import numpy as np
from ..mbase import BaseModel
from ..pakbase import Package
from .mpsim import ModpathSim
from .mpbas import ModpathBas
import os


class ModpathList(Package):
    """
    List package class
    """

    def __init__(self, model, extension='list', listunit=7):
        """
        Package constructor.

        """
        # Call ancestor's init to set self.parent, extension, name and
        # unit number
        Package.__init__(self, model, extension, 'LIST', listunit)
        # self.parent.add_package(self) This package is not added to the base
        # model so that it is not included in get_name_file_entries()
        return

    def write_file(self):
        # Not implemented for list class
        return


class Modpath(BaseModel):
    """
    Modpath base class

    """

    def __init__(self, modelname='modpathtest', simfile_ext='mpsim',
                 namefile_ext='mpnam',
                 version='modpath', exe_name='mp6.exe', modflowmodel=None,
                 dis_file=None, dis_unit=87, head_file=None, budget_file=None,
                 model_ws=None, external_path=None, verbose=False,
                 load=True, listunit=7):
        """
        Model constructor.

        """
        BaseModel.__init__(self, modelname, simfile_ext, exe_name,
                           model_ws=model_ws, verbose=verbose)

        self.version_types = {'modpath': 'MODPATH'}
        self.set_version(version)

        self.__mf = modflowmodel
        self.lst = ModpathList(self, listunit=listunit)
        self.mpnamefile = '{}.{}'.format(self.name, namefile_ext)
        self.mpbas_file = '{}.mpbas'.format(modelname)
        if self.__mf is not None:
            # ensure that user-specified files are used
            iu = self.__mf.oc.iuhead
            head_file = self.__mf.get_output(unit=iu)
            p = self.__mf.get_package('LPF')
            if p is None:
                p = self.__mf.get_package('BCF6')
            if p is None:
                p = self.__mf.get_package('UPW')
            if p is None:
                msg = 'LPF, BCF6, or UPW packages must be included in the ' + \
                      'passed MODFLOW model'
                raise Exception(msg)
            iu = p.ipakcb
            budget_file = self.__mf.get_output(unit=iu)
            dis_file = self.__mf.dis.file_name[0] \
                if dis_file is None else dis_file
            dis_unit = self.__mf.dis.unit_number[0]
        self.head_file = head_file
        self.budget_file = budget_file
        self.dis_file = dis_file
        self.dis_unit = dis_unit
        # make sure the valid files are available
        if self.head_file is None:
            msg = 'the head file in the MODFLOW model or passed ' + \
                  'to __init__ cannot be None'
            raise ValueError(msg)
        if self.budget_file is None:
            msg = 'the budget file in the MODFLOW model or passed ' + \
                  'to __init__ cannot be None'
            raise ValueError(msg)
        if self.dis_file is None:
            msg = 'the dis file in the MODFLOW model or passed ' + \
                  'to __init__ cannot be None'
            raise ValueError(msg)

        # set the rest of the attributes
        self.__sim = None
        self.array_free_format = False
        self.array_format = 'modflow'
        self.external_path = external_path
        self.external = False
        self.external_fnames = []
        self.external_units = []
        self.external_binflag = []
        self.load = load
        self.__next_ext_unit = 500
        if external_path is not None:
            assert os.path.exists(
                external_path), 'external_path does not exist'
            self.external = True
        return

    def __repr__(self):
        return 'Modpath model'

    # function to encapsulate next_ext_unit attribute
    def next_ext_unit(self):
        self.__next_ext_unit += 1
        return self.__next_ext_unit

    def getsim(self):
        if (self.__sim == None):
            for p in (self.packagelist):
                if isinstance(p, ModpathSim):
                    self.__sim = p
        return self.__sim

    def getmf(self):
        return self.__mf

    def write_name_file(self):
        """
        Write the name file

        Returns
        -------
        None

        """
        fn_path = os.path.join(self.model_ws, self.mpnamefile)
        f_nam = open(fn_path, 'w')
        f_nam.write('%s\n' % (self.heading))
        if self.mpbas_file is not None:
            f_nam.write('%s %3i %s\n' % ('MPBAS', 86, self.mpbas_file))
        if self.dis_file is not None:
            f_nam.write('%s %3i %s\n' % ('DIS', self.dis_unit, self.dis_file))
        if self.head_file is not None:
            f_nam.write('%s %3i %s\n' % ('HEAD', 88, self.head_file))
        if self.budget_file is not None:
            f_nam.write('%s %3i %s\n' % ('BUDGET', 89, self.budget_file))
        for u, f in zip(self.external_units, self.external_fnames):
            f_nam.write('DATA  {0:3d}  '.format(u) + f + '\n')
        f_nam.close()

    sim = property(getsim)  # Property has no setter, so read-only
    mf = property(getmf)  # Property has no setter, so read-only

    def create_mpsim(self, simtype='pathline', trackdir='forward',
                     packages='WEL', start_time=0, default_ifaces=None,
                     ParticleColumnCount=4, ParticleRowCount=4,
                     MinRow=0, MinColumn=0, MaxRow=None, MaxColumn=None,
                     ):
        """
        Create a MODPATH simulation file using available MODFLOW boundary
        package data.

        Parameters
        ----------
        simtype : str
            Keyword defining the MODPATH simulation type. Available simtype's
             are 'endpoint', 'pathline', and 'timeseries'.
             (default is 'PATHLINE')
        trackdir : str
            Keyword that defines the MODPATH particle tracking direction.
            Available trackdir's are 'backward' and 'forward'.
            (default is 'forward')
        packages : str or list of strings
            Keyword defining the modflow packages used to create initial
            particle locations. Supported packages are 'WEL', 'MNW2' and 'RCH'.
            (default is 'WEL').
        start_time : float or tuple
            Sets the value of MODPATH reference time relative to MODFLOW time.
            float : value of MODFLOW simulation time at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 1.
            tuple : (period, step, time fraction) MODFLOW stress period, time step and fraction
                    between 0 and 1 at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 2.
        default_ifaces : list
            List of cell faces (1-6; see MODPATH6 manual, fig. 7) on which to start particles.
            (default is None, meaning ifaces will vary depending on packages argument above)
        ParticleRowCount : int
            Rows of particles to start on each cell index face (iface).
        ParticleColumnCount : int
            Columns of particles to start on each cell index face (iface).

        Returns
        -------
        mpsim : ModpathSim object

        """
        if isinstance(packages, str):
            packages = [packages]
        pak_list = self.__mf.get_package_list()

        # not sure if this is the best way to handle this
        ReferenceTimeOption = 1
        ref_time = 0
        ref_time_per_stp = (0, 0, 1.)
        if isinstance(start_time, tuple):
            ReferenceTimeOption = 2  # 1: specify value for ref. time, 2: specify kper, kstp, rel. time pos
            ref_time_per_stp = start_time
        else:
            ref_time = start_time

        # set iface particle grids
        ptrow = ParticleRowCount
        ptcol = ParticleColumnCount
        side_faces = [[1, ptrow, ptcol], [2, ptrow, ptcol],
                      [3, ptrow, ptcol], [4, ptrow, ptcol]]
        top_face = [5, ptrow, ptcol]
        botm_face = [6, ptrow, ptcol]
        if default_ifaces is not None:
            default_ifaces = [[ifc, ptrow, ptcol] for ifc in default_ifaces]

        Grid = 1
        GridCellRegionOption = 1
        PlacementOption = 1
        ReleaseStartTime = 0.
        ReleaseOption = 1
        CHeadOption = 1
        nper = self.__mf.dis.nper
        nlay, nrow, ncol = self.__mf.dis.nlay, \
                           self.__mf.dis.nrow, \
                           self.__mf.dis.ncol
        arr = np.zeros((nlay, nrow, ncol), dtype=np.int)
        group_name = []
        group_region = []
        group_placement = []
        ifaces = []
        face_ct = []
        strt_file = None
        for package in packages:

            if package.upper() == 'WEL':
                ParticleGenerationOption = 1
                if 'WEL' not in pak_list:
                    raise Exception(
                        'Error: no well package in the passed model')
                for kper in range(nper):
                    mflist = self.__mf.wel.stress_period_data[kper]
                    idx = (mflist['k'], mflist['i'], mflist['j'])
                    arr[idx] = 1
                ngrp = arr.sum()
                icnt = 0
                for k in range(nlay):
                    for i in range(nrow):
                        for j in range(ncol):
                            if arr[k, i, j] < 1:
                                continue
                            group_name.append('wc{}'.format(icnt))
                            group_placement.append([Grid, GridCellRegionOption,
                                                    PlacementOption,
                                                    ReleaseStartTime,
                                                    ReleaseOption,
                                                    CHeadOption])
                            group_region.append([k, i, j, k, i, j])
                            if default_ifaces is None:
                                ifaces.append(
                                    side_faces + [top_face, botm_face])
                                face_ct.append(6)
                            else:
                                ifaces.append(default_ifaces)
                                face_ct.append(len(default_ifaces))
                            icnt += 1
            # this is kind of a band aid pending refactoring of mpsim class
            elif 'MNW' in package.upper():
                ParticleGenerationOption = 1
                if 'MNW2' not in pak_list:
                    raise Exception(
                        'Error: no MNW2 package in the passed model')
                node_data = self.__mf.mnw2.get_allnode_data()
                node_data.sort(order=['wellid', 'k'])
                wellids = np.unique(node_data.wellid)

                def append_node(ifaces_well, wellid, node_number, k, i, j):
                    """add a single MNW node"""
                    group_region.append([k, i, j, k, i, j])
                    if default_ifaces is None:
                        ifaces.append(ifaces_well)
                        face_ct.append(len(ifaces_well))
                    else:
                        ifaces.append(default_ifaces)
                        face_ct.append(len(default_ifaces))
                    group_name.append('{}{}'.format(wellid, node_number))
                    group_placement.append([Grid, GridCellRegionOption,
                                            PlacementOption,
                                            ReleaseStartTime,
                                            ReleaseOption,
                                            CHeadOption])

                for wellid in wellids:
                    nd = node_data[node_data.wellid == wellid]
                    k, i, j = nd.k[0], nd.i[0], nd.j[0]
                    if len(nd) == 1:
                        append_node(side_faces + [top_face, botm_face],
                                    wellid, 0, k, i, j)
                    else:
                        append_node(side_faces + [top_face],
                                    wellid, 0, k, i, j)
                        for n in range(len(nd))[1:]:
                            k, i, j = nd.k[n], nd.i[n], nd.j[n]
                            if n == len(nd) - 1:
                                append_node(side_faces + [botm_face],
                                            wellid, n, k, i, j)
                            else:
                                append_node(side_faces,
                                            wellid, n, k, i, j)
            elif package.upper() == 'RCH':
                ParticleGenerationOption = 1
                # for j in range(nrow):
                #    for i in range(ncol):
                #        group_name.append('rch')
                group_name.append('rch')
                group_placement.append([Grid, GridCellRegionOption,
                                        PlacementOption,
                                        ReleaseStartTime,
                                        ReleaseOption, CHeadOption])
                group_region.append([0, 0, 0, 0, nrow - 1, ncol - 1])
                if default_ifaces is None:
                    face_ct.append(1)
                    ifaces.append([[6, 1, 1]])
                else:
                    ifaces.append(default_ifaces)
                    face_ct.append(len(default_ifaces))


            else:
                model_ws = ''
                if self.__mf is not None:
                    model_ws = self.__mf.model_ws
                if os.path.exists(os.path.join(model_ws, package)):
                    print(
                        "detected a particle starting locations file in packages")
                    assert len(
                        packages) == 1, "if a particle starting locations file is passed" + \
                                        ", other packages cannot be specified"
                    ParticleGenerationOption = 2
                    strt_file = package
                else:
                    raise Exception(
                        "package '{0}' not supported".format(package))

        SimulationType = 1
        if simtype.lower() == 'endpoint':
            SimulationType = 1
        elif simtype.lower() == 'pathline':
            SimulationType = 2
        elif simtype.lower() == 'timeseries':
            SimulationType = 3
        if trackdir.lower() == 'forward':
            TrackingDirection = 1
        elif trackdir.lower() == 'backward':
            TrackingDirection = 2
        WeakSinkOption = 2
        WeakSourceOption = 1

        StopOption = 2

        if SimulationType == 1:
            TimePointOption = 1
        else:
            TimePointOption = 3
        BudgetOutputOption = 1
        ZoneArrayOption = 1
        RetardationOption = 1
        AdvectiveObservationsOption = 1

        mpoptions = [SimulationType, TrackingDirection, WeakSinkOption,
                     WeakSourceOption, ReferenceTimeOption, StopOption,
                     ParticleGenerationOption, TimePointOption,
                     BudgetOutputOption, ZoneArrayOption, RetardationOption,
                     AdvectiveObservationsOption]

        return ModpathSim(self,
                          ref_time=ref_time,
                          ref_time_per_stp=ref_time_per_stp,
                          option_flags=mpoptions,
                          group_placement=group_placement,
                          group_name=group_name,
                          group_region=group_region,
                          face_ct=face_ct, ifaces=ifaces,
                          strt_file=strt_file)

cd671474040114db4c1ce3f7305c17904a20e2a7
<mask token>


class Modpath(BaseModel):
    <mask token>

    def __init__(self, modelname='modpathtest', simfile_ext='mpsim',
        namefile_ext='mpnam', version='modpath', exe_name='mp6.exe',
        modflowmodel=None, dis_file=None, dis_unit=87, head_file=None,
        budget_file=None, model_ws=None, external_path=None, verbose=False,
        load=True, listunit=7):
        """
        Model constructor.

        """
        BaseModel.__init__(self, modelname, simfile_ext, exe_name, model_ws
            =model_ws, verbose=verbose)
        self.version_types = {'modpath': 'MODPATH'}
        self.set_version(version)
        self.__mf = modflowmodel
        self.lst = ModpathList(self, listunit=listunit)
        self.mpnamefile = '{}.{}'.format(self.name, namefile_ext)
        self.mpbas_file = '{}.mpbas'.format(modelname)
        if self.__mf is not None:
            iu = self.__mf.oc.iuhead
            head_file = self.__mf.get_output(unit=iu)
            p = self.__mf.get_package('LPF')
            if p is None:
                p = self.__mf.get_package('BCF6')
            if p is None:
                p = self.__mf.get_package('UPW')
            if p is None:
                msg = (
                    'LPF, BCF6, or UPW packages must be included in the ' +
                    'passed MODFLOW model')
                raise Exception(msg)
            iu = p.ipakcb
            budget_file = self.__mf.get_output(unit=iu)
            dis_file = self.__mf.dis.file_name[0
                ] if dis_file is None else dis_file
            dis_unit = self.__mf.dis.unit_number[0]
        self.head_file = head_file
        self.budget_file = budget_file
        self.dis_file = dis_file
        self.dis_unit = dis_unit
        if self.head_file is None:
            msg = ('the head file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        if self.budget_file is None:
            msg = ('the budget file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        if self.dis_file is None:
            msg = ('the dis file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        self.__sim = None
        self.array_free_format = False
        self.array_format = 'modflow'
        self.external_path = external_path
        self.external = False
        self.external_fnames = []
        self.external_units = []
        self.external_binflag = []
        self.load = load
        self.__next_ext_unit = 500
        if external_path is not None:
            assert os.path.exists(external_path
                ), 'external_path does not exist'
            self.external = True
        return

    def __repr__(self):
        return 'Modpath model'

    def next_ext_unit(self):
        self.__next_ext_unit += 1
        return self.__next_ext_unit

    def getsim(self):
        if self.__sim == None:
            for p in self.packagelist:
                if isinstance(p, ModpathSim):
                    self.__sim = p
        return self.__sim

    def getmf(self):
        return self.__mf

    def write_name_file(self):
        """
        Write the name file

        Returns
        -------
        None

        """
        fn_path = os.path.join(self.model_ws, self.mpnamefile)
        f_nam = open(fn_path, 'w')
        f_nam.write('%s\n' % self.heading)
        if self.mpbas_file is not None:
            f_nam.write('%s %3i %s\n' % ('MPBAS', 86, self.mpbas_file))
        if self.dis_file is not None:
            f_nam.write('%s %3i %s\n' % ('DIS', self.dis_unit, self.dis_file))
        if self.head_file is not None:
            f_nam.write('%s %3i %s\n' % ('HEAD', 88, self.head_file))
        if self.budget_file is not None:
            f_nam.write('%s %3i %s\n' % ('BUDGET', 89, self.budget_file))
        for u, f in zip(self.external_units, self.external_fnames):
            f_nam.write('DATA  {0:3d}  '.format(u) + f + '\n')
        f_nam.close()
    sim = property(getsim)
    mf = property(getmf)

    def create_mpsim(self, simtype='pathline', trackdir='forward', packages
        ='WEL', start_time=0, default_ifaces=None, ParticleColumnCount=4,
        ParticleRowCount=4, MinRow=0, MinColumn=0, MaxRow=None, MaxColumn=None
        ):
        """
        Create a MODPATH simulation file using available MODFLOW boundary
        package data.

        Parameters
        ----------
        simtype : str
            Keyword defining the MODPATH simulation type. Available simtype's
             are 'endpoint', 'pathline', and 'timeseries'.
             (default is 'PATHLINE')
        trackdir : str
            Keyword that defines the MODPATH particle tracking direction.
            Available trackdir's are 'backward' and 'forward'.
            (default is 'forward')
        packages : str or list of strings
            Keyword defining the modflow packages used to create initial
            particle locations. Supported packages are 'WEL', 'MNW2' and 'RCH'.
            (default is 'WEL').
        start_time : float or tuple
            Sets the value of MODPATH reference time relative to MODFLOW time.
            float : value of MODFLOW simulation time at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 1.
            tuple : (period, step, time fraction) MODFLOW stress period, time step and fraction
                    between 0 and 1 at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 2.
        default_ifaces : list
            List of cell faces (1-6; see MODPATH6 manual, fig. 7) on which to start particles.
            (default is None, meaning ifaces will vary depending on packages argument above)
        ParticleRowCount : int
            Rows of particles to start on each cell index face (iface).
        ParticleColumnCount : int
            Columns of particles to start on each cell index face (iface).

        Returns
        -------
        mpsim : ModpathSim object

        """
        if isinstance(packages, str):
            packages = [packages]
        pak_list = self.__mf.get_package_list()
        ReferenceTimeOption = 1
        ref_time = 0
        ref_time_per_stp = 0, 0, 1.0
        if isinstance(start_time, tuple):
            ReferenceTimeOption = 2
            ref_time_per_stp = start_time
        else:
            ref_time = start_time
        ptrow = ParticleRowCount
        ptcol = ParticleColumnCount
        side_faces = [[1, ptrow, ptcol], [2, ptrow, ptcol], [3, ptrow,
            ptcol], [4, ptrow, ptcol]]
        top_face = [5, ptrow, ptcol]
        botm_face = [6, ptrow, ptcol]
        if default_ifaces is not None:
            default_ifaces = [[ifc, ptrow, ptcol] for ifc in default_ifaces]
        Grid = 1
        GridCellRegionOption = 1
        PlacementOption = 1
        ReleaseStartTime = 0.0
        ReleaseOption = 1
        CHeadOption = 1
        nper = self.__mf.dis.nper
        nlay, nrow, ncol = (self.__mf.dis.nlay, self.__mf.dis.nrow, self.
            __mf.dis.ncol)
        arr = np.zeros((nlay, nrow, ncol), dtype=np.int)
        group_name = []
        group_region = []
        group_placement = []
        ifaces = []
        face_ct = []
        strt_file = None
        for package in packages:
            if package.upper() == 'WEL':
                ParticleGenerationOption = 1
                if 'WEL' not in pak_list:
                    raise Exception(
                        'Error: no well package in the passed model')
                for kper in range(nper):
                    mflist = self.__mf.wel.stress_period_data[kper]
                    idx = mflist['k'], mflist['i'], mflist['j']
                    arr[idx] = 1
                ngrp = arr.sum()
                icnt = 0
                for k in range(nlay):
                    for i in range(nrow):
                        for j in range(ncol):
                            if arr[k, i, j] < 1:
                                continue
                            group_name.append('wc{}'.format(icnt))
                            group_placement.append([Grid,
                                GridCellRegionOption, PlacementOption,
                                ReleaseStartTime, ReleaseOption, CHeadOption])
                            group_region.append([k, i, j, k, i, j])
                            if default_ifaces is None:
                                ifaces.append(side_faces + [top_face,
                                    botm_face])
                                face_ct.append(6)
                            else:
                                ifaces.append(default_ifaces)
                                face_ct.append(len(default_ifaces))
                            icnt += 1
            elif 'MNW' in package.upper():
                ParticleGenerationOption = 1
                if 'MNW2' not in pak_list:
                    raise Exception(
                        'Error: no MNW2 package in the passed model')
                node_data = self.__mf.mnw2.get_allnode_data()
                node_data.sort(order=['wellid', 'k'])
                wellids = np.unique(node_data.wellid)

                def append_node(ifaces_well, wellid, node_number, k, i, j):
                    """add a single MNW node"""
                    group_region.append([k, i, j, k, i, j])
                    if default_ifaces is None:
                        ifaces.append(ifaces_well)
                        face_ct.append(len(ifaces_well))
                    else:
                        ifaces.append(default_ifaces)
                        face_ct.append(len(default_ifaces))
                    group_name.append('{}{}'.format(wellid, node_number))
                    group_placement.append([Grid, GridCellRegionOption,
                        PlacementOption, ReleaseStartTime, ReleaseOption,
                        CHeadOption])
                for wellid in wellids:
                    nd = node_data[node_data.wellid == wellid]
                    k, i, j = nd.k[0], nd.i[0], nd.j[0]
                    if len(nd) == 1:
                        append_node(side_faces + [top_face, botm_face],
                            wellid, 0, k, i, j)
                    else:
                        append_node(side_faces + [top_face], wellid, 0, k, i, j
                            )
                        for n in range(len(nd))[1:]:
                            k, i, j = nd.k[n], nd.i[n], nd.j[n]
                            if n == len(nd) - 1:
                                append_node(side_faces + [botm_face],
                                    wellid, n, k, i, j)
                            else:
                                append_node(side_faces, wellid, n, k, i, j)
            elif package.upper() == 'RCH':
                ParticleGenerationOption = 1
                group_name.append('rch')
                group_placement.append([Grid, GridCellRegionOption,
                    PlacementOption, ReleaseStartTime, ReleaseOption,
                    CHeadOption])
                group_region.append([0, 0, 0, 0, nrow - 1, ncol - 1])
                if default_ifaces is None:
                    face_ct.append(1)
                    ifaces.append([[6, 1, 1]])
                else:
                    ifaces.append(default_ifaces)
                    face_ct.append(len(default_ifaces))
            else:
                model_ws = ''
                if self.__mf is not None:
                    model_ws = self.__mf.model_ws
                if os.path.exists(os.path.join(model_ws, package)):
                    print(
                        'detected a particle starting locations file in packages'
                        )
                    assert len(packages
                        ) == 1, 'if a particle starting locations file is passed' + ', other packages cannot be specified'
                    ParticleGenerationOption = 2
                    strt_file = package
                else:
                    raise Exception("package '{0}' not supported".format(
                        package))
        SimulationType = 1
        if simtype.lower() == 'endpoint':
            SimulationType = 1
        elif simtype.lower() == 'pathline':
            SimulationType = 2
        elif simtype.lower() == 'timeseries':
            SimulationType = 3
        if trackdir.lower() == 'forward':
            TrackingDirection = 1
        elif trackdir.lower() == 'backward':
            TrackingDirection = 2
        WeakSinkOption = 2
        WeakSourceOption = 1
        StopOption = 2
        if SimulationType == 1:
            TimePointOption = 1
        else:
            TimePointOption = 3
        BudgetOutputOption = 1
        ZoneArrayOption = 1
        RetardationOption = 1
        AdvectiveObservationsOption = 1
        mpoptions = [SimulationType, TrackingDirection, WeakSinkOption,
            WeakSourceOption, ReferenceTimeOption, StopOption,
            ParticleGenerationOption, TimePointOption, BudgetOutputOption,
            ZoneArrayOption, RetardationOption, AdvectiveObservationsOption]
        return ModpathSim(self, ref_time=ref_time, ref_time_per_stp=
            ref_time_per_stp, option_flags=mpoptions, group_placement=
            group_placement, group_name=group_name, group_region=
            group_region, face_ct=face_ct, ifaces=ifaces, strt_file=strt_file)

<mask token>


class ModpathList(Package):
    <mask token>

    def __init__(self, model, extension='list', listunit=7):
        """
        Package constructor.

        """
        Package.__init__(self, model, extension, 'LIST', listunit)
        return
    <mask token>


class Modpath(BaseModel):
    """
    Modpath base class

    """

    def __init__(self, modelname='modpathtest', simfile_ext='mpsim',
        namefile_ext='mpnam', version='modpath', exe_name='mp6.exe',
        modflowmodel=None, dis_file=None, dis_unit=87, head_file=None,
        budget_file=None, model_ws=None, external_path=None, verbose=False,
        load=True, listunit=7):
        """
        Model constructor.

        """
        BaseModel.__init__(self, modelname, simfile_ext, exe_name, model_ws
            =model_ws, verbose=verbose)
        self.version_types = {'modpath': 'MODPATH'}
        self.set_version(version)
        self.__mf = modflowmodel
        self.lst = ModpathList(self, listunit=listunit)
        self.mpnamefile = '{}.{}'.format(self.name, namefile_ext)
        self.mpbas_file = '{}.mpbas'.format(modelname)
        if self.__mf is not None:
            iu = self.__mf.oc.iuhead
            head_file = self.__mf.get_output(unit=iu)
            p = self.__mf.get_package('LPF')
            if p is None:
                p = self.__mf.get_package('BCF6')
            if p is None:
                p = self.__mf.get_package('UPW')
            if p is None:
                msg = (
                    'LPF, BCF6, or UPW packages must be included in the ' +
                    'passed MODFLOW model')
                raise Exception(msg)
            iu = p.ipakcb
            budget_file = self.__mf.get_output(unit=iu)
            dis_file = self.__mf.dis.file_name[0
                ] if dis_file is None else dis_file
            dis_unit = self.__mf.dis.unit_number[0]
        self.head_file = head_file
        self.budget_file = budget_file
        self.dis_file = dis_file
        self.dis_unit = dis_unit
        if self.head_file is None:
            msg = ('the head file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        if self.budget_file is None:
            msg = ('the budget file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        if self.dis_file is None:
            msg = ('the dis file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        self.__sim = None
        self.array_free_format = False
        self.array_format = 'modflow'
        self.external_path = external_path
        self.external = False
        self.external_fnames = []
        self.external_units = []
        self.external_binflag = []
        self.load = load
        self.__next_ext_unit = 500
        if external_path is not None:
            assert os.path.exists(external_path
                ), 'external_path does not exist'
            self.external = True
        return

    def __repr__(self):
        return 'Modpath model'

    def next_ext_unit(self):
        self.__next_ext_unit += 1
        return self.__next_ext_unit

    def getsim(self):
        if self.__sim == None:
            for p in self.packagelist:
                if isinstance(p, ModpathSim):
                    self.__sim = p
        return self.__sim

    def getmf(self):
        return self.__mf

    def write_name_file(self):
        """
        Write the name file

        Returns
        -------
        None

        """
        fn_path = os.path.join(self.model_ws, self.mpnamefile)
        f_nam = open(fn_path, 'w')
        f_nam.write('%s\n' % self.heading)
        if self.mpbas_file is not None:
            f_nam.write('%s %3i %s\n' % ('MPBAS', 86, self.mpbas_file))
        if self.dis_file is not None:
            f_nam.write('%s %3i %s\n' % ('DIS', self.dis_unit, self.dis_file))
        if self.head_file is not None:
            f_nam.write('%s %3i %s\n' % ('HEAD', 88, self.head_file))
        if self.budget_file is not None:
            f_nam.write('%s %3i %s\n' % ('BUDGET', 89, self.budget_file))
        for u, f in zip(self.external_units, self.external_fnames):
            f_nam.write('DATA  {0:3d}  '.format(u) + f + '\n')
        f_nam.close()
    sim = property(getsim)
    mf = property(getmf)

    def create_mpsim(self, simtype='pathline', trackdir='forward', packages
        ='WEL', start_time=0, default_ifaces=None, ParticleColumnCount=4,
        ParticleRowCount=4, MinRow=0, MinColumn=0, MaxRow=None, MaxColumn=None
        ):
        """
        Create a MODPATH simulation file using available MODFLOW boundary
        package data.

        Parameters
        ----------
        simtype : str
            Keyword defining the MODPATH simulation type. Available simtype's
             are 'endpoint', 'pathline', and 'timeseries'.
             (default is 'PATHLINE')
        trackdir : str
            Keyword that defines the MODPATH particle tracking direction.
            Available trackdir's are 'backward' and 'forward'.
            (default is 'forward')
        packages : str or list of strings
            Keyword defining the modflow packages used to create initial
            particle locations. Supported packages are 'WEL', 'MNW2' and 'RCH'.
            (default is 'WEL').
        start_time : float or tuple
            Sets the value of MODPATH reference time relative to MODFLOW time.
            float : value of MODFLOW simulation time at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 1.
            tuple : (period, step, time fraction) MODFLOW stress period, time step and fraction
                    between 0 and 1 at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 2.
        default_ifaces : list
            List of cell faces (1-6; see MODPATH6 manual, fig. 7) on which to start particles.
            (default is None, meaning ifaces will vary depending on packages argument above)
        ParticleRowCount : int
            Rows of particles to start on each cell index face (iface).
        ParticleColumnCount : int
            Columns of particles to start on each cell index face (iface).

        Returns
        -------
        mpsim : ModpathSim object

        """
        if isinstance(packages, str):
            packages = [packages]
        pak_list = self.__mf.get_package_list()
        ReferenceTimeOption = 1
        ref_time = 0
        ref_time_per_stp = 0, 0, 1.0
        if isinstance(start_time, tuple):
            ReferenceTimeOption = 2
            ref_time_per_stp = start_time
        else:
            ref_time = start_time
        ptrow = ParticleRowCount
        ptcol = ParticleColumnCount
        side_faces = [[1, ptrow, ptcol], [2, ptrow, ptcol], [3, ptrow,
            ptcol], [4, ptrow, ptcol]]
        top_face = [5, ptrow, ptcol]
        botm_face = [6, ptrow, ptcol]
        if default_ifaces is not None:
            default_ifaces = [[ifc, ptrow, ptcol] for ifc in default_ifaces]
        Grid = 1
        GridCellRegionOption = 1
        PlacementOption = 1
        ReleaseStartTime = 0.0
        ReleaseOption = 1
        CHeadOption = 1
        nper = self.__mf.dis.nper
        nlay, nrow, ncol = (self.__mf.dis.nlay, self.__mf.dis.nrow, self.
            __mf.dis.ncol)
        arr = np.zeros((nlay, nrow, ncol), dtype=np.int)
        group_name = []
        group_region = []
        group_placement = []
        ifaces = []
        face_ct = []
        strt_file = None
        for package in packages:
            if package.upper() == 'WEL':
                ParticleGenerationOption = 1
                if 'WEL' not in pak_list:
                    raise Exception(
                        'Error: no well package in the passed model')
                for kper in range(nper):
                    mflist = self.__mf.wel.stress_period_data[kper]
                    idx = mflist['k'], mflist['i'], mflist['j']
                    arr[idx] = 1
                ngrp = arr.sum()
                icnt = 0
                for k in range(nlay):
                    for i in range(nrow):
                        for j in range(ncol):
                            if arr[k, i, j] < 1:
                                continue
                            group_name.append('wc{}'.format(icnt))
                            group_placement.append([Grid,
                                GridCellRegionOption, PlacementOption,
                                ReleaseStartTime, ReleaseOption, CHeadOption])
                            group_region.append([k, i, j, k, i, j])
                            if default_ifaces is None:
                                ifaces.append(side_faces + [top_face,
                                    botm_face])
                                face_ct.append(6)
                            else:
                                ifaces.append(default_ifaces)
                                face_ct.append(len(default_ifaces))
                            icnt += 1
            elif 'MNW' in package.upper():
                ParticleGenerationOption = 1
                if 'MNW2' not in pak_list:
                    raise Exception(
                        'Error: no MNW2 package in the passed model')
                node_data = self.__mf.mnw2.get_allnode_data()
                node_data.sort(order=['wellid', 'k'])
                wellids = np.unique(node_data.wellid)

                def append_node(ifaces_well, wellid, node_number, k, i, j):
                    """add a single MNW node"""
                    group_region.append([k, i, j, k, i, j])
                    if default_ifaces is None:
                        ifaces.append(ifaces_well)
                        face_ct.append(len(ifaces_well))
                    else:
                        ifaces.append(default_ifaces)
                        face_ct.append(len(default_ifaces))
                    group_name.append('{}{}'.format(wellid, node_number))
                    group_placement.append([Grid, GridCellRegionOption,
                        PlacementOption, ReleaseStartTime, ReleaseOption,
                        CHeadOption])
                for wellid in wellids:
                    nd = node_data[node_data.wellid == wellid]
                    k, i, j = nd.k[0], nd.i[0], nd.j[0]
                    if len(nd) == 1:
                        append_node(side_faces + [top_face, botm_face],
                            wellid, 0, k, i, j)
                    else:
                        append_node(side_faces + [top_face], wellid, 0, k, i, j
                            )
                        for n in range(len(nd))[1:]:
                            k, i, j = nd.k[n], nd.i[n], nd.j[n]
                            if n == len(nd) - 1:
                                append_node(side_faces + [botm_face],
                                    wellid, n, k, i, j)
                            else:
                                append_node(side_faces, wellid, n, k, i, j)
            elif package.upper() == 'RCH':
                ParticleGenerationOption = 1
                group_name.append('rch')
                group_placement.append([Grid, GridCellRegionOption,
                    PlacementOption, ReleaseStartTime, ReleaseOption,
                    CHeadOption])
                group_region.append([0, 0, 0, 0, nrow - 1, ncol - 1])
                if default_ifaces is None:
                    face_ct.append(1)
                    ifaces.append([[6, 1, 1]])
                else:
                    ifaces.append(default_ifaces)
                    face_ct.append(len(default_ifaces))
            else:
                model_ws = ''
                if self.__mf is not None:
                    model_ws = self.__mf.model_ws
                if os.path.exists(os.path.join(model_ws, package)):
                    print(
                        'detected a particle starting locations file in packages'
                        )
                    assert len(packages
                        ) == 1, 'if a particle starting locations file is passed' + ', other packages cannot be specified'
                    ParticleGenerationOption = 2
                    strt_file = package
                else:
                    raise Exception("package '{0}' not supported".format(
                        package))
        SimulationType = 1
        if simtype.lower() == 'endpoint':
            SimulationType = 1
        elif simtype.lower() == 'pathline':
            SimulationType = 2
        elif simtype.lower() == 'timeseries':
            SimulationType = 3
        if trackdir.lower() == 'forward':
            TrackingDirection = 1
        elif trackdir.lower() == 'backward':
            TrackingDirection = 2
        WeakSinkOption = 2
        WeakSourceOption = 1
        StopOption = 2
        if SimulationType == 1:
            TimePointOption = 1
        else:
            TimePointOption = 3
        BudgetOutputOption = 1
        ZoneArrayOption = 1
        RetardationOption = 1
        AdvectiveObservationsOption = 1
        mpoptions = [SimulationType, TrackingDirection, WeakSinkOption,
            WeakSourceOption, ReferenceTimeOption, StopOption,
            ParticleGenerationOption, TimePointOption, BudgetOutputOption,
            ZoneArrayOption, RetardationOption, AdvectiveObservationsOption]
        return ModpathSim(self, ref_time=ref_time, ref_time_per_stp=
            ref_time_per_stp, option_flags=mpoptions, group_placement=
            group_placement, group_name=group_name, group_region=
            group_region, face_ct=face_ct, ifaces=ifaces, strt_file=strt_file)

<mask token>


class ModpathList(Package):
    """
    List package class
    """

    def __init__(self, model, extension='list', listunit=7):
        """
        Package constructor.

        """
        Package.__init__(self, model, extension, 'LIST', listunit)
        return

    def write_file(self):
        return


class Modpath(BaseModel):
    """
    Modpath base class

    """

    def __init__(self, modelname='modpathtest', simfile_ext='mpsim',
        namefile_ext='mpnam', version='modpath', exe_name='mp6.exe',
        modflowmodel=None, dis_file=None, dis_unit=87, head_file=None,
        budget_file=None, model_ws=None, external_path=None, verbose=False,
        load=True, listunit=7):
        """
        Model constructor.

        """
        BaseModel.__init__(self, modelname, simfile_ext, exe_name, model_ws
            =model_ws, verbose=verbose)
        self.version_types = {'modpath': 'MODPATH'}
        self.set_version(version)
        self.__mf = modflowmodel
        self.lst = ModpathList(self, listunit=listunit)
        self.mpnamefile = '{}.{}'.format(self.name, namefile_ext)
        self.mpbas_file = '{}.mpbas'.format(modelname)
        if self.__mf is not None:
            iu = self.__mf.oc.iuhead
            head_file = self.__mf.get_output(unit=iu)
            p = self.__mf.get_package('LPF')
            if p is None:
                p = self.__mf.get_package('BCF6')
            if p is None:
                p = self.__mf.get_package('UPW')
            if p is None:
                msg = (
                    'LPF, BCF6, or UPW packages must be included in the ' +
                    'passed MODFLOW model')
                raise Exception(msg)
            iu = p.ipakcb
            budget_file = self.__mf.get_output(unit=iu)
            dis_file = self.__mf.dis.file_name[0
                ] if dis_file is None else dis_file
            dis_unit = self.__mf.dis.unit_number[0]
        self.head_file = head_file
        self.budget_file = budget_file
        self.dis_file = dis_file
        self.dis_unit = dis_unit
        if self.head_file is None:
            msg = ('the head file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        if self.budget_file is None:
            msg = ('the budget file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        if self.dis_file is None:
            msg = ('the dis file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        self.__sim = None
        self.array_free_format = False
        self.array_format = 'modflow'
        self.external_path = external_path
        self.external = False
        self.external_fnames = []
        self.external_units = []
        self.external_binflag = []
        self.load = load
        self.__next_ext_unit = 500
        if external_path is not None:
            assert os.path.exists(external_path
                ), 'external_path does not exist'
            self.external = True
        return

    def __repr__(self):
        return 'Modpath model'

    def next_ext_unit(self):
        self.__next_ext_unit += 1
        return self.__next_ext_unit

    def getsim(self):
        if self.__sim == None:
            for p in self.packagelist:
                if isinstance(p, ModpathSim):
                    self.__sim = p
        return self.__sim

    def getmf(self):
        return self.__mf

    def write_name_file(self):
        """
        Write the name file

        Returns
        -------
        None

        """
        fn_path = os.path.join(self.model_ws, self.mpnamefile)
        f_nam = open(fn_path, 'w')
        f_nam.write('%s\n' % self.heading)
        if self.mpbas_file is not None:
            f_nam.write('%s %3i %s\n' % ('MPBAS', 86, self.mpbas_file))
        if self.dis_file is not None:
            f_nam.write('%s %3i %s\n' % ('DIS', self.dis_unit, self.dis_file))
        if self.head_file is not None:
            f_nam.write('%s %3i %s\n' % ('HEAD', 88, self.head_file))
        if self.budget_file is not None:
            f_nam.write('%s %3i %s\n' % ('BUDGET', 89, self.budget_file))
        for u, f in zip(self.external_units, self.external_fnames):
            f_nam.write('DATA  {0:3d}  '.format(u) + f + '\n')
        f_nam.close()
    sim = property(getsim)
    mf = property(getmf)

    def create_mpsim(self, simtype='pathline', trackdir='forward', packages
        ='WEL', start_time=0, default_ifaces=None, ParticleColumnCount=4,
        ParticleRowCount=4, MinRow=0, MinColumn=0, MaxRow=None, MaxColumn=None
        ):
        """
        Create a MODPATH simulation file using available MODFLOW boundary
        package data.

        Parameters
        ----------
        simtype : str
            Keyword defining the MODPATH simulation type. Available simtype's
             are 'endpoint', 'pathline', and 'timeseries'.
             (default is 'PATHLINE')
        trackdir : str
            Keyword that defines the MODPATH particle tracking direction.
            Available trackdir's are 'backward' and 'forward'.
            (default is 'forward')
        packages : str or list of strings
            Keyword defining the modflow packages used to create initial
            particle locations. Supported packages are 'WEL', 'MNW2' and 'RCH'.
            (default is 'WEL').
        start_time : float or tuple
            Sets the value of MODPATH reference time relative to MODFLOW time.
            float : value of MODFLOW simulation time at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 1.
            tuple : (period, step, time fraction) MODFLOW stress period, time step and fraction
                    between 0 and 1 at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 2.
        default_ifaces : list
            List of cell faces (1-6; see MODPATH6 manual, fig. 7) on which to start particles.
            (default is None, meaning ifaces will vary depending on packages argument above)
        ParticleRowCount : int
            Rows of particles to start on each cell index face (iface).
        ParticleColumnCount : int
            Columns of particles to start on each cell index face (iface).

        Returns
        -------
        mpsim : ModpathSim object

        """
        if isinstance(packages, str):
            packages = [packages]
        pak_list = self.__mf.get_package_list()
        ReferenceTimeOption = 1
        ref_time = 0
        ref_time_per_stp = 0, 0, 1.0
        if isinstance(start_time, tuple):
            ReferenceTimeOption = 2
            ref_time_per_stp = start_time
        else:
            ref_time = start_time
        ptrow = ParticleRowCount
        ptcol = ParticleColumnCount
        side_faces = [[1, ptrow, ptcol], [2, ptrow, ptcol], [3, ptrow,
            ptcol], [4, ptrow, ptcol]]
        top_face = [5, ptrow, ptcol]
        botm_face = [6, ptrow, ptcol]
        if default_ifaces is not None:
            default_ifaces = [[ifc, ptrow, ptcol] for ifc in default_ifaces]
        Grid = 1
        GridCellRegionOption = 1
        PlacementOption = 1
        ReleaseStartTime = 0.0
        ReleaseOption = 1
        CHeadOption = 1
        nper = self.__mf.dis.nper
        nlay, nrow, ncol = (self.__mf.dis.nlay, self.__mf.dis.nrow, self.
            __mf.dis.ncol)
        arr = np.zeros((nlay, nrow, ncol), dtype=np.int)
        group_name = []
        group_region = []
        group_placement = []
        ifaces = []
        face_ct = []
        strt_file = None
        for package in packages:
            if package.upper() == 'WEL':
                ParticleGenerationOption = 1
                if 'WEL' not in pak_list:
                    raise Exception(
                        'Error: no well package in the passed model')
                for kper in range(nper):
                    mflist = self.__mf.wel.stress_period_data[kper]
                    idx = mflist['k'], mflist['i'], mflist['j']
                    arr[idx] = 1
                ngrp = arr.sum()
                icnt = 0
                for k in range(nlay):
                    for i in range(nrow):
                        for j in range(ncol):
                            if arr[k, i, j] < 1:
                                continue
                            group_name.append('wc{}'.format(icnt))
                            group_placement.append([Grid,
                                GridCellRegionOption, PlacementOption,
                                ReleaseStartTime, ReleaseOption, CHeadOption])
                            group_region.append([k, i, j, k, i, j])
                            if default_ifaces is None:
                                ifaces.append(side_faces + [top_face,
                                    botm_face])
                                face_ct.append(6)
                            else:
                                ifaces.append(default_ifaces)
                                face_ct.append(len(default_ifaces))
                            icnt += 1
            elif 'MNW' in package.upper():
                ParticleGenerationOption = 1
                if 'MNW2' not in pak_list:
                    raise Exception(
                        'Error: no MNW2 package in the passed model')
                node_data = self.__mf.mnw2.get_allnode_data()
                node_data.sort(order=['wellid', 'k'])
                wellids = np.unique(node_data.wellid)

                def append_node(ifaces_well, wellid, node_number, k, i, j):
                    """add a single MNW node"""
                    group_region.append([k, i, j, k, i, j])
                    if default_ifaces is None:
                        ifaces.append(ifaces_well)
                        face_ct.append(len(ifaces_well))
                    else:
                        ifaces.append(default_ifaces)
                        face_ct.append(len(default_ifaces))
                    group_name.append('{}{}'.format(wellid, node_number))
                    group_placement.append([Grid, GridCellRegionOption,
                        PlacementOption, ReleaseStartTime, ReleaseOption,
                        CHeadOption])
                for wellid in wellids:
                    nd = node_data[node_data.wellid == wellid]
                    k, i, j = nd.k[0], nd.i[0], nd.j[0]
                    if len(nd) == 1:
                        append_node(side_faces + [top_face, botm_face],
                            wellid, 0, k, i, j)
                    else:
                        append_node(side_faces + [top_face], wellid, 0, k, i, j
                            )
                        for n in range(len(nd))[1:]:
                            k, i, j = nd.k[n], nd.i[n], nd.j[n]
                            if n == len(nd) - 1:
                                append_node(side_faces + [botm_face],
                                    wellid, n, k, i, j)
                            else:
                                append_node(side_faces, wellid, n, k, i, j)
            elif package.upper() == 'RCH':
                ParticleGenerationOption = 1
                group_name.append('rch')
                group_placement.append([Grid, GridCellRegionOption,
                    PlacementOption, ReleaseStartTime, ReleaseOption,
                    CHeadOption])
                group_region.append([0, 0, 0, 0, nrow - 1, ncol - 1])
                if default_ifaces is None:
                    face_ct.append(1)
                    ifaces.append([[6, 1, 1]])
                else:
                    ifaces.append(default_ifaces)
                    face_ct.append(len(default_ifaces))
            else:
                model_ws = ''
                if self.__mf is not None:
                    model_ws = self.__mf.model_ws
                if os.path.exists(os.path.join(model_ws, package)):
                    print(
                        'detected a particle starting locations file in packages'
                        )
                    assert len(packages
                        ) == 1, 'if a particle starting locations file is passed' + ', other packages cannot be specified'
                    ParticleGenerationOption = 2
                    strt_file = package
                else:
                    raise Exception("package '{0}' not supported".format(
                        package))
        SimulationType = 1
        if simtype.lower() == 'endpoint':
            SimulationType = 1
        elif simtype.lower() == 'pathline':
            SimulationType = 2
        elif simtype.lower() == 'timeseries':
            SimulationType = 3
        if trackdir.lower() == 'forward':
            TrackingDirection = 1
        elif trackdir.lower() == 'backward':
            TrackingDirection = 2
        WeakSinkOption = 2
        WeakSourceOption = 1
        StopOption = 2
        if SimulationType == 1:
            TimePointOption = 1
        else:
            TimePointOption = 3
        BudgetOutputOption = 1
        ZoneArrayOption = 1
        RetardationOption = 1
        AdvectiveObservationsOption = 1
        mpoptions = [SimulationType, TrackingDirection, WeakSinkOption,
            WeakSourceOption, ReferenceTimeOption, StopOption,
            ParticleGenerationOption, TimePointOption, BudgetOutputOption,
            ZoneArrayOption, RetardationOption, AdvectiveObservationsOption]
        return ModpathSim(self, ref_time=ref_time, ref_time_per_stp=
            ref_time_per_stp, option_flags=mpoptions, group_placement=
            group_placement, group_name=group_name, group_region=
            group_region, face_ct=face_ct, ifaces=ifaces, strt_file=strt_file)

import numpy as np
from ..mbase import BaseModel
from ..pakbase import Package
from .mpsim import ModpathSim
from .mpbas import ModpathBas
import os


class ModpathList(Package):
    """
    List package class
    """

    def __init__(self, model, extension='list', listunit=7):
        """
        Package constructor.

        """
        Package.__init__(self, model, extension, 'LIST', listunit)
        return

    def write_file(self):
        return


class Modpath(BaseModel):
    """
    Modpath base class

    """

    def __init__(self, modelname='modpathtest', simfile_ext='mpsim',
        namefile_ext='mpnam', version='modpath', exe_name='mp6.exe',
        modflowmodel=None, dis_file=None, dis_unit=87, head_file=None,
        budget_file=None, model_ws=None, external_path=None, verbose=False,
        load=True, listunit=7):
        """
        Model constructor.

        """
        BaseModel.__init__(self, modelname, simfile_ext, exe_name, model_ws
            =model_ws, verbose=verbose)
        self.version_types = {'modpath': 'MODPATH'}
        self.set_version(version)
        self.__mf = modflowmodel
        self.lst = ModpathList(self, listunit=listunit)
        self.mpnamefile = '{}.{}'.format(self.name, namefile_ext)
        self.mpbas_file = '{}.mpbas'.format(modelname)
        if self.__mf is not None:
            iu = self.__mf.oc.iuhead
            head_file = self.__mf.get_output(unit=iu)
            p = self.__mf.get_package('LPF')
            if p is None:
                p = self.__mf.get_package('BCF6')
            if p is None:
                p = self.__mf.get_package('UPW')
            if p is None:
                msg = (
                    'LPF, BCF6, or UPW packages must be included in the ' +
                    'passed MODFLOW model')
                raise Exception(msg)
            iu = p.ipakcb
            budget_file = self.__mf.get_output(unit=iu)
            dis_file = self.__mf.dis.file_name[0
                ] if dis_file is None else dis_file
            dis_unit = self.__mf.dis.unit_number[0]
        self.head_file = head_file
        self.budget_file = budget_file
        self.dis_file = dis_file
        self.dis_unit = dis_unit
        if self.head_file is None:
            msg = ('the head file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        if self.budget_file is None:
            msg = ('the budget file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        if self.dis_file is None:
            msg = ('the dis file in the MODFLOW model or passed ' +
                'to __init__ cannot be None')
            raise ValueError(msg)
        self.__sim = None
        self.array_free_format = False
        self.array_format = 'modflow'
        self.external_path = external_path
        self.external = False
        self.external_fnames = []
        self.external_units = []
        self.external_binflag = []
        self.load = load
        self.__next_ext_unit = 500
        if external_path is not None:
            assert os.path.exists(external_path
                ), 'external_path does not exist'
            self.external = True
        return

    def __repr__(self):
        return 'Modpath model'

    def next_ext_unit(self):
        self.__next_ext_unit += 1
        return self.__next_ext_unit

    def getsim(self):
        if self.__sim == None:
            for p in self.packagelist:
                if isinstance(p, ModpathSim):
                    self.__sim = p
        return self.__sim

    def getmf(self):
        return self.__mf

    def write_name_file(self):
        """
        Write the name file

        Returns
        -------
        None

        """
        fn_path = os.path.join(self.model_ws, self.mpnamefile)
        f_nam = open(fn_path, 'w')
        f_nam.write('%s\n' % self.heading)
        if self.mpbas_file is not None:
            f_nam.write('%s %3i %s\n' % ('MPBAS', 86, self.mpbas_file))
        if self.dis_file is not None:
            f_nam.write('%s %3i %s\n' % ('DIS', self.dis_unit, self.dis_file))
        if self.head_file is not None:
            f_nam.write('%s %3i %s\n' % ('HEAD', 88, self.head_file))
        if self.budget_file is not None:
            f_nam.write('%s %3i %s\n' % ('BUDGET', 89, self.budget_file))
        for u, f in zip(self.external_units, self.external_fnames):
            f_nam.write('DATA  {0:3d}  '.format(u) + f + '\n')
        f_nam.close()
    sim = property(getsim)
    mf = property(getmf)

    def create_mpsim(self, simtype='pathline', trackdir='forward', packages
        ='WEL', start_time=0, default_ifaces=None, ParticleColumnCount=4,
        ParticleRowCount=4, MinRow=0, MinColumn=0, MaxRow=None, MaxColumn=None
        ):
        """
        Create a MODPATH simulation file using available MODFLOW boundary
        package data.

        Parameters
        ----------
        simtype : str
            Keyword defining the MODPATH simulation type. Available simtype's
             are 'endpoint', 'pathline', and 'timeseries'.
             (default is 'PATHLINE')
        trackdir : str
            Keyword that defines the MODPATH particle tracking direction.
            Available trackdir's are 'backward' and 'forward'.
            (default is 'forward')
        packages : str or list of strings
            Keyword defining the modflow packages used to create initial
            particle locations. Supported packages are 'WEL', 'MNW2' and 'RCH'.
            (default is 'WEL').
        start_time : float or tuple
            Sets the value of MODPATH reference time relative to MODFLOW time.
            float : value of MODFLOW simulation time at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 1.
            tuple : (period, step, time fraction) MODFLOW stress period, time step and fraction
                    between 0 and 1 at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 2.
        default_ifaces : list
            List of cell faces (1-6; see MODPATH6 manual, fig. 7) on which to start particles.
            (default is None, meaning ifaces will vary depending on packages argument above)
        ParticleRowCount : int
            Rows of particles to start on each cell index face (iface).
        ParticleColumnCount : int
            Columns of particles to start on each cell index face (iface).

        Returns
        -------
        mpsim : ModpathSim object

        """
        if isinstance(packages, str):
            packages = [packages]
        pak_list = self.__mf.get_package_list()
        ReferenceTimeOption = 1
        ref_time = 0
        ref_time_per_stp = 0, 0, 1.0
        if isinstance(start_time, tuple):
            ReferenceTimeOption = 2
            ref_time_per_stp = start_time
        else:
            ref_time = start_time
        ptrow = ParticleRowCount
        ptcol = ParticleColumnCount
        side_faces = [[1, ptrow, ptcol], [2, ptrow, ptcol], [3, ptrow,
            ptcol], [4, ptrow, ptcol]]
        top_face = [5, ptrow, ptcol]
        botm_face = [6, ptrow, ptcol]
        if default_ifaces is not None:
            default_ifaces = [[ifc, ptrow, ptcol] for ifc in default_ifaces]
        Grid = 1
        GridCellRegionOption = 1
        PlacementOption = 1
        ReleaseStartTime = 0.0
        ReleaseOption = 1
        CHeadOption = 1
        nper = self.__mf.dis.nper
        nlay, nrow, ncol = (self.__mf.dis.nlay, self.__mf.dis.nrow, self.
            __mf.dis.ncol)
        arr = np.zeros((nlay, nrow, ncol), dtype=np.int)
        group_name = []
        group_region = []
        group_placement = []
        ifaces = []
        face_ct = []
        strt_file = None
        for package in packages:
            if package.upper() == 'WEL':
                ParticleGenerationOption = 1
                if 'WEL' not in pak_list:
                    raise Exception(
                        'Error: no well package in the passed model')
                for kper in range(nper):
                    mflist = self.__mf.wel.stress_period_data[kper]
                    idx = mflist['k'], mflist['i'], mflist['j']
                    arr[idx] = 1
                ngrp = arr.sum()
                icnt = 0
                for k in range(nlay):
                    for i in range(nrow):
                        for j in range(ncol):
                            if arr[k, i, j] < 1:
                                continue
                            group_name.append('wc{}'.format(icnt))
                            group_placement.append([Grid,
                                GridCellRegionOption, PlacementOption,
                                ReleaseStartTime, ReleaseOption, CHeadOption])
                            group_region.append([k, i, j, k, i, j])
                            if default_ifaces is None:
                                ifaces.append(side_faces + [top_face,
                                    botm_face])
                                face_ct.append(6)
                            else:
                                ifaces.append(default_ifaces)
                                face_ct.append(len(default_ifaces))
                            icnt += 1
            elif 'MNW' in package.upper():
                ParticleGenerationOption = 1
                if 'MNW2' not in pak_list:
                    raise Exception(
                        'Error: no MNW2 package in the passed model')
                node_data = self.__mf.mnw2.get_allnode_data()
                node_data.sort(order=['wellid', 'k'])
                wellids = np.unique(node_data.wellid)

                def append_node(ifaces_well, wellid, node_number, k, i, j):
                    """add a single MNW node"""
                    group_region.append([k, i, j, k, i, j])
                    if default_ifaces is None:
                        ifaces.append(ifaces_well)
                        face_ct.append(len(ifaces_well))
                    else:
                        ifaces.append(default_ifaces)
                        face_ct.append(len(default_ifaces))
                    group_name.append('{}{}'.format(wellid, node_number))
                    group_placement.append([Grid, GridCellRegionOption,
                        PlacementOption, ReleaseStartTime, ReleaseOption,
                        CHeadOption])
                for wellid in wellids:
                    nd = node_data[node_data.wellid == wellid]
                    k, i, j = nd.k[0], nd.i[0], nd.j[0]
                    if len(nd) == 1:
                        append_node(side_faces + [top_face, botm_face],
                            wellid, 0, k, i, j)
                    else:
                        append_node(side_faces + [top_face], wellid, 0, k, i, j
                            )
                        for n in range(len(nd))[1:]:
                            k, i, j = nd.k[n], nd.i[n], nd.j[n]
                            if n == len(nd) - 1:
                                append_node(side_faces + [botm_face],
                                    wellid, n, k, i, j)
                            else:
                                append_node(side_faces, wellid, n, k, i, j)
            elif package.upper() == 'RCH':
                ParticleGenerationOption = 1
                group_name.append('rch')
                group_placement.append([Grid, GridCellRegionOption,
                    PlacementOption, ReleaseStartTime, ReleaseOption,
                    CHeadOption])
                group_region.append([0, 0, 0, 0, nrow - 1, ncol - 1])
                if default_ifaces is None:
                    face_ct.append(1)
                    ifaces.append([[6, 1, 1]])
                else:
                    ifaces.append(default_ifaces)
                    face_ct.append(len(default_ifaces))
            else:
                model_ws = ''
                if self.__mf is not None:
                    model_ws = self.__mf.model_ws
                if os.path.exists(os.path.join(model_ws, package)):
                    print(
                        'detected a particle starting locations file in packages'
                        )
                    assert len(packages
                        ) == 1, 'if a particle starting locations file is passed' + ', other packages cannot be specified'
                    ParticleGenerationOption = 2
                    strt_file = package
                else:
                    raise Exception("package '{0}' not supported".format(
                        package))
        SimulationType = 1
        if simtype.lower() == 'endpoint':
            SimulationType = 1
        elif simtype.lower() == 'pathline':
            SimulationType = 2
        elif simtype.lower() == 'timeseries':
            SimulationType = 3
        if trackdir.lower() == 'forward':
            TrackingDirection = 1
        elif trackdir.lower() == 'backward':
            TrackingDirection = 2
        WeakSinkOption = 2
        WeakSourceOption = 1
        StopOption = 2
        if SimulationType == 1:
            TimePointOption = 1
        else:
            TimePointOption = 3
        BudgetOutputOption = 1
        ZoneArrayOption = 1
        RetardationOption = 1
        AdvectiveObservationsOption = 1
        mpoptions = [SimulationType, TrackingDirection, WeakSinkOption,
            WeakSourceOption, ReferenceTimeOption, StopOption,
            ParticleGenerationOption, TimePointOption, BudgetOutputOption,
            ZoneArrayOption, RetardationOption, AdvectiveObservationsOption]
        return ModpathSim(self, ref_time=ref_time, ref_time_per_stp=
            ref_time_per_stp, option_flags=mpoptions, group_placement=
            group_placement, group_name=group_name, group_region=
            group_region, face_ct=face_ct, ifaces=ifaces, strt_file=strt_file)

import numpy as np
from ..mbase import BaseModel
from ..pakbase import Package
from .mpsim import ModpathSim
from .mpbas import ModpathBas
import os


class ModpathList(Package):
    """
    List package class
    """

    def __init__(self, model, extension='list', listunit=7):
        """
        Package constructor.

        """
        # Call ancestor's init to set self.parent, extension, name and
        # unit number
        Package.__init__(self, model, extension, 'LIST', listunit)
        # self.parent.add_package(self) This package is not added to the base
        # model so that it is not included in get_name_file_entries()
        return

    def write_file(self):
        # Not implemented for list class
        return


class Modpath(BaseModel):
    """
    Modpath base class

    """

    def __init__(self, modelname='modpathtest', simfile_ext='mpsim',
                 namefile_ext='mpnam',
                 version='modpath', exe_name='mp6.exe', modflowmodel=None,
                 dis_file=None, dis_unit=87, head_file=None, budget_file=None,
                 model_ws=None, external_path=None, verbose=False,
                 load=True, listunit=7):
        """
        Model constructor.

        """
        BaseModel.__init__(self, modelname, simfile_ext, exe_name,
                           model_ws=model_ws, verbose=verbose)

        self.version_types = {'modpath': 'MODPATH'}
        self.set_version(version)

        self.__mf = modflowmodel
        self.lst = ModpathList(self, listunit=listunit)
        self.mpnamefile = '{}.{}'.format(self.name, namefile_ext)
        self.mpbas_file = '{}.mpbas'.format(modelname)
        if self.__mf is not None:
            # ensure that user-specified files are used
            iu = self.__mf.oc.iuhead
            head_file = self.__mf.get_output(unit=iu)
            p = self.__mf.get_package('LPF')
            if p is None:
                p = self.__mf.get_package('BCF6')
            if p is None:
                p = self.__mf.get_package('UPW')
            if p is None:
                msg = 'LPF, BCF6, or UPW packages must be included in the ' + \
                      'passed MODFLOW model'
                raise Exception(msg)
            iu = p.ipakcb
            budget_file = self.__mf.get_output(unit=iu)
            dis_file = self.__mf.dis.file_name[0] \
                if dis_file is None else dis_file
            dis_unit = self.__mf.dis.unit_number[0]
        self.head_file = head_file
        self.budget_file = budget_file
        self.dis_file = dis_file
        self.dis_unit = dis_unit
        # make sure the valid files are available
        if self.head_file is None:
            msg = 'the head file in the MODFLOW model or passed ' + \
                  'to __init__ cannot be None'
            raise ValueError(msg)
        if self.budget_file is None:
            msg = 'the budget file in the MODFLOW model or passed ' + \
                  'to __init__ cannot be None'
            raise ValueError(msg)
        if self.dis_file is None:
            msg = 'the dis file in the MODFLOW model or passed ' + \
                  'to __init__ cannot be None'
            raise ValueError(msg)

        # set the rest of the attributes
        self.__sim = None
        self.array_free_format = False
        self.array_format = 'modflow'
        self.external_path = external_path
        self.external = False
        self.external_fnames = []
        self.external_units = []
        self.external_binflag = []
        self.load = load
        self.__next_ext_unit = 500
        if external_path is not None:
            assert os.path.exists(
                external_path), 'external_path does not exist'
            self.external = True
        return

    def __repr__(self):
        return 'Modpath model'

    # function to encapsulate next_ext_unit attribute
    def next_ext_unit(self):
        self.__next_ext_unit += 1
        return self.__next_ext_unit

    def getsim(self):
        if (self.__sim == None):
            for p in (self.packagelist):
                if isinstance(p, ModpathSim):
                    self.__sim = p
        return self.__sim

    def getmf(self):
        return self.__mf

    def write_name_file(self):
        """
        Write the name file

        Returns
        -------
        None

        """
        fn_path = os.path.join(self.model_ws, self.mpnamefile)
        f_nam = open(fn_path, 'w')
        f_nam.write('%s\n' % (self.heading))
        if self.mpbas_file is not None:
            f_nam.write('%s %3i %s\n' % ('MPBAS', 86, self.mpbas_file))
        if self.dis_file is not None:
            f_nam.write('%s %3i %s\n' % ('DIS', self.dis_unit, self.dis_file))
        if self.head_file is not None:
            f_nam.write('%s %3i %s\n' % ('HEAD', 88, self.head_file))
        if self.budget_file is not None:
            f_nam.write('%s %3i %s\n' % ('BUDGET', 89, self.budget_file))
        for u, f in zip(self.external_units, self.external_fnames):
            f_nam.write('DATA  {0:3d}  '.format(u) + f + '\n')
        f_nam.close()

    sim = property(getsim)  # Property has no setter, so read-only
    mf = property(getmf)  # Property has no setter, so read-only

    def create_mpsim(self, simtype='pathline', trackdir='forward',
                     packages='WEL', start_time=0, default_ifaces=None,
                     ParticleColumnCount=4, ParticleRowCount=4,
                     MinRow=0, MinColumn=0, MaxRow=None, MaxColumn=None,
                     ):
        """
        Create a MODPATH simulation file using available MODFLOW boundary
        package data.

        Parameters
        ----------
        simtype : str
            Keyword defining the MODPATH simulation type. Available simtype's
             are 'endpoint', 'pathline', and 'timeseries'.
             (default is 'PATHLINE')
        trackdir : str
            Keyword that defines the MODPATH particle tracking direction.
            Available trackdir's are 'backward' and 'forward'.
            (default is 'forward')
        packages : str or list of strings
            Keyword defining the modflow packages used to create initial
            particle locations. Supported packages are 'WEL', 'MNW2' and 'RCH'.
            (default is 'WEL').
        start_time : float or tuple
            Sets the value of MODPATH reference time relative to MODFLOW time.
            float : value of MODFLOW simulation time at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 1.
            tuple : (period, step, time fraction) MODFLOW stress period, time step and fraction
                    between 0 and 1 at which to start the particle tracking simulation.
                    Sets the value of MODPATH ReferenceTimeOption to 2.
        default_ifaces : list
            List of cell faces (1-6; see MODPATH6 manual, fig. 7) on which to start particles.
            (default is None, meaning ifaces will vary depending on packages argument above)
        ParticleRowCount : int
            Rows of particles to start on each cell index face (iface).
        ParticleColumnCount : int
            Columns of particles to start on each cell index face (iface).

        Returns
        -------
        mpsim : ModpathSim object

        """
        if isinstance(packages, str):
            packages = [packages]
        pak_list = self.__mf.get_package_list()

        # not sure if this is the best way to handle this
        ReferenceTimeOption = 1
        ref_time = 0
        ref_time_per_stp = (0, 0, 1.)
        if isinstance(start_time, tuple):
            ReferenceTimeOption = 2  # 1: specify value for ref. time, 2: specify kper, kstp, rel. time pos
            ref_time_per_stp = start_time
        else:
            ref_time = start_time

        # set iface particle grids
        ptrow = ParticleRowCount
        ptcol = ParticleColumnCount
        side_faces = [[1, ptrow, ptcol], [2, ptrow, ptcol],
                      [3, ptrow, ptcol], [4, ptrow, ptcol]]
        top_face = [5, ptrow, ptcol]
        botm_face = [6, ptrow, ptcol]
        if default_ifaces is not None:
            default_ifaces = [[ifc, ptrow, ptcol] for ifc in default_ifaces]

        Grid = 1
        GridCellRegionOption = 1
        PlacementOption = 1
        ReleaseStartTime = 0.
        ReleaseOption = 1
        CHeadOption = 1
        nper = self.__mf.dis.nper
        nlay, nrow, ncol = self.__mf.dis.nlay, \
                           self.__mf.dis.nrow, \
                           self.__mf.dis.ncol
        arr = np.zeros((nlay, nrow, ncol), dtype=np.int)
        group_name = []
        group_region = []
        group_placement = []
        ifaces = []
        face_ct = []
        strt_file = None
        for package in packages:

            if package.upper() == 'WEL':
                ParticleGenerationOption = 1
                if 'WEL' not in pak_list:
                    raise Exception(
                        'Error: no well package in the passed model')
                for kper in range(nper):
                    mflist = self.__mf.wel.stress_period_data[kper]
                    idx = (mflist['k'], mflist['i'], mflist['j'])
                    arr[idx] = 1
                ngrp = arr.sum()
                icnt = 0
                for k in range(nlay):
                    for i in range(nrow):
                        for j in range(ncol):
                            if arr[k, i, j] < 1:
                                continue
                            group_name.append('wc{}'.format(icnt))
                            group_placement.append([Grid, GridCellRegionOption,
                                                    PlacementOption,
                                                    ReleaseStartTime,
                                                    ReleaseOption,
                                                    CHeadOption])
                            group_region.append([k, i, j, k, i, j])
                            if default_ifaces is None:
                                ifaces.append(
                                    side_faces + [top_face, botm_face])
                                face_ct.append(6)
                            else:
                                ifaces.append(default_ifaces)
                                face_ct.append(len(default_ifaces))
                            icnt += 1
            # this is kind of a band aid pending refactoring of mpsim class
            elif 'MNW' in package.upper():
                ParticleGenerationOption = 1
                if 'MNW2' not in pak_list:
                    raise Exception(
                        'Error: no MNW2 package in the passed model')
                node_data = self.__mf.mnw2.get_allnode_data()
                node_data.sort(order=['wellid', 'k'])
                wellids = np.unique(node_data.wellid)

                def append_node(ifaces_well, wellid, node_number, k, i, j):
                    """add a single MNW node"""
                    group_region.append([k, i, j, k, i, j])
                    if default_ifaces is None:
                        ifaces.append(ifaces_well)
                        face_ct.append(len(ifaces_well))
                    else:
                        ifaces.append(default_ifaces)
                        face_ct.append(len(default_ifaces))
                    group_name.append('{}{}'.format(wellid, node_number))
                    group_placement.append([Grid, GridCellRegionOption,
                                            PlacementOption,
                                            ReleaseStartTime,
                                            ReleaseOption,
                                            CHeadOption])

                for wellid in wellids:
                    nd = node_data[node_data.wellid == wellid]
                    k, i, j = nd.k[0], nd.i[0], nd.j[0]
                    if len(nd) == 1:
                        append_node(side_faces + [top_face, botm_face],
                                    wellid, 0, k, i, j)
                    else:
                        append_node(side_faces + [top_face],
                                    wellid, 0, k, i, j)
                        for n in range(len(nd))[1:]:
                            k, i, j = nd.k[n], nd.i[n], nd.j[n]
                            if n == len(nd) - 1:
                                append_node(side_faces + [botm_face],
                                            wellid, n, k, i, j)
                            else:
                                append_node(side_faces,
                                            wellid, n, k, i, j)
            elif package.upper() == 'RCH':
                ParticleGenerationOption = 1
                # for j in range(nrow):
                #    for i in range(ncol):
                #        group_name.append('rch')
                group_name.append('rch')
                group_placement.append([Grid, GridCellRegionOption,
                                        PlacementOption,
                                        ReleaseStartTime,
                                        ReleaseOption, CHeadOption])
                group_region.append([0, 0, 0, 0, nrow - 1, ncol - 1])
                if default_ifaces is None:
                    face_ct.append(1)
                    ifaces.append([[6, 1, 1]])
                else:
                    ifaces.append(default_ifaces)
                    face_ct.append(len(default_ifaces))


            else:
                model_ws = ''
                if self.__mf is not None:
                    model_ws = self.__mf.model_ws
                if os.path.exists(os.path.join(model_ws, package)):
                    print(
                        "detected a particle starting locations file in packages")
                    assert len(
                        packages) == 1, "if a particle starting locations file is passed" + \
                                        ", other packages cannot be specified"
                    ParticleGenerationOption = 2
                    strt_file = package
                else:
                    raise Exception(
                        "package '{0}' not supported".format(package))

        SimulationType = 1
        if simtype.lower() == 'endpoint':
            SimulationType = 1
        elif simtype.lower() == 'pathline':
            SimulationType = 2
        elif simtype.lower() == 'timeseries':
            SimulationType = 3
        if trackdir.lower() == 'forward':
            TrackingDirection = 1
        elif trackdir.lower() == 'backward':
            TrackingDirection = 2
        WeakSinkOption = 2
        WeakSourceOption = 1

        StopOption = 2

        if SimulationType == 1:
            TimePointOption = 1
        else:
            TimePointOption = 3
        BudgetOutputOption = 1
        ZoneArrayOption = 1
        RetardationOption = 1
        AdvectiveObservationsOption = 1

        mpoptions = [SimulationType, TrackingDirection, WeakSinkOption,
                     WeakSourceOption, ReferenceTimeOption, StopOption,
                     ParticleGenerationOption, TimePointOption,
                     BudgetOutputOption, ZoneArrayOption, RetardationOption,
                     AdvectiveObservationsOption]

        return ModpathSim(self,
                          ref_time=ref_time,
                          ref_time_per_stp=ref_time_per_stp,
                          option_flags=mpoptions,
                          group_placement=group_placement,
                          group_name=group_name,
                          group_region=group_region,
                          face_ct=face_ct, ifaces=ifaces,
                          strt_file=strt_file)
