# pyerrors.input.hadrons API documentation

# pyerrors.input.hadrons

View Source

      1import os
      2import warnings
      3from collections import Counter
      4import h5py
      5from pathlib import Path
      6import numpy as np
      7from ..obs import Obs, CObs
      8from ..correlators import Corr
      9from ..dirac import epsilon_tensor_rank4
     10
     11
     12def _get_files(path, filestem, idl):
     13    ls = os.listdir(path)
     14
     15    # Clean up file list
     16    files = list(filter(lambda x: x.startswith(filestem + "."), ls))
     17
     18    if not files:
     19        raise Exception('No files starting with', filestem, 'in folder', path)
     20
     21    def get_cnfg_number(n):
     22        return int(n.replace(".h5", "")[len(filestem) + 1:])  # From python 3.9 onward the safer 'removesuffix' method can be used.
     23
     24    # Sort according to configuration number
     25    files.sort(key=get_cnfg_number)
     26
     27    cnfg_numbers = []
     28    filtered_files = []
     29    for line in files:
     30        no = get_cnfg_number(line)
     31        if idl:
     32            if no in list(idl):
     33                filtered_files.append(line)
     34                cnfg_numbers.append(no)
     35        else:
     36            filtered_files.append(line)
     37            cnfg_numbers.append(no)
     38
     39    if idl:
     40        if Counter(list(idl)) != Counter(cnfg_numbers):
     41            raise Exception("Not all configurations specified in idl found, configurations " + str(list(Counter(list(idl)) - Counter(cnfg_numbers))) + " are missing.")
     42
     43    # Check that configurations are evenly spaced
     44    dc = np.unique(np.diff(cnfg_numbers))
     45    if np.any(dc < 0):
     46        raise Exception("Unsorted files")
     47    if len(dc) == 1:
     48        idx = range(cnfg_numbers[0], cnfg_numbers[-1] + dc[0], dc[0])
     49    elif idl:
     50        idx = idl
     51        warnings.warn("Configurations are not evenly spaced.", RuntimeWarning)
     52    else:
     53        raise Exception("Configurations are not evenly spaced.")
     54
     55    return filtered_files, idx
     56
     57
     58def read_meson_hd5(path, filestem, ens_id, meson='meson_0', idl=None, gammas=None):
     59    r'''Read hadrons meson hdf5 file and extract the meson labeled 'meson'
     60
     61    Parameters
     62    -----------------
     63    path : str
     64        path to the files to read
     65    filestem : str
     66        namestem of the files to read
     67    ens_id : str
     68        name of the ensemble, required for internal bookkeeping
     69    meson : str
     70        label of the meson to be extracted, standard value meson_0 which
     71        corresponds to the pseudoscalar pseudoscalar two-point function.
     72    gammas : tuple of strings
     73        Instrad of a meson label one can also provide a tuple of two strings
     74        indicating the gamma matrices at source and sink.
     75        ("Gamma5", "Gamma5") corresponds to the pseudoscalar pseudoscalar
     76        two-point function. The gammas argument dominateds over meson.
     77    idl : range
     78        If specified only configurations in the given range are read in.
     79    '''
     80
     81    files, idx = _get_files(path, filestem, idl)
     82
     83    tree = meson.rsplit('_')[0]
     84    if gammas is not None:
     85        h5file = h5py.File(path + '/' + files[0], "r")
     86        found_meson = None
     87        for key in h5file[tree].keys():
     88            if gammas[0] == h5file[tree][key].attrs["gamma_snk"][0].decode() and h5file[tree][key].attrs["gamma_src"][0].decode() == gammas[1]:
     89                found_meson = key
     90                break
     91        h5file.close()
     92        if found_meson:
     93            meson = found_meson
     94        else:
     95            raise Exception("Source Sink combination " + str(gammas) + " not found.")
     96
     97    corr_data = []
     98    infos = []
     99    for hd5_file in files:
    100        h5file = h5py.File(path + '/' + hd5_file, "r")
    101        if not tree + '/' + meson in h5file:
    102            raise Exception("Entry '" + meson + "' not contained in the files.")
    103        raw_data = h5file[tree + '/' + meson + '/corr']
    104        real_data = raw_data[:]["re"].astype(np.double)
    105        corr_data.append(real_data)
    106        if not infos:
    107            for k, i in h5file[tree + '/' + meson].attrs.items():
    108                infos.append(k + ': ' + i[0].decode())
    109        h5file.close()
    110    corr_data = np.array(corr_data)
    111
    112    l_obs = []
    113    for c in corr_data.T:
    114        l_obs.append(Obs([c], [ens_id], idl=[idx]))
    115
    116    corr = Corr(l_obs)
    117    corr.tag = r", ".join(infos)
    118    return corr
    119
    120
    121def read_DistillationContraction_hd5(path, ens_id, diagrams=["direct"], idl=None):
    122    """Read hadrons DistillationContraction hdf5 files in given directory structure
    123
    124    Parameters
    125    -----------------
    126    path : str
    127        path to the directories to read
    128    ens_id : str
    129        name of the ensemble, required for internal bookkeeping
    130    diagrams : list
    131        List of strings of the diagrams to extract, e.g. ["direct", "box", "cross"].
    132    idl : range
    133        If specified only configurations in the given range are read in.
    134    """
    135
    136    res_dict = {}
    137
    138    directories, idx = _get_files(path, "data", idl)
    139
    140    explore_path = Path(path + "/" + directories[0])
    141
    142    for explore_file in explore_path.iterdir():
    143        if explore_file.is_file():
    144            stem = explore_file.with_suffix("").with_suffix("").as_posix().split("/")[-1]
    145
    146        file_list = []
    147        for dir in directories:
    148            tmp_path = Path(path + "/" + dir)
    149            file_list.append((tmp_path / stem).as_posix() + tmp_path.suffix + ".h5")
    150
    151        corr_data = {}
    152
    153        for diagram in diagrams:
    154            corr_data[diagram] = []
    155
    156        for n_file, (hd5_file, n_traj) in enumerate(zip(file_list, list(idx))):
    157            h5file = h5py.File(hd5_file)
    158
    159            if n_file == 0:
    160                if h5file["DistillationContraction/Metadata"].attrs.get("TimeSources")[0].decode() != "0...":
    161                    raise Exception("Routine is only implemented for files containing inversions on all timeslices.")
    162
    163                Nt = h5file["DistillationContraction/Metadata"].attrs.get("Nt")[0]
    164
    165                identifier = []
    166                for in_file in range(4):
    167                    encoded_info = h5file["DistillationContraction/Metadata/DmfInputFiles"].attrs.get("DmfInputFiles_" + str(in_file))
    168                    full_info = encoded_info[0].decode().split("/")[-1].replace(".h5", "").split("_")
    169                    my_tuple = (full_info[0], full_info[1][1:], full_info[2], full_info[3])
    170                    identifier.append(my_tuple)
    171                identifier = tuple(identifier)
    172                # "DistillationContraction/Metadata/DmfSuffix" contains info about different quarks, irrelevant in the SU(3) case.
    173
    174            for diagram in diagrams:
    175                real_data = np.zeros(Nt)
    176                for x0 in range(Nt):
    177                    raw_data = h5file["DistillationContraction/Correlators/" + diagram + "/" + str(x0)]
    178                    real_data += np.roll(raw_data[:]["re"].astype(np.double), -x0)
    179                real_data /= Nt
    180
    181                corr_data[diagram].append(real_data)
    182            h5file.close()
    183
    184        res_dict[str(identifier)] = {}
    185
    186        for diagram in diagrams:
    187
    188            tmp_data = np.array(corr_data[diagram])
    189
    190            l_obs = []
    191            for c in tmp_data.T:
    192                l_obs.append(Obs([c], [ens_id], idl=[idx]))
    193
    194            corr = Corr(l_obs)
    195            corr.tag = str(identifier)
    196
    197            res_dict[str(identifier)][diagram] = corr
    198
    199    return res_dict
    200
    201
    202class Npr_matrix(np.ndarray):
    203
    204    def __new__(cls, input_array, mom_in=None, mom_out=None):
    205        obj = np.asarray(input_array).view(cls)
    206        obj.mom_in = mom_in
    207        obj.mom_out = mom_out
    208        return obj
    209
    210    @property
    211    def g5H(self):
    212        """Gamma_5 hermitean conjugate
    213
    214        Uses the fact that the propagator is gamma5 hermitean, so just the
    215        in and out momenta of the propagator are exchanged.
    216        """
    217        return Npr_matrix(self,
    218                          mom_in=self.mom_out,
    219                          mom_out=self.mom_in)
    220
    221    def _propagate_mom(self, other, name):
    222        s_mom = getattr(self, name, None)
    223        o_mom = getattr(other, name, None)
    224        if s_mom is not None and o_mom is not None:
    225            if not np.allclose(s_mom, o_mom):
    226                raise Exception(name + ' does not match.')
    227        return o_mom if o_mom is not None else s_mom
    228
    229    def __matmul__(self, other):
    230        return self.__new__(Npr_matrix,
    231                            super().__matmul__(other),
    232                            self._propagate_mom(other, 'mom_in'),
    233                            self._propagate_mom(other, 'mom_out'))
    234
    235    def __array_finalize__(self, obj):
    236        if obj is None:
    237            return
    238        self.mom_in = getattr(obj, 'mom_in', None)
    239        self.mom_out = getattr(obj, 'mom_out', None)
    240
    241
    242def read_ExternalLeg_hd5(path, filestem, ens_id, idl=None):
    243    """Read hadrons ExternalLeg hdf5 file and output an array of CObs
    244
    245    Parameters
    246    ----------
    247    path : str
    248        path to the files to read
    249    filestem : str
    250        namestem of the files to read
    251    ens_id : str
    252        name of the ensemble, required for internal bookkeeping
    253    idl : range
    254        If specified only configurations in the given range are read in.
    255    """
    256
    257    files, idx = _get_files(path, filestem, idl)
    258
    259    mom = None
    260
    261    corr_data = []
    262    for hd5_file in files:
    263        file = h5py.File(path + '/' + hd5_file, "r")
    264        raw_data = file['ExternalLeg/corr'][0][0].view('complex')
    265        corr_data.append(raw_data)
    266        if mom is None:
    267            mom = np.array(str(file['ExternalLeg/info'].attrs['pIn'])[3:-2].strip().split(), dtype=float)
    268        file.close()
    269    corr_data = np.array(corr_data)
    270
    271    rolled_array = np.rollaxis(corr_data, 0, 5)
    272
    273    matrix = np.empty((rolled_array.shape[:-1]), dtype=object)
    274    for si, sj, ci, cj in np.ndindex(rolled_array.shape[:-1]):
    275        real = Obs([rolled_array[si, sj, ci, cj].real], [ens_id], idl=[idx])
    276        imag = Obs([rolled_array[si, sj, ci, cj].imag], [ens_id], idl=[idx])
    277        matrix[si, sj, ci, cj] = CObs(real, imag)
    278
    279    return Npr_matrix(matrix, mom_in=mom)
    280
    281
    282def read_Bilinear_hd5(path, filestem, ens_id, idl=None):
    283    """Read hadrons Bilinear hdf5 file and output an array of CObs
    284
    285    Parameters
    286    ----------
    287    path : str
    288        path to the files to read
    289    filestem : str
    290        namestem of the files to read
    291    ens_id : str
    292        name of the ensemble, required for internal bookkeeping
    293    idl : range
    294        If specified only configurations in the given range are read in.
    295    """
    296
    297    files, idx = _get_files(path, filestem, idl)
    298
    299    mom_in = None
    300    mom_out = None
    301
    302    corr_data = {}
    303    for hd5_file in files:
    304        file = h5py.File(path + '/' + hd5_file, "r")
    305        for i in range(16):
    306            name = file['Bilinear/Bilinear_' + str(i) + '/info'].attrs['gamma'][0].decode('UTF-8')
    307            if name not in corr_data:
    308                corr_data[name] = []
    309            raw_data = file['Bilinear/Bilinear_' + str(i) + '/corr'][0][0].view('complex')
    310            corr_data[name].append(raw_data)
    311            if mom_in is None:
    312                mom_in = np.array(str(file['Bilinear/Bilinear_' + str(i) + '/info'].attrs['pIn'])[3:-2].strip().split(), dtype=float)
    313            if mom_out is None:
    314                mom_out = np.array(str(file['Bilinear/Bilinear_' + str(i) + '/info'].attrs['pOut'])[3:-2].strip().split(), dtype=float)
    315
    316        file.close()
    317
    318    result_dict = {}
    319
    320    for key, data in corr_data.items():
    321        local_data = np.array(data)
    322
    323        rolled_array = np.rollaxis(local_data, 0, 5)
    324
    325        matrix = np.empty((rolled_array.shape[:-1]), dtype=object)
    326        for si, sj, ci, cj in np.ndindex(rolled_array.shape[:-1]):
    327            real = Obs([rolled_array[si, sj, ci, cj].real], [ens_id], idl=[idx])
    328            imag = Obs([rolled_array[si, sj, ci, cj].imag], [ens_id], idl=[idx])
    329            matrix[si, sj, ci, cj] = CObs(real, imag)
    330
    331        result_dict[key] = Npr_matrix(matrix, mom_in=mom_in, mom_out=mom_out)
    332
    333    return result_dict
    334
    335
    336def read_Fourquark_hd5(path, filestem, ens_id, idl=None, vertices=["VA", "AV"]):
    337    """Read hadrons FourquarkFullyConnected hdf5 file and output an array of CObs
    338
    339    Parameters
    340    ----------
    341    path : str
    342        path to the files to read
    343    filestem : str
    344        namestem of the files to read
    345    ens_id : str
    346        name of the ensemble, required for internal bookkeeping
    347    idl : range
    348        If specified only configurations in the given range are read in.
    349    vertices : list
    350        Vertex functions to be extracted.
    351    """
    352
    353    files, idx = _get_files(path, filestem, idl)
    354
    355    mom_in = None
    356    mom_out = None
    357
    358    vertex_names = []
    359    for vertex in vertices:
    360        vertex_names += _get_lorentz_names(vertex)
    361
    362    corr_data = {}
    363
    364    tree = 'FourQuarkFullyConnected/FourQuarkFullyConnected_'
    365
    366    for hd5_file in files:
    367        file = h5py.File(path + '/' + hd5_file, "r")
    368
    369        for i in range(32):
    370            name = (file[tree + str(i) + '/info'].attrs['gammaA'][0].decode('UTF-8'), file[tree + str(i) + '/info'].attrs['gammaB'][0].decode('UTF-8'))
    371            if name in vertex_names:
    372                if name not in corr_data:
    373                    corr_data[name] = []
    374                raw_data = file[tree + str(i) + '/corr'][0][0].view('complex')
    375                corr_data[name].append(raw_data)
    376                if mom_in is None:
    377                    mom_in = np.array(str(file[tree + str(i) + '/info'].attrs['pIn'])[3:-2].strip().split(), dtype=float)
    378                if mom_out is None:
    379                    mom_out = np.array(str(file[tree + str(i) + '/info'].attrs['pOut'])[3:-2].strip().split(), dtype=float)
    380
    381        file.close()
    382
    383    intermediate_dict = {}
    384
    385    for vertex in vertices:
    386        lorentz_names = _get_lorentz_names(vertex)
    387        for v_name in lorentz_names:
    388            if v_name in [('SigmaXY', 'SigmaZT'),
    389                          ('SigmaXT', 'SigmaYZ'),
    390                          ('SigmaYZ', 'SigmaXT'),
    391                          ('SigmaZT', 'SigmaXY')]:
    392                sign = -1
    393            else:
    394                sign = 1
    395            if vertex not in intermediate_dict:
    396                intermediate_dict[vertex] = sign * np.array(corr_data[v_name])
    397            else:
    398                intermediate_dict[vertex] += sign * np.array(corr_data[v_name])
    399
    400    result_dict = {}
    401
    402    for key, data in intermediate_dict.items():
    403
    404        rolled_array = np.moveaxis(data, 0, 8)
    405
    406        matrix = np.empty((rolled_array.shape[:-1]), dtype=object)
    407        for index in np.ndindex(rolled_array.shape[:-1]):
    408            real = Obs([rolled_array[index].real], [ens_id], idl=[idx])
    409            imag = Obs([rolled_array[index].imag], [ens_id], idl=[idx])
    410            matrix[index] = CObs(real, imag)
    411
    412        result_dict[key] = Npr_matrix(matrix, mom_in=mom_in, mom_out=mom_out)
    413
    414    return result_dict
    415
    416
    417def _get_lorentz_names(name):
    418    lorentz_index = ['X', 'Y', 'Z', 'T']
    419
    420    res = []
    421
    422    if name == "TT":
    423        for i in range(4):
    424            for j in range(i + 1, 4):
    425                res.append(("Sigma" + lorentz_index[i] + lorentz_index[j], "Sigma" + lorentz_index[i] + lorentz_index[j]))
    426        return res
    427
    428    if name == "TTtilde":
    429        for i in range(4):
    430            for j in range(i + 1, 4):
    431                for k in range(4):
    432                    for o in range(k + 1, 4):
    433                        fac = epsilon_tensor_rank4(i, j, k, o)
    434                        if not np.isclose(fac, 0.0):
    435                            res.append(("Sigma" + lorentz_index[i] + lorentz_index[j], "Sigma" + lorentz_index[k] + lorentz_index[o]))
    436        return res
    437
    438    assert len(name) == 2
    439
    440    if 'S' in name or 'P' in name:
    441        if not set(name) <= set(['S', 'P']):
    442            raise Exception("'" + name + "' is not a Lorentz scalar")
    443
    444        g_names = {'S': 'Identity',
    445                   'P': 'Gamma5'}
    446
    447        res.append((g_names[name[0]], g_names[name[1]]))
    448
    449    else:
    450        if not set(name) <= set(['V', 'A']):
    451            raise Exception("'" + name + "' is not a Lorentz scalar")
    452
    453        for ind in lorentz_index:
    454            res.append(('Gamma' + ind + (name[0] == 'A') * 'Gamma5',
    455                        'Gamma' + ind + (name[1] == 'A') * 'Gamma5'))
    456
    457    return res

def read_meson_hd5(path, filestem, ens_id, meson='meson_0', idl=None, gammas=None) View Source

     59def read_meson_hd5(path, filestem, ens_id, meson='meson_0', idl=None, gammas=None):
     60    r'''Read hadrons meson hdf5 file and extract the meson labeled 'meson'
     61
     62    Parameters
     63    -----------------
     64    path : str
     65        path to the files to read
     66    filestem : str
     67        namestem of the files to read
     68    ens_id : str
     69        name of the ensemble, required for internal bookkeeping
     70    meson : str
     71        label of the meson to be extracted, standard value meson_0 which
     72        corresponds to the pseudoscalar pseudoscalar two-point function.
     73    gammas : tuple of strings
     74        Instrad of a meson label one can also provide a tuple of two strings
     75        indicating the gamma matrices at source and sink.
     76        ("Gamma5", "Gamma5") corresponds to the pseudoscalar pseudoscalar
     77        two-point function. The gammas argument dominateds over meson.
     78    idl : range
     79        If specified only configurations in the given range are read in.
     80    '''
     81
     82    files, idx = _get_files(path, filestem, idl)
     83
     84    tree = meson.rsplit('_')[0]
     85    if gammas is not None:
     86        h5file = h5py.File(path + '/' + files[0], "r")
     87        found_meson = None
     88        for key in h5file[tree].keys():
     89            if gammas[0] == h5file[tree][key].attrs["gamma_snk"][0].decode() and h5file[tree][key].attrs["gamma_src"][0].decode() == gammas[1]:
     90                found_meson = key
     91                break
     92        h5file.close()
     93        if found_meson:
     94            meson = found_meson
     95        else:
     96            raise Exception("Source Sink combination " + str(gammas) + " not found.")
     97
     98    corr_data = []
     99    infos = []
    100    for hd5_file in files:
    101        h5file = h5py.File(path + '/' + hd5_file, "r")
    102        if not tree + '/' + meson in h5file:
    103            raise Exception("Entry '" + meson + "' not contained in the files.")
    104        raw_data = h5file[tree + '/' + meson + '/corr']
    105        real_data = raw_data[:]["re"].astype(np.double)
    106        corr_data.append(real_data)
    107        if not infos:
    108            for k, i in h5file[tree + '/' + meson].attrs.items():
    109                infos.append(k + ': ' + i[0].decode())
    110        h5file.close()
    111    corr_data = np.array(corr_data)
    112
    113    l_obs = []
    114    for c in corr_data.T:
    115        l_obs.append(Obs([c], [ens_id], idl=[idx]))
    116
    117    corr = Corr(l_obs)
    118    corr.tag = r", ".join(infos)
    119    return corr

Read hadrons meson hdf5 file and extract the meson labeled 'meson'

###### Parameters

- path (str): path to the files to read
- filestem (str): namestem of the files to read
- ens_id (str): name of the ensemble, required for internal bookkeeping
- meson (str): label of the meson to be extracted, standard value meson_0 which corresponds to the pseudoscalar pseudoscalar two-point function.
- gammas (tuple of strings): Instrad of a meson label one can also provide a tuple of two strings indicating the gamma matrices at source and sink. ("Gamma5", "Gamma5") corresponds to the pseudoscalar pseudoscalar two-point function. The gammas argument dominateds over meson.
- idl (range): If specified only configurations in the given range are read in.

def read_DistillationContraction_hd5(path, ens_id, diagrams=['direct'], idl=None) View Source

    122def read_DistillationContraction_hd5(path, ens_id, diagrams=["direct"], idl=None):
    123    """Read hadrons DistillationContraction hdf5 files in given directory structure
    124
    125    Parameters
    126    -----------------
    127    path : str
    128        path to the directories to read
    129    ens_id : str
    130        name of the ensemble, required for internal bookkeeping
    131    diagrams : list
    132        List of strings of the diagrams to extract, e.g. ["direct", "box", "cross"].
    133    idl : range
    134        If specified only configurations in the given range are read in.
    135    """
    136
    137    res_dict = {}
    138
    139    directories, idx = _get_files(path, "data", idl)
    140
    141    explore_path = Path(path + "/" + directories[0])
    142
    143    for explore_file in explore_path.iterdir():
    144        if explore_file.is_file():
    145            stem = explore_file.with_suffix("").with_suffix("").as_posix().split("/")[-1]
    146
    147        file_list = []
    148        for dir in directories:
    149            tmp_path = Path(path + "/" + dir)
    150            file_list.append((tmp_path / stem).as_posix() + tmp_path.suffix + ".h5")
    151
    152        corr_data = {}
    153
    154        for diagram in diagrams:
    155            corr_data[diagram] = []
    156
    157        for n_file, (hd5_file, n_traj) in enumerate(zip(file_list, list(idx))):
    158            h5file = h5py.File(hd5_file)
    159
    160            if n_file == 0:
    161                if h5file["DistillationContraction/Metadata"].attrs.get("TimeSources")[0].decode() != "0...":
    162                    raise Exception("Routine is only implemented for files containing inversions on all timeslices.")
    163
    164                Nt = h5file["DistillationContraction/Metadata"].attrs.get("Nt")[0]
    165
    166                identifier = []
    167                for in_file in range(4):
    168                    encoded_info = h5file["DistillationContraction/Metadata/DmfInputFiles"].attrs.get("DmfInputFiles_" + str(in_file))
    169                    full_info = encoded_info[0].decode().split("/")[-1].replace(".h5", "").split("_")
    170                    my_tuple = (full_info[0], full_info[1][1:], full_info[2], full_info[3])
    171                    identifier.append(my_tuple)
    172                identifier = tuple(identifier)
    173                # "DistillationContraction/Metadata/DmfSuffix" contains info about different quarks, irrelevant in the SU(3) case.
    174
    175            for diagram in diagrams:
    176                real_data = np.zeros(Nt)
    177                for x0 in range(Nt):
    178                    raw_data = h5file["DistillationContraction/Correlators/" + diagram + "/" + str(x0)]
    179                    real_data += np.roll(raw_data[:]["re"].astype(np.double), -x0)
    180                real_data /= Nt
    181
    182                corr_data[diagram].append(real_data)
    183            h5file.close()
    184
    185        res_dict[str(identifier)] = {}
    186
    187        for diagram in diagrams:
    188
    189            tmp_data = np.array(corr_data[diagram])
    190
    191            l_obs = []
    192            for c in tmp_data.T:
    193                l_obs.append(Obs([c], [ens_id], idl=[idx]))
    194
    195            corr = Corr(l_obs)
    196            corr.tag = str(identifier)
    197
    198            res_dict[str(identifier)][diagram] = corr
    199
    200    return res_dict

Read hadrons DistillationContraction hdf5 files in given directory structure

###### Parameters

- path (str): path to the directories to read
- ens_id (str): name of the ensemble, required for internal bookkeeping
- diagrams (list): List of strings of the diagrams to extract, e.g. ["direct", "box", "cross"].
- idl (range): If specified only configurations in the given range are read in.

class Npr_matrix(numpy.ndarray): View Source

    203class Npr_matrix(np.ndarray):
    204
    205    def __new__(cls, input_array, mom_in=None, mom_out=None):
    206        obj = np.asarray(input_array).view(cls)
    207        obj.mom_in = mom_in
    208        obj.mom_out = mom_out
    209        return obj
    210
    211    @property
    212    def g5H(self):
    213        """Gamma_5 hermitean conjugate
    214
    215        Uses the fact that the propagator is gamma5 hermitean, so just the
    216        in and out momenta of the propagator are exchanged.
    217        """
    218        return Npr_matrix(self,
    219                          mom_in=self.mom_out,
    220                          mom_out=self.mom_in)
    221
    222    def _propagate_mom(self, other, name):
    223        s_mom = getattr(self, name, None)
    224        o_mom = getattr(other, name, None)
    225        if s_mom is not None and o_mom is not None:
    226            if not np.allclose(s_mom, o_mom):
    227                raise Exception(name + ' does not match.')
    228        return o_mom if o_mom is not None else s_mom
    229
    230    def __matmul__(self, other):
    231        return self.__new__(Npr_matrix,
    232                            super().__matmul__(other),
    233                            self._propagate_mom(other, 'mom_in'),
    234                            self._propagate_mom(other, 'mom_out'))
    235
    236    def __array_finalize__(self, obj):
    237        if obj is None:
    238            return
    239        self.mom_in = getattr(obj, 'mom_in', None)
    240        self.mom_out = getattr(obj, 'mom_out', None)

ndarray(shape, dtype=float, buffer=None, offset=0, strides=None, order=None)

An array object represents a multidimensional, homogeneous array of fixed-size items. An associated data-type object describes the format of each element in the array (its byte-order, how many bytes it occupies in memory, whether it is an integer, a floating point number, or something else, etc.)

Arrays should be constructed using `array`, `zeros` or `empty` (refer to the See Also section below). The parameters given here refer to a low-level method (`ndarray(...)`) for instantiating an array.

For more information, refer to the `numpy` module and examine the methods and attributes of an array.

###### Parameters

- (for the __new__ method; see Notes below)
- shape (tuple of ints): Shape of created array.
- dtype (data-type, optional): Any object that can be interpreted as a numpy data type.
- buffer (object exposing buffer interface, optional): Used to fill the array with data.
- offset (int, optional): Offset of array data in buffer.
- strides (tuple of ints, optional): Strides of data in memory.
- order ({'C', 'F'}, optional): Row-major (C-style) or column-major (Fortran-style) order.

###### Attributes

- T (ndarray): Transpose of the array.
- data (buffer): The array's elements, in memory.
- dtype (dtype object): Describes the format of the elements in the array.
- flags (dict): Dictionary containing information related to memory use, e.g., 'C_CONTIGUOUS', 'OWNDATA', 'WRITEABLE', etc.
- flat (numpy.flatiter object): Flattened version of the array as an iterator. The iterator allows assignments, e.g., `x.flat = 3` (See `ndarray.flat` for assignment examples; TODO).
- imag (ndarray): Imaginary part of the array.
- real (ndarray): Real part of the array.
- size (int): Number of elements in the array.
- itemsize (int): The memory use of each array element in bytes.
- nbytes (int): The total number of bytes required to store the array data, i.e., `itemsize * size`.
- ndim (int): The array's number of dimensions.
- shape (tuple of ints): Shape of the array.
- strides (tuple of ints): The step-size required to move from one element to the next in memory. For example, a contiguous `(3, 4)` array of type `int16` in C-order has strides `(8, 2)`. This implies that to move from element to element in memory requires jumps of 2 bytes. To move from row-to-row, one needs to jump 8 bytes at a time (`2 * 4`).
- ctypes (ctypes object): Class containing properties of the array needed for interaction with ctypes.
- base (ndarray): If the array is a view into another array, that array is its `base` (unless that array is also a view). The `base` array is where the array data is actually stored.

###### See Also

`array`: Construct an array.
`zeros`: Create an array, each element of which is zero.
`empty`: Create an array, but leave its allocated memory unchanged (i.e., it contains "garbage").
`dtype`: Create a data-type.
`numpy.typing.NDArray`: An ndarray alias :term:`generic <generic type>` w.r.t. its `dtype.type <numpy.dtype.type>`.

###### Notes

There are two modes of creating an array using `__new__`:

1. If `buffer` is None, then only `shape`, `dtype`, and `order` are used.
2. If `buffer` is an object exposing the buffer interface, then all keywords are interpreted.

No `__init__` method is needed because the array is fully initialized after the `__new__` method.

###### Examples

These examples illustrate the low-level `ndarray` constructor. Refer to the `See Also` section above for easier ways of constructing an ndarray.

First mode, `buffer` is None:

    >>> np.ndarray(shape=(2,2), dtype=float, order='F')
    array([[0.0e+000, 0.0e+000], # random
           [     nan, 2.5e-323]])

Second mode:

    >>> np.ndarray((2,), buffer=np.array([1,2,3]),
    ...            offset=np.int_().itemsize,
    ...            dtype=int) # offset = 1*itemsize, i.e. skip first element
    array([2, 3])

Npr_matrix()
g5H

Gamma_5 hermitean conjugate

Uses the fact that the propagator is gamma5 hermitean, so just the in and out momenta of the propagator are exchanged.

##### Inherited Members

numpy.ndarray
  dumps
  dump
  all
  any
  argmax
  argmin
  argpartition
  argsort
  astype
  byteswap
  choose
  clip
  compress
  conj
  conjugate
  copy
  cumprod
  cumsum
  diagonal
  dot
  fill
  flatten
  getfield
  item
  itemset
  max
  mean
  min
  newbyteorder
  nonzero
  partition
  prod
  ptp
  put
  ravel
  repeat
  reshape
  resize
  round
  searchsorted
  setfield
  setflags
  sort
  squeeze
  std
  sum
  swapaxes
  take
  tobytes
  tofile
  tolist
  tostring
  trace
  transpose
  var
  view
  ndim
  flags
  shape
  strides
  data
  itemsize
  size
  nbytes
  base
  dtype
  real
  imag
  flat
  ctypes
  T

def read_ExternalLeg_hd5(path, filestem, ens_id, idl=None) View Source

    243def read_ExternalLeg_hd5(path, filestem, ens_id, idl=None):
    244    """Read hadrons ExternalLeg hdf5 file and output an array of CObs
    245
    246    Parameters
    247    ----------
    248    path : str
    249        path to the files to read
    250    filestem : str
    251        namestem of the files to read
    252    ens_id : str
    253        name of the ensemble, required for internal bookkeeping
    254    idl : range
    255        If specified only configurations in the given range are read in.
    256    """
    257
    258    files, idx = _get_files(path, filestem, idl)
    259
    260    mom = None
    261
    262    corr_data = []
    263    for hd5_file in files:
    264        file = h5py.File(path + '/' + hd5_file, "r")
    265        raw_data = file['ExternalLeg/corr'][0][0].view('complex')
    266        corr_data.append(raw_data)
    267        if mom is None:
    268            mom = np.array(str(file['ExternalLeg/info'].attrs['pIn'])[3:-2].strip().split(), dtype=float)
    269        file.close()
    270    corr_data = np.array(corr_data)
    271
    272    rolled_array = np.rollaxis(corr_data, 0, 5)
    273
    274    matrix = np.empty((rolled_array.shape[:-1]), dtype=object)
    275    for si, sj, ci, cj in np.ndindex(rolled_array.shape[:-1]):
    276        real = Obs([rolled_array[si, sj, ci, cj].real], [ens_id], idl=[idx])
    277        imag = Obs([rolled_array[si, sj, ci, cj].imag], [ens_id], idl=[idx])
    278        matrix[si, sj, ci, cj] = CObs(real, imag)
    279
    280    return Npr_matrix(matrix, mom_in=mom)

Read hadrons ExternalLeg hdf5 file and output an array of CObs

###### Parameters

- path (str): path to the files to read
- filestem (str): namestem of the files to read
- ens_id (str): name of the ensemble, required for internal bookkeeping
- idl (range): If specified only configurations in the given range are read in.

def read_Bilinear_hd5(path, filestem, ens_id, idl=None) View Source

    283def read_Bilinear_hd5(path, filestem, ens_id, idl=None):
    284    """Read hadrons Bilinear hdf5 file and output an array of CObs
    285
    286    Parameters
    287    ----------
    288    path : str
    289        path to the files to read
    290    filestem : str
    291        namestem of the files to read
    292    ens_id : str
    293        name of the ensemble, required for internal bookkeeping
    294    idl : range
    295        If specified only configurations in the given range are read in.
    296    """
    297
    298    files, idx = _get_files(path, filestem, idl)
    299
    300    mom_in = None
    301    mom_out = None
    302
    303    corr_data = {}
    304    for hd5_file in files:
    305        file = h5py.File(path + '/' + hd5_file, "r")
    306        for i in range(16):
    307            name = file['Bilinear/Bilinear_' + str(i) + '/info'].attrs['gamma'][0].decode('UTF-8')
    308            if name not in corr_data:
    309                corr_data[name] = []
    310            raw_data = file['Bilinear/Bilinear_' + str(i) + '/corr'][0][0].view('complex')
    311            corr_data[name].append(raw_data)
    312            if mom_in is None:
    313                mom_in = np.array(str(file['Bilinear/Bilinear_' + str(i) + '/info'].attrs['pIn'])[3:-2].strip().split(), dtype=float)
    314            if mom_out is None:
    315                mom_out = np.array(str(file['Bilinear/Bilinear_' + str(i) + '/info'].attrs['pOut'])[3:-2].strip().split(), dtype=float)
    316
    317        file.close()
    318
    319    result_dict = {}
    320
    321    for key, data in corr_data.items():
    322        local_data = np.array(data)
    323
    324        rolled_array = np.rollaxis(local_data, 0, 5)
    325
    326        matrix = np.empty((rolled_array.shape[:-1]), dtype=object)
    327        for si, sj, ci, cj in np.ndindex(rolled_array.shape[:-1]):
    328            real = Obs([rolled_array[si, sj, ci, cj].real], [ens_id], idl=[idx])
    329            imag = Obs([rolled_array[si, sj, ci, cj].imag], [ens_id], idl=[idx])
    330            matrix[si, sj, ci, cj] = CObs(real, imag)
    331
    332        result_dict[key] = Npr_matrix(matrix, mom_in=mom_in, mom_out=mom_out)
    333
    334    return result_dict

Read hadrons Bilinear hdf5 file and output an array of CObs

###### Parameters

- path (str): path to the files to read
- filestem (str): namestem of the files to read
- ens_id (str): name of the ensemble, required for internal bookkeeping
- idl (range): If specified only configurations in the given range are read in.

def read_Fourquark_hd5(path, filestem, ens_id, idl=None, vertices=['VA', 'AV']) View Source

    337def read_Fourquark_hd5(path, filestem, ens_id, idl=None, vertices=["VA", "AV"]):
    338    """Read hadrons FourquarkFullyConnected hdf5 file and output an array of CObs
    339
    340    Parameters
    341    ----------
    342    path : str
    343        path to the files to read
    344    filestem : str
    345        namestem of the files to read
    346    ens_id : str
    347        name of the ensemble, required for internal bookkeeping
    348    idl : range
    349        If specified only configurations in the given range are read in.
    350    vertices : list
    351        Vertex functions to be extracted.
    352    """
    353
    354    files, idx = _get_files(path, filestem, idl)
    355
    356    mom_in = None
    357    mom_out = None
    358
    359    vertex_names = []
    360    for vertex in vertices:
    361        vertex_names += _get_lorentz_names(vertex)
    362
    363    corr_data = {}
    364
    365    tree = 'FourQuarkFullyConnected/FourQuarkFullyConnected_'
    366
    367    for hd5_file in files:
    368        file = h5py.File(path + '/' + hd5_file, "r")
    369
    370        for i in range(32):
    371            name = (file[tree + str(i) + '/info'].attrs['gammaA'][0].decode('UTF-8'), file[tree + str(i) + '/info'].attrs['gammaB'][0].decode('UTF-8'))
    372            if name in vertex_names:
    373                if name not in corr_data:
    374                    corr_data[name] = []
    375                raw_data = file[tree + str(i) + '/corr'][0][0].view('complex')
    376                corr_data[name].append(raw_data)
    377                if mom_in is None:
    378                    mom_in = np.array(str(file[tree + str(i) + '/info'].attrs['pIn'])[3:-2].strip().split(), dtype=float)
    379                if mom_out is None:
    380                    mom_out = np.array(str(file[tree + str(i) + '/info'].attrs['pOut'])[3:-2].strip().split(), dtype=float)
    381
    382        file.close()
    383
    384    intermediate_dict = {}
    385
    386    for vertex in vertices:
    387        lorentz_names = _get_lorentz_names(vertex)
    388        for v_name in lorentz_names:
    389            if v_name in [('SigmaXY', 'SigmaZT'),
    390                          ('SigmaXT', 'SigmaYZ'),
    391                          ('SigmaYZ', 'SigmaXT'),
    392                          ('SigmaZT', 'SigmaXY')]:
    393                sign = -1
    394            else:
    395                sign = 1
    396            if vertex not in intermediate_dict:
    397                intermediate_dict[vertex] = sign * np.array(corr_data[v_name])
    398            else:
    399                intermediate_dict[vertex] += sign * np.array(corr_data[v_name])
    400
    401    result_dict = {}
    402
    403    for key, data in intermediate_dict.items():
    404
    405        rolled_array = np.moveaxis(data, 0, 8)
    406
    407        matrix = np.empty((rolled_array.shape[:-1]), dtype=object)
    408        for index in np.ndindex(rolled_array.shape[:-1]):
    409            real = Obs([rolled_array[index].real], [ens_id], idl=[idx])
    410            imag = Obs([rolled_array[index].imag], [ens_id], idl=[idx])
    411            matrix[index] = CObs(real, imag)
    412
    413        result_dict[key] = Npr_matrix(matrix, mom_in=mom_in, mom_out=mom_out)
    414
    415    return result_dict

Read hadrons FourquarkFullyConnected hdf5 file and output an array of CObs

###### Parameters

- path (str): path to the files to read
- filestem (str): namestem of the files to read
- ens_id (str): name of the ensemble, required for internal bookkeeping
- idl (range): If specified only configurations in the given range are read in.
- vertices (list): Vertex functions to be extracted.