Merge branch 'feature/joint-vec-statistics' into develop

bfps/PP.py

@@ -117,7 +117,7 @@ class PP(_code):
             outfile.write(self.main + '\n')
         return None
     def generate_default_parameters(self):
-        # these parameters are relevant for all DNS classes
+        # these parameters are relevant for all PP classes
         self.parameters['dealias_type'] = int(1)
         self.parameters['dkx'] = float(1.0)
         self.parameters['dky'] = float(1.0)
@@ -131,6 +131,15 @@ class PP(_code):
         self.pp_parameters = {}
         self.pp_parameters['iteration_list'] = np.zeros(1).astype(np.int)
         return None
+    def extra_postprocessing_parameters(
+            self,
+            dns_type = 'joint_acc_vel_stats'):
+        pars = {}
+        if dns_type == 'joint_acc_vel_stats':
+            pars['max_acceleration_estimate'] = float(10)
+            pars['max_velocity_estimate'] = float(1)
+            pars['histogram_bins'] = int(129)
+        return pars
     def get_data_file_name(self):
         return os.path.join(self.work_dir, self.simname + '.h5')
     def get_data_file(self):
@@ -426,6 +435,15 @@ class PP(_code):
         self.simulation_parser_arguments(parser_get_rfields)
         self.job_parser_arguments(parser_get_rfields)
         self.parameters_to_parser_arguments(parser_get_rfields)
+        parser_joint_acc_vel_stats = subparsers.add_parser(
+                'joint_acc_vel_stats',
+                help = 'get joint acceleration and velocity statistics')
+        self.simulation_parser_arguments(parser_joint_acc_vel_stats)
+        self.job_parser_arguments(parser_joint_acc_vel_stats)
+        self.parameters_to_parser_arguments(parser_joint_acc_vel_stats)
+        self.parameters_to_parser_arguments(
+                parser_joint_acc_vel_stats,
+                parameters = self.extra_postprocessing_parameters('joint_acc_vel_stats'))
         return None
     def prepare_launch(
             self,
@@ -463,7 +481,8 @@ class PP(_code):
         for k in self.pp_parameters.keys():
              self.parameters[k] = self.pp_parameters[k]
         self.pars_from_namespace(opt)
-        niter_out = self.get_data_file()['parameters/niter_todo'].value
+        niter_out = self.get_data_file()['parameters/niter_out'].value
+        assert(opt.iter0 % niter_out == 0)
         self.pp_parameters['iteration_list'] = np.arange(
                 opt.iter0, opt.iter1+niter_out, niter_out, dtype = np.int)
         return opt
@@ -622,13 +641,170 @@ class PP(_code):
                 dst_file[dst_dset_name][kz,:min_shape[1], :min_shape[2]] = \
                         src_file[src_dset_name][kz, :min_shape[1], :min_shape[2]]
         return None
+    def prepare_post_file(
+            self,
+            opt = None):
+        self.pp_parameters.update(
+                self.extra_postprocessing_parameters(self.dns_type))
+        self.pars_from_namespace(
+                opt,
+                parameters = self.pp_parameters,
+                get_sim_info = False)
+        for kk in ['nx', 'ny', 'nz']:
+            self.parameters[kk] = self.get_data_file()['parameters/' + kk].value
+        n = self.parameters['nx']
+        if self.dns_type in ['filtered_slices',
+                             'filtered_acceleration']:
+            if type(opt.klist_kmax) == type(None):
+                opt.klist_kmax = n / 3.
+            if type(opt.klist_kmin) == type(None):
+                opt.klist_kmin = 6.
+            kvals = bfps_addons.tools.power_space_array(
+                    power = opt.klist_power,
+                    size = opt.klist_size,
+                    vmin = opt.klist_kmin,
+                    vmax = opt.klist_kmax)
+            if opt.test_klist:
+                for i in range(opt.klist_size):
+                    print('kcut{0} = {1}, ell{0} = {2:.3e}'.format(
+                        i, kvals[i], 2*np.pi / kvals[i]))
+                opt.no_submit = True
+            self.pp_parameters['kcut'] = kvals
+        self.rewrite_par(
+                group = self.dns_type + '/parameters',
+                parameters = self.pp_parameters,
+                file_name = os.path.join(self.work_dir, self.simname + '_post.h5'))
+        histogram_bins = opt.histogram_bins
+        if (type(histogram_bins) == type(None) and
+            'histogram_bins' in self.pp_parameters.keys()):
+            histogram_bins = self.pp_parameters['histogram_bins']
+        with h5py.File(os.path.join(self.work_dir, self.simname + '_post.h5'), 'r+') as ofile:
+            group = ofile[self.dns_type]
+            group.require_group('histograms')
+            group.require_group('moments')
+            group.require_group('spectra')
+            vec_spectra_stats = []
+            vec4_rspace_stats = []
+            scal_rspace_stats = []
+            if self.dns_type == 'joint_acc_vel_stats':
+                vec_spectra_stats.append('velocity')
+                vec4_rspace_stats.append('velocity')
+                vec_spectra_stats.append('acceleration')
+                vec4_rspace_stats.append('acceleration')
+            for quantity in scal_rspace_stats:
+                if quantity not in group['histograms'].keys():
+                    time_chunk = 2**20 // (8*histogram_bins)
+                    time_chunk = max(time_chunk, 1)
+                    group['histograms'].create_dataset(
+                            quantity,
+                            (1, histogram_bins),
+                            chunks = (time_chunk, histogram_bins),
+                            maxshape = (None, histogram_bins),
+                            dtype = np.int64)
+                else:
+                    assert(histogram_bins ==
+                           group['histograms/' + quantity].shape[1])
+                if quantity not in group['moments'].keys():
+                    time_chunk = 2**20 // (8*10)
+                    time_chunk = max(time_chunk, 1)
+                    group['moments'].create_dataset(
+                            quantity,
+                            (1, 10),
+                            chunks = (time_chunk, 10),
+                            maxshape = (None, 10),
+                            dtype = np.float64)
+            if self.dns_type == 'joint_acc_vel_stats':
+                quantity = 'acceleration_and_velocity_components'
+                if quantity not in group['histograms'].keys():
+                    time_chunk = 2**20 // (8*9*histogram_bins**2)
+                    time_chunk = max(time_chunk, 1)
+                    group['histograms'].create_dataset(
+                            quantity,
+                            (1, histogram_bins, histogram_bins, 3, 3),
+                            chunks = (time_chunk, histogram_bins, histogram_bins, 3, 3),
+                            maxshape = (None, histogram_bins, histogram_bins, 3, 3),
+                            dtype = np.int64)
+                quantity = 'acceleration_and_velocity_magnitudes'
+                if quantity not in group['histograms'].keys():
+                    time_chunk = 2**20 // (8*histogram_bins**2)
+                    time_chunk = max(time_chunk, 1)
+                    group['histograms'].create_dataset(
+                            quantity,
+                            (1, histogram_bins, histogram_bins),
+                            chunks = (time_chunk, histogram_bins, histogram_bins),
+                            maxshape = (None, histogram_bins, histogram_bins),
+                            dtype = np.int64)
+            ncomps = 4
+            for quantity in vec4_rspace_stats:
+                if quantity not in group['histograms'].keys():
+                    time_chunk = 2**20 // (8*histogram_bins*ncomps)
+                    time_chunk = max(time_chunk, 1)
+                    group['histograms'].create_dataset(
+                            quantity,
+                            (1, histogram_bins, ncomps),
+                            chunks = (time_chunk, histogram_bins, ncomps),
+                            maxshape = (None, histogram_bins, ncomps),
+                            dtype = np.int64)
+                if quantity not in group['moments'].keys():
+                    time_chunk = 2**20 // (8*10*ncomps)
+                    time_chunk = max(time_chunk, 1)
+                    group['moments'].create_dataset(
+                            quantity,
+                            (1, 10, ncomps),
+                            chunks = (time_chunk, 10, ncomps),
+                            maxshape = (None, 10, ncomps),
+                            dtype = np.float64)
+                time_chunk = 2**20 // (
+                        4*3*
+                        self.parameters['nx']*self.parameters['ny'])
+                time_chunk = max(time_chunk, 1)
+            for quantity in vec_spectra_stats:
+                df = self.get_data_file()
+                if quantity + '_' + quantity not in group['spectra'].keys():
+                    spec_chunks = df['statistics/spectra/velocity_velocity'].chunks
+                    spec_shape = df['statistics/spectra/velocity_velocity'].shape
+                    spec_maxshape = df['statistics/spectra/velocity_velocity'].maxshape
+                    group['spectra'].create_dataset(
+                            quantity + '_' + quantity,
+                            spec_shape,
+                            chunks = spec_chunks,
+                            maxshape = spec_maxshape,
+                            dtype = np.float64)
+                df.close()
+        return None
+    def prepare_field_file(self):
+        df = self.get_data_file()
+        if 'field_dtype' in df.keys():
+            # we don't need to do anything, raw binary files are used
+            return None
+        last_iteration = df['iteration'].value
+        cppf = df['parameters/checkpoints_per_file'].value
+        niter_out = df['parameters/niter_out'].value
+        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 = 0
+            while True:
+                cpf_name = os.path.join(
+                        self.work_dir,
+                        self.simname + '_checkpoint_{0}.h5'.format(checkpoint))
+                if os.path.exists(cpf_name):
+                    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)
+                    checkpoint += 1
+                else:
+                    break
+        return None
     def launch_jobs(
             self,
             opt = None,
             particle_initial_condition = None):
-        self.rewrite_par(
-                group = self.dns_type,
-                parameters = self.pp_parameters)
+        self.prepare_post_file(opt)
+        self.prepare_field_file()
         self.run(
                 nb_processes = opt.nb_processes,
                 nb_threads_per_process = opt.nb_threads_per_process,

bfps/cpp/field.cpp

@@ -1135,6 +1135,231 @@ int invert_curl(
     return EXIT_SUCCESS;
 }
 
+template <typename rnumber,
+          field_backend be,
+          field_components fc>
+int joint_rspace_PDF(
+        field<rnumber, be, fc> *f1,
+        field<rnumber, be, fc> *f2,
+        const hid_t group,
+        const std::string dset_name,
+        const hsize_t toffset,
+        const std::vector<double> max_f1_estimate,
+        const std::vector<double> max_f2_estimate)
+{
+    TIMEZONE("joint_rspace_PDF");
+    assert(f1->real_space_representation);
+    assert(f2->real_space_representation);
+    if (fc == THREE)
+    {
+        assert(max_f1_estimate.size() == 4);
+        assert(max_f2_estimate.size() == 4);
+    }
+    else if (fc == ONE)
+    {
+        assert(max_f1_estimate.size() == 1);
+        assert(max_f2_estimate.size() == 1);
+    }
+    int nbins;
+    std::string dsetc, dsetm;
+    dsetc = "histograms/" + dset_name + "_components";
+    if (fc == THREE)
+        dsetm = "histograms/" + dset_name + "_magnitudes";
+    else
+        dsetm = "histograms/" + dset_name;
+    if (f1->myrank == 0)
+    {
+        hid_t dset, wspace;
+        hsize_t dims[5];
+        int ndims;
+        if (fc == THREE)
+        {
+            dset = H5Dopen(
+                    group,
+                    dsetc.c_str(),
+                    H5P_DEFAULT);
+            wspace = H5Dget_space(dset);
+            ndims = H5Sget_simple_extent_dims(wspace, dims, NULL);
+            DEBUG_MSG("number of dimensions is %d\n", ndims);
+            assert(ndims == 5);
+            assert(dims[3] == 3);
+            assert(dims[4] == 3);
+            H5Sclose(wspace);
+            H5Dclose(dset);
+        }
+        dset = H5Dopen(
+                group,
+                dsetm.c_str(),
+                H5P_DEFAULT);
+        wspace = H5Dget_space(dset);
+        ndims = H5Sget_simple_extent_dims(wspace, dims, NULL);
+        assert(ndims == 3);
+        H5Sclose(wspace);
+        H5Dclose(dset);
+        nbins = dims[1];
+    }
+    {
+        TIMEZONE("MPI_Bcast");
+        MPI_Bcast(&nbins, 1, MPI_INT, 0, f1->comm);
+    }
+
+        /// histogram components
+        shared_array<ptrdiff_t> local_histc_threaded(
+                nbins*nbins*9,
+                [&](ptrdiff_t* local_hist){
+                    std::fill_n(local_hist, nbins*nbins*9, 0);
+                    });
+
+    /// histogram magnitudes
+    shared_array<ptrdiff_t> local_histm_threaded(
+            nbins*nbins,
+            [&](ptrdiff_t* local_hist){
+                std::fill_n(local_hist, nbins*nbins, 0);
+                });
+
+    /// set up bin sizes
+    std::vector<double> bin1size, bin2size;
+    bin1size.resize(4);
+    bin2size.resize(4);
+    if (fc == THREE)
+    {
+        for (unsigned int i=0; i<3; i++)
+        {
+            bin1size[i] = 2*max_f1_estimate[i] / nbins;
+            bin2size[i] = 2*max_f2_estimate[i] / nbins;
+        }
+        bin1size[3] = max_f1_estimate[3] / nbins;
+        bin2size[3] = max_f2_estimate[3] / nbins;
+    }
+    else if (fc == ONE)
+    {
+        for (unsigned int i=0; i<4; i++)
+        {
+            bin1size[i] = max_f1_estimate[0] / nbins;
+            bin2size[i] = max_f2_estimate[0] / nbins;
+        }
+    }
+
+
+    {
+        TIMEZONE("field::RLOOP");
+        f1->RLOOP(
+                [&](ptrdiff_t rindex,
+                    ptrdiff_t xindex,
+                    ptrdiff_t yindex,
+                    ptrdiff_t zindex){
+            ptrdiff_t *local_histm = local_histm_threaded.getMine();
+            int bin1 = 0;
+            int bin2 = 0;
+            if (fc == THREE)
+            {
+                ptrdiff_t *local_histc = local_histc_threaded.getMine();
+
+                double mag1, mag2;
+                mag1 = 0.0;
+                mag2 = 0.0;
+                for (unsigned int i=0; i<3; i++)
+                {
+                    double val1 = f1->rval(rindex, i);
+                    mag1 += val1*val1;
+                    int bin1 = int(floor((val1 + max_f1_estimate[i])/bin1size[i]));
+                    mag2 = 0.0;
+                    for (unsigned int j=0; j<3; j++)
+                    {
+                        double val2 = f2->rval(rindex, j);
+                        mag2 += val2*val2;
+                        int bin2 = int(floor((val2 + max_f2_estimate[j])/bin2size[j]));
+                        if ((bin1 >= 0 && bin1 < nbins) &&
+                            (bin2 >= 0 && bin2 < nbins))
+                            local_histc[(bin1*nbins + bin2)*9 + i*3 + j]++;
+                    }
+                }
+                bin1 = int(floor(sqrt(mag1)/bin1size[3]));
+                bin2 = int(floor(sqrt(mag2)/bin2size[3]));
+            }
+            else if (fc == ONE)
+            {
+                bin1 = int(floor(f1->rval(rindex)/bin1size[3]));
+                bin2 = int(floor(f2->rval(rindex)/bin2size[3]));
+            }
+            if ((bin1 >= 0 && bin1 < nbins) &&
+                (bin2 >= 0 && bin2 < nbins))
+                local_histm[bin1*nbins + bin2]++;
+            });
+    }
+    local_histm_threaded.mergeParallel();
+    ptrdiff_t *histm = new ptrdiff_t[nbins*nbins];
+    ptrdiff_t *histc = NULL;
+    if (fc == THREE)
+    {
+        local_histc_threaded.mergeParallel();
+        histc = new ptrdiff_t[nbins*nbins*9];
+    }
+    {
+        MPI_Allreduce(
+                (void*)local_histm_threaded.getMasterData(),
+                (void*)histm,
+                nbins*nbins,
+                MPI_INT64_T, MPI_SUM, f1->comm);
+        if (fc == THREE)
+            MPI_Allreduce(
+                    (void*)local_histc_threaded.getMasterData(),
+                    (void*)histc,
+                    nbins*nbins*9,
+                    MPI_INT64_T, MPI_SUM, f1->comm);
+    }
+
+    if (f1->myrank == 0)
+    {
+        TIMEZONE("root-work");
+        hid_t dset, wspace, mspace;
+        hsize_t count[5], offset[5];
+        if (fc == THREE)
+        {
+            dset = H5Dopen(group, dsetc.c_str(), H5P_DEFAULT);
+            assert(dset > 0);
+            wspace = H5Dget_space(dset);
+            offset[0] = toffset;
+            offset[1] = 0;
+            offset[2] = 0;
+            offset[3] = 0;
+            offset[4] = 0;
+            count[0] = 1;
+            count[1] = nbins;
+            count[2] = nbins;
+            count[3] = 3;
+            count[4] = 3;
+            mspace = H5Screate_simple(5, count, NULL);
+            H5Sselect_hyperslab(wspace, H5S_SELECT_SET, offset, NULL, count, NULL);
+            H5Dwrite(dset, H5T_NATIVE_INT64, mspace, wspace, H5P_DEFAULT, histc);
+            H5Sclose(wspace);
+            H5Sclose(mspace);
+            H5Dclose(dset);
+        }
+        dset = H5Dopen(group, dsetm.c_str(), H5P_DEFAULT);
+        assert(dset > 0);
+        offset[0] = toffset;
+        offset[1] = 0;
+        offset[2] = 0;
+        count[0] = 1;
+        count[1] = nbins;
+        count[2] = nbins;
+        mspace = H5Screate_simple(3, count, NULL);
+        wspace = H5Dget_space(dset);
+        H5Sselect_hyperslab(wspace, H5S_SELECT_SET, offset, NULL, count, NULL);
+        H5Dwrite(dset, H5T_NATIVE_INT64, mspace, wspace, H5P_DEFAULT, histm);
+        H5Sclose(wspace);
+        H5Sclose(mspace);
+        H5Dclose(dset);
+    }
+
+    delete[] histm;
+    if (fc == THREE)
+        delete[] histc;
+
+    return EXIT_SUCCESS;
+}
+
 template class field<float, FFTW, ONE>;
 template class field<float, FFTW, THREE>;
 template class field<float, FFTW, THREExTHREE>;
@@ -1209,3 +1434,37 @@ template int invert_curl<double, FFTW, SMOOTH>(
         field<double, FFTW, THREE> *,
         field<double, FFTW, THREE> *);
 
+template int joint_rspace_PDF<float, FFTW, THREE>(
+        field<float, FFTW, THREE> *,
+        field<float, FFTW, THREE> *,
+        const hid_t,
+        const std::string,
+        const hsize_t,
+        const std::vector<double>,
+        const std::vector<double>);
+template int joint_rspace_PDF<double, FFTW, THREE>(
+        field<double, FFTW, THREE> *,
+        field<double, FFTW, THREE> *,
+        const hid_t,
+        const std::string,
+        const hsize_t,
+        const std::vector<double>,
+        const std::vector<double>);
+
+template int joint_rspace_PDF<float, FFTW, ONE>(
+        field<float, FFTW, ONE> *,
+        field<float, FFTW, ONE> *,
+        const hid_t,
+        const std::string,
+        const hsize_t,
+        const std::vector<double>,
+        const std::vector<double>);
+template int joint_rspace_PDF<double, FFTW, ONE>(
+        field<double, FFTW, ONE> *,
+        field<double, FFTW, ONE> *,
+        const hid_t,
+        const std::string,
+        const hsize_t,
+        const std::vector<double>,
+        const std::vector<double>);
+

bfps/cpp/field.hpp

@@ -306,5 +306,17 @@ int invert_curl(
         field<rnumber, be, THREE> *source,
         field<rnumber, be, THREE> *destination);
 
+template <typename rnumber,
+          field_backend be,
+          field_components fc>
+int joint_rspace_PDF(
+        field<rnumber, be, fc> *f1,
+        field<rnumber, be, fc> *f2,
+        const hid_t group,
+        const std::string dset_name,
+        const hsize_t toffset,
+        const std::vector<double> max_f1_estimate,
+        const std::vector<double> max_f2_estimate);
+
 #endif//FIELD_HPP
 

bfps/cpp/full_code/joint_acc_vel_stats.cpp

+#include <string>
+#include <cmath>
+#include "joint_acc_vel_stats.hpp"
+#include "scope_timer.hpp"
+
+
+template <typename rnumber>
+int joint_acc_vel_stats<rnumber>::initialize(void)
+{
+    this->NSVE_field_stats<rnumber>::initialize();
+    this->kk = new kspace<FFTW, SMOOTH>(
+            this->vorticity->clayout, this->dkx, this->dky, this->dkz);
+    this->ve = new vorticity_equation<rnumber, FFTW>(
+            this->simname.c_str(),
+            this->nx,
+            this->ny,
+            this->nz,
+            this->dkx,
+            this->dky,
+            this->dkz,
+            this->vorticity->fftw_plan_rigor);
+    hid_t parameter_file = H5Fopen(
+            (this->simname + std::string(".h5")).c_str(),
+            H5F_ACC_RDONLY,
+            H5P_DEFAULT);
+    hid_t dset = H5Dopen(parameter_file, "/parameters/niter_out", H5P_DEFAULT);
+    H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->niter_out);
+    H5Dclose(dset);
+    if (H5Lexists(parameter_file, "/parameters/checkpoints_per_file", H5P_DEFAULT))
+    {
+        dset = H5Dopen(parameter_file, "/parameters/checkpoints_per_file", H5P_DEFAULT);
+        H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->checkpoints_per_file);
+        H5Dclose(dset);
+    }
+    else
+        this->checkpoints_per_file = 1;
+    H5Fclose(parameter_file);
+    parameter_file = H5Fopen(
+            (this->simname + std::string("_post.h5")).c_str(),
+            H5F_ACC_RDONLY,
+            H5P_DEFAULT);
+    this->iteration_list = hdf5_tools::read_vector<int>(
+            parameter_file,
+            "/joint_acc_vel_stats/parameters/iteration_list");
+    dset = H5Dopen(parameter_file, "joint_acc_vel_stats/parameters/max_acceleration_estimate", H5P_DEFAULT);
+    H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->max_acceleration_estimate);
+    H5Dclose(dset);
+    dset = H5Dopen(parameter_file, "joint_acc_vel_stats/parameters/max_velocity_estimate", H5P_DEFAULT);
+    H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->max_velocity_estimate);
+    H5Dclose(dset);
+    H5Fclose(parameter_file);
+    if (this->myrank == 0)
+    {
+        // set caching parameters
+        hid_t fapl = H5Pcreate(H5P_FILE_ACCESS);
+        herr_t cache_err = H5Pset_cache(fapl, 0, 521, 134217728, 1.0);
+        DEBUG_MSG("when setting stat_file cache I got %d\n", cache_err);
+        this->stat_file = H5Fopen(
+                (this->simname + "_post.h5").c_str(),
+                H5F_ACC_RDWR,
+                fapl);
+    }
+    else
+    {
+        this->stat_file = 0;
+    }
+    int data_file_problem;
+    if (this->myrank == 0)
+        data_file_problem = hdf5_tools::require_size_file_datasets(
+                this->stat_file,
+                "joint_acc_vel_stats",
+                (this->iteration_list.back() / this->niter_out) + 1);
+    MPI_Bcast(&data_file_problem, 1, MPI_INT, 0, this->comm);
+    if (data_file_problem > 0)
+    {
+        std::cerr <<
+            data_file_problem <<
+            " problems setting sizes of file datasets.\ntrying to exit now." <<
+            std::endl;
+        return EXIT_FAILURE;
+    }
+    return EXIT_SUCCESS;
+}
+