - simulation of turbulence: Reynolds number dependence of - one-point velocity gradient statistics*. - J. Fluid Mech., - **592**, 335-366, 2007 """ self.statistics['Uint(t)'] = np.sqrt(2*self.statistics['energy(t)'] / 3) for key in ['energy', @@ -820,7 +817,7 @@ class DNS(_code): kM = opt.n * 0.5 if opt.dealias_type == 1: kM *= 0.8 - # tweak forcing/viscosity based on forcint type + # tweak forcing/viscosity based on forcing type if opt.forcing_type == 'linear': # custom famplitude for 288 and 576 if opt.n == 288: @@ -833,6 +830,11 @@ class DNS(_code): opt.nu = ( opt.injection_rate * (opt.kMeta / kM)**4)**(1./3) + if opt.injection_rate == 0: + opt.nu = ( + (opt.kMeta / kM)**(4./3) * + (np.pi / 1.5)**(1./3) * + (2*self.parameters['energy'] / 3)**0.5) elif opt.forcing_type == 'fixed_energy': kf = 1. / (1./opt.fk0 + 1./opt.fk1) @@ -1128,7 +1130,7 @@ class DNS(_code): f = h5py.File(self.get_checkpoint_0_fname(), 'r') try: dset = f[checkpoint_field + '/complex/0'] - need_field = (dset.shape == (self.parameters['ny'], + need_field = (dset.shape != (self.parameters['ny'], self.parameters['nz'], self.parameters['nx']//2+1, 3)) @@ -1213,12 +1215,13 @@ class DNS(_code): return None def launch_jobs( self, - opt = None): + opt = None, + iter0 = 0): if not os.path.exists(self.get_data_file_name()): if not os.path.isdir(self.work_dir): os.makedirs(self.work_dir) self.generate_initial_condition(opt = opt) - self.write_par() + self.write_par(iter0 = iter0) if (('test' in self.dns_type) or (self.dns_type in ['kraichnan_field'])): self.check_current_vorticity_exists = False diff --git a/TurTLE/PP.py b/TurTLE/PP.py index 8382ab13619972c66ac5c2c456122115964e8dac..4699b52d8cd9f662f380bf0eff337e3595f9572c 100644 --- a/TurTLE/PP.py +++ b/TurTLE/PP.py @@ -238,7 +238,7 @@ class PP(_code): Further computation of statistics based on the contents of ``simname_postprocess.h5``. Standard quantities are as follows - (consistent with [Ishihara]_): + (consistent with [ishihara2007jfm]_): .. math:: @@ -254,13 +254,6 @@ class PP(_code): Re = \\frac{U_{\\textrm{int}} L_{\\textrm{int}}}{\\nu}, \\hskip .5cm R_{\\lambda} = \\frac{U_{\\textrm{int}} \\lambda}{\\nu} - - .. [Ishihara] T. Ishihara et al, - *Small-scale statistics in high-resolution direct numerical - simulation of turbulence: Reynolds number dependence of - one-point velocity gradient statistics*. - J. Fluid Mech., - **592**, 335-366, 2007 """ for key in ['energy', 'enstrophy']: self.statistics[key + '(t)'] = (self.statistics['dk'] * @@ -783,9 +776,9 @@ class PP(_code): if 'field_dtype' in df.keys(): # we don't need to do anything, raw binary files are used return None - last_iteration = df['iteration'][...] - cppf = df['parameters/checkpoints_per_file'][...] - niter_out = df['parameters/niter_out'][...] + 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: ff.require_group('vorticity') ff.require_group('vorticity/complex') @@ -807,7 +800,13 @@ class PP(_code): if self.dns_type == 'resize': with h5py.File(os.path.join(self.work_dir, self.pp_parameters['new_simname'] + '.h5'), 'a') as ff: for kk in df['parameters'].keys(): - ff['parameters/' + kk] = df['parameters/' + kk][...] + ff['parameters/' + kk] = df['parameters/' + kk][()] + ff['parameters/nx'][()] = self.pp_parameters['new_nx'] + ff['parameters/ny'][()] = self.pp_parameters['new_ny'] + ff['parameters/nz'][()] = self.pp_parameters['new_nz'] + if 'iteration' not in ff.keys(): + ff['iteration'] = last_iteration + ff['checkpoint'] = df['checkpoint'][()] return None def launch_jobs( self, diff --git a/TurTLE/test/particle_set/NSVEparticle_set.cpp b/TurTLE/test/particle_set/NSVEparticle_set.cpp index ee89c2e36df943fd38dc04372dd2b459d5e21632..da986349dbe84e1db8e4945a4cf4e475ec894ea3 100644 --- a/TurTLE/test/particle_set/NSVEparticle_set.cpp +++ b/TurTLE/test/particle_set/NSVEparticle_set.cpp @@ -205,6 +205,7 @@ int NSVEparticle_set<rnumber>::read_parameters(void) this->tracers0_neighbours = hdf5_tools::read_value<int>(parameter_file, "parameters/tracers0_neighbours"); this->tracers0_smoothness = hdf5_tools::read_value<int>(parameter_file, "parameters/tracers0_smoothness"); H5Fclose(parameter_file); + MPI_Barrier(this->comm); return EXIT_SUCCESS; } diff --git a/TurTLE/tools.py b/TurTLE/tools.py index 7ddbf32d2e6d0beee57d11db75c5b07dbd0e5f86..6d3869854a9070eaeca2c1bc8149e38637730df7 100644 --- a/TurTLE/tools.py +++ b/TurTLE/tools.py @@ -230,13 +230,8 @@ def get_fornberg_coeffs( """compute finite difference coefficients Compute finite difference coefficients for a generic grid specified - by ``x``, according to [Fornberg]_. + by ``x``, according to [fornberg1988mc]_. The function is used by :func:`particle_finite_diff_test`. - - .. [Fornberg] B. Fornberg, - *Generation of Finite Difference Formulas on Arbitrarily Spaced Grids*. - Mathematics of Computation, - **51:184**, 699-706, 1988 """ N = len(a) - 1 d = [] diff --git a/cpp/field.cpp b/cpp/field.cpp index 6e950ad450553dbfccfa3ba33f0ae0bab168c58b..7dd5889f0f57bbf270f55baa0507205694e9cc77 100644 --- a/cpp/field.cpp +++ b/cpp/field.cpp @@ -210,7 +210,7 @@ int field<rnumber, be, fc>::io( } if (read) { - DEBUG_MSG("field::io trying to read field from file %s\n", fname.c_str()); + DEBUG_MSG("field::io trying to read field %s from file %s\n", dset_name.c_str(), fname.c_str()); assert(file_exists); file_id = H5Fopen(fname.c_str(), H5F_ACC_RDONLY, plist_id); } diff --git a/cpp/full_code/NSE.cpp b/cpp/full_code/NSE.cpp index 25a4c3956f98143bba4be477490499fa67533921..fac9a0b3c622d46bdbddd5e91fd9c7f40bed0140 100644 --- a/cpp/full_code/NSE.cpp +++ b/cpp/full_code/NSE.cpp @@ -460,7 +460,7 @@ int NSE<rnumber>::ShuOsher(void) *this->tmp_velocity2 = rnumber(0); this->add_nonlinear_term(this->tmp_velocity1, this->tmp_velocity2); - this->add_forcing_term(this->velocity, this->tmp_velocity2); + this->add_forcing_term(this->tmp_velocity1, this->tmp_velocity2); this->kk->CLOOP_K2( [&](const ptrdiff_t cindex, const ptrdiff_t xindex, @@ -482,7 +482,7 @@ int NSE<rnumber>::ShuOsher(void) *this->tmp_velocity1 = rnumber(0); this->add_nonlinear_term(this->tmp_velocity2, this->tmp_velocity1); - this->add_forcing_term(this->velocity, this->tmp_velocity1); + this->add_forcing_term(this->tmp_velocity2, this->tmp_velocity1); this->kk->CLOOP_K2( [&](const ptrdiff_t cindex, const ptrdiff_t xindex, diff --git a/cpp/full_code/NSVEparticles.cpp b/cpp/full_code/NSVEparticles.cpp index f2c53a4eadb5770ffecb4bb440fbc5e899b662a6..3f24be4060ac03b45bdd55f13a81d46482327037 100644 --- a/cpp/full_code/NSVEparticles.cpp +++ b/cpp/full_code/NSVEparticles.cpp @@ -98,6 +98,7 @@ int NSVEparticles<rnumber>::initialize(void) this->particles_output_writer_mpi->close_file(); } + DEBUG_MSG("fs->iteration = %d\n", this->fs->iteration); DEBUG_MSG_WAIT(MPI_COMM_WORLD, "about to call particles_system_builder\n"); this->ps = particles_system_builder( this->fs->cvelocity, // (field object) diff --git a/cpp/kspace.cpp b/cpp/kspace.cpp index 921e498de2330bc64b97fc76ccd3492955448ede..369db6236fb8eaad52c9e0c2a7fdca35fb5d5198 100644 --- a/cpp/kspace.cpp +++ b/cpp/kspace.cpp @@ -28,6 +28,7 @@ #include <cstdlib> #include <algorithm> #include <cassert> +#include <stdexcept> #include "kspace.hpp" #include "scope_timer.hpp" #include "shared_array.hpp" @@ -201,8 +202,9 @@ int kspace<be, dt>::store(hid_t stat_file) if (this->nshells != int(dims[0])) { DEBUG_MSG( - "ERROR: computed nshells %d not equal to data file nshells %d\n", - this->nshells, dims[0]); + "ERROR: computed nshells %d not equal to data file nshells %d for dealiasing %d\n", + this->nshells, dims[0], dt); + throw std::runtime_error("Computed nshells not equal to data file nshells. Something is probably wrong with the dealiasing option.\n"); } H5Dwrite( dset, diff --git a/documentation/index.rst b/documentation/index.rst index 0566f7b4dad43652deef3c17020987a4ae0b896b..7788a2f226901d8a66b728ff6aa45dda63e8ff33 100644 --- a/documentation/index.rst +++ b/documentation/index.rst @@ -18,6 +18,10 @@ Contents: chapters/api chapters/cpp_doxygen + sphinx_static/convergence + + sphinx_static/bibliography + Indices and tables ================== diff --git a/documentation/sphinx_static/bibliography.rst b/documentation/sphinx_static/bibliography.rst new file mode 100644 index 0000000000000000000000000000000000000000..1b90b08284d75040e5732b0d84351946eb983036 --- /dev/null +++ b/documentation/sphinx_static/bibliography.rst @@ -0,0 +1,21 @@ +Bibliography +============ + +.. [fornberg1988mc] B. Fornberg, + *Generation of Finite Difference Formulas on Arbitrarily Spaced Grids*. + Mathematics of Computation, + **51:184**, 699-706, 1988 + +.. [ishihara2007jfm] T. Ishihara et al, + *Small-scale statistics in high-resolution direct numerical + simulation of turbulence: Reynolds number dependence of + one-point velocity gradient statistics*. + J. Fluid Mech., + **592**, 335-366, 2007 + +.. [lalescu2010jcp] C. C. Lalescu, B. Teaca and D. Carati + *Implementation of high order spline interpolations for tracking test + particles in discretized fields*. + J. Comput. Phys. + **229**, 5862-5869, 2010 + diff --git a/documentation/sphinx_static/convergence.rst b/documentation/sphinx_static/convergence.rst new file mode 100644 index 0000000000000000000000000000000000000000..5d0b9574ed83d8efb1465766e800f98b13de628e --- /dev/null +++ b/documentation/sphinx_static/convergence.rst @@ -0,0 +1,114 @@ +Tutorial: convergence test +========================== + +An essential property of numerical methods is their accuracy. With +standard approaches to differential equations, one may use +generic convergence tests to characterize algorithms and/or +implementations. + +As an example usage of TurTLE, we show here how to characterize +convergence for the field solver, or the AdamsBashforth +particle solver. +The purpose of this tutorial is to introduce TurTLE users to nontrivial +workflows that involve keeping track of a number of simulations and +prescribing their initial conditions. + +The field solver test is a fairly simple pursuit, showing basic +operations with the `turtle` launcher. + +The particle solver test is also minimal within the methodological +constraints imposed by the use of the Adams Bashforth integration +method, leading to a relatively increased complexity. +The example shows how to account for a number of technical details: full +control over multi-step method initialization and full control of fluid +solver forcing parameters. + + +Navier-Stokes solution +---------------------- + +TurTLE implements two distinct solvers of the Navier-Stokes equations: +one for their vorticity formulation, and one for the more common velocity +formulation. +While there are inescapable differences in the two implementations, they +both use the same time-stepping algorithm (a 3rd order RungeKutta +method). + +We test convergence properties for a "statistically stationary initial +condition", since the smoothness properties of the field will influence +convergence properties in general. +As an example of the variety of questions that we can address with +TurTLE, we also perform a direct comparison of the NSVE (vorticity +solver) and NSE (velocity solver) results. + +A basic Python script that performs this convergence test is provided +under `examples/convergence/fields_temporal.py`, and it is discussed +below. +In brief, simulations are performed using the same initial conditions, +but different time steps. +Error estimates are computed as differences between the different +solutions. +The figure shows the L2 norm of these differences, normalized by +the root-mean-squared velocity magnitude. +Note that the actual value of this "relative error" is irrelevant +(it depends on total integration time, spatial resolution, etc), but the +plot shows that (1) solutions converge with the 3rd order of the +timestep and (2) the systematic difference between NSE and NSVE behaves +quite differently from the two individual error estimates. + +.. image:: err_vs_dt_field.svg + +Particle tracking errors +------------------------ + +There is a more complex mechanism that generates numerical errors for +particle tracking in this setting. +In particular, the accuracy of the field itself is relevant, as well as +the accuracy of the interpolation method coupled to the ODE solver. +For instance the default particle tracking solver is a 4th order +Adams Bashforth method in TurTLE, which seems at first unnecessary since the +fluid only provides a 3rd order solution. +The default interpolation method is that of cubic splines, which should +in principle limit ODE error convergence to 2nd order (because convergence +relies on existence of relevant Taylor expansion terms, and interpolated +fields only have a finite number of continuous derivatives). +This discussion is briefly continued below, but we will not do it justice +in this tutorial. + +We present below a Python script that performs a particle tracking +convergence test, provided as +`examples/convergence/particles_temporal.py`. +The figure shows trajectory integration errors, in a fairly simple +setting, for two interpolation methods: cubic splines (I4O3) and 5th +order splines on a kernel of 8 points (I8O5). +Furthermore, we show both the maximum and the mean errors for the same +set of trajectories. +While both mean errors seem to converge with the 3rd order of the +timestep (consistent with the error of the velocity field), the maximum +error obtained for cubic splines converges with the second order --- +which is the expected behavior for particle tracking in a field that +only has one continuous derivative. + +.. image:: err_vs_dt_particle.svg + +The results would merit a longer and more careful analysis outside the +scope of this particular tutorial, so we limit ourselves to noting that +(1) different ODEs will have different numerical properties (i.e. +rotating particles, or inertial particles) and (2) interpolation errors +may in general grow with the Reynolds number, since interpolation +errors depend on values of gradients (however the distribution of +extreme gradient values also changes with Reynolds number, so the +overall behavior is complex). + + +Python code for fields +---------------------- + +.. include:: convergence_fields.rst + + +Python code for particles +------------------------- + +.. include:: convergence_particles.rst + diff --git a/documentation/sphinx_static/convergence_fields.rst b/documentation/sphinx_static/convergence_fields.rst new file mode 100644 index 0000000000000000000000000000000000000000..5830e4e7dff3e479d4e050678870cd68649d7e0d --- /dev/null +++ b/documentation/sphinx_static/convergence_fields.rst @@ -0,0 +1,281 @@ +We present here a Python script that performs simple convergence tests +with TurTLE. The script itself is provided as the file +`examples/convergence/fields_temporal.py`. + +The preamble imports standard packages, TurTLE itself, and a few simple +tools from `examples/convergence/fields_base.py` (not discussed here): + +.. code:: python + + import numpy as np + import h5py + import matplotlib.pyplot as plt + + import TurTLE + from TurTLE import DNS, PP + + from fields_base import * + +As explained above, we should test convergence for a statistically +stationary regime. +The base simulation will use a real-space grid of :math:`128 \times 128 \times 128` points, +and experience shows that reasonable quasistationarity is reached for this +problem-size in a few hundred iterations (here `base_niterations`). +For the convergence test itself, we use a relatively small number +of iterations (i.e. `test_niterations`), otherwise deterministic chaos will dominate the +difference between different solutions (rather than numerical integration +errors). + +.. code:: python + + base_niterations = 512 + test_niterations = 32 + grid_size = 128 + +We distinguish between three steps of this script. +First, we generate the statistically quasistationary regime. +Second, we run the fluid solver. +Finally, we "analyze" the results (i.e. we generate simple error plots). + +.. code:: python + + def main(): + generate_initial_conditions() + + run_simulations_field( + err_vs_t = False) + plot_error_field( + err_vs_t = False) + return None + +The `err_vs_t` parameter may be used if one is interested in looking at +the difference between the NSE and NSVE solutions as a function of time. +It turns on a fine-grained output of the fields in +`run_simulations_field` and it turns on the corresponding plot in +`plot_error_field`. + +`generate_initial_conditions` performs a few calls to C++ executable +codes generated with TurTLE. In brief, it + + * generates a vorticity field in a quasistationary Navier-Stokes + regime (using the NSVE solver). + * generates the corresponding velocity field needed for the NSE solver + +We use the `launch` method of the `DNS` and `PP` Python +classes --- the wrappers around the C++ `direct_numerical_simulation` +and `postprocess` functionality. +This means that the current Python code may be translated to a shell +script directly, only by writing out the arguments (rather than placing +them in a list of Python strings). +The full function is given below: + +.. code:: python + + def generate_initial_conditions(): + # change these two values as needed. + # number of MPI processes to use + nprocesses = 8 + # number of OpenMP threads per MPI process to use + nthreads_per_process = 1 + + # 1. Generate quasistationary state to use for initial conditions. + # create a dns object + c0 = DNS() + # launch the simulation + c0.launch([ + 'NSVE', + '-n', '{0}'.format(grid_size), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--precision', 'double', + '--src-simname', 'B32p1e4', + '--src-wd', TurTLE.data_dir, + '--src-iteration', '0', + '--simname', 'base', + '--niter_todo', '{0}'.format(base_niterations), + '--niter_out', '{0}'.format(base_niterations), + '--overwrite-src-parameters', + '--kMeta', '1.5', + '--fk0', '2', + '--fk1', '3', + '--niter_stat', '16', + '--checkpoints_per_file', '{0}'.format(64)]) + + # 3. Generate initial conditions for NSE runs. + # create postprocess object + cc = PP() + # launches code to compute velocity field at last iteration + cc.launch([ + 'get_velocity', + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--simname', 'base', + '--precision', 'double', + '--iter0', '{0}'.format(base_niterations), + '--iter1', '{0}'.format(base_niterations)]) + return None + +`run_simulations_field` runs six DNS (3 resolutions for each of NSE and +NSVE solvers): + +.. code:: python + + def run_simulations_field(err_vs_t = False): + # change these two values as needed. + # number of MPI processes to use + nprocesses = 8 + # number of OpenMP threads per MPI process to use + nthreads_per_process = 1 + + if err_vs_t: + niter_out_factor = 1 + else: + niter_out_factor = test_niterations + + # 1. Run NSVE for the three resolutions. + for factor in [1, 2, 4]: + # create dns object + cc = DNS() + # launch simulation + cc.launch([ + 'NSVE', + '-n', '{0}'.format(grid_size), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--src-simname', 'base', + '--src-iteration', '{0}'.format(base_niterations), + '--simname', 'nsve_{0}x'.format(factor), + '--precision', 'double', + '--dtfactor', '{0}'.format(0.5 / factor), + '--niter_todo', '{0}'.format(test_niterations*factor), + '--niter_out', '{0}'.format(niter_out_factor*factor), + '--niter_stat', '{0}'.format(factor)]) + + # 2. Run NSE for the three resolutions. + for factor in [1, 2, 4]: + # create dns object + cc = DNS() + # launch simulation + cc.launch([ + 'NSE', + '-n', '{0}'.format(grid_size), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--src-simname', 'base', + '--src-iteration', '{0}'.format(base_niterations), + '--simname', 'nse_{0}x'.format(factor), + '--precision', 'double', + '--dtfactor', '{0}'.format(0.5 / factor), + '--niter_todo', '{0}'.format(test_niterations*factor), + '--niter_out', '{0}'.format(niter_out_factor*factor), + '--niter_out', '{0}'.format(test_niterations*factor), + '--niter_stat', '{0}'.format(factor)]) + return None + +Once the runs are finished successfully, the code calls +`plot_error_field`. +Here we first read the output of the six different runs, and we compute +their statistics, since the call to `compute_statistics` will also +perform some sanity checks on the output. +We then compute the error analysis for each of the two solvers, and also +compare the two solutions. +The `get_velocity` and `compute_vector_field_distance` methods are defined in +`examples/convergence/fields_base.py`. + +.. code:: python + + def plot_error_field(err_vs_t = False): + factor_list = [1, 2, 4] + c0_list = [DNS(simname = 'nsve_{0}x'.format(factor)) + for factor in factor_list] + c1_list = [DNS(simname = 'nse_{0}x'.format(factor)) + for factor in factor_list] + cl = [c0_list, c1_list] + # sanity checks + for cc in c0_list + c1_list: + cc.compute_statistics() + + # errors for individual solvers + error_list = [[], [], []] + for ii in range(len(factor_list)-1): + factor = factor_list[ii] + for jj in [0, 1]: + vel1 = get_velocity(cl[jj][ii ], iteration = test_niterations*factor) + vel2 = get_velocity(cl[jj][ii+1], iteration = 2*test_niterations*factor) + dd = compute_vector_field_distance(vel1, vel2, figname = cl[jj][ii].simname + '_vs_' + cl[jj][ii+1].simname) + error_list[jj].append(dd['L2_rel']) + + # comparisons of two solutions + for ii in range(len(factor_list)): + factor = factor_list[ii] + vel1 = get_velocity(cl[0][ii], iteration = test_niterations*factor) + vel2 = get_velocity(cl[1][ii], iteration = test_niterations*factor) + dd = compute_vector_field_distance(vel1, vel2) + error_list[2].append(dd['L2_rel']) + + f = plt.figure(figsize = (4, 4)) + a = f.add_subplot(111) + a.plot(factor_list[:len(error_list[0])], + error_list[0], + marker = '.', + dashes = (2, 3), + label = 'NSVE') + a.plot(factor_list[:len(error_list[1])], + error_list[1], + marker = '.', + dashes = (3, 5), + label = 'NSE') + a.plot(factor_list, + error_list[2], + marker = '.', + label = 'NSVE vs NSE') + fl = np.array(factor_list).astype(np.float) + for ee in [2, 3]: + a.plot(fl[:2], error_list[0][0] * fl[:2]**(-ee), + dashes = (ee, ee), + color = 'black', + label = '$\propto f^{{-{0}}}$'.format(ee), + zorder = -ee) + a.set_ylabel('relative error') + a.set_xlabel('resolution factor $f$') + a.set_xscale('log') + a.set_yscale('log') + a.legend(loc = 'best', fontsize = 6) + f.tight_layout() + f.savefig('err_vs_dt_field.pdf') + f.savefig('err_vs_dt_field.svg') + plt.close(f) + + if err_vs_t: + t = range(test_niterations+1) + err_vs_t = [[], [], []] + # comparisons of two solvers + for ii in range(len(factor_list)): + factor = factor_list[ii] + for tt in t: + vel1 = get_velocity(cl[0][ii], iteration = tt*factor) + vel2 = get_velocity(cl[1][ii], iteration = tt*factor) + dd = compute_vector_field_distance(vel1, vel2) + err_vs_t[ii].append(dd['L2_rel']) + # distance between NSVE and NSE as a function of time + f = plt.figure(figsize = (4, 4)) + a = f.add_subplot(111) + a.plot(t, err_vs_t[0], label = 'f = 1') + a.plot(t, err_vs_t[1], label = 'f = 2') + a.plot(t, err_vs_t[2], label = 'f = 4') + a.set_yscale('log') + a.legend(loc = 'best', fontsize = 6) + f.tight_layout() + f.savefig('err_vs_t_field.pdf') + f.savefig('err_vs_t_field.svg') + plt.close(f) + return None + + +Finally, the script ends with a standard call to `main`: + +.. code:: python + + if __name__ == '__main__': + main() + diff --git a/documentation/sphinx_static/convergence_particles.rst b/documentation/sphinx_static/convergence_particles.rst new file mode 100644 index 0000000000000000000000000000000000000000..45fd4dab443a3dd3e51c911090ad0cfd1c01e316 --- /dev/null +++ b/documentation/sphinx_static/convergence_particles.rst @@ -0,0 +1,405 @@ +We present here a Python script that performs a particle tracking +convergence test with TurTLE, in the current default configuration (a +`particles_system` object coupled with an NSVE fluid solver). + +The preamble imports standard packages, and TurTLE itself: + +.. code:: python + + import numpy as np + import h5py + import matplotlib.pyplot as plt + + import TurTLE + from TurTLE import DNS + +We then set a few basic parameters, including a list of interpolation +parameters. +In brief, the spline interpolations used in TurTLE are parametrized by +the size :math:`I` of the interpolation kernel and the order :math:`O` of +the polynomial. +In this example code we emphasize two equivalences: + +* :math:`I = 2 n + 2` where :math:`n` is the number of neighbouring + points (in one orientation) required to interpolate the field + within one cell. +* :math:`O = 2 m + 1` where :math:`m` is the order of highest + continuous derivative of the interpolating polynomial. + +More details on the interpolation method can be found in +[lalescu2010jcp]_. + +.. code:: python + + base_niterations = 256 + + nparticles = 1000 + particle_random_seed = 15 + base_particle_dt = 0.5 + test_niterations_particles = 128 + + neighbours_smoothness_list = [ + (1, 1), + (3, 2)] + +We distinguish between three main parts of this script: generation of +initial conditions with statistically stationary regime, computation of +numerical solutions, analysis of results (plot commands): + +.. code:: python + + def main(): + generate_initial_conditions() + + run_simulations_particles() + + plot_error_particles() + plot_traj_particles() + return None + +`generate_initial_conditions` consists of a single launch of an NSVE +run: + +.. code:: python + + def generate_initial_conditions(): + # change these two values as needed. + # number of MPI processes to use + nprocesses = 8 + # number of OpenMP threads per MPI process to use + nthreads_per_process = 1 + + # 1. Generate quasistationary state to use for initial conditions. + # create a dns object + c0 = DNS() + # launch the simulation + c0.launch([ + 'NSVE', + '-n', '32', + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--precision', 'double', + '--src-simname', 'B32p1e4', + '--src-wd', TurTLE.data_dir, + '--src-iteration', '0', + '--simname', 'base', + '--niter_todo', '{0}'.format(base_niterations), + '--niter_out', '{0}'.format(base_niterations), + '--overwrite-src-parameters', + '--kMeta', '1.', + '--niter_stat', '16', + '--checkpoints_per_file', '{0}'.format(16)]) + return None + +We then define the function that runs the particle simulations, +`run_simulations_particles`. +Because we use an Adams-Bashforth method, we need to know the values of +the particle velocity (i.e. the right-hand-side of the ODE) at previous +steps. +By default TurTLE accomplishes this by using the Euler integration scheme +for "time step 0", then using a 2nd order Adams-Bashforth, etc, until +the desired number of right-hand-side values is stored. +Thus the code first integrates trajectories for 8 iterations, and the +output will contain the additional information. +This happens because such information is crucial for checkpointing --- +i.e. stopping/restarting the simulation at arbitrary iterations without +affecting the numerical solution. + +To put it simply, for the simulation "nsvep_base" the dataset +"tracers0/rhs/0" contains only zeros, and TurTLE ignores them. +However, the "tracers0/rhs/8" dataset for simulation "nsvep_1x" contains +meaningful values (that **are** used because we request that `iter0` is +different from 0). +In order to generate consistent values of the "rhs" datasets, we first +run a simulation at the highest resolution (smallest time-step), and +then we extract the appropriate snapshots --- see also the second part +of the trajectory plot function. + +Finally, the `launch` method is called in an unusual way for TurTLE. +Firstly, we demand a DNS that starts at an iteration different from 0. +Secondly, we manually copy the forcing parameters from the source +simulation; since the source cannot be specified explicitly, the `DNS` +class cannot search for the source parameters itself. +Thirdly, I will note that one may in fact break this call by modifying +the `iter0` and `checkpoints_per_file` values, since we have explicitly +placed `iter0` in the `checkpoint` 0 file. +While a full discussion of the `iter0` and `checkpoint` subtleties is +beyond the scope of this tutorial, I will mention that it was a +conscious choice to use a simple `iteration` to `checkpoint` +correspondence, since we don't actually need anything smarter outside of +extreme scenarios that need to be addressed individually anyway +due to other complexities. + +.. code:: python + + def run_simulations_particles(): + # change these two values as needed. + # number of MPI processes to use + nprocesses = 8 + # number of OpenMP threads per MPI process to use + nthreads_per_process = 1 + + # 1. Run NSVEparticles for a few iterations, to build up rhs values, consistent + # with the relevant velocity field. + factor = 1 + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + # create dns object + cc = DNS() + # launch simulation + cc.launch([ + 'NSVEparticles', + '-n', '{0}'.format(factor*32), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--src-simname', 'base', + '--src-iteration', '{0}'.format(base_niterations), + '--simname', 'nsvep_base_' + interp_name, + '--precision', 'double', + '--dtfactor', '{0}'.format(base_particle_dt/4), + '--kMeta', '{0}'.format(factor*1.0), + '--niter_todo', '{0}'.format(20), + '--niter_out', '{0}'.format(1), + '--niter_stat', '{0}'.format(1), + '--nparticles', '{0}'.format(nparticles), + '--niter_part', '{0}'.format(1), + '--tracers0_neighbours', '{0}'.format(neighbours), + '--tracers0_smoothness', '{0}'.format(smoothness), + '--tracers0_integration_steps', '4', + '--cpp_random_particles', '{0}'.format(particle_random_seed), + '--checkpoints_per_file', '{0}'.format(16)]) + + # 2. Prepare initial conditions + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + for factor in [1, 2, 4]: + df = h5py.File('nsvep_{0}x_{1}_checkpoint_0.h5'.format(factor, interp_name), 'w') + # field + field_iteration = 16 + df['vorticity/complex/{0}'.format(8*factor)] = h5py.ExternalLink( + 'nsvep_base_{0}_checkpoint_0.h5'.format(interp_name), + 'vorticity/complex/{0}'.format(field_iteration)) + # particles + df['tracers0/state/{0}'.format(8*factor)] = h5py.ExternalLink( + 'nsvep_base_{0}_checkpoint_0.h5'.format(interp_name), + 'tracers0/state/16') + # copy rhs + source_file = h5py.File( + 'nsvep_base_{0}_checkpoint_0.h5'.format(interp_name), 'r') + rhs = source_file['tracers0/rhs/16'][()] + for tt in range(1, rhs.shape[0]): + ii = 16 - tt*4//factor + 1 + #print(factor, tt, ii) + rhs[tt] = source_file['tracers0/rhs/{0}'.format(16 - tt*4//factor + 1)][1] + df['tracers0/rhs/{0}'.format(8*factor)] = rhs + df.close() + + # 3. Run NSVEparticles + for factor in [1, 2, 4]: + # Test different interpolations. + # The loop iterates over number of neighbours and smoothness. + # The simulation names are defined based on "kernel size" and "order + # of polynomial". + # We do this to emphasize the one-to-one correspondence between + # neighbours and kernel size, and smoothness and order of polynomial. + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + source_file = h5py.File('nsvep_base_{0}.h5'.format(interp_name), 'r') + # create dns object + cc = DNS() + # launch simulation + cc.launch([ + 'NSVEparticles', + '-n', '{0}'.format(source_file['parameters/nx'][()]), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--simname', 'nsvep_{0}x_{1}'.format(factor, interp_name), + '--precision', 'double', + '--dtfactor', '{0}'.format(base_particle_dt/factor), + '--niter_todo', '{0}'.format(test_niterations_particles*factor+8*factor), + '--niter_out', '{0}'.format(test_niterations_particles*factor+8*factor), + '--niter_stat', '{0}'.format(1), + ## ensure fluid physics is the same + '--dealias_type', '{0}'.format(source_file['parameters/dealias_type'][()]), + '--energy', '{0}'.format(source_file['parameters/energy'][()]), + '--famplitude', '{0}'.format(source_file['parameters/famplitude'][()]), + '--fk0', '{0}'.format(source_file['parameters/fk0'][()]), + '--fk1', '{0}'.format(source_file['parameters/fk1'][()]), + '--fmode', '{0}'.format(source_file['parameters/fmode'][()]), + '--friction_coefficient', '{0}'.format(source_file['parameters/friction_coefficient'][()]), + '--injection_rate', '{0}'.format(source_file['parameters/injection_rate'][()]), + '--nu', '{0}'.format(source_file['parameters/nu'][()]), + '--forcing_type', '{0}'.format(str(source_file['parameters/forcing_type'][()], 'ascii')), + ## particle params + '--nparticles', '{0}'.format(nparticles), + '--niter_part', '{0}'.format(1), + '--tracers0_neighbours', '{0}'.format(neighbours), + '--tracers0_smoothness', '{0}'.format(smoothness), + '--tracers0_integration_steps', '4', + '--cpp_random_particles', '0', # turn off C++ particle initialization + '--checkpoints_per_file', '{0}'.format(16)], + iter0 = 8*factor) + source_file.close() + return None + +To compute the trajectory integration error, we proceed as explained +above, and compare each DNS with its corresponding double-the-resolution DNS: + +.. code:: python + + def plot_error_particles(): + f = plt.figure() + a = f.add_subplot(111) + factor_list = [1, 2] + factor_list = np.array(factor_list).astype(np.float) + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + err_max_list = [] + err_mean_list = [] + for factor in factor_list: + factor = int(factor) + c1 = DNS(simname = 'nsvep_{0}x_'.format(int(factor)) + interp_name) + c2 = DNS(simname = 'nsvep_{0}x_'.format(int(factor)*2) + interp_name) + for cc in [c1, c2]: + cc.parameters['niter_part'] = cc.get_data_file()['parameters/niter_part'][()] + c1.compute_statistics(iter0 = 8*factor) + c2.compute_statistics(iter0 = 8*factor*2) + final_iter_x1 = c1.get_data_file()['iteration'][()] + final_iter_x2 = c2.get_data_file()['iteration'][()] + f1 = h5py.File(c1.simname + '_checkpoint_0.h5', 'r') + f2 = h5py.File(c2.simname + '_checkpoint_0.h5', 'r') + x1 = f1['tracers0/state/{0}'.format(final_iter_x1)][()] + x2 = f2['tracers0/state/{0}'.format(final_iter_x2)][()] + diff = np.sqrt(np.sum((x2-x1)**2, axis = -1)) + err_max_list.append(np.max(diff)) + err_mean_list.append(np.mean(diff)) + f1.close() + f2.close() + err_max_list = np.array(err_max_list) + err_mean_list = np.array(err_mean_list) + a.plot(factor_list, err_max_list, marker = '.', label = 'max error ' + interp_name) + a.plot(factor_list, err_mean_list, marker = '.', label = 'mean error ' + interp_name) + for ee in [2, 3, 4]: + a.plot(factor_list, + (1e-4)*factor_list**(-ee), + color = 'black', + dashes = (ee, ee), + label = '$\propto f^{{-{0}}}$'.format(ee)) + a.set_xscale('log') + a.set_yscale('log') + a.set_xlabel('resolution factor f') + a.set_ylabel('absolute trajectory error [DNS units]') + a.legend(loc = 'best', fontsize = 7) + f.tight_layout() + f.savefig('err_vs_dt_particle.pdf') + f.savefig('err_vs_dt_particle.svg') + plt.close(f) + return None + +For the beginner's convenience, we also provide a method to plot +individual particle trajectories. +Note that the second part of this function is in fact a sanity check for +the initial conditions: the plot confirms that the data required for the +multi-step method (explicitly placed in the checkpoint file) is +consistent with the simulation parameters. + +.. code:: python + + def plot_traj_particles(): + ########################################################################### + f = plt.figure() + a = f.add_subplot(111) + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + for factor in [1, 2, 4]: + cc = DNS(simname = 'nsvep_{0}x_'.format(factor) + interp_name) + cc.compute_statistics(iter0 = 8*factor) + tt = 3 + xx = read_trajectory(cc, tt, iter0 = 8*factor) + a.plot(xx[:, 0], + xx[:, 1], + label = interp_name + '$f = {0}$'.format(factor), + marker = 'x', + dashes = (4/factor, 3, 4/factor), + alpha = 0.2) + #a.plot(xx[:, 0], xx[:, 1], dashes = (4/factor, 3, 4/factor), alpha = 0.2) + a.legend(loc = 'best', fontsize = 7) + a.set_xlabel('$x$ [code units]') + a.set_ylabel('$y$ [code units]') + f.tight_layout() + f.savefig('trajectories.pdf') + f.savefig('trajectories.svg') + plt.close(f) + ########################################################################### + ########################################################################### + traj_index = 3 + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + cc = DNS(simname = 'nsvep_base_' + interp_name) + cc.compute_statistics() + xx_base = read_trajectory(cc, traj_index, iter0 = 0, dset_name = 'velocity') + iter0 = 16 + tt_base = np.array(range(iter0, iter0 + xx_base.shape[0]))*cc.parameters['dt'] + f = plt.figure() + ax_counter = 1 + for factor in [1, 2, 4]: + a = f.add_subplot(310 + ax_counter) + ax_counter += 1 + a.plot(tt_base, + xx_base[:, 2], + label = 'base_' + interp_name, + marker = '+', + linewidth = 0.5, + alpha = 0.2) + cc = DNS(simname = 'nsvep_{0}x_'.format(factor) + interp_name) + cc.compute_statistics(iter0 = 8*factor) + xx = read_trajectory(cc, traj_index, iter0 = 8*factor, dset_name = 'velocity') + tt = np.array(range(8*factor, xx.shape[0]+8*factor))*cc.parameters['dt'] + a.plot(tt, + xx[:, 2], + label = interp_name + '$f = {0}$'.format(factor), + marker = 'x', + dashes = (4/factor, 3, 4/factor), + alpha = 0.2) + df = h5py.File(cc.simname + '_checkpoint_0.h5', 'r') + xx = df['tracers0/rhs/{0}'.format(8*factor)][()] + for rhs_index in [1, 2, 3]: + a.scatter((8*factor - rhs_index)*cc.parameters['dt'], + xx[rhs_index, traj_index, 2], + marker = '*', + zorder = -10, + alpha = 0.5, + color = 'black') + df.close() + a.legend(loc = 'best', fontsize = 7) + a.set_xlabel('$t$ [code units]') + a.set_ylabel('$v_y$ [code units]') + f.tight_layout() + f.savefig('velocities_{0}.pdf'.format(interp_name)) + plt.close(f) + ########################################################################### + return None + + def read_trajectory( + cc, + traj_index, + iter0, + dset_name = 'position'): + cc.parameters['niter_part'] = cc.get_data_file()['parameters/niter_part'][()] + df = cc.get_particle_file() + xx = [] + for ii in range(iter0, cc.get_data_file()['iteration'][()]+1, cc.parameters['niter_part']): + xx.append(df['tracers0/' + dset_name + '/{0}'.format(ii)][traj_index]) + df.close() + return np.array(xx) + +.. image:: trajectories.svg + +Finally, the script ends 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a/examples/convergence/fields_base.py b/examples/convergence/fields_base.py new file mode 100644 index 0000000000000000000000000000000000000000..d2225d3245c01f2b2ff24cad482dae7cc364d6e4 --- /dev/null +++ b/examples/convergence/fields_base.py @@ -0,0 +1,78 @@ +import numpy as np +import h5py +import matplotlib.pyplot as plt + +def main(): + return None + +def get_velocity( + cc, + iteration = 0): + data_file = h5py.File( + cc.get_checkpoint_fname(iteration = iteration), + 'r') + if 'velocity' in data_file.keys(): + if 'real' in data_file['velocity'].keys(): + vel = data_file['velocity/real/{0}'.format(iteration)][()] + else: + cvel = data_file['velocity/complex/{0}'.format(iteration)][()] + vel = ift(cvel) + else: + assert('complex' in data_file['vorticity'].keys()) + cvort = data_file['vorticity/complex/{0}'.format(iteration)][()] + cvel = compute_curl(cc, cvort, inverse_curl = True) + vel = ift(cvel) + data_file.close() + return vel + +def ift(cfield): + ff = np.fft.irfftn(cfield, axes = (0, 1, 2)) + field = np.transpose(ff, (1, 0, 2, 3)).copy() + return field*(field.shape[0]*field.shape[1]*field.shape[2]) + +def compute_curl( + cc, + cfield, + inverse_curl = False): + kx = cc.get_data_file()['kspace/kx'][()] + ky = cc.get_data_file()['kspace/ky'][()] + kz = cc.get_data_file()['kspace/kz'][()] + ff = cfield.copy() + ff[..., 0] = 1j*(ky[:, None, None]*cfield[..., 2] - kz[None, :, None]*cfield[..., 1]) + ff[..., 1] = 1j*(kz[None, :, None]*cfield[..., 0] - kx[None, None, :]*cfield[..., 2]) + ff[..., 2] = 1j*(kx[None, None, :]*cfield[..., 1] - ky[:, None, None]*cfield[..., 0]) + if inverse_curl: + k2 = (kx[None, None, :]**2 + + ky[ :, None, None]**2 + + kz[None, :, None]**2) + k2[0, 0, 0] = 1. + ff /= k2[:, :, :, None] + return ff + +def compute_vector_field_distance( + f1, f2, + figname = None): + diff = f1 - f2 + rms1 = np.mean(np.sum(f1**2, axis = 3))**0.5 + rms2 = np.mean(np.sum(f2**2, axis = 3))**0.5 + rms = np.sqrt(rms1 * rms2) + dd = np.sum(diff**2, axis = 3) + L2 = np.sqrt(np.mean(dd)) + max_val = np.max(np.sqrt(dd)) + if type(figname) != type(None): + fig = plt.figure(figsize = (8, 4)) + a = fig.add_subplot(121) + a.imshow(f1[:, 5, :, 2], vmin = -1, vmax = 1, interpolation = 'none') + a = fig.add_subplot(122) + a.imshow(f2[:, 5, :, 2], vmin = -1, vmax = 1, interpolation = 'none') + fig.tight_layout() + fig.savefig('field_slice_' + figname + '.pdf') + plt.close(fig) + return {'L2' : L2, + 'L2_rel' : L2 / rms, + 'max' : max_val, + 'max_rel' : max_val / rms} + +if __name__ == '__main__': + main() + diff --git a/examples/convergence/fields_temporal.py b/examples/convergence/fields_temporal.py new file mode 100644 index 0000000000000000000000000000000000000000..d5e271be336b70303c6e2845a438293930834a6e --- /dev/null +++ b/examples/convergence/fields_temporal.py @@ -0,0 +1,208 @@ +import numpy as np +import h5py +import matplotlib.pyplot as plt + +import TurTLE +from TurTLE import DNS, PP + +from fields_base import * + +base_niterations = 512 +test_niterations = 32 +grid_size = 128 + +def main(): + generate_initial_conditions() + + run_simulations_field( + err_vs_t = False) + plot_error_field( + err_vs_t = False) + return None + +def generate_initial_conditions(): + # change these two values as needed. + # number of MPI processes to use + nprocesses = 8 + # number of OpenMP threads per MPI process to use + nthreads_per_process = 1 + +# 1. Generate quasistationary state to use for initial conditions. + # create a dns object + c0 = DNS() + # launch the simulation + c0.launch([ + 'NSVE', + '-n', '{0}'.format(grid_size), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--precision', 'double', + '--src-simname', 'B32p1e4', + '--src-wd', TurTLE.data_dir, + '--src-iteration', '0', + '--simname', 'base', + '--niter_todo', '{0}'.format(base_niterations), + '--niter_out', '{0}'.format(base_niterations), + '--overwrite-src-parameters', + '--kMeta', '1.5', + '--fk0', '2', + '--fk1', '3', + '--niter_stat', '16', + '--checkpoints_per_file', '{0}'.format(64)]) + +# 3. Generate initial conditions for NSE runs. + # create postprocess object + cc = PP() + # launches code to compute velocity field at last iteration + cc.launch([ + 'get_velocity', + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--simname', 'base', + '--precision', 'double', + '--iter0', '{0}'.format(base_niterations), + '--iter1', '{0}'.format(base_niterations)]) + return None + +def run_simulations_field(err_vs_t = False): + # change these two values as needed. + # number of MPI processes to use + nprocesses = 8 + # number of OpenMP threads per MPI process to use + nthreads_per_process = 1 + + if err_vs_t: + niter_out_factor = 1 + else: + niter_out_factor = test_niterations + +# 1. Run NSVE for the three resolutions. + for factor in [1, 2, 4]: + # create dns object + cc = DNS() + # launch simulation + cc.launch([ + 'NSVE', + '-n', '{0}'.format(grid_size), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--src-simname', 'base', + '--src-iteration', '{0}'.format(base_niterations), + '--simname', 'nsve_{0}x'.format(factor), + '--precision', 'double', + '--dtfactor', '{0}'.format(0.5 / factor), + '--niter_todo', '{0}'.format(test_niterations*factor), + '--niter_out', '{0}'.format(niter_out_factor*factor), + '--niter_stat', '{0}'.format(factor)]) + +# 2. Run NSE for the three resolutions. + for factor in [1, 2, 4]: + # create dns object + cc = DNS() + # launch simulation + cc.launch([ + 'NSE', + '-n', '{0}'.format(grid_size), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--src-simname', 'base', + '--src-iteration', '{0}'.format(base_niterations), + '--simname', 'nse_{0}x'.format(factor), + '--precision', 'double', + '--dtfactor', '{0}'.format(0.5 / factor), + '--niter_todo', '{0}'.format(test_niterations*factor), + '--niter_out', '{0}'.format(niter_out_factor*factor), + '--niter_out', '{0}'.format(test_niterations*factor), + '--niter_stat', '{0}'.format(factor)]) + return None + +def plot_error_field(err_vs_t = False): + factor_list = [1, 2, 4] + c0_list = [DNS(simname = 'nsve_{0}x'.format(factor)) + for factor in factor_list] + c1_list = [DNS(simname = 'nse_{0}x'.format(factor)) + for factor in factor_list] + cl = [c0_list, c1_list] + # sanity checks + for cc in c0_list + c1_list: + cc.compute_statistics() + + # errors for individual solvers + error_list = [[], [], []] + for ii in range(len(factor_list)-1): + factor = factor_list[ii] + for jj in [0, 1]: + vel1 = get_velocity(cl[jj][ii ], iteration = test_niterations*factor) + vel2 = get_velocity(cl[jj][ii+1], iteration = 2*test_niterations*factor) + dd = compute_vector_field_distance(vel1, vel2, figname = cl[jj][ii].simname + '_vs_' + cl[jj][ii+1].simname) + error_list[jj].append(dd['L2_rel']) + + # comparisons of two solutions + for ii in range(len(factor_list)): + factor = factor_list[ii] + vel1 = get_velocity(cl[0][ii], iteration = test_niterations*factor) + vel2 = get_velocity(cl[1][ii], iteration = test_niterations*factor) + dd = compute_vector_field_distance(vel1, vel2) + error_list[2].append(dd['L2_rel']) + + f = plt.figure(figsize = (4, 4)) + a = f.add_subplot(111) + a.plot(factor_list[:len(error_list[0])], + error_list[0], + marker = '.', + dashes = (2, 3), + label = 'NSVE') + a.plot(factor_list[:len(error_list[1])], + error_list[1], + marker = '.', + dashes = (3, 5), + label = 'NSE') + a.plot(factor_list, + error_list[2], + marker = '.', + label = 'NSVE vs NSE') + fl = np.array(factor_list).astype(np.float) + for ee in [2, 3]: + a.plot(fl[:2], error_list[0][0] * fl[:2]**(-ee), + dashes = (ee, ee), + color = 'black', + label = '$\propto f^{{-{0}}}$'.format(ee), + zorder = -ee) + a.set_ylabel('relative error') + a.set_xlabel('resolution factor $f$') + a.set_xscale('log') + a.set_yscale('log') + a.legend(loc = 'best', fontsize = 6) + f.tight_layout() + f.savefig('err_vs_dt_field.pdf') + f.savefig('err_vs_dt_field.svg') + plt.close(f) + + if err_vs_t: + t = range(test_niterations+1) + err_vs_t = [[], [], []] + # comparisons of two solvers + for ii in range(len(factor_list)): + factor = factor_list[ii] + for tt in t: + vel1 = get_velocity(cl[0][ii], iteration = tt*factor) + vel2 = get_velocity(cl[1][ii], iteration = tt*factor) + dd = compute_vector_field_distance(vel1, vel2) + err_vs_t[ii].append(dd['L2_rel']) + # distance between NSVE and NSE as a function of time + f = plt.figure(figsize = (4, 4)) + a = f.add_subplot(111) + a.plot(t, err_vs_t[0], label = 'f = 1') + a.plot(t, err_vs_t[1], label = 'f = 2') + a.plot(t, err_vs_t[2], label = 'f = 4') + a.set_yscale('log') + a.legend(loc = 'best', fontsize = 6) + f.tight_layout() + f.savefig('err_vs_t_field.pdf') + f.savefig('err_vs_t_field.svg') + plt.close(f) + return None + +if __name__ == '__main__': + main() + diff --git a/examples/convergence/particles_temporal.py b/examples/convergence/particles_temporal.py new file mode 100644 index 0000000000000000000000000000000000000000..c7b0ac15573a97031bd9a72e706674d03f6d8a8f --- /dev/null +++ b/examples/convergence/particles_temporal.py @@ -0,0 +1,304 @@ +import numpy as np +import h5py +import matplotlib.pyplot as plt + +import TurTLE +from TurTLE import DNS + +base_niterations = 256 + +nparticles = 1000 +particle_random_seed = 15 +base_particle_dt = 0.5 +test_niterations_particles = 128 + +neighbours_smoothness_list = [ + (1, 1), + (3, 2)] + +def main(): + generate_initial_conditions() + + run_simulations_particles() + + plot_error_particles() + plot_traj_particles() + return None + +def generate_initial_conditions(): + # change these two values as needed. + # number of MPI processes to use + nprocesses = 8 + # number of OpenMP threads per MPI process to use + nthreads_per_process = 1 + +# 1. Generate quasistationary state to use for initial conditions. + # create a dns object + c0 = DNS() + # launch the simulation + c0.launch([ + 'NSVE', + '-n', '32', + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--precision', 'double', + '--src-simname', 'B32p1e4', + '--src-wd', TurTLE.data_dir, + '--src-iteration', '0', + '--simname', 'base', + '--niter_todo', '{0}'.format(base_niterations), + '--niter_out', '{0}'.format(base_niterations), + '--overwrite-src-parameters', + '--kMeta', '1.', + '--niter_stat', '16', + '--checkpoints_per_file', '{0}'.format(16)]) + return None + +def run_simulations_particles(): + # change these two values as needed. + # number of MPI processes to use + nprocesses = 8 + # number of OpenMP threads per MPI process to use + nthreads_per_process = 1 + +# 1. Run NSVEparticles for a few iterations, to build up rhs values, consistent +# with the relevant velocity field. + factor = 1 + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + # create dns object + cc = DNS() + # launch simulation + cc.launch([ + 'NSVEparticles', + '-n', '{0}'.format(factor*32), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--src-simname', 'base', + '--src-iteration', '{0}'.format(base_niterations), + '--simname', 'nsvep_base_' + interp_name, + '--precision', 'double', + '--dtfactor', '{0}'.format(base_particle_dt/4), + '--kMeta', '{0}'.format(factor*1.0), + '--niter_todo', '{0}'.format(20), + '--niter_out', '{0}'.format(1), + '--niter_stat', '{0}'.format(1), + '--nparticles', '{0}'.format(nparticles), + '--niter_part', '{0}'.format(1), + '--tracers0_neighbours', '{0}'.format(neighbours), + '--tracers0_smoothness', '{0}'.format(smoothness), + '--tracers0_integration_steps', '4', + '--cpp_random_particles', '{0}'.format(particle_random_seed)]) + +# 2. Prepare initial conditions + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + for factor in [1, 2, 4]: + df = h5py.File('nsvep_{0}x_{1}_checkpoint_0.h5'.format(factor, interp_name), 'w') + # field + field_iteration = 16 + df['vorticity/complex/{0}'.format(8*factor)] = h5py.ExternalLink( + 'nsvep_base_{0}_checkpoint_0.h5'.format(interp_name), + 'vorticity/complex/{0}'.format(field_iteration)) + # particles + df['tracers0/state/{0}'.format(8*factor)] = h5py.ExternalLink( + 'nsvep_base_{0}_checkpoint_0.h5'.format(interp_name), + 'tracers0/state/16') + # copy rhs + source_file = h5py.File( + 'nsvep_base_{0}_checkpoint_0.h5'.format(interp_name), 'r') + rhs = source_file['tracers0/rhs/16'][()] + for tt in range(1, rhs.shape[0]): + ii = 16 - tt*4//factor + 1 + #print(factor, tt, ii) + rhs[tt] = source_file['tracers0/rhs/{0}'.format(16 - tt*4//factor + 1)][1] + df['tracers0/rhs/{0}'.format(8*factor)] = rhs + df.close() + +# 3. Run NSVEparticles + for factor in [1, 2, 4]: + # Test different interpolations. + # The loop iterates over number of neighbours and smoothness. + # The simulation names are defined based on "kernel size" and "order + # of polynomial". + # We do this to emphasize the one-to-one correspondence between + # neighbours and kernel size, and smoothness and order of polynomial. + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + source_file = h5py.File('nsvep_base_{0}.h5'.format(interp_name), 'r') + # create dns object + cc = DNS() + # launch simulation + cc.launch([ + 'NSVEparticles', + '-n', '{0}'.format(source_file['parameters/nx'][()]), + '--np', '{0}'.format(nprocesses), + '--ntpp', '{0}'.format(nthreads_per_process), + '--simname', 'nsvep_{0}x_{1}'.format(factor, interp_name), + '--precision', 'double', + '--dtfactor', '{0}'.format(base_particle_dt/factor), + '--niter_todo', '{0}'.format(test_niterations_particles*factor+8*factor), + '--niter_out', '{0}'.format(test_niterations_particles*factor+8*factor), + '--niter_stat', '{0}'.format(1), + ## ensure fluid physics is the same + '--dealias_type', '{0}'.format(source_file['parameters/dealias_type'][()]), + '--energy', '{0}'.format(source_file['parameters/energy'][()]), + '--famplitude', '{0}'.format(source_file['parameters/famplitude'][()]), + '--fk0', '{0}'.format(source_file['parameters/fk0'][()]), + '--fk1', '{0}'.format(source_file['parameters/fk1'][()]), + '--fmode', '{0}'.format(source_file['parameters/fmode'][()]), + '--friction_coefficient', '{0}'.format(source_file['parameters/friction_coefficient'][()]), + '--injection_rate', '{0}'.format(source_file['parameters/injection_rate'][()]), + '--nu', '{0}'.format(source_file['parameters/nu'][()]), + '--forcing_type', '{0}'.format(str(source_file['parameters/forcing_type'][()], 'ascii')), + ## particle params + '--nparticles', '{0}'.format(nparticles), + '--niter_part', '{0}'.format(1), + '--tracers0_neighbours', '{0}'.format(neighbours), + '--tracers0_smoothness', '{0}'.format(smoothness), + '--tracers0_integration_steps', '4', + '--cpp_random_particles', '0'], # turn off C++ particle initialization + iter0 = 8*factor) + source_file.close() + return None + +def plot_error_particles(): + f = plt.figure() + a = f.add_subplot(111) + factor_list = [1, 2] + factor_list = np.array(factor_list).astype(np.float) + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + err_max_list = [] + err_mean_list = [] + for factor in factor_list: + factor = int(factor) + c1 = DNS(simname = 'nsvep_{0}x_'.format(int(factor)) + interp_name) + c2 = DNS(simname = 'nsvep_{0}x_'.format(int(factor)*2) + interp_name) + for cc in [c1, c2]: + cc.parameters['niter_part'] = cc.get_data_file()['parameters/niter_part'][()] + c1.compute_statistics(iter0 = 8*factor) + c2.compute_statistics(iter0 = 8*factor*2) + final_iter_x1 = c1.get_data_file()['iteration'][()] + final_iter_x2 = c2.get_data_file()['iteration'][()] + f1 = h5py.File(c1.simname + '_checkpoint_0.h5', 'r') + f2 = h5py.File(c2.simname + '_checkpoint_0.h5', 'r') + x1 = f1['tracers0/state/{0}'.format(final_iter_x1)][()] + x2 = f2['tracers0/state/{0}'.format(final_iter_x2)][()] + diff = np.sqrt(np.sum((x2-x1)**2, axis = -1)) + err_max_list.append(np.max(diff)) + err_mean_list.append(np.mean(diff)) + f1.close() + f2.close() + err_max_list = np.array(err_max_list) + err_mean_list = np.array(err_mean_list) + a.plot(factor_list, err_max_list, marker = '.', label = 'max error ' + interp_name) + a.plot(factor_list, err_mean_list, marker = '.', label = 'mean error ' + interp_name) + for ee in [2, 3, 4]: + a.plot(factor_list, + (1e-4)*factor_list**(-ee), + color = 'black', + dashes = (ee, ee), + label = '$\propto f^{{-{0}}}$'.format(ee)) + a.set_xscale('log') + a.set_yscale('log') + a.set_xlabel('resolution factor f') + a.set_ylabel('absolute trajectory error [DNS units]') + a.legend(loc = 'best', fontsize = 7) + f.tight_layout() + f.savefig('err_vs_dt_particle.pdf') + f.savefig('err_vs_dt_particle.svg') + plt.close(f) + return None + +def plot_traj_particles(): + ########################################################################### + f = plt.figure() + a = f.add_subplot(111) + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + for factor in [1, 2, 4]: + cc = DNS(simname = 'nsvep_{0}x_'.format(factor) + interp_name) + cc.compute_statistics(iter0 = 8*factor) + tt = 3 + xx = read_trajectory(cc, tt, iter0 = 8*factor) + a.plot(xx[:, 0], + xx[:, 1], + label = interp_name + '$f = {0}$'.format(factor), + marker = 'x', + dashes = (4/factor, 3, 4/factor), + alpha = 0.2) + #a.plot(xx[:, 0], xx[:, 1], dashes = (4/factor, 3, 4/factor), alpha = 0.2) + a.legend(loc = 'best', fontsize = 7) + a.set_xlabel('$x$ [code units]') + a.set_ylabel('$y$ [code units]') + f.tight_layout() + f.savefig('trajectories.pdf') + f.savefig('trajectories.svg') + plt.close(f) + ########################################################################### + ########################################################################### + traj_index = 3 + for neighbours, smoothness in neighbours_smoothness_list: + interp_name = 'I{0}O{1}'.format(2*neighbours+2, 2*smoothness+1) + cc = DNS(simname = 'nsvep_base_' + interp_name) + cc.compute_statistics() + xx_base = read_trajectory(cc, traj_index, iter0 = 0, dset_name = 'velocity') + iter0 = 16 + tt_base = np.array(range(iter0, iter0 + xx_base.shape[0]))*cc.parameters['dt'] + f = plt.figure() + ax_counter = 1 + for factor in [1, 2, 4]: + a = f.add_subplot(310 + ax_counter) + ax_counter += 1 + a.plot(tt_base, + xx_base[:, 2], + label = 'base_' + interp_name, + marker = '+', + linewidth = 0.5, + alpha = 0.2) + cc = DNS(simname = 'nsvep_{0}x_'.format(factor) + interp_name) + cc.compute_statistics(iter0 = 8*factor) + xx = read_trajectory(cc, traj_index, iter0 = 8*factor, dset_name = 'velocity') + tt = np.array(range(8*factor, xx.shape[0]+8*factor))*cc.parameters['dt'] + a.plot(tt, + xx[:, 2], + label = interp_name + '$f = {0}$'.format(factor), + marker = 'x', + dashes = (4/factor, 3, 4/factor), + alpha = 0.2) + df = h5py.File(cc.simname + '_checkpoint_0.h5', 'r') + xx = df['tracers0/rhs/{0}'.format(8*factor)][()] + for rhs_index in [1, 2, 3]: + a.scatter((8*factor - rhs_index)*cc.parameters['dt'], + xx[rhs_index, traj_index, 2], + marker = '*', + zorder = -10, + alpha = 0.5, + color = 'black') + df.close() + a.legend(loc = 'best', fontsize = 7) + a.set_xlabel('$t$ [code units]') + a.set_ylabel('$v_y$ [code units]') + f.tight_layout() + f.savefig('velocities_{0}.pdf'.format(interp_name)) + plt.close(f) + ########################################################################### + return None + +def read_trajectory( + cc, + traj_index, + iter0, + dset_name = 'position'): + cc.parameters['niter_part'] = cc.get_data_file()['parameters/niter_part'][()] + df = cc.get_particle_file() + xx = [] + for ii in range(iter0, cc.get_data_file()['iteration'][()]+1, cc.parameters['niter_part']): + xx.append(df['tracers0/' + dset_name + '/{0}'.format(ii)][traj_index]) + df.close() + return np.array(xx) + +if __name__ == '__main__': + main() +