diff --git a/pyerrors/input/openQCD.py b/pyerrors/input/openQCD.py
index 3c50a3d2..36bdd552 100644
--- a/pyerrors/input/openQCD.py
+++ b/pyerrors/input/openQCD.py
@@ -217,8 +217,7 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
     return result
 
 
-def extract_t0(path, prefix, dtr_read, xmin,
-               spatial_extent, fit_range=5, **kwargs):
+def extract_t0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, **kwargs):
     """Extract t0 from given .ms.dat files. Returns t0 as Obs.
 
     It is assumed that all boundary effects have
@@ -226,7 +225,6 @@ def extract_t0(path, prefix, dtr_read, xmin,
     The data around the zero crossing of t^2<E> - 0.3
     is fitted with a linear function
     from which the exact root is extracted.
-    Only works with openQCD
 
     It is assumed that one measurement is performed for each config.
     If this is not the case, the resulting idl, as well as the handling
@@ -510,8 +508,289 @@ def _read_array_openQCD2(fp):
     return {'d': d, 'n': n, 'size': size, 'arr': arr}
 
 
-def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
-    """Read qtop format from given folder structure.
+def read_qtop(path, prefix, c, dtr_cnfg=1, version="openQCD", **kwargs):
+    """Read the topologial charge based on openQCD gradient flow measurements.
+
+    Parameters
+    ----------
+    path : str
+        path of the measurement files
+    prefix : str
+        prefix of the measurement files, e.g. <prefix>_id0_r0.ms.dat.
+        Ignored if file names are passed explicitly via keyword files.
+    c : double
+        Smearing radius in units of the lattice extent, c = sqrt(8 t0) / L.
+    dtr_cnfg : int
+        (optional) parameter that specifies the number of measurements
+        between two configs.
+        If it is not set, the distance between two measurements
+        in the file is assumed to be the distance between two configurations.
+    steps : int
+        (optional) Distance between two configurations in units of trajectories /
+         cycles. Assumed to be the distance between two measurements * dtr_cnfg if not given
+    version : str
+        Either openQCD or sfqcd, depending on the data.
+    L : int
+        spatial length of the lattice in L/a.
+        HAS to be set if version != sfqcd, since openQCD does not provide
+        this in the header
+    r_start : list
+        list which contains the first config to be read for each replicum.
+    r_stop : list
+        list which contains the last config to be read for each replicum.
+    files : list
+        specify the exact files that need to be read
+        from path, practical if e.g. only one replicum is needed
+    names : list
+        Alternative labeling for replicas/ensembles.
+        Has to have the appropriate length.
+    Zeuthen_flow : bool
+        (optional) If True, the Zeuthen flow is used for Qtop. Only possible
+        for version=='sfqcd' If False, the Wilson flow is used.
+    integer_charge : bool
+        If True, the charge is rounded towards the nearest integer on each config.
+    """
+    known_versions = ["openQCD", "sfqcd"]
+
+    if version not in known_versions:
+        raise Exception("Unknown openQCD version.")
+    if "steps" in kwargs:
+        steps = kwargs.get("steps")
+    if version == "sfqcd":
+        if "L" in kwargs:
+            supposed_L = kwargs.get("L")
+        else:
+            supposed_L = None
+        postfix = ".gfms.dat"
+    else:
+        if "L" not in kwargs:
+            raise Exception("This version of openQCD needs you to provide the spatial length of the lattice as parameter 'L'.")
+        else:
+            L = kwargs.get("L")
+        postfix = ".ms.dat"
+
+    if "files" in kwargs:
+        files = kwargs.get("files")
+        postfix = ''
+    else:
+        found = []
+        files = []
+        for (dirpath, dirnames, filenames) in os.walk(path + "/"):
+            # print(filenames)
+            found.extend(filenames)
+            break
+        for f in found:
+            if fnmatch.fnmatch(f, prefix + "*" + postfix):
+                files.append(f)
+
+    if 'r_start' in kwargs:
+        r_start = kwargs.get('r_start')
+        if len(r_start) != len(files):
+            raise Exception('r_start does not match number of replicas')
+        r_start = [o if o else None for o in r_start]
+    else:
+        r_start = [None] * len(files)
+
+    if 'r_stop' in kwargs:
+        r_stop = kwargs.get('r_stop')
+        if len(r_stop) != len(files):
+            raise Exception('r_stop does not match number of replicas')
+    else:
+        r_stop = [None] * len(files)
+    rep_names = []
+
+    zeuthen = kwargs.get('Zeuthen_flow', False)
+    if zeuthen and version not in ['sfqcd']:
+        raise Exception('Zeuthen flow can only be used for version==sfqcd')
+
+    r_start_index = []
+    r_stop_index = []
+    deltas = []
+    configlist = []
+    for rep, file in enumerate(files):
+        with open(path + "/" + file, "rb") as fp:
+
+            Q = []
+            traj_list = []
+            if version in ['sfqcd']:
+                if zeuthen:
+                    obspos = 0
+                else:
+                    obspos = 8
+                t = fp.read(12)
+                header = struct.unpack('<iii', t)
+                zthfl = header[0]  # Zeuthen flow -> if it's equal to 2 it means that the Zeuthen flow is also 'measured' (apart from the Wilson flow)
+                ncs = header[1]  # number of different values for c in t_flow=1/8 c² L² -> measurements done for ncs c's
+                tmax = header[2]  # lattice T/a
+
+                t = fp.read(12)
+                Ls = struct.unpack('<iii', t)
+                if(Ls[0] == Ls[1] and Ls[1] == Ls[2]):
+                    L = Ls[0]
+                    if not (supposed_L == L) and supposed_L:
+                        raise Exception("It seems the length given in the header and by you contradict each other")
+                else:
+                    raise Exception("Found more than one spatial length in header!")
+
+                t = fp.read(16)
+                header2 = struct.unpack('<dd', t)
+                tol = header2[0]
+                cmax = header2[1]  # highest value of c used
+
+                if c > cmax:
+                    raise Exception('Flow has been determined between c=0 and c=%lf with tolerance %lf' % (cmax, tol))
+
+                if(zthfl == 2):
+                    nfl = 2  # number of flows
+                else:
+                    nfl = 1
+                iobs = 8 * nfl  # number of flow observables calculated
+
+                while 0 < 1:
+                    t = fp.read(4)
+                    if(len(t) < 4):
+                        break
+                    traj_list.append(struct.unpack('i', t)[0])   # trajectory number when measurement was done
+
+                    for j in range(ncs + 1):
+                        for i in range(iobs):
+                            t = fp.read(8 * tmax)
+                            if (i == obspos):  # determines the flow observable -> i=0 <-> Zeuthen flow
+                                Q.append(struct.unpack('d' * tmax, t))
+
+            else:
+                t = fp.read(12)
+                header = struct.unpack('<iii', t)
+                # step size in integration steps "dnms"
+                dn = header[0]
+                # number of measurements, so "ntot"/dn
+                nn = header[1]
+                # lattice T/a
+                tmax = header[2]
+
+                t = fp.read(8)
+                eps = struct.unpack('d', t)[0]
+
+                while 0 < 1:
+                    t = fp.read(4)
+                    if(len(t) < 4):
+                        break
+                    traj_list.append(struct.unpack('i', t)[0])
+                    # Wsl
+                    t = fp.read(8 * tmax * (nn + 1))
+                    # Ysl
+                    t = fp.read(8 * tmax * (nn + 1))
+                    # Qsl, which is asked for in this method
+                    t = fp.read(8 * tmax * (nn + 1))
+                    # unpack the array of Qtops,
+                    # on each timeslice t=0,...,tmax-1 and the
+                    # measurement number in = 0...nn (see README.qcd1)
+                    tmpd = struct.unpack('d' * tmax * (nn + 1), t)
+                    Q.append(tmpd)
+
+        if len(np.unique(np.diff(traj_list))) != 1:
+            raise Exception("Irregularities in stepsize found")
+        else:
+            if 'steps' in kwargs:
+                if steps != traj_list[1] - traj_list[0]:
+                    raise Exception("steps and the found stepsize are not the same")
+            else:
+                steps = traj_list[1] - traj_list[0]
+
+        configlist.append([tr // steps / dtr_cnfg for tr in traj_list])
+        if configlist[-1][0] > 1:
+            offset = configlist[-1][0] - 1
+            warnings.warn('Assume thermalization and that the first measurement belongs to the first config. Offset = %d configs (%d trajectories / cycles)' % (
+                offset, offset * steps))
+            configlist[-1] = [item - offset for item in configlist[-1]]
+
+        if r_start[rep] is None:
+            r_start_index.append(0)
+        else:
+            try:
+                r_start_index.append(configlist[-1].index(r_start[rep]))
+            except ValueError:
+                raise Exception('Config %d not in file with range [%d, %d]' % (
+                    r_start[rep], configlist[-1][0], configlist[-1][-1])) from None
+
+        if r_stop[rep] is None:
+            r_stop_index.append(len(configlist[-1]) - 1)
+        else:
+            try:
+                r_stop_index.append(configlist[-1].index(r_stop[rep]))
+            except ValueError:
+                raise Exception('Config %d not in file with range [%d, %d]' % (
+                    r_stop[rep], configlist[-1][0], configlist[-1][-1])) from None
+
+        if version in ['sfqcd']:
+            cstepsize = cmax / ncs
+            index_aim = round(c / cstepsize)
+        else:
+            t_aim = (c * L) ** 2 / 8
+            index_aim = round(t_aim / eps / dn)
+
+        Q_sum = []
+        for i, item in enumerate(Q):
+            Q_sum.append([sum(item[current:current + tmax])
+                         for current in range(0, len(item), tmax)])
+        Q_top = []
+        if version in ['sfqcd']:
+            for i in range(len(Q_sum) // (ncs + 1)):
+                Q_top.append(Q_sum[i * (ncs + 1) + index_aim][0])
+        else:
+            for i in range(len(Q) // dtr_cnfg):
+                Q_top.append(Q_sum[dtr_cnfg * i][index_aim])
+        if len(Q_top) != len(traj_list) // dtr_cnfg:
+            raise Exception("qtops and traj_list dont have the same length")
+
+        if kwargs.get('integer_charge', False):
+            Q_top = [round(q) for q in Q_top]
+
+        truncated_file = file[:-len(postfix)]
+
+        if "names" not in kwargs:
+            try:
+                idx = truncated_file.index('r')
+            except Exception:
+                if "names" not in kwargs:
+                    raise Exception("Automatic recognition of replicum failed, please enter the key word 'names'.")
+            ens_name = truncated_file[:idx]
+            rep_names.append(ens_name + '|' + truncated_file[idx:])
+        else:
+            names = kwargs.get("names")
+            rep_names = names
+        deltas.append(Q_top)
+
+    idl = [range(int(configlist[rep][r_start_index[rep]]), int(configlist[rep][r_stop_index[rep]]), 1) for rep in range(len(deltas))]
+    deltas = [deltas[nrep][r_start_index[nrep]:r_stop_index[nrep]] for nrep in range(len(deltas))]
+    result = Obs(deltas, rep_names, idl=idl)
+    return result
+
+
+def qtop_projection(qtop, target=0):
+    """Returns the projection to the topological charge sector defined by target.
+
+    Parameters
+    ----------
+    path : Obs
+        Topological charge, rounded to nearest integer on each config.
+    target : int
+        Specifies the topological sector to be reweighted to (default 0)
+    """
+    if qtop.reweighted:
+        raise Exception('You can not use a reweighted observable for reweighting!')
+
+    proj_qtop = []
+    for n in qtop.deltas:
+        proj_qtop.append(np.array([1 if int(qtop.value + q) == target else 0 for q in qtop.deltas[n]]))
+
+    reto = Obs(proj_qtop, qtop.names, idl=[qtop.idl[name] for name in qtop.names])
+    reto.is_merged = qtop.is_merged
+    return reto
+
+
+def read_qtop_sector(path, prefix, c, target=0, **kwargs):
+    """Constructs reweighting factors to a specified topological sector.
 
     Parameters
     ----------
@@ -521,18 +800,19 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
         prefix of the measurement files, e.g. <prefix>_id0_r0.ms.dat
     c : double
         Smearing radius in units of the lattice extent, c = sqrt(8 t0) / L
+    target : int
+        Specifies the topological sector to be reweighted to (default 0)
     dtr_cnfg : int
         (optional) parameter that specifies the number of trajectories
         between two configs.
         if it is not set, the distance between two measurements
-        in the file is assumed to be
-        the distance between two configurations.
+        in the file is assumed to be the distance between two configurations.
     steps : int
-        (optional) (maybe only necessary for openQCD2.0)
-        nt step size, guessed if not given
+        (optional) Distance between two configurations in units of trajectories /
+         cycles. Assumed to be the distance between two measurements * dtr_cnfg if not given
     version : str
         version string of the openQCD (sfqcd) version used to create
-        the ensemble
+        the ensemble. Default is 2.0. May also be set to sfqcd.
     L : int
         spatial length of the lattice in L/a.
         HAS to be set if version != sfqcd, since openQCD does not provide
@@ -548,200 +828,17 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="1.2", **kwargs):
     names : list
         Alternative labeling for replicas/ensembles.
         Has to have the appropriate length
-    """
-    known_versions = ["1.0", "1.2", "1.4", "1.6", "2.0", "sfqcd"]
-
-    if version not in known_versions:
-        raise Exception("Unknown openQCD version.")
-    if "steps" in kwargs:
-        steps = kwargs.get("steps")
-    if version == "sfqcd":
-        if "L" in kwargs:
-            supposed_L = kwargs.get("L")
-    else:
-        if "L" not in kwargs:
-            raise Exception("This version of openQCD needs you to provide the spatial length of the lattice as parameter 'L'.")
-        else:
-            L = kwargs.get("L")
-    r_start = 1
-    if "r_start" in kwargs:
-        r_start = kwargs.get("r_start")
-    if "r_stop" in kwargs:
-        r_stop = kwargs.get("r_stop")
-    if "files" in kwargs:
-        files = kwargs.get("files")
-    else:
-        found = []
-        files = []
-        for (dirpath, dirnames, filenames) in os.walk(path + "/"):
-            # print(filenames)
-            found.extend(filenames)
-            break
-        for f in found:
-            if fnmatch.fnmatch(f, prefix + "*" + ".ms.dat"):
-                files.append(f)
-        print(files)
-    rep_names = []
-
-    deltas = []
-    idl = []
-    for rep, file in enumerate(files):
-        with open(path + "/" + file, "rb") as fp:
-            t = fp.read(12)
-            header = struct.unpack('<iii', t)
-            # step size in integration steps "dnms"
-            dn = header[0]
-            # number of measurements, so "ntot"/dn
-            nn = header[1]
-            # lattice T/a
-            tmax = header[2]
-            if version == "sfqcd":
-                t = fp.read(12)
-                Ls = struct.unpack('<iii', t)
-                if(Ls[0] == Ls[1] and Ls[1] == Ls[2]):
-                    L = Ls[0]
-                    if not (supposed_L == L):
-                        raise Exception("It seems the length given in the header and by you contradict each other")
-                else:
-                    raise Exception("Found more than one spatial length in header!")
-
-            print('dnms:', dn)
-            print('nn:', nn)
-            print('tmax:', tmax)
-            t = fp.read(8)
-            eps = struct.unpack('d', t)[0]
-            print('eps:', eps)
-
-            Q = []
-            ncs = []
-            while 0 < 1:
-                t = fp.read(4)
-                if(len(t) < 4):
-                    break
-                ncs.append(struct.unpack('i', t)[0])
-                # Wsl
-                t = fp.read(8 * tmax * (nn + 1))
-                # Ysl
-                t = fp.read(8 * tmax * (nn + 1))
-                # Qsl, which is asked for in this method
-                t = fp.read(8 * tmax * (nn + 1))
-                # unpack the array of Qtops,
-                # on each timeslice t=0,...,tmax-1 and the
-                # measurement number in = 0...nn (see README.qcd1)
-                tmpd = struct.unpack('d' * tmax * (nn + 1), t)
-                Q.append(tmpd)
-
-        if not len(set([ncs[i] - ncs[i - 1] for i in range(1, len(ncs))])):
-            raise Exception("Irregularities in stepsize found")
-        else:
-            if 'steps' in kwargs:
-                if steps != ncs[1] - ncs[0]:
-                    raise Exception("steps and the found stepsize are not the same")
-            else:
-                steps = ncs[1] - ncs[0]
-
-        print(len(Q))
-        print('max_t:', dn * (nn) * eps)
-
-        t_aim = (c * L) ** 2 / 8
-
-        print('t_aim:', t_aim)
-        index_aim = round(t_aim / eps / dn)
-        print('index_aim:', index_aim)
-
-        Q_sum = []
-        for i, item in enumerate(Q):
-            Q_sum.append([sum(item[current:current + tmax])
-                         for current in range(0, len(item), tmax)])
-        print(len(Q_sum))
-        print(len(Q_sum[0]))
-        Q_round = []
-        for i in range(len(Q) // dtr_cnfg):
-            Q_round.append(round(Q_sum[dtr_cnfg * i][index_aim]))
-        if len(Q_round) != len(ncs) // dtr_cnfg:
-            raise Exception("qtops and ncs dont have the same length")
-
-        truncated_file = file[:-7]
-        print(truncated_file)
-        idl_start = 1
-
-        if "r_start" in kwargs:
-            Q_round = Q_round[r_start[rep]:]
-            idl_start = r_start[rep]
-        if "r_stop" in kwargs:
-            Q_round = Q_round[:r_stop[rep]]
-        idl_stop = idl_start + len(Q_round)
-        # keyword "names" prevails over "ens_name"
-        if "names" not in kwargs:
-            try:
-                idx = truncated_file.index('r')
-            except Exception:
-                if "names" not in kwargs:
-                    raise Exception("Automatic recognition of replicum failed, please enter the key word 'names'.")
-            if "ens_name" in kwargs:
-                ens_name = kwargs.get("ens_name")
-            else:
-                ens_name = truncated_file[:idx]
-            rep_names.append(ens_name + '|' + truncated_file[idx:])
-        else:
-            names = kwargs.get("names")
-            rep_names = names
-        deltas.append(np.array(Q_round))
-        idl.append(range(idl_start, idl_stop))
-    result = Obs(deltas, rep_names, idl=idl)
-    return result
-
-
-def read_qtop_sector(target=0, **kwargs):
-    """Constructs reweighting factors to a specified topological sector.
-
-    Parameters
-    ----------
-    target : int
-        Specifies the topological sector to be reweighted to (default 0)
-    q_top : Obs
-        Alternatively takes args of read_qtop method as kwargs
+    Zeuthen_flow : bool
+        (optional) If True, the Zeuthen flow is used for Qtop. Only possible
+        for version=='sfqcd' If False, the Wilson flow is used.
+    integer_charge : bool
+        If True, the charge is rounded towards the nearest integer on each config.
     """
 
     if not isinstance(target, int):
         raise Exception("'target' has to be an integer.")
 
-    if "q_top" in kwargs:
-        qtop = kwargs.get("q_top")
-    else:
-        if "path" in kwargs:
-            path = kwargs.get("path")
-            del kwargs["path"]
-        else:
-            raise Exception("If you are not providing q_top, please provide path")
-        if "prefix" in kwargs:
-            prefix = kwargs.get("prefix")
-            del kwargs["prefix"]
-        else:
-            raise Exception("If you are not providing q_top, please provide prefix")
-        if "c" in kwargs:
-            c = kwargs.get("c")
-            del kwargs["c"]
-        else:
-            raise Exception("If you are not providing q_top, please provide c")
-        if "version" in kwargs:
-            version = kwargs.get("version")
-            del kwargs["version"]
-        else:
-            version = "1.2"
-        if "dtr_cnfg" in kwargs:
-            dtr_cnfg = kwargs.get("dtr_cnfg")
-            del kwargs["dtr_cnfg"]
-        else:
-            dtr_cnfg = 1
-        qtop = read_qtop(path, prefix, c, dtr_cnfg=dtr_cnfg,
-                         version=version, **kwargs)
-    names = qtop.names
-    print(names)
-    print(qtop.deltas.keys())
-    proj_qtop = []
-    for n in qtop.deltas:
-        proj_qtop.append(np.array([1 if int(qtop.value + q) == target else 0 for q in qtop.deltas[n]]))
+    kwargs['integer_charge'] = True
+    qtop = read_qtop(path, prefix, c, **kwargs)
 
-    result = Obs(proj_qtop, qtop.names)
-    return result
+    return qtop_projection(qtop, target=target)