# Copyright 2010 Torbjorn Bjorkman
# This file is part of cif2cell
#
# cif2cell is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# cif2cell is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with cif2cell.  If not, see <http://www.gnu.org/licenses/>.
#
# ******************************************************************************************
#  Description: Interfaces for a number of electronic structure programs. Currently only
#               reads CIF and outputs to the ESP's. Supported programs are: ABINIT, ATAT,
#               CASTEP, CPMD, Crystal09, Elk, EMTO, Exciting, Fleur, Hutsepot, NCOL,
#               Quantum Espresso, RSPt, Siesta, VASP, xyz
#
#  Author:      Torbjorn Bjorkman
#  ORCID:       0000-0002-1154-9846
# ******************************************************************************************
import os
import math
import string
from math import pi, sin, cos
import sys
from re import search

from cif2cell.utils import Vector, LatticeMatrix, mvmult3, deletenewline, AtomSite, SetupError, det3, minv3, third, mmmult3
from cif2cell.elementdata import ElementData
from cif2cell.spacegroupdata import Number2AP

__all__ = (
    'GeometryOutputFile',
    'ATATFile',
    'HUTSEPOTFile',
    'ASEFile',
    'CFGFile',
    'COOFile',
    'LAMMPSFile',
    'XYZFile',
    'OldNCOLFile',
    'BSTRFile',
    'CellgenFile',
    'SymtFile',
    'SymtFile2',
    'Crystal09File',
    'SpacegroupFile',
    'ElkFile',
    'ExcitingFile',
    'FleurFile',
    'CASTEPFile',
    'PWSCFFile',
    'CP2KFile',
    'CPMDFile',
    'SiestaFile',
    'ABINITFile',
    'AIMSFile',
    'MCSQSFile',
    'POSCARFile',
    'POTCARFile',
    'KPOINTSFile',
    'INCARFile',
    'KFCDFile',
    'KGRNFile',
    'ShapeFile',
    'BMDLFile',
    'KSTRFile',
    'XBandSysFile',
    'SPCFile',
    'MOPACFile',
    'CRYMOLFile',
)

################################################################################################
ed = ElementData()
suspiciouslist = set(["Cr", "Mn", "Fe", "Co", "Ni",
                      "Ce", "Pr", "Nd", "Pm", "Sm", "Eu",
                      "Gd", "Tb", "Dy", "Ho", "Er", "Tm",
                      "Th", "Pa", "U", "Np", "Pu"])
initialmoments = {"Cr": 3, "Mn": 3, "Fe": 3, "Co": 3, "Ni": 1,
                  "Ce": 1, "Pr": 2, "Nd": 3, "Pm": 4, "Sm": 5, "Eu": 6,
                  "Gd": 7, "Tb": 8, "Dy": 9, "Ho": 10, "Er": 11, "Tm": 12,
                  "Th": 1, "Pa": 2, "U": 3, "Np": 4, "Pu": 5}

################################################################################################


class GeometryOutputFile:
    """
    Parent class for electronic struture code files generated from geometrical information.
    A CrystalStructure object and a documentation string are required input.
    """

    def __init__(self, crystalstructure, string):
        self.cell = crystalstructure
        self.docstring = string

################################################################################################
# ATAT FILE


class ATATFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting an ATAT input file
    and the method __str__ that outputs the contents of the file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Document string on first line after '//'
        self.programdoc = string.rstrip("\n")
        # set up species list
        tmp = set([])
        for a in self.cell.atomdata:
            for b in a:
                tmp.add(b.spcstring())
        self.species = list(tmp)
        # make sure the docstring goes on one line
        self.cell.newunit("bohr")

    def __str__(self):
        filestring = str(self.cell.a)+" "+str(self.cell.b)+" "+str(self.cell.c)+" " + \
            str(self.cell.alpha)+" "+str(self.cell.beta) + \
            " "+str(self.cell.gamma)+"\n"
        filestring += str(self.cell.lattrans)
        for a in self.cell.atomdata:
            for b in a:
                filestring += str(b.position)
                if b.alloy():
                    for k, v in b.species.items():
                        filestring += k+"="+str(v)+","
                    filestring = filestring.rstrip(",")+"\n"
                else:
                    filestring += " "+b.spcstring(separator=',')+"\n"
        return filestring

################################################################################################
# HUTSEPOT FILE


class HUTSEPOTFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting a hutsepot input file
    and the method __str__ that outputs the contents of the file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Document string on first line after '//'
        self.programdoc = string.rstrip("\n")
        # set up species list
        tmp = set([])
        for a in self.cell.atomdata:
            for b in a:
                tmp.add(b.spcstring())
        self.species = list(tmp)
        # make sure the docstring goes on one line
        self.cell.newunit("bohr")

    def __str__(self):
        streck = "-------------------------------------------------------------------------------"
        filestring = streck+"\n"
        filestring += "------------------------- Generated by cif2cell -------------------------------\n"
        filestring = streck+"\n"
        t = self.cell.lengthscale
        filestring += "3D unit cell alat=%18.12f blat=%18.12f clat=%18.12f\n" % (
            t, t, t)
        filestring += "   rb=" + \
            str(self.cell.latticevectors[0].scalmult(t))+"ascale=1.0\n"
        filestring += "      " + \
            str(self.cell.latticevectors[1].scalmult(t))+"bscale=1.0\n"
        filestring += "      " + \
            str(self.cell.latticevectors[2].scalmult(t))+"cscale=1.0\n"
        # positions
        filestring += "-------------------------------------------------------------------------------\n"
        filestring += "------------------------------- atomic positions ------------------------------\n"
        filestring += "-------------------------------------------------------------------------------\n"
        positionstring = ""
        species = 0
        atom = 0
        for sp in self.species:
            nr = 0
            species += 1
            for a in self.cell.atomdata:
                for b in a:
                    if b.spcstring() == sp:
                        atom += 1
                        nr += 1
                        p = Vector(mvmult3(self.cell.latticevectors,
                                           b.position.scalmult(self.cell.lengthscale)))
                        positionstring += str(species)+"."+b.spcstring() + \
                            "_"+str(nr)+" type=%i" % (atom) + \
                            " nat=60 tau="+str(p)
                        positionstring += "\n"
        filestring += positionstring
        filestring += "-------------------------------------------------------------------------------\n"
        filestring += "---------------------------- atomic configurations ----------------------------\n"
        filestring += "-------------------------------------------------------------------------------\n"
        species = 0
        for sp in self.species:
            species += 1
            filestring += str(species)+". "+ed.hutsepotelements[sp]+"\n"
        filestring += "-------------------------------------------------------------------------------\n"
        filestring += "------------------------------- atomic options --------------------------------\n"
        filestring += "-------------------------------------------------------------------------------\n"
        species = 0
        atom = 0
        for sp in self.species:
            species += 1
            for a in self.cell.atomdata:
                for b in a:
                    if b.spcstring() == sp:
                        atom += 1
                        filestring += str(species)+". atom=" + \
                            sp+" type="+str(atom)
                        filestring += " fix=F lmax=3 lmaxv=0 conc=1.0 mtz=T sort=" + \
                            str(atom)+"\n"
        filestring += "-------------------------------------------------------------------------------\n"
        filestring += "--------------------------------- potentials ----------------------------------\n"
        filestring += "-------------------------------------------------------------------------------\n"
        species = 0
        atom = 0
        for sp in self.species:
            species += 1
            nr = 0
            for a in self.cell.atomdata:
                for b in a:
                    if b.spcstring() == sp:
                        atom += 1
                        nr += 1
                        filestring += str(species)+". type="+str(atom)
                        filestring += " np=1001 r1=1.0E-05 rnp=-2 pfile=" + \
                            sp+str(nr)+".pot\n"
        filestring += "-------------------------------------------------------------------------------\n"
        return filestring

################################################################################################
# ASE FILE


class ASEFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting data for ASE
    and the method __str__ that outputs the contents of the file as a string of
    python code.
    """

    def __init__(self, crystalstructure, docstring):
        GeometryOutputFile.__init__(self, crystalstructure, docstring)
        # Variables
        self.cartesian = True  # Cartesian coordinates?
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string
        # set up species list
        tmp = set([])
        for a in self.cell.atomdata:
            for b in a:
                tmp.add(b.spcstring())
        self.species = list(tmp)

    def __str__(self):
        filestring = "from ase import *\n\n"
        # Cartesian or lattice coordinates?
        if self.cartesian:
            transmtx = []
            for i in range(3):
                transmtx.append([])
                for j in range(3):
                    transmtx[i].append(
                        self.cell.latticevectors[i][j] * self.cell.lengthscale)
        else:
            transmtx = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
        # positions and number of species
        nspcs = []
        positionstring = ""
        for sp in self.species:
            nsp = 0
            for a in self.cell.atomdata:
                for b in a:
                    if b.spcstring() == sp:
                        nsp += 1
                        p = Vector(mvmult3(transmtx, b.position))
                        positionstring += "%11f, %11f, %11f),\n               (" % (
                            p[0], p[1], p[2])
            nspcs.append(nsp)
        positionstring = positionstring.rstrip("\n (,")+"],\n"

        # Atoms object
        filestring += "atoms = Atoms("
        # Species
        for i in range(len(self.species)):
            filestring += "['"+self.species[i] + \
                "' for i in range("+str(nspcs[i])+")]+"
        filestring = filestring.rstrip("+")+",\n"
        # Positions
        filestring += "              [("
        filestring += positionstring
        # Boundary conditions
        filestring += "              pbc = (True,True,True))\n"
        # Set lattice vectors
        filestring += "atoms.set_cell([["
        for i in range(3):
            for j in range(3):
                filestring += "%12f, " % (
                    self.cell.latticevectors[i][j]*self.cell.lengthscale)
            filestring = filestring.rstrip(", ")+"],\n                ["
        filestring = filestring.rstrip(",[ ]\n")+"]],\n"
        filestring += "                scale_atoms = %s)\n" % str(
            not self.cartesian)

        return filestring

################################################################################################
# CFG FILE


class CFGFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting a .cfg file
    and the method __str__ that outputs the contents of the .coo file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string

    def __str__(self):
        # Set up atom list for printing.
        tmplist = list(self.cell.atomset)
        atomlist = []
        for a in tmplist:
            if a.alloy():
                for sp, occ in a.species.items():
                    atomlist.append(AtomSite(position=a.position, species={
                                    sp: occ}, charges={sp: a.charges[sp]}))
            else:
                atomlist.append(a)
        atomlist.sort(key=lambda x: max(
            [ed.elementnr[sp] for sp in x.species]), reverse=True)
        prevsp = ""
        natoms = len(atomlist)
        # Make string
        filestring = self.docstring
        filestring += "Number of particles = %i \n" % (natoms)
        filestring += "A = 1.0 Angstrom\n"
        filestring += "H0(1,1) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[0][0])
        filestring += "H0(1,2) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[0][1])
        filestring += "H0(1,3) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[0][2])
        filestring += "H0(2,1) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[1][0])
        filestring += "H0(2,2) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[1][1])
        filestring += "H0(2,3) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[1][2])
        filestring += "H0(3,1) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[2][0])
        filestring += "H0(3,2) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[2][1])
        filestring += "H0(3,3) = %f A\n" % (self.cell.lengthscale *
                                            self.cell.latticevectors[2][2])
        filestring += ".NO_VELOCITY.\n"
        # Cut the fancy stuff for now, stick with just the positions
        ## filestring += "entry_count = 3\n"
        filestring += "entry_count = 6\n"
        for a in atomlist:
            for sp, occ in a.species.items():
                if prevsp != sp:
                    filestring += "%i\n" % (int(round(ed.elementweight[sp])))
                    filestring += sp+"\n"
                prevsp = sp
                # Debye-Waller factor, QSTEM prescription
                DW = 0.45*ed.elementnr['Si']/ed.elementnr[sp]
                filestring += str(a.position)+" %f " % (DW) + \
                    " %f " % (occ)+" %f\n" % (a.charges[sp])
                ## filestring += str(a.position)+"\n"
        return filestring

################################################################################################
# COO FILE


class COOFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting a .coo file
    and the method __str__ that outputs the contents of the .coo file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Document string on first line after '//'
        self.programdoc = string.rstrip("\n")

    def __str__(self):
        filestring = "//"+self.programdoc+"\n"
        a = self.cell.latticevectors[0].length()*self.cell.lengthscale
        b = self.cell.latticevectors[1].length()*self.cell.lengthscale
        c = self.cell.latticevectors[2].length()*self.cell.lengthscale
        alpha = abs(self.cell.latticevectors[1].angle(
            self.cell.latticevectors[2]))*180/pi
        beta = abs(self.cell.latticevectors[2].angle(
            self.cell.latticevectors[0]))*180/pi
        gamma = abs(self.cell.latticevectors[0].angle(
            self.cell.latticevectors[1]))*180/pi
        filestring += " %10.7f %10.7f %10.7f" % (a, b, c)
        filestring += " %10.7f %10.7f %10.7f %i\n" % (
            alpha, beta, gamma, len(self.cell.atomset))
        for a in self.cell.atomdata:
            for b in a:
                filestring += str(b.position) + \
                    " %3i  0.500 0.000 1.000\n" % (ed.elementnr[b.spcstring()])
        return filestring

################################################################################################
# LAMMPS FILE


class LAMMPSFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting an .data LAMMPS file
    and the method __str__ that outputs the contents of the .data file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # To be put on the second line
        self.programdoc = ""

    def __str__(self):
        filestring = ""
        filestring += "#"+self.docstring+"\n\n"
        filestring += "%i atoms\n" % sum([len(v) for v in self.cell.atomdata])
        atomTypes = {}
        nextAtomTypeId = 1

        for a in self.cell.atomdata:
            for b in a:
                atomType = str(b).split()[0]
                if not atomType in atomTypes:
                    atomTypes[atomType] = nextAtomTypeId
                    nextAtomTypeId += 1
        filestring += "%i atom types\n\n" % len(atomTypes)

        if self.cell.latticevectors[0][1] != 0:
            theta = math.atan2(-self.cell.latticevectors[0]
                               [1], self.cell.latticevectors[0][0])
            c = cos(theta)
            s = sin(theta)
            R = LatticeMatrix([[c, s, 0],
                               [-s, c, 0],
                               [0, 0, 1]])
            self.cell.latticevectors[0] = Vector(
                mvmult3(R, self.cell.latticevectors[0]))
            self.cell.latticevectors[1] = Vector(
                mvmult3(R, self.cell.latticevectors[1]))
            self.cell.latticevectors[2] = Vector(
                mvmult3(R, self.cell.latticevectors[2]))

        if self.cell.latticevectors[0][2] != 0:
            theta = math.atan2(-self.cell.latticevectors[0]
                               [2], self.cell.latticevectors[0][0])
            c = cos(theta)
            s = sin(theta)
            R = LatticeMatrix([[c, s, 0],
                               [0, 1, 0],
                               [-s, c, 0]])
            self.cell.latticevectors[0] = Vector(
                mvmult3(R, self.cell.latticevectors[0]))
            self.cell.latticevectors[1] = Vector(
                mvmult3(R, self.cell.latticevectors[1]))
            self.cell.latticevectors[2] = Vector(
                mvmult3(R, self.cell.latticevectors[2]))

        if self.cell.latticevectors[1][2] != 0:
            theta = math.atan2(-self.cell.latticevectors[1]
                               [2], self.cell.latticevectors[1][1])
            c = cos(theta)
            s = sin(theta)
            R = LatticeMatrix([[1, 0, 0],
                               [0, c, s],
                               [0, -s, c]])
            self.cell.latticevectors[0] = Vector(
                mvmult3(R, self.cell.latticevectors[0]))
            self.cell.latticevectors[1] = Vector(
                mvmult3(R, self.cell.latticevectors[1]))
            self.cell.latticevectors[2] = Vector(
                mvmult3(R, self.cell.latticevectors[2]))

        if self.cell.latticevectors[0][1] != 0 or self.cell.latticevectors[0][2] != 0 or self.cell.latticevectors[1][2] != 0 or self.cell.latticevectors[0][0] <= 0 or self.cell.latticevectors[1][1] <= 0 or self.cell.latticevectors[2][2] <= 0:
            print("Error in triclinic box. Vectors should follow these rules: http://lammps.sandia.gov/doc/Section_howto.html#howto-12")
            print(
                "Ideally, this program should solve this, but it doesn't yet. You need to fix it.")
            exit()

        xy = self.cell.lengthscale*self.cell.latticevectors[1][0]
        xz = self.cell.lengthscale*self.cell.latticevectors[2][0]
        yz = self.cell.lengthscale*self.cell.latticevectors[2][1]

        a = self.cell.latticevectors[0][0]*self.cell.lengthscale
        b = self.cell.latticevectors[1][1]*self.cell.lengthscale
        c = self.cell.latticevectors[2][2]*self.cell.lengthscale

        filestring += "0.0 %f xlo xhi\n" % a
        filestring += "0.0 %f ylo yhi\n" % b
        filestring += "0.0 %f zlo zhi\n" % c
        if xy != 0 or xz != 0 or yz != 0:
            filestring += str(xy) + " " + str(xz) + " " + \
                str(yz) + " xy xz yz\n"

        filestring += "\n"
        filestring += "Atoms\n\n"

        nextAtomId = 1

        # for b in [a for a in self.cell.atomdata]:
        # print str(b).split()[0]
        # atomTypes str(b).split()[0]

        lv = []
        for i in range(3):
            lv.append([])
            for j in range(3):
                lv[i].append(self.cell.lengthscale *
                             self.cell.latticevectors[i][j])
        for a in self.cell.atomdata:
            for b in a:
                t = Vector(mvmult3(lv, b.position))
                atomType = str(b).split()[0]
                atomTypeId = atomTypes[atomType]
                filestring += str(nextAtomId)+" " + \
                    str(atomTypeId)+" "+str(t)+"\n"
                nextAtomId += 1
        return filestring

################################################################################################
# XYZ FILE


class XYZFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting an .xyz file
    and the method __str__ that outputs the contents of the .xyz file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # To be put on the second line
        self.programdoc = ""

    def __str__(self):
        filestring = ""
        filestring += "%i \n" % sum([len(v) for v in self.cell.atomdata])
        filestring += self.docstring+"\n"
        lv = []
        for i in range(3):
            lv.append([])
            for j in range(3):
                lv[i].append(self.cell.lengthscale *
                             self.cell.latticevectors[i][j])
        for a in self.cell.atomdata:
            for b in a:
                t = Vector(mvmult3(lv, b.position))
                filestring += str(b).split()[0]+"  "+str(t)+"\n"
        return filestring

################################################################################################
# NCOL FILES


class OldNCOLFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].dat file for the ncol program
    and the method __str__ that outputs the contents of the .dat file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.jobnam = "default"
        self.bstrjobnam = "default"
        # To be put on the first line
        self.programdoc = ""
        # Set atomic units for length scale
        self.cell.newunit("bohr")

    def __str__(self):
        # Element data
        ed = ElementData()
        # l quantum number setup (same as from bstr)
        l = {"s": 2, "p": 2, "d": 3, "f": 4}
        filestring = ""
        tmpstring = "BULK      IDSYST=  7 SCRATCH=R"
        tmpstring = tmpstring.ljust(
            25)+"    "+deletenewline(self.programdoc, replace=" ")+"\n"
        filestring += tmpstring
        tmpstring = "JOBNAM...=" + \
            self.jobnam.ljust(
                10)+" MSGL.=  1 BSAVE..=N COLD...=Y DOS...=N SPO...=N ISM...=G RCLCR...=Y\n"
        filestring += tmpstring
        filestring += "FOR001=./"+self.bstrjobnam+".tfm\n"
        filestring += "FOR002=\n"
        filestring += "FOR003=\n"
        filestring += "FOR004=\n"
        filestring += "FOR006=\n"
        filestring += "FOR010=\n"
        filestring += "Band: 4 lines, " + \
            deletenewline(self.docstring, replace=" ")+"\n"
        filestring += "NITER.=200 NOB..=  2 NPRN.=  0 NFIX.=  0 MIXKEY=  2 NCOL.=Y  PMODE=K\n"
        filestring += "REP.....=B FIXD...=Y CRT....=S NB...= 16 CLSIZE= 32 NPROW= 0 NPCOL= 0\n"
        filestring += "NKX...=  1 NKY..=  1 NKZ..=  1 TFERMI..= 2000.0(K)\n"
        filestring += "AMIX.....=     0.100 TOLE....= 0.0000100 TOLEL...= 0.0000010\n"
        # average wigner-seitz radius
        nosites = 0
        for a in self.cell.atomdata:
            nosites += len(a)
        volume = abs(det3(self.cell.latticevectors))
        wsr = self.cell.lengthscale * (3*volume/(nosites * 4 * pi))**third
        filestring += "SWS......= %9f NP...=  1 SMIX.= 0.500 TMIX.= 0.0000\n" % wsr
        filestring += "Setup: 3 + NQ*NS*NP lines\n"
        filestring += "EFGS.....=    0.0000 EFGS....=   0.00000 FTMAG...=  0.000000\n"
        filestring += "DEO(l)...=     0.020     0.010     0.005     0.001      0.02\n"
        filestring += "Symb IQ IT NL IP NSP   SWP  QTRO  SPLT NFIX NDWF     Eny(spdf)\n"
        # set first species
        if self.cell.atomdata[0][0].alloy():
            prevspecies = "??"
        else:
            for v in self.cell.atomdata[0][0].species:
                prevspecies = v
        # type loop
        iq = 1
        it = 1
        nsp = 1
        for a in self.cell.atomdata:
            for b in a:
                if b.alloy():
                    species = "??"
                else:
                    species = b.spcstring()
                if species != prevspecies:
                    prevspecies = species
                    nsp += 1
                tmpstring = species.ljust(
                    2)+"    "+str(iq).ljust(3)+str(it).ljust(3)
                try:
                    tmpstring += str(l[ed.elementblock[species]]
                                     ).ljust(3)+str(1).ljust(3)
                except KeyError:
                    tmpstring += "  ?  1"
                tmpstring += str(nsp).ljust(3)
                tmpstring += "  1.000 .000 0.00 0000 1111   .0   .0   .0   .0"
                if b.alloy():
                    # print alloy components at the end of the line
                    tmpstring += "       "+b.spcstring()
                filestring += tmpstring+"\n"
                iq += 1
            it += 1
        for a in self.cell.atomdata:
            filestring += "Theta....=     90.00 Phia....=      0.00 FIXMOM..=         N moment..=      0.0\n"
        filestring += "PQX......=      0.00 PQY.....=      0.00 PQZ.....=   0.00000 COORD...=L\n"
        filestring += "Atom: 4 lines + NT*6 lines\n"
        filestring += "IEX...=  4  NP..=500 NES..= 15 NITER=250 IWAT.=  0\n"
        filestring += "VMIX.....=  0.300000 RWAT....=  3.500000 RMAX....= 20.000000\n"
        filestring += "DPAS.....=  0.049000 DR1.....=  1.00E-08 TEST....=  1.00E-08\n"
        filestring += "TESTE....=  1.00E-07 TESTY...=  1.00E-08 TESTV...=  1.00E-07\n"
        for a in self.cell.atomdata:
            for comp in a[0].species:
                filestring += comp+"\n"
                try:
                    filestring += ed.emtoelements[comp]
                except KeyError:
                    filestring += "\n\n\n\n\n"
        return filestring


class BSTRFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].dat file for the bstr program
    and the method __str__ that outputs the contents of the .dat file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        self.jobnam = "default"
        self.a = 1
        self.b = 1
        self.c = 1
        # To be put on the first line
        self.programdoc = ""

    def __str__(self):
        ed = ElementData()
        filestring = ""
        tmpstring = "BSTR      IDSYST=  7"
        tmpstring = tmpstring.ljust(
            40)+deletenewline(self.programdoc, replace=" ")+"\n"
        filestring += tmpstring
        tmpstring = "JOBNAM...="+self.jobnam.ljust(9)+" MSGL.=   1 \n"
        filestring += tmpstring
        filestring += "MODE....=B STORE..=Y SCREEN.=B CMBC...=Y\n"
        filestring += "FOR001=\n"
        filestring += "FOR006=\n"
        filestring += deletenewline(self.docstring, replace=" ")+"\n"
        # Get number of sites
        nosites = 0
        for a in self.cell.atomdata:
            nosites += len(a)
        # Setting the real space summation cutoff to 4.5*(wigner-seitz radius)
        volume = abs(det3(self.cell.latticevectors))
        wsr = (3*volume/(nosites * 4 * pi))**third
        tmpstring = "IALF...= 0 NPRN..= 1 DMAX....=%10.5f \n" % (wsr*4.5)
        filestring += tmpstring
        filestring += "ALF(spdf)= 0.3205350 0.0413320 0.0084290 0.0015370\nDKAPPA...= 0.00010\n"
        tmpstring = "NQ3....=%3i LAT...= 0 IPRIM.= 0" % nosites
        filestring += tmpstring
        # Set up basis functions. Just setting lmax = 2 for s-/p-, 3 for d- and 4 for f- blocks
        tmpstring = "\nNLX(IQ)..="
        for a in self.cell.atomdata:
            for b in a:
                for k in b.species:
                    l = 1
                    if ed.elementblock[k] == "s" or ed.elementblock[k] == "p":
                        l = max(l, 2)
                    elif ed.elementblock[k] == "d":
                        l = max(l, 3)
                    elif ed.elementblock[k] == "f":
                        l = max(l, 4)
                tmpstring += " %1i" % l
                if len(tmpstring) % 69 == 0:
                    tmpstring += "\n          "
        # Need to strip newline character if the last line was 69 characters long...
        tmpstring = tmpstring.rstrip(string.whitespace)
        tmpstring = tmpstring+"\n"
        filestring += tmpstring
        # Print lattice vectors
        coa = self.c / self.a
        boa = self.b / self.a
        filestring += "A........=  1.00000000 B.......=  1.00000000 C.......=  1.00000000\n"
        tmpstring = ""
        lv = self.cell.latticevectors
        for i in range(3):
            tmpstring += "BSX......=%12.7f BSY.....=%12.7f BSZ.....=%12.7f\n" % (
                lv[i][0], lv[i][1], lv[i][2])
        filestring += tmpstring
        # All positions
        it = 1
        for a in self.cell.atomdata:
            for b in a:
                pos = mvmult3(lv, b.position)
                tmpstring = "QX.......=%12.7f QY......=%12.7f QZ......=%12.7f" % (
                    pos[0], pos[1], pos[2])
                tmpstring += "      "+b.spcstring()+"\n"
                filestring += tmpstring
            it += 1
        filestring += "LAMDA....=    2.5000 AMAX....=    5.5000 BMAX....=    5.5000\n"
        return filestring

################################################################################################
# RSPT FILES


class CellgenFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a cellgen.inp file and the method
    __str__ that outputs the contents of an cellgen.inp file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.supercellmap = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
        self.referencevector = [0, 0, 0]
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string

    def __str__(self):
        # Initialize element data
        ed = ElementData()
        # Add docstring
        filestring = self.docstring
        # Add lattice constant
        filestring += "# Lattice constant in a.u.: " + \
            str(self.cell.lengthscale)+"\n"
        # RSPt reads the lattice vectors as columns...
        filestring += "# Lattice vectors (columns)\n"
        tmpstring = ""
        for i in range(3):
            for j in range(3):
                tmpstring += "%19.15f " % self.cell.latticevectors[j][i]
            tmpstring += "\n"
        filestring += tmpstring
        # Get number of sites
        nosites = 0
        for a in self.cell.atomdata:
            nosites += len(a)
        filestring += "# Sites\n"
        filestring += str(nosites)+"\n"
        it = 1
        for a in self.cell.atomdata:
            for b in a:
                tmpstring = ""
                tmpstring += str(b.position)+" "
                if b.alloy():
                    # don't know what to put for an alloy
                    tmpstring += "???"
                else:
                    tmpstring += "%3i" % ed.elementnr[b.spcstring()]
                tmpstring += " l "+chr(it+96)+"   # "+b.spcstring()+"\n"
                filestring += tmpstring
            it += 1
        filestring += "# Supercell map\n"
        tmpstring = ""
        for i in self.supercellmap:
            for j in i:
                tmpstring += str(j).rjust(4)
            tmpstring += "\n"
        filestring += tmpstring
        filestring += "# Reference vector\n"
        tmpstring = ""
        for i in self.referencevector:
            tmpstring += "%19.15f " % i
        tmpstring += "\n"
        filestring += tmpstring
        return filestring

################################################################################################


class SymtFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in an old format symt.inp file and the method
    __str__ that outputs the contents of an symt.inp file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string
        # Default spin axis is [0,0,0]
        self.spinaxis = [0.0, 0.0, 0.0]
        self.rsptcartlatvects = False
        self.passwyckoff = False
        self.printlabels = False

    def __str__(self):
        # Initialize element data
        ed = ElementData()
        # Add docstring
        filestring = self.docstring
        # Add lattice constant
        filestring += "# Lattice constant in a.u.: " + \
            str(self.cell.lengthscale)+"\n"
        # RSPt reads the lattice vectors as columns...
        filestring += "# Lattice vectors (columns)\n"
        if self.rsptcartlatvects:
            fac = self.cell.lengthscale
        else:
            fac = 1.0
        tmpstring = ""
        for i in range(3):
            for j in range(3):
                tmpstring += "%19.15f " % (self.cell.latticevectors[j][i]*fac)
            tmpstring += "\n"
        filestring += tmpstring
        filestring += "# Spin axis\n"
        filestring += "%19.15f %19.15f %19.15f  l\n" % (
            self.spinaxis[0], self.spinaxis[1], self.spinaxis[2])
        # Get number of sites
        nosites = 0
        for a in self.cell.atomdata:
            nosites += len(a)
        filestring += "# Sites\n"
        filestring += str(nosites)+"\n"
        it = 1
        label = "a"
        for a in self.cell.atomdata:
            for b in a:
                tmpstring = ""
                tmpstring += str(b.position)+" "
                if b.alloy():
                    # don't know what to put for an alloy
                    tmpstring += "???"
                else:
                    tmpstring += "%3i" % ed.elementnr[b.spcstring()]
                if self.passwyckoff:
                    label = chr(it+96)
                if self.printlabels:
                    tmpstring += " l "+label+"   # "+b.label+"\n"
                else:
                    tmpstring += " l "+label+"   # "+b.spcstring()+"\n"
                filestring += tmpstring
            it += 1
        return filestring

################################################################################################


class SymtFile2(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a new format symt.inp file and the method
    __str__ that outputs the contents of an symt.inp file as a string.
    """

    def __init__(self, crystalstructure, string, kresolution=0.1):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string
        # Default spin axis is [0,0,0]
        self.spinaxis = Vector([0.0, 0.0, 0.0])
        # parameters for spin polarization
        self.spinpol = False
        self.relativistic = False
        self.forcenospin = False
        self.rsptcartlatvects = False
        self.mtradii = 0
        self.passwyckoff = False
        # k-mesh generation etc.
        self.setupall = False
        self.kresolution = kresolution
        self.nokshifts = False
        self.kshifts = [[0, 0, 0], [1, 1, 1]]
        self.printlabels = False

    def __str__(self):
        # Initialize element data
        ed = ElementData()
        # Add docstring
        filestring = self.docstring
        # Add lattice constant
        filestring += "# Lattice constant in a.u.\n"
        filestring += "lengthscale\n"
        if self.rsptcartlatvects:
            filestring += "1.000 \n"
        else:
            filestring += str(self.cell.lengthscale)+"\n"
        if self.spinpol and not self.forcenospin:
            filestring += "# Spin polarized calculation\nspinpol\n"
            filestring += "# Spin polarize atomic densities\nspinpol_atomdens\n"
        if self.relativistic:
            if self.setupall:
                filestring += "# Relativistic symmetries\nspinorbit\n"
            else:
                filestring += "# Relativistic symmetries\nfullrel\n"
            # Default to z-direction for relativistic calculations...
            t = self.spinaxis - Vector([0., 0., 0.])
            if t.length() < 1e-7:
                self.spinaxis = mvmult3(
                    minv3(self.cell.latticevectors), Vector([0., 0., 1.]))
                # ... unless these space group settings, when we pick a more likely high-symmetry axis
                if self.cell.spacegroupsetting == "A":
                    self.spinaxis = mvmult3(
                        minv3(self.cell.latticevectors), Vector([1., 0., 0.]))
                elif self.cell.spacegroupsetting == "B":
                    self.spinaxis = mvmult3(
                        minv3(self.cell.latticevectors), Vector([0., 1., 0.]))
        if self.mtradii != 0:
            filestring += "# Choice of MT radii\n"
            filestring += "mtradii\n"+str(self.mtradii)+"\n"
        # RSPt reads the lattice vectors as columns...
        filestring += "# Lattice vectors (columns)\n"
        filestring += "latticevectors\n"
        tmpstring = ""
        if self.rsptcartlatvects:
            fac = self.cell.lengthscale
        else:
            fac = 1.0
        for i in range(3):
            for j in range(3):
                tmpstring += "%19.15f " % (self.cell.latticevectors[j][i]*fac)
            tmpstring += "\n"
        filestring += tmpstring
        filestring += "# Spin axis\n"
        filestring += "spinaxis\n"
        filestring += "%19.15f %19.15f %19.15f  l\n" % (
            self.spinaxis[0], self.spinaxis[1], self.spinaxis[2])
        # Get number of sites
        nosites = 0
        for a in self.cell.atomdata:
            nosites += len(a)
        filestring += "# Sites\n"
        filestring += "atoms\n"
        filestring += str(nosites)+"\n"
        it = 1
        label = "a"
        for a in self.cell.atomdata:
            for b in a:
                label = "a"
                tmpstring = ""
                tmpstring += str(b.position)+" "
                if b.alloy():
                    # don't know what to put for an alloy
                    tmpstring += "???"
                else:
                    tmpstring += "%3i" % ed.elementnr[b.spcstring()]
                if self.passwyckoff:
                    label = chr(it+96)
                if self.setupall and b.spcstring() in suspiciouslist and not self.forcenospin:
                    label = "up"
                if self.printlabels:
                    tmpstring += " l "+label+"   # "+b.label+"\n"
                else:
                    tmpstring += " l "+label+"   # "+b.spcstring()+"\n"
                filestring += tmpstring
            it += 1
        # k-mesh setup for new input
        if self.setupall:
            # Using k-resolution together with Froyen map needs supervised choice of mesh,
            # or they easily become unnecessarily dense, so don't use this feature.
            ## filestring += "\n"
            # filestring += "# k space resolution\n"
            ## filestring += "kresolution\n"
            ## filestring += "  %f\n"%(self.kresolution)
            # Guess a suitable Froyen map !!! Column vectors for RSPt !!!
            mapmatrix = LatticeMatrix([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
            if self.cell.primcell:
                if self.cell.spacegroupsetting == 'F':
                    mapmatrix = LatticeMatrix(
                        [[1, 1, 0], [1, 0, 1], [0, 1, 1]])
                elif self.cell.spacegroupsetting == 'I':
                    if self.cell.crystal_system() == 'cubic':
                        mapmatrix = LatticeMatrix(
                            [[-1, 1, 1], [1, -1, 1], [1, 1, -1]])
                    else:
                        mapmatrix = LatticeMatrix(
                            [[2, 0, 1], [0, 2, 1], [0, 0, 2]])
                elif self.cell.spacegroupsetting == 'A':
                    mapmatrix = LatticeMatrix(
                        [[1, 0, 0], [0, 1, -1], [0, 1, 1]])
                elif self.cell.spacegroupsetting == 'B':
                    mapmatrix = LatticeMatrix(
                        [[1, 0, -1], [0, 1, 0], [1, 0, 1]])
                elif self.cell.spacegroupsetting == 'C':
                    mapmatrix = LatticeMatrix(
                        [[1, -1, 0], [1, 1, 0], [0, 0, 1]])
                elif self.cell.spacegroupsetting == 'R' and abs(self.cell.latticevectors[0].angle(self.cell.latticevectors[1])*180/pi) > 10:
                    # Generate in hexagonal supercell unless the rhombohedral angle is close to 90 degrees.
                    mapmatrix = LatticeMatrix(
                        [[1, 0, 1], [-1, 1, 1], [0, -1, 1]])
            # Determine mesh
            reclatvect = LatticeMatrix(mmmult3(
                self.cell.reciprocal_latticevectors().transpose(), mapmatrix)).transpose()
            for j in range(3):
                for i in range(3):
                    reclatvect[j][i] = reclatvect[j][i] / self.cell.lengthscale
            # Lengths of reciprocal lattice vectors
            reclatvectlen = [elem.length() for elem in reclatvect]
            kgrid = [max(1, int(round(elem/self.kresolution)))
                     for elem in reclatvectlen]
            # Manual adjustments to make the choice work well with the Froyen mesh.
            # Some centerings should have even meshes, for rhombohedral it should be dividable by 3
            # along c.
            if self.cell.primcell:
                if self.cell.spacegroupsetting == 'F' or self.cell.spacegroupsetting == "I":
                    for i in range(3):
                        kgrid[i] += kgrid[i] % 2
                elif self.cell.spacegroupsetting == 'A':
                    kgrid[1] += kgrid[1] % 2
                    kgrid[2] += kgrid[2] % 2
                elif self.cell.spacegroupsetting == 'B':
                    kgrid[0] += kgrid[0] % 2
                    kgrid[2] += kgrid[2] % 2
                elif self.cell.spacegroupsetting == 'C':
                    kgrid[0] += kgrid[0] % 2
                    kgrid[1] += kgrid[1] % 2
                elif self.cell.spacegroupsetting == 'R' and abs(self.cell.latticevectors[0].angle(self.cell.latticevectors[1])*180/pi) > 10:
                    for i in range(3):
                        # This rounds to nearest multiple of 3
                        if kgrid[i] % 3 == 1:
                            kgrid[i] -= 1
                        elif kgrid[i] % 3 == 2:
                            kgrid[i] += 1
            filestring += "\n# k-points\n"
            filestring += "kpoints\n"
            filestring += " %i %i %i\n\n" % (kgrid[0], kgrid[1], kgrid[2])
            # Write Froyen map.
            filestring += "# Froyen map\n"
            filestring += "kmapmatrix\n"
            for v in mapmatrix:
                filestring += " %4i %4i %4i\n" % (v[0], v[1], v[2])
        # Return
        return filestring

################################################################################################


class Crystal09File(GeometryOutputFile):
    """
    Class for storing the geometrical data needed by Crystal09 and the method
    __str__ that outputs the contents of an Crystal09 input file as a string.
    Presently only handles standard settings (space group numbers, not H-M symbols),
    and the special case of rhombohedral settings for relevant trigonal space groups.
    """

    def __init__(self, crystalstructure, string, rhombohedral=False):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("angstrom")
        # Rhombohedral cell setting
        self.rhombohedral = rhombohedral
        # Make sure the docstring has the form of a f90 comment
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("!")
            string = "!"+string+"\n"
            self.docstring += string

    def __str__(self):
        # Initialize element data
        ed = ElementData()
        # Add docstring
        filestring = self.docstring
        filestring += "CRYSTAL\n"
        # Space group setting and crystal parameters
        if self.cell.is_spacegroup("triclinic"):
            filestring += "0 0 0\n"
            filestring += str(self.spacegroupnr)+"\n"
            filestring += "%13.8f %13.8f %13.8f %13.8f %13.8f %13.8f\n" % (
                self.cell.a, self.cell.b, self.cell.c, self.cell.alpha, self.cell.beta, self.cell.gamma)
        elif self.cell.is_spacegroup("monoclinic"):
            filestring += "0 0 0\n"
            filestring += str(self.spacegroupnr)+"\n"
            filestring += "%13.8f %13.8f %13.8f %13.8f\n" % (
                self.cell.a, self.cell.b, self.cell.c, self.cell.beta)
        elif self.cell.is_spacegroup("orthorhombic"):
            filestring += "0 0 0\n"
            filestring += str(self.spacegroupnr)+"\n"
            filestring += "%13.8f %13.8f %13.8f\n" % (
                self.cell.a, self.cell.b, self.cell.c)
        elif self.cell.is_spacegroup("tetragonal"):
            filestring += "0 0 0\n"
            filestring += str(self.spacegroupnr)+"\n"
            filestring += "%13.8f %13.8f\n" % (self.cell.a, self.cell.c)
        elif self.cell.is_spacegroup("trigonal") and not (self.cell.is_spacegroup("rhombohedral") and self.rhombohedral):
            filestring += "0 0 0\n"
            filestring += str(self.spacegroupnr)+"\n"
            filestring += "%13.8f %13.8f\n" % (self.cell.a, self.cell.c)
        elif self.cell.is_spacegroup("rhombohedral") and self.rhombohedral:
            filestring += "0 1 0\n"
            filestring += str(self.spacegroupnr)+"\n"
            filestring += "%13.8f %13.8f\n" % (self.cell.latticevectors[0].length(
            )*self.cell.lengthscale, self.cell.latticevectors[1].angle(self.cell.latticevectors[2])*180/pi)
        elif self.cell.is_spacegroup("hexagonal"):
            filestring += "0 0 0\n"
            filestring += str(self.spacegroupnr)+"\n"
            filestring += "%13.8f %13.8f\n" % (self.cell.a, self.cell.c)
        elif self.cell.is_spacegroup("cubic"):
            filestring += "0 0 0\n"
            filestring += str(self.spacegroupnr)+"\n"
            filestring += "%13.8f\n" % (self.cell.a)
        else:
            if self.force:
                sys.stderr.write(
                    "***Warning: Could not determine crystal system corresponding to space group "+str(self.spacegroupnr)+".")
                filestring += "0 0 0\n"
                filestring += str(self.spacegroupnr)+"\n"
                filestring += "%13.8f %13.8f %13.8f %13.8f %13.8f %13.8f\n" % (
                    self.cell.a, self.cell.b, self.cell.c, self.cell.alpha, self.cell.beta, self.cell.gamma)
            else:
                return "***Error: Could not determine crystal system corresponding to space group "+str(self.spacegroupnr)+"."
        # Number of atoms
        filestring += str(len(self.cell.ineqsites))+"\n"
        # Atomic numbers and representative positions
        for a in self.cell.atomdata:
            if len(a[0].species) > 1:
                # don't know what to put for an alloy
                filestring += "??"
            else:
                for k in a[0].species:
                    filestring += str(ed.elementnr[k]).rjust(2)
            filestring += "  "+str(a[0].position) + \
                "      ! "+a[0].spcstring()+"\n"
        filestring += "END\n"
        return filestring

################################################################################################


class SpacegroupFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a spacegroup.in file and the method
    __str__ that outputs the contents of an spacegroup.in file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.HermannMauguin = ""
        self.a = 1
        self.b = 1
        self.c = 1
        self.alpha = 90
        self.beta = 90
        self.gamma = 90
        self.supercelldims = [1, 1, 1]
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        # Make sure the docstring has the form of a f90 comment
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("!")
            string = "!"+string+"\n"
            self.docstring += string

    def __str__(self):
        filestring = ""
        if (self.HermannMauguin[-1] == 'R' or self.HermannMauguin[-1] == 'H') and self.HermannMauguin[-2] != ':':
            self.HermannMauguin = self.HermannMauguin[0:len(
                self.HermannMauguin)-1]+':'+self.HermannMauguin[-1]
        tmpstring = " '"+self.HermannMauguin+"'"
        tmpstring = tmpstring.ljust(50)+": hrmg\n"
        filestring += tmpstring
        tmpstring = ""
        tmpstring += " %15.11f" % (self.a)
        tmpstring += " %15.11f" % (self.b)
        tmpstring += " %15.11f" % (self.c)
        tmpstring = tmpstring.ljust(50)+": a, b, c\n"
        filestring += tmpstring
        tmpstring = " %15.9f %15.9f %15.9f" % (
            self.gamma, self.beta, self.alpha)
        tmpstring = tmpstring.ljust(50)+": ab, ac, bc\n"
        filestring += tmpstring
        tmpstring = ""
        for i in self.supercelldims:
            tmpstring += str(i)+"  "
        tmpstring = tmpstring.ljust(50)
        tmpstring += ": ncell\n"
        filestring += tmpstring
        filestring += ".true.".ljust(50)+": primcell\n"
        # Get species info
        species = set([])
        for occ in self.cell.occupations:
            spcstring = ""
            for k in occ:
                spcstring += k+"/"
            spcstring = spcstring.rstrip("/")
            species.add(spcstring)
        tmpstring = str(len(species)).ljust(50)+": nspecies\n"
        filestring += tmpstring
        for spcs in species:
            # find number of representative sites for this species
            spcsites = 0
            positionstring = ""
            i = 0
            for occ in self.cell.occupations:
                spcstring = ""
                for k in occ:
                    spcstring += k+"/"
                spcstring = spcstring.rstrip("/")
                if spcstring == spcs:
                    spcsites += 1
                    positionstring += str(self.cell.ineqsites[i])+"\n"
                i += 1
            # output species info
            if len(spcs) > 2:
                # alloy
                spcsheader = "'??'".ljust(50)+"! "+spcs+"\n"+str(spcsites)+"\n"
            else:
                spcsheader = "'"+spcs+"'\n"+str(spcsites)+"\n"
            filestring += spcsheader
            filestring += positionstring
        filestring += "\n"+self.docstring
        return filestring

################################################################################################


class ElkFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in an elk.in file and the method
    __str__ that outputs the contents of an elk.in file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        # Make sure the docstring has the form of a f90 comment
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("!")
            string = "!"+string+"\n"
            self.docstring += string

    def __str__(self):
        filestring = self.docstring
        # Lattice vectors
        filestring += "avec\n"
        tmpstring = ""
        for pos in self.cell.latticevectors:
            for coord in pos:
                tmpstring += "  %13.10f" % coord
            tmpstring += "\n"
        tmpstring += "\n"
        filestring += tmpstring
        # Scale factor
        filestring += "scale\n"
        filestring += "  %13.10f\n\n" % self.cell.lengthscale
        # Atoms
        filestring += "atoms\n"
        # Get number of species
        species = set([])
        for a in self.cell.atomdata:
            for b in a:
                species.add(b.spcstring())
        tmpstring = ("  "+str(len(species))).ljust(37)+": nspecies\n"
        filestring += tmpstring
        # local B-field string
        bfcmtstring = "   0.00000000  0.00000000  0.00000000"
        # initialize some stuff
        natoms = 0
        spcstring = self.cell.atomdata[0][0].spcstring()
        positionstring = ""
        for a in self.cell.atomdata:
            for b in a:
                spcs = b.spcstring()
                # Accumulate for this species
                if spcs == spcstring:
                    ## natoms += len(a)
                    natoms += 1
                    positionstring += str(b.position)+bfcmtstring+"\n"
                else:
                    # Print species
                    if len(spcstring) > 2:
                        # alloy
                        filestring += "'??.in'".ljust(37) + \
                            ": spfname = "+spcstring+"\n"
                    else:
                        filestring += ("'"+spcstring +
                                       ".in'").ljust(37)+": spfname \n"
                    filestring += "  "+str(natoms)+"\n"
                    filestring += positionstring
                    # Initialize next species
                    spcstring = spcs
                    natoms = 1
                    positionstring = str(b.position)+bfcmtstring+"\n"
        # Print last species
        if len(spcstring) > 2:
            # alloy
            filestring += "'??.in'".ljust(37)+": spfname = "+spcstring+"\n"
        else:
            filestring += ("'"+spcstring+".in'").ljust(37)+": spfname\n"
        filestring += "  "+str(natoms)+"\n"
        filestring += positionstring
        return filestring

################################################################################################


class ExcitingFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in an input.xml file and the method
    __str__ that outputs the contents of an input.xml file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        self.title = ""
        self.docstring = self.docstring.rstrip("\n")+"\n"

    def __str__(self):
        filestring = "<input>\n"
        filestring += "  <title>\n"
        filestring += self.docstring
        filestring += "  </title>\n"
        # Add title if there is one
        if self.title != "":
            filestring += "  <title>"+self.title+"</title>\n"
        filestring += "  <structure>\n"
        # scale factor
        filestring += "    <crystal scale="+str(self.cell.lengthscale)+">\n"
        # Lattice vectors
        tmpstring = ""
        for pos in self.cell.latticevectors:
            tmpstring += "      <basevect>"
            for coord in pos:
                tmpstring += " %13.10f" % coord
            tmpstring += "</basevect>\n"
        filestring += tmpstring
        filestring += "    </crystal>\n"
        # Atoms
        # local B-field string
        bfcmtstring = "   0.00000000  0.00000000  0.00000000"
        # initialize some stuff
        spcstring = self.cell.atomdata[0][0].spcstring()
        positionstring = ""
        for a in self.cell.atomdata:
            for b in a:
                spcs = b.spcstring()
                # Accumulate for this species
                if spcs == spcstring:
                    positionstring += "      <atom coord=\""
                    positionstring += str(b.position)+"\"/>\n"
                else:
                    # Print species
                    if len(spcstring) > 2:
                        # alloy
                        filestring += "    <species speciesfile=\"??.xml\">"
                        filestring += "       <!-- "+spcstring+" -->\n"
                    else:
                        filestring += "    <species speciesfile=\""+spcstring+".xml\">\n"
                    filestring += positionstring+"    </species>\n"
                    # Initialize next species
                    spcstring = spcs
                    positionstring = "      <atom coord=\"" + \
                        str(b.position)+"\"/>\n"
        # Print last species
        if len(spcstring) > 2:
            # alloy
            filestring += "    <species speciesfile=\"??.xml\">"
            filestring += "       <!-- "+spcstring+" -->\n"
        else:
            filestring += "    <species speciesfile=\""+spcstring+".xml\">\n"
        filestring += positionstring
        filestring += "    </species>\n"
        filestring += "  </structure>\n"
        filestring += "</input>\n"
        return filestring

################################################################################################


class FleurFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a Fleur input generator input file (how about
    that, we generate input for the generator of the input...) and the method
    __str__ that outputs the contents as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        # make sure the docstring goes on one line
        self.docstring = self.docstring.replace("\n", " ")
        if len(self.docstring) > 80:
            self.docstring = self.docstring[0:78]+"...\n"

    def __str__(self):
        ed = ElementData()
        filestring = self.docstring+"\n"
        filestring += "&input cartesian=f oldfleur=f\n\n"
        # Lattice vectors
        tmpstring = ""
        n = 1
        for pos in self.cell.latticevectors:
            tmpstring += str(pos)
            tmpstring += "    !  a%1i\n" % n
            n += 1
        filestring += tmpstring
        # Scale factor
        filestring += "%13.9f    ! aa\n" % self.cell.lengthscale
        filestring += "1.0  1.0  1.0 ! scale(1), scale(2), scale(3)\n"
        # Atoms
        natom = 0
        for a in self.cell.atomdata:
            natom += len(a)
        filestring += str(natom)+"\n"
        nspcs = 0
        spcs = ""
        coordstring = ""
        for a in self.cell.atomdata:
            for b in a:
                # Check for alloy
                if b.alloy():
                    prestring = "??"
                    poststring = "  ! "
                    for k in b.species:
                        poststring += str(ed.elementnr[k])+"/"
                    poststring = poststring.rstrip(
                        "/")+" "+str(b.spcstring())+"\n"
                else:
                    prestring = str(ed.elementnr[b.spcstring()]).ljust(2)
                    poststring = "  ! "+b.spcstring()+"\n"
                coordstring += prestring+str(b.position)+poststring
        # To filestring
        filestring += coordstring
        return filestring

################################################################################################


class CASTEPFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a CASTEP run and the method
    __str__ that outputs to a .cell file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Cartesian units?
        self.cartesian = False
        # What units?
        self.unit = "angstrom"
        self.cell.newunit("angstrom")
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string
        # VCA calculation?
        self.vca = False
        # Print labels?
        self.printlabels = False

    def __str__(self):
        # Set units
        self.cell.newunit(self.unit)
        # Assign some local variables
        a = self.cell.lengthscale
        lattice = self.cell.latticevectors
        ed = ElementData()
        # docstring
        filestring = self.docstring+"\n"
        filestring += "%BLOCK LATTICE_CART\n"
        # units
        if self.cell.unit == "angstrom":
            filestring += "ang    # angstrom units\n"
        elif self.cell.unit == "bohr":
            filestring += "bohr   # atomic units\n"
        # lattice
        for vec in lattice:
            for coord in vec:
                filestring += " %19.15f" % (coord*a)
            filestring += "\n"
        # Cutoff
        filestring += "%ENDBLOCK LATTICE_CART\n\n"
        # The atom position info
        if self.cartesian:
            # Correct block name and units
            filestring += "%BLOCK POSITIONS_ABS\n"
            if self.cell.unit == "angstrom":
                filestring += "ang    # angstrom units\n"
            elif self.cell.unit == "bohr":
                filestring += "bohr   # atomic units\n"
            # Set transformation matrix
            transmat = LatticeMatrix(self.cell.latticevectors)
            scalfac = self.cell.a
        else:
            filestring += "%BLOCK POSITIONS_FRAC\n"
            transmat = LatticeMatrix([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
            scalfac = 1.0
        i = 0
        for a in self.cell.atomdata:
            for b in a:
                pos = Vector(mvmult3(transmat, b.position)).scalmult(scalfac)
                # Check for VCA calculation
                if self.cell.alloy and self.vca:
                    if len(b.species) > 1:
                        i = i + 1
                        for sp, conc in b.species.items():
                            filestring += sp.ljust(2)+" "+str(pos) + \
                                "  MIXTURE:( %i %6.5f )" % (i, conc)
                    else:
                        filestring += b.spcstring().ljust(2)+" "+str(pos)
                else:
                    filestring += b.spcstring().ljust(2)+" "+str(pos)
                if self.printlabels and b.label != "":
                    filestring += " ID="+b.label
                filestring += "\n"
        if self.cartesian:
            filestring += "%ENDBLOCK POSITIONS_ABS\n"
        else:
            filestring += "%ENDBLOCK POSITIONS_FRAC\n"
        # pseudo-potential block
        species = set([])
        for a in self.cell.atomdata:
            if self.vca:
                for sp, conc in a[0].species.items():
                    species.add(sp)
            else:
                species.add(a[0].spcstring())
        filestring += "\n"
        filestring += "# Commented out pseudopotential block for easy editing\n"
        filestring += "#%BLOCK SPECIES_POT\n"
        for sp in species:
            filestring += "# "+sp.ljust(2)+"  "+sp+"_00.usp\n"
        filestring += "#%ENDBLOCK SPECIES_POT\n"
        # Put in the symmetry operations
        filestring += "\n%BLOCK SYMMETRY_OPS\n"
        latvect = self.cell.conventional_latticevectors()
        # make list and make sure that identity comes first
        symoplist = sorted(list(self.cell.symops))
        k = 1
        for op in symoplist:
            filestring += "# Symm. op. %i\n" % k
            filestring += str(op)
            k += 1
        filestring += "%ENDBLOCK SYMMETRY_OPS\n"
        return filestring

################################################################################################
# PWSCF (Quantum Espresso)


class PWSCFFile(GeometryOutputFile):
    """
    Class for storing the geometrical data for a PWSCF run and the method
    __str__ that outputs to a .in file as a string.
    """

    def __init__(self, crystalstructure, string, kresolution=0.2):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        #
        self.setupall = False
        # Cartesian units?
        self.cartesian = False
        self.cartesianpositions = False
        self.cartesianlatvects = False
        self.scaledcartesianpositions = False
        # What units?
        self.unit = "angstrom"
        self.cell.newunit("angstrom")
        # Pseudopotential string
        self.pseudostring = "_PSEUDO"
        # set up species list
        tmp = set([])
        for a in self.cell.atomdata:
            for b in a:
                tmp.add(b.spcstring())
        self.species = list(tmp)
        # k-space information
        reclatvect = self.cell.reciprocal_latticevectors()
        for j in range(3):
            for i in range(3):
                reclatvect[j][i] = reclatvect[j][i] / self.cell.lengthscale
        # Lengths of reciprocal lattice vectors
        reclatvectlen = [elem.length() for elem in reclatvect]
        self.kgrid = [max(1, int(round(elem/kresolution)))
                      for elem in reclatvectlen]
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string
        self.docstring += "\n"

    def __str__(self):
        filestring = self.docstring
        # Set current units and stuff
        if self.cartesian:
            self.cartesianpositions = True
            self.cartesianlatvects = True
        self.cell.newunit(self.unit)
        # Determine max width of spcstring
        width = 0
        for a in self.cell.atomdata:
            for b in a:
                width = max(width, len(b.spcstring()))
        #
        filestring += "&SYSTEM\n"
        filestring += "  ibrav = %i\n" % (0)
        if self.unit == "bohr":
            filestring += "  celldm(1) = %10.5f\n" % (self.cell.lengthscale)
        elif self.unit == "angstrom":
            filestring += "  A = %10.5f\n" % (self.cell.lengthscale)
        filestring += "  nat = %i\n" % (self.cell.natoms())
        filestring += "  ntyp = %i\n" % (len(self.species))
        filestring += "/\n"
        if self.cartesianlatvects:
            if self.unit == "bohr":
                filestring += "CELL_PARAMETERS {bohr}\n"
            elif self.unit == "angstrom":
                filestring += "CELL_PARAMETERS {angstrom}\n"
            t = LatticeMatrix(self.cell.latticevectors)
            for i in range(3):
                for j in range(3):
                    t[i][j] = self.cell.latticevectors[i][j] * \
                        self.cell.lengthscale
            filestring += str(t)
        else:
            filestring += "CELL_PARAMETERS {alat}\n"
            filestring += str(self.cell.latticevectors)
        filestring += "ATOMIC_SPECIES\n"
        for sp in self.species:
            filestring += "  %2s" % (sp.rjust(width))
            try:
                filestring += ("  %8.5f" % (ed.elementweight[sp])).rjust(11)
            except:
                filestring += "   ???".rjust(11)
            filestring += "  %2s%s\n" % (sp.rjust(width), self.pseudostring)
        if self.cartesianpositions:
            if self.scaledcartesianpositions:
                filestring += "ATOMIC_POSITIONS {alat}\n"
            else:
                if self.unit == "bohr":
                    filestring += "ATOMIC_POSITIONS {bohr}\n"
                elif self.unit == "angstrom":
                    filestring += "ATOMIC_POSITIONS {angstrom}\n"
        else:
            if self.scaledcartesianpositions:
                filestring += "ATOMIC_POSITIONS {alat}\n"
            else:
                filestring += "ATOMIC_POSITIONS {crystal}\n"
        for a in self.cell.atomdata:
            for b in a:
                if self.cartesianpositions:
                    t = Vector(mvmult3(self.cell.latticevectors, b.position))
                    if self.scaledcartesianpositions:
                        filestring += b.spcstring().rjust(width)+" "+str(t)+"\n"
                    else:
                        for i in range(3):
                            t[i] = self.cell.lengthscale*t[i]
                        filestring += b.spcstring().rjust(width)+" "+str(t)+"\n"
                else:
                    if self.scaledcartesianpositions:
                        t = Vector(
                            mvmult3(self.cell.latticevectors, b.position))
                        filestring += b.spcstring().rjust(width)+" "+str(t)+"\n"
                    else:
                        filestring += b.spcstring().rjust(width)+" "+str(b.position)+"\n"
        # Add k-space mesh
        if self.setupall:
            filestring += "\n# k-space resolution ~" + \
                str(self.kresolution)+"/A.\n"
            # Opt for gamma-point run if possible
            if self.kgrid[0]*self.kgrid[1]*self.kgrid[2] == 1:
                filestring += "K_POINTS gamma\n"
            else:
                filestring += "K_POINTS automatic\n"
                filestring += str(self.kgrid[0])+" "+str(self.kgrid[1]
                                                         )+" "+str(self.kgrid[2])+"  0 0 0\n"
        return filestring
    # Return the PWscf internal bravais lattice number

    def ibrav(self):
        system = self.cell.crystal_system()
        setting = self.cell.spacegroupsetting
        if self.supercell:
            return 14
        if system == 'cubic':
            if self.primcell:
                if setting == 'P':
                    return 1
                elif setting == 'F':
                    return 2
                elif setting == 'I':
                    return 3
            else:
                return 1
        if system == 'hexagonal':
            if self.primcell:
                if setting == 'P':
                    return 4
                elif setting == 'R':
                    return 5

################################################################################################
# CP2K


class CP2KFile(GeometryOutputFile):
    """
    Class for storing the geometrical data for a CP2k run and the method
    __str__ that outputs to a .inp file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.cell.newunit("angstrom")
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string
        self.docstring += "\n"

    def __str__(self):
        filestring = self.docstring
        filestring += "&CELL\n"
        filestring += "  PERIODIC XYZ\n"
        filestring += "  A " + \
            str(self.cell.latticevectors[0].scalmult(
                self.cell.lengthscale))+"\n"
        filestring += "  B " + \
            str(self.cell.latticevectors[1].scalmult(
                self.cell.lengthscale))+"\n"
        filestring += "  C " + \
            str(self.cell.latticevectors[2].scalmult(
                self.cell.lengthscale))+"\n"
        filestring += "&END CELL\n\n"
        filestring += "&COORD\n"
        for a in self.cell.atomdata:
            for b in a:
                filestring += b.spcstring()+str(Vector(mvmult3(self.cell.latticevectors,
                                                               b.position)).scalmult(self.cell.lengthscale))+"\n"
        filestring += "&END COORD\n"
        return filestring

################################################################################################


class CPMDFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a CPMD run and the method
    __str__ that outputs to a .inp file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.cell.newunit("bohr")
        self.cutoff = 100.0

    def __str__(self):
        # Assign some local variables
        a = self.cell.lengthscale
        lattice = self.cell.latticevectors
        ed = ElementData()
        # Transformation to cartesian coordinates
        transmtx = []
        for i in range(3):
            transmtx.append([])
            for j in range(3):
                transmtx[i].append(lattice[i][j] * a)
        # docstring
        filestring = self.docstring+"\n"
        filestring += "&SYSTEM\n"
        # lattice
        filestring += " CELL VECTORS\n"
        for vec in transmtx:
            for coord in vec:
                filestring += " %19.15f" % coord
            filestring += "\n"
        # Cutoff
        filestring += " CUTOFF\n"
        filestring += " "+str(self.cutoff)+"\n"
        filestring += "&END\n\n"
        # The atom position info
        filestring += "&ATOMS\n"
        # get all species
        species = set([])
        for a in self.cell.atomdata:
            for b in a:
                species.add(b.spcstring())
        for spc in species:
            filestring += "*[pseudopotential file for "+spc+" here]\n"
            # Find maximal angular momentum
            spcs = spc.split("/")
            l = "s"
            for s in spcs:
                if ed.angularmomentum[ed.elementblock[s]] > ed.angularmomentum[l]:
                    l = ed.elementblock[s]
            natoms = 0
            posstring = ""
            for a in self.cell.atomdata:
                for b in a:
                    if b.spcstring() == spc:
                        natoms += 1
                        posstring += str(Vector(mvmult3(transmtx,
                                                        b.position)))+"\n"
            # Print
            filestring += str(natoms)+"\n"
            filestring += posstring
        filestring += "&END\n"
        return filestring

################################################################################################


class SiestaFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a Siesta run and the method
    __str__ that outputs to a .fdf file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.cell.newunit("angstrom")
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string

    def __str__(self):
        # Assign some local variables
        lattice = self.cell.latticevectors
        ed = ElementData()
        # docstring
        filestring = self.docstring
        filestring += "AtomicCoordinatesFormat".ljust(28)+"Fractional\n"
        species = set([])
        natom = 0
        for a in self.cell.atomdata:
            natom += len(a)
            for b in a:
                species.add(b.spcstring())
        species = list(species)
        nspcs = len(species)
        filestring += "LatticeConstant".ljust(28) + \
            str(self.cell.lengthscale)+" Ang\n"
        filestring += "NumberOfAtoms".ljust(28)+str(natom)+"\n"
        filestring += "NumberOfSpecies".ljust(28)+str(nspcs)+"\n"
        # lattice
        filestring += "%block LatticeVectors\n"
        for vec in lattice:
            filestring += str(vec)+"\n"
        filestring += "%endblock LatticeVectors\n"
        # Atomic coordinates
        filestring += "%block AtomicCoordinatesAndAtomicSpecies\n"
        i = 1
        for sp in species:
            for a in self.cell.atomdata:
                for b in a:
                    if b.spcstring() == sp:
                        filestring += str(b.position)
                        filestring += "   %i\n" % i
            i += 1
        filestring += "%endblock AtomicCoordinatesAndAtomicSpecies\n"
        # Chemical species
        filestring += "%block ChemicalSpeciesLabel\n"
        i = 1
        for sp in species:
            filestring += str(i).ljust(8)
            if len(sp) > 2:
                filestring += "??      ??    # "
                tsp = sp.split("/")
                for t in tsp:
                    filestring += str(ed.elementnr[t])+"/"
                filestring = filestring.rstrip("/")
                filestring += "      "+sp+"\n"
            else:
                filestring += str(ed.elementnr[sp]).ljust(8)+sp.ljust(8)+"\n"
            i += 1
        filestring += "%endblock ChemicalSpeciesLabel\n"
        return filestring

################################################################################################


class ABINITFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in an abinit run and the method
    __str__ that outputs the contents of a abinit input file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.cell.newunit("bohr")
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string
        self.printbraces = False

    def __str__(self):
        # Assign some local variables
        a = self.cell.lengthscale
        lattice = self.cell.latticevectors
        ed = ElementData()
        # docstring
        filestring = self.docstring
        # VASP needs lattice vector matrix to have positive triple product
        if det3(lattice) < 0:
            if lattice[0].length() == lattice[1].length() == lattice[2].length():
                # Shift the first and last for cubic lattices
                transmtx = [[0, 0, 1],
                            [0, 1, 0],
                            [1, 0, 0]]
            else:
                # Else shift the two shortest
                if lattice[0].length() > lattice[1].length() and lattice[0].length() > lattice[2].length():
                    transmtx = [[1, 0, 0],
                                [0, 0, 1],
                                [0, 1, 0]]
                elif lattice[1].length() > lattice[2].length() and lattice[1].length() > lattice[0].length():
                    transmtx = [[0, 0, 1],
                                [0, 1, 0],
                                [1, 0, 0]]
                else:
                    transmtx = [[0, 1, 0],
                                [1, 0, 0],
                                [0, 0, 1]]
        else:
            transmtx = [[1, 0, 0],
                        [0, 1, 0],
                        [0, 0, 1]]
        lattice = mmmult3(transmtx, lattice)
        # Print braces around values (or not)
        if self.printbraces:
            lbrace = "{"
            rbrace = "}"
        else:
            lbrace = " "
            rbrace = ""
        # length scale and lattice
        filestring += "# Structural parameters\n"
        filestring += "acell "+lbrace+"  3*"+str(a)+" "+rbrace+" \n\n"
        filestring += "rprim "+lbrace
        for vec in lattice:
            filestring += str(Vector(vec))+"\n       "
        filestring = filestring[:-1]
        filestring += rbrace+" \n"
        # The atom position info
        alloy = False
        spcs = ""
        typatstring = "typat  "+lbrace+" "
        natom = 0
        ntypat = 0
        znuclstring = "znucl  "+lbrace+" "
        alloystring = ""
        xredstring = "xred "+lbrace+" "
        for a in self.cell.atomdata:
            for b in a:
                natom += 1
                if spcs != b.spcstring():
                    ntypat += 1
                    if b.alloy():
                        znuclstring += "?? "
                        alloystring += b.spcstring()+" "
                        alloy = True
                    else:
                        znuclstring += str(ed.elementnr[b.spcstring()])+" "
                typatstring += str(ntypat)+" "
                xredstring += str(Vector(mvmult3(transmtx,
                                                 b.position)))+"\n       "
                spcs = b.spcstring()
        filestring += "natom  "+lbrace+" "+str(natom)+" "+rbrace+" \n"
        filestring += "ntypat "+lbrace+" "+str(ntypat)+" "+rbrace+" \n"
        filestring += typatstring+rbrace+" \n"
        filestring += znuclstring+rbrace+" "
        if alloy:
            filestring += "    # "+alloystring
        filestring += "\n"
        filestring += xredstring
        filestring = filestring[:-2]+rbrace+" \n"
        return filestring

################################################################################################


class AIMSFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a FHI-AIMS run and the method
    __str__ that outputs the contents of a abinit input file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.cell.newunit("angstrom")
        self.cartesian = False
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string

    def __str__(self):
        filestring = self.docstring+"\n"
        latvecs = self.cell.latticevectors
        for i in range(3):
            for j in range(3):
                latvecs[i][j] = latvecs[i][j] * self.cell.lengthscale
        for vec in latvecs:
            filestring += "lattice_vector  "+str(vec)+"\n"
        for a in self.cell.atomdata:
            for b in a:
                if self.cartesian:
                    filestring += "atom  " + \
                        str(Vector(mvmult3(latvecs, b.position))) + \
                        " "+b.spcstring()+"\n"
                else:
                    filestring += "atom_frac  " + \
                        str(b.position)+" "+b.spcstring()+"\n"
        return filestring

################################################################################################
# UNFINISHED!


class MCSQSFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed by the mcsqs SQS generator and the method
    __str__ that outputs the contents of a mcsqs input file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.cell.newunit("angstrom")
        self.cartesian = False
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        self.docstring = ""
        for string in tmpstrings:
            string = string.lstrip("#")
            string = "#"+string+"\n"
            self.docstring += string

    def __str__(self):
        l = self.cell.lengthscale
        filestring = "%12.8f %12.8f %12.8f 90.0 90.0 90.0"
        filestring += str(self.cell.latticevectors)
        for a in self.cell.atomdata:
            for b in a:
                filestring += +str(b.position)+" "
                for k, v in b.species.items():
                    filestring += k+"="+str(v)
        return filestring

################################################################################################


class POSCARFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a POSCAR file and the method
    __str__ that outputs the contents of a POSCAR file as a string.
    If you want POSCAR to be printed with the atomic positions in Cartesian form,
    then set
    POSCARFile.printcartpos = True
    If you want to put the overall length scale on the lattice vectors and print 1.0
    for the length scale, then set
    POSCARFile.printcartvecs = True
    """

    def __init__(self, crystalstructure, string, vca=False):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.cell.newunit("angstrom")
        self.printcartvecs = False
        self.printcartpos = False
        self.vasp5format = False
        self.selectivedyn = False
        self.vca = vca
        # set up species list
        tmp = set([])
        for a in self.cell.atomdata:
            for b in a:
                if self.vca:
                    for k, v in b.species.items():
                        tmp.add(k)
                else:
                    tmp.add(b.spcstring())
        self.species = list(tmp)
        # make sure the docstring goes on one line
        self.docstring = self.docstring.replace("\n", " ")

    def SpeciesOrder(self):
        """
        Return a string with the species in the order they appear in POSCAR.
        """
        returnstring = ""
        for sp in self.species:
            returnstring += sp+" "
        return returnstring

    def __str__(self):
        # Assign some local variables
        lattice = self.cell.latticevectors
        # VASP needs lattice vector matrix to have positive triple product
        if det3(lattice) < 0:
            if lattice[0].length() == lattice[1].length() == lattice[2].length():
                # Shift the first and last for cubic lattices
                transmtx = [[0, 0, 1],
                            [0, 1, 0],
                            [1, 0, 0]]
            else:
                # Else shift the two shortest
                if lattice[0].length() > lattice[1].length() and lattice[0].length() > lattice[2].length():
                    transmtx = [[1, 0, 0],
                                [0, 0, 1],
                                [0, 1, 0]]
                elif lattice[1].length() > lattice[2].length() and lattice[1].length() > lattice[0].length():
                    transmtx = [[0, 0, 1],
                                [0, 1, 0],
                                [1, 0, 0]]
                else:
                    transmtx = [[0, 1, 0],
                                [1, 0, 0],
                                [0, 0, 1]]
        else:
            transmtx = [[1, 0, 0],
                        [0, 1, 0],
                        [0, 0, 1]]
        lattice = mmmult3(transmtx, lattice)

        # For output of atomic positions
        a = self.cell.lengthscale
        positionunits = ""
        if self.selectivedyn:
            positionunits += "Selective dynamics\n"
        if self.printcartpos:
            positionunits += "Cartesian\n"
            coordmat = []
            for i in range(3):
                coordmat.append([])
                for j in range(3):
                    coordmat[i].append(lattice[i][j] * a)
        else:
            coordmat = [[1, 0, 0],
                        [0, 1, 0],
                        [0, 0, 1]]
            positionunits += "Direct\n"
        # The first line with info from input docstring
        filestring = self.docstring
        if not self.vasp5format:
            filestring += " Species order: "
            for sp in self.species:
                filestring += sp+" "
        filestring += "\n"
        # Lattice parameter and vectors
        if self.printcartvecs:
            latticestring = " 1.0\n"
            for i in range(3):
                latticestring += "%19.15f %19.15f %19.15f\n" % (
                    a*lattice[i][0], a*lattice[i][1], a*lattice[i][2])
        else:
            latticestring = " %10f\n" % a
            for i in range(3):
                latticestring += "%19.15f %19.15f %19.15f\n" % (
                    lattice[i][0], lattice[i][1], lattice[i][2])
        filestring += latticestring
        # print species here if vasp 5 format
        if self.vasp5format:
            for sp in self.species:
                filestring += (" "+sp).rjust(4)
            filestring += "\n"
        # positions and number of species
        nspstring = ""
        positionstring = ""
        for sp in self.species:
            nsp = 0
            for a in self.cell.atomdata:
                for b in a:
                    if self.vca:
                        for k, v in b.species.items():
                            if k == sp:
                                nsp += 1
                                p = Vector(
                                    mvmult3(coordmat, mvmult3(transmtx, b.position)))
                                positionstring += str(p)
                                if self.selectivedyn:
                                    positionstring += "   T  T  T"
                                positionstring += "\n"
                    else:
                        if b.spcstring() == sp:
                            nsp += 1
                            p = Vector(
                                mvmult3(coordmat, mvmult3(transmtx, b.position)))
                            positionstring += str(p)
                            if self.selectivedyn:
                                positionstring += "   T  T  T"
                            positionstring += "\n"
            nspstring += (" "+str(nsp)).rjust(4)
        filestring += nspstring+"\n"
        filestring += positionunits
        filestring += positionstring
        return filestring


class POTCARFile:
    """
    Class for representing and outputting a POTCAR file for VASP.
    """

    def __init__(self, crystalstructure, directory="", vca=False,
                 prioritylist=["_d", "_pv", "_sv", "", "_h", "_s"]):
        self.cell = crystalstructure
        self.vca = vca
        self.prioritylist = prioritylist
        # POTCAR library
        if directory != "":
            self.dir = directory
        else:
            try:
                self.dir = os.environ['VASP_PSEUDOLIB']
            except:
                try:
                    self.dir = os.environ['VASP_PAWLIB']
                except:
                    self.dir = ""
        # check directory
        if self.dir == "":
            raise SetupError(
                "No path to the VASP pseudopotential library specified.\n")
        if not os.path.exists(self.dir):
            raise SetupError(
                "The specified path to the VASP pseudopotential library does not exist.\n"+self.dir)
        # set up species list
        poscarfile = POSCARFile(self.cell, "", vca=self.vca)
        self.species = poscarfile.species

    def __str__(self):
        # get all files
        potcarlist = []
        for a in self.species:
            for version in self.prioritylist:
                potcarfile = self.dir+"/"+a+version+"/POTCAR"
                if os.path.exists(potcarfile):
                    potcarlist.append(potcarfile)
                    break
        # read potcar files and put in outstring
        outstring = ""
        for f in potcarlist:
            potcar = open(f, "r")
            outstring += potcar.read()
            potcar.close()
        return outstring


class KPOINTSFile:
    """
    Class for representing and outputting a KPOINTS file for VASP.
    """

    def __init__(self, crystalstructure, docstring="", kresolution=0.2):
        self.docstring = docstring
        self.kresolution = kresolution
        # set reciprocal lattice vectors in reciprocal angstroms
        reclatvect = crystalstructure.reciprocal_latticevectors()
        for j in range(3):
            for i in range(3):
                reclatvect[j][i] = reclatvect[j][i] / \
                    crystalstructure.lengthscale
        # Lengths of reciprocal lattice vectors
        reclatvectlen = [elem.length() for elem in reclatvect]
        self.kgrid = [max(1, int(round(elem/self.kresolution)))
                      for elem in reclatvectlen]

    def __str__(self):
        tmp = self.docstring
        tmp += " k-space resolution ~"+str(self.kresolution)+"/A\n"
        tmp += " 0\n"
        tmp += "Gamma\n"
        tmp += str(self.kgrid[0])+" "+str(self.kgrid[1]) + \
            " "+str(self.kgrid[2])+"\n"
        tmp += "0 0 0\n"
        return tmp


class INCARFile:
    """
    Class for representing and outputting a INCAR file for VASP.
    """

    def __init__(self, crystalstructure, docstring="", potcardir="", vca=False,
                 prioritylist=["_d", "_pv", "_sv", "", "_h", "_s"], encutfac=1.5):
        self.cell = crystalstructure
        self.docstring = "# "+docstring.lstrip("#").rstrip("\n")+"\n"
        self.prioritylist = prioritylist
        self.vca = vca
        self.vcaspecies = None
        # ecut = max(encuts found in potcars)*encutfac
        self.encutfac = encutfac
        poscarfile = POSCARFile(self.cell, "", vca=self.vca)
        # we need the potcar directory
        if potcardir != "":
            self.potcardir = potcardir
        else:
            try:
                self.potcardir = os.environ['VASP_PSEUDOLIB']
            except:
                try:
                    self.potcardir = os.environ['VASP_PAWLIB']
                except:
                    self.potcardir = ""
        # check directory
        if self.potcardir == "":
            raise SetupError(
                "No path to the VASP pseudopotential library specified.\n")
        if not os.path.exists(self.potcardir):
            raise SetupError(
                "The specified path to the VASP pseudopotential library does not exist.\n"+self.dir)

        if self.vca:
            # set up species list
            tmp = set([])
            for a in self.cell.atomdata:
                for b in a:
                    for k, v in b.species.items():
                        tmp.add((k, v))
            tmp = list(tmp)
            self.vcaspecies = []
            for s in poscarfile.species:
                for t in tmp:
                    if t[0] == s:
                        self.vcaspecies.append(t)
        # set up species dict
        speciesdict = dict([])
        for a in self.cell.atomdata:
            for b in a:
                if self.vca:
                    for k, v in b.species.items():
                        spcstr = k
                        if spcstr in speciesdict:
                            t = speciesdict[spcstr] + 1
                            speciesdict[spcstr] = t
                        else:
                            speciesdict[spcstr] = 1
                else:
                    spcstr = b.spcstring()
                    if spcstr in speciesdict:
                        t = speciesdict[spcstr] + 1
                        speciesdict[spcstr] = t
                    else:
                        speciesdict[spcstr] = 1
        # species list in the same order as poscar
        self.species = []
        for s in poscarfile.species:
            for k, v in speciesdict.items():
                if k == s:
                    self.species.append((k, v))
        # get potcar list
        potcars = dict([])
        specieslist = []
        for a in speciesdict:
            for version in self.prioritylist:
                potcarfile = self.potcardir+"/"+a+version+"/POTCAR"
                if os.path.exists(potcarfile):
                    potcars[a] = potcarfile
                    specieslist.append(a)
                    break
        # get maximal encut and number of electrons from potcars
        enmaxs = dict([])
        zvals = dict([])
        for a, f in potcars.items():
            potcar = open(f, "r")
            for line in potcar:
                if search("ZVAL", line):
                    zvals[a] = float(line.split("ZVAL")[1].lstrip(
                        "= ").split()[0].strip(string.punctuation))
                if search("ENMAX", line):
                    enmaxs[a] = float(line.split("ENMAX")[1].lstrip(
                        "= ").split()[0].strip(string.punctuation))
                if search("END of PSCTR", line):
                    break
            potcar.close()
        self.maxencut = max([k for v, k in enmaxs.items()])
        # do we suspect that this might be magnetic?
        self.magnetic = False
        self.magmomlist = []
        for s in self.species:
            if s[0] in suspiciouslist:
                self.magnetic = True
                self.magmomlist.append(str(s[1])+"*"+str(initialmoments[s[0]]))
            else:
                self.magmomlist.append(str(s[1])+"*0")
        # Determine NBANDS
        nmag = sum([eval(i) for i in self.magmomlist])
        nelect = 0.0
        for sp, z in zvals.items():
            for a in self.cell.atomdata:
                for b in a:
                    if sp == b.spcstring():
                        nelect += z
        if nmag > 0:
            nstates = int(math.ceil(nelect))
        else:
            nstates = int(math.ceil(nelect/2))
        # NBANDS is max of the default VASP definition and occupied bands+20
        natoms = sum([len(a) for a in self.cell.atomdata])
        self.nbands = max(max(max(int(math.ceil(nelect/2)) +
                                  int(natoms/2), 3), math.ceil(0.6*nelect))+nmag, nstates+20)

    def __str__(self):
        tmp = self.docstring
        tmp += "ENCUT = "+str(self.maxencut*self.encutfac)+"\n"
        tmp += "#NBANDS = "+str(self.nbands)+"\n"
        ## tmp += "IBRION = 1\n"
        ## tmp += "POTIM = 0.4\n"
        ## tmp += "ISIF = 2\n"
        ## tmp += "NSW = 30\n"
        ## tmp += "NELMIN = 4\n"
        tmp += "PREC = Accurate\n"
        tmp += "LREAL = Auto\n"
        tmp += "ISMEAR = 0\n"
        tmp += "SIGMA = 0.1\n"
        if self.magnetic:
            tmp += "ISPIN = 2\n"
            tmp += "MAGMOM = "
            for species in self.magmomlist:
                tmp += species+" "
            tmp += "\n"
        if self.vca:
            tmp += "VCA = "
            for s in self.vcaspecies:
                tmp += str(s[1])+" "
            tmp += "\n"
            tmp += "LVCADER = .True.\n"
        return tmp


################################################################################################
# EMTO
class KFCDFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].dat file for the kfcd program
    and the method __str__ that outputs the contents of the .dat file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.jobnam = "default"
        self.kstrjobnam = "default"
        # To be put on the first line
        self.programdoc = ""

    def __str__(self):
        filestring = ""
        tmpstring = "KFCD      MSGL..=  0"
        tmpstring = tmpstring.ljust(25)+self.programdoc.replace("\n", " ")+"\n"
        filestring += tmpstring
        tmpstring = "JOBNAM...="+self.jobnam+"\n"
        filestring += tmpstring
        tmpstring = "STRNAM...="+self.kstrjobnam+"\n"
        filestring += tmpstring
        filestring += "DIR001=../kstr/smx/\n"
        filestring += "DIR002=../kgrn/chd/\n"
        filestring += "DIR003=../shape/shp/\n"
        filestring += "DIR004=../bmdl/mdl/\n"
        filestring += "DIR006=./\n"
        filestring += "Lmaxs.= 30 NTH..= 41 NFI..= 81 FPOT..= N\n"
        filestring += "OVCOR.=  Y UBG..=  N NPRN.=  0\n"
        return filestring


class KGRNFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].dat file for the kgrn program
    and the method __str__ that outputs the contents of the .dat file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.jobnam = "default"
        self.kstrjobnam = "default"
        # To be put on the first line
        self.programdoc = ""
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        self.latticenr = 14

    def __str__(self):
        ed = ElementData()
        filestring = ""
        tmpstring = "KGRN"
        tmpstring = tmpstring.ljust(25)+self.programdoc.replace("\n", " ")+"\n"
        filestring += tmpstring
        tmpstring = "JOBNAM="+self.jobnam+"\n"
        filestring += tmpstring
        filestring += "STRT..=  A MSGL.=  0 EXPAN.= S FCD..=  Y FUNC..= SCA\n"
        tmpstring = "FOR001=../kstr/smx/"+self.kstrjobnam+".tfh\n"
        tmpstring += "FOR001=../kstr/smx/"+self.kstrjobnam+"10.tfh\n"
        filestring += tmpstring
        filestring += "DIR002=pot/\n"
        filestring += "DIR003=pot/\n"
        tmpstring = "FOR004=../bmdl/mdl/"+self.kstrjobnam+".mdl\n"
        filestring += tmpstring
        filestring += "DIR006=\n"
        filestring += "DIR009=pot/\n"
        filestring += "DIR010=chd/\n"
        # Use environment variable TMPDIR if possible
        tmpstring = "DIR011="
        if "TMPDIR" in os.environ:
            tmpstring += os.environ["TMPDIR"]
            # Make sure the string will end with a single /
            tmpstring = tmpstring.rstrip("/")
        else:
            # ...else check for /tmp
            if os.path.isdir("/tmp"):
                tmpstring += "/tmp"
            else:
                # ...and last resort is ./
                tmpstring += "."
        tmpstring += "/\n"
        filestring += tmpstring
        filestring += self.docstring.replace("\n", " ")+"\n"
        filestring += "Band: 10 lines\n"
        tmpstring = "NITER.= 50 NLIN.= 31 NPRN.=  0 NCPA.= 20 NT...=%3i" % len(
            self.cell.atomdata)+" MNTA.="
        # Work out maximal number of species occupying a site
        mnta = 1
        for a in self.cell.atomdata:
            for b in a:
                mnta = max(mnta, len(b.species))
        tmpstring += "%3i" % mnta+"\n"
        filestring += tmpstring
        filestring += "MODE..= 3D FRC..=  N DOS..=  N OPS..=  N AFM..=  P CRT..=  M\n"
        filestring += "Lmaxh.=  8 Lmaxt=  4 NFI..= 31 FIXG.=  2 SHF..=  0 SOFC.=  N\n"
        # Choose brillouin zone by lattice type
        # Output the smallest allowed n for each direction in this lattice type
        if self.latticenr == 1:
            nkx = 0
            nky = 2
            nkz = 0
        elif self.latticenr == 2:
            nkx = 0
            nky = 5
            nkz = 0
        elif self.latticenr == 3:
            nkx = 0
            nky = 3
            nkz = 0
        elif self.latticenr == 4:
            nkx = 0
            nky = 3
            nkz = 2
        elif self.latticenr == 5:
            nkx = 0
            nky = 2
            nkz = 2
        elif self.latticenr == 6:
            nkx = 0
            nky = 3
            nkz = 2
        elif self.latticenr == 7:
            nkx = 0
            nky = 3
            nkz = 3
        elif self.latticenr == 8:
            nkx = 2
            nky = 2
            nkz = 1
        elif self.latticenr == 9:
            nkx = 2
            nky = 2
            nkz = 1
        elif self.latticenr == 10:
            nkx = 2
            nky = 2
            nkz = 1
        elif self.latticenr == 11:
            nkx = 1
            nky = 1
            nkz = 1
        elif self.latticenr == 12:
            nkx = 1
            nky = 2
            nkz = 1
        elif self.latticenr == 13:
            nkx = 3
            nky = 3
            nkz = 0
        else:
            nkx = 2
            nky = 2
            nkz = 2
        filestring += "KMSH...= G IBZ..= %2i NKX..= %2i NKY..= %2i NKZ..= %2i FBZ..=  N\n" % (
            self.latticenr, nkx, nky, nkz)
        filestring += "KMSH2..= G IBZ2.=  1 NKX2.=  4 NKY2.=  0 NKZ2.= 51\n"
        filestring += "ZMSH...= C NZ1..= 16 NZ2..= 16 NZ3..=  8 NRES.=  4 NZD.= 500\n"
        filestring += "DEPTH..=  1.500 IMAGZ.=  0.020 EPS...=  0.200 ELIM..= -1.000\n"
        filestring += "AMIX...=  0.100 EFMIX.=  1.000 VMTZ..=  0.000 MMOM..=  0.000\n"
        filestring += "TOLE...= 1.d-05 TOLEF.= 1.d-05 TOLCPA= 1.d-05 TFERMI=  500.0 (K)\n"
        # Get number of sites
        nosites = 0
        for a in self.cell.atomdata:
            nosites += len(a)
        # average wigner-seitz radius
        volume = abs(det3(self.cell.latticevectors))
        wsr = self.cell.lengthscale * 3*volume/(nosites * 4 * pi)**third
        filestring += "SWS......=%8f   NSWS.=  1 DSWS..=   0.05 ALPCPA= 0.9020\n" % wsr
        filestring += "Setup: 2 + NQ*NS lines\n"
        filestring += "EFGS...=  0.000 HX....=  0.100 NX...= 11 NZ0..=  6 STMP..= Y\n"
        # atom info
        filestring += "Symb   IQ IT ITA NZ  CONC   Sm(s)  S(ws) WS(wst) QTR SPLT\n"
        iq = 1
        it = 1
        for a in self.cell.atomdata:
            ita = 1
            # THIS MAKES ASSUMPTIONS ABOUT THE ORDERING OF ATOMDATA
            # But we're OK for all orderings implemented so far
            for comp in a[0].spcstring().split("/"):
                for b in a:
                    if comp in b.species:
                        tmpstring = comp.ljust(
                            4)+"  "+"%3i%3i%3i" % (iq, it, ita)
                        tmpstring += "%4i" % ed.elementnr[comp]
                        tmpstring += "%7.3f%7.3f%7.3f%7.3f" % (
                            a[0].species[comp], 1, 1, 1)
                        tmpstring += "%5.2f%5.2f\n" % (0, 0)
                        filestring += tmpstring
                        iq += 1
                ita += 1
                iq -= len(a)
            iq += len(a)
            it += 1
        filestring += "Atom:  4 lines + NT*NTA*6 lines\n"
        filestring += "IEX...=  4 NP..= 251 NES..= 15 NITER=100 IWAT.=  0 NPRNA=  0\n"
        filestring += "VMIX.....=  0.300000 RWAT....=  3.500000 RMAX....= 20.000000\n"
        filestring += "DX.......=  0.030000 DR1.....=  0.002000 TEST....=  1.00E-12\n"
        filestring += "TESTE....=  1.00E-12 TESTY...=  1.00E-12 TESTV...=  1.00E-12\n"
        for a in self.cell.atomdata:
            for comp in a[0].species:
                filestring += comp+"\n"
                try:
                    filestring += ed.emtoelements[comp]
                except KeyError:
                    filestring += "\n\n\n\n\n"
        return filestring


class ShapeFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].dat file for the shape program
    and the method __str__ that outputs the contents of the .dat file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.jobnam = "default"
        # To be put on the first line
        self.programdoc = ""

    def __str__(self):
        filestring = ""
        tmpstring = "SHAPE     HP......=N"
        tmpstring = tmpstring.ljust(25)+self.programdoc.replace("\n", " ")+"\n"
        filestring += tmpstring
        tmpstring = "JOBNAM...="+self.jobnam.ljust(10)+" MSGL.=  1\n"
        filestring += tmpstring
        filestring += "FOR001=../kstr/smx/"+self.jobnam+".tfh\n"
        filestring += "DIR002=shp/\n"
        filestring += "DIR006=./\n"
        filestring += "Lmax..= 30 NSR..=129 NFI..= 11\n"
        filestring += "NPRN..=  0 IVEF.=  3\n"
        return filestring


class BMDLFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].dat file for the bmdl program
    and the method __str__ that outputs the contents of the .dat file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        self.jobnam = "default"
        self.latticenr = 14
        self.a = 1
        self.b = 1
        self.c = 1
        self.alpha = 90
        self.beta = 90
        self.gamma = 90
        # To be put on the first line
        self.programdoc = ""

    def __str__(self):
        lv = self.cell.latticevectors
        ed = ElementData()
        filestring = ""
        tmpstring = "BMDL      HP......=N"
        tmpstring = tmpstring.ljust(25)+self.programdoc.replace("\n", " ")+"\n"
        filestring += tmpstring
        tmpstring = "JOBNAM...="+self.jobnam.ljust(10)+" MSGL.=  1 NPRN.=  0\n"
        filestring += tmpstring
        filestring += "DIR001=mdl/\n"
        filestring += "DIR006=./\n"
        filestring += "Madelung potential, " + \
            self.docstring.replace("\n", " ")+"\n"
        filestring += "NL.....= 7\n"
        filestring += "LAMDA....=    2.5000 AMAX....=    4.5000 BMAX....=    4.5000\n"
        # Get number of sites
        nosites = 0
        for a in self.cell.atomdata:
            nosites += len(a)
        if self.latticenr == 0:
            tmpstring = "NQ3...=%3i LAT...= 0 IPRIM.= 0 NGHBP.=13 NQR2..= 0\n" % (
                nosites, self.latticenr)
        else:
            tmpstring = "NQ3...=%3i LAT...=%2i IPRIM.= 1 NGHBP.=13 NQR2..= 0\n" % (
                nosites, self.latticenr)
        filestring += tmpstring
        boa = self.b/self.a
        coa = self.c/self.a
        filestring += "A........= 1.0000000 B.......=%10f C.......=%10f\n" % (
            boa, coa)
        tmpstring = ""
        if self.latticenr == 0:
            for i in range(3):
                tmpstring += "BSX......=%10f BSY.....=%10f BSZ.....=%10f\n" % (
                    lv[i][0], lv[i][1], lv[i][2])
        else:
            tmpstring += "ALPHA....=%10f BETA....=%10f GAMMA...=%10f\n" % (
                self.alpha, self.beta, self.gamma)
        filestring += tmpstring
        for a in self.cell.atomdata:
            for b in a:
                v = mvmult3(lv, b.position)
                filestring += "QX(IQ)...=%10f QY......=%10f QZ......=%10f" % (
                    v[0], v[1], v[2])
                filestring += "      "+b.spcstring()+"\n"
        return filestring


class KSTRFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].dat file for the kstr program
    and the method __str__ that outputs the contents of the .dat file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        self.jobnam = "default"
        self.latticenr = 14
        self.a = 1
        self.b = 1
        self.c = 1
        self.alpha = 90
        self.beta = 90
        self.gamma = 90
        self.hardsphere = 0.67
        self.iprim = 0
        # To be put on the first line
        self.programdoc = ""

    def __str__(self):
        lv = self.cell.latticevectors
        ed = ElementData()
        filestring = ""
        tmpstring = "KSTR      HP......=N"
        tmpstring = tmpstring.ljust(25)+self.programdoc.replace("\n", " ")+"\n"
        filestring += tmpstring
        tmpstring = "JOBNAM...=" + \
            self.jobnam.ljust(10)+" MSGL.=  1 MODE...=B STORE..=Y HIGH...=Y\n"
        filestring += tmpstring
        filestring += "DIR001=smx/\n"
        filestring += "DIR006=./\n"
        filestring += "Slope matrices, "+self.docstring.replace("\n", " ")+"\n"
        # NL = maximal l from element blocks
        maxl = 1
        for a in self.cell.atomdata:
            for b in a:
                for i in b.species:
                    if ed.elementblock[i] == "p":
                        maxl = max(maxl, 2)
                    elif ed.elementblock[i] == "d":
                        maxl = max(maxl, 3)
                    elif ed.elementblock[i] == "f":
                        maxl = max(maxl, 4)
        tmpstring = "NL.....= %1i NLH...=11 NLW...= 9 NDER..= 6 ITRANS= 3 NPRN..= 0\n" % maxl
        filestring += tmpstring
        # Setting the real space summation cutoff to 4.5*(wigner-seitz radius)
        volume = abs(det3(lv))
        wsr = (3*volume/(self.cell.natoms() * 4 * pi))**third
        tmpstring = "(K*W)^2..=  0.000000 DMAX....=%10f RWATS...=      0.10\n" % (wsr*4.5)
        filestring += tmpstring
        tmpstring = "NQ3...=%3i LAT...=%2i IPRIM.=%2i NGHBP.=13 NQR2..= 0\n" % (
            self.cell.natoms(), self.latticenr, self.iprim)
        filestring += tmpstring
        boa = self.b/self.a
        coa = self.c/self.a
        filestring += "A........= 1.0000000 B.......=%10f C.......=%10f\n" % (
            boa, coa)
        tmpstring = ""
        if self.iprim == 0:
            for i in range(3):
                tmpstring += "BSX......=%10f BSY.....=%10f BSZ.....=%10f\n" % (
                    lv[i][0], lv[i][1], lv[i][2])
        else:
            tmpstring += "ALPHA....=%10f BETA....=%10f GAMMA...=%10f\n" % (
                self.alpha, self.beta, self.gamma)
        filestring += tmpstring
        for a in self.cell.atomdata:
            for b in a:
                v = mvmult3(lv, b.position)
                filestring += "QX(IQ)...=%10f QY......=%10f QZ......=%10f" % (
                    v[0], v[1], v[2])
                filestring += "      "+b.spcstring()+"\n"
        for i in range(self.cell.natoms()):
            filestring += "a/w(IQ)..="
            for i in range(4):
                filestring += "%5.2f" % self.hardsphere
            filestring += "\n"
        filestring += "LAMDA....=    2.5000 AMAX....=    4.5000 BMAX....=    4.5000\n"
        return filestring

################################################################################################
# SPRKKR


class XBandSysFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].sys file for the xband program
    and the method __str__ that outputs the contents of the .sys file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Set atomic units for length scale
        self.cell.newunit("bohr")
        self.jobnam = "default"
        self.a = 1
        self.b = 1
        self.c = 1
        self.alpha = 90
        self.beta = 90
        self.gamma = 90
        self.minangmom = None
        self.filename = ""
        # To be put on the first line
        self.programdoc = ""

    def __str__(self):
        ed = ElementData()
        # First identify any site which is not filled (concentrations add to 1.0)
        # and fill up with vacuum sphere (Vc)
        self.cell.fill_out_empty(label='Vc')
        # docstring on a single line
        filestring = deletenewline(self.docstring, replace=" ")
        filestring += "\n"+self.filename+"\n"
        filestring += "xband-version\n"
        filestring += "5.0\n"
        # It would be really cool to support lower dimensions...one day.
        filestring += "dimension\n"
        filestring += "3D\n"
        filestring += "Bravais lattice\n"
        if self.cell.crystal_system() == 'triclinic':
            filestring += "1  triclinic   primitive      -1     C_i \n"
        elif self.cell.crystal_system() == 'monoclinic':
            if self.cell.spacegroupsetting == 'P':
                filestring += "2  monoclinic  primitive      2/m    C_2h\n"
            elif self.cell.spacegroupsetting == 'A' or self.cell.spacegroupsetting == 'B' or \
                    self.cell.spacegroupsetting == 'C':
                filestring += "3  monoclinic  primitive      2/m    C_2h\n"
            else:
                sys.stderr.write(
                    "xband only knows primitive and base-centered monoclinic settings!\n")
                sys.exit(43)
        elif self.cell.crystal_system() == 'orthorhombic':
            if self.cell.spacegroupsetting == 'P':
                filestring += "4  orthorombic primitive      mmm    D_2h\n"
            elif self.cell.spacegroupsetting == 'A' or self.cell.spacegroupsetting == 'B' or \
                    self.cell.spacegroupsetting == 'C':
                filestring += "5  orthorombic body-centered  mmm    D_2h\n"
            elif self.cell.spacegroupsetting == "I":
                filestring += "6  orthorombic body-centered  mmm    D_2h\n"
            elif self.cell.spacegroupsetting == "F":
                filestring += "7  orthorombic face-centered  mmm    D_2h\n"
            else:
                sys.stderr.write(
                    "xband does not know %1s centering of an orthorhombic cell.\n" % self.cell.spacegroupsetting)
                sys.exit(43)
        elif self.cell.crystal_system() == "tetragonal":
            if self.cell.spacegroupsetting == "P":
                filestring += "8  tetragonal  primitive      4/mmm  D_4h\n"
            elif self.cell.spacegroupsetting == "I":
                filestring += "9  tetragonal  body-centered  4/mmm  D_4h\n"
            else:
                sys.stderr.write(
                    "xband only knows primitive and body-centered tetragonal settings!\n")
                sys.exit(43)
        elif self.cell.crystal_system() == "trigonal":
            filestring += "10 trigonal    primitive      -3m    D_3d\n"
        elif self.cell.crystal_system() == "hexagonal":
            filestring += "11 hexagonal   primitive      6/mmm  D_6h\n"
        elif self.cell.crystal_system() == "cubic":
            if self.cell.spacegroupsetting == "P":
                filestring += "12 cubic       primitive      m3m    O_h \n"
            elif self.cell.spacegroupsetting == "F":
                filestring += "13 cubic       face-centered  m3m    O_h \n"
            elif self.cell.spacegroupsetting == "I":
                filestring += "14 cubic       body-centered  m3m    O_h \n"
            else:
                sys.stderr.write(
                    "xband does not know %1s centering of a cubic cell.\n" % self.cell.spacegroupsetting)
                sys.exit(43)
        filestring += "space group number (ITXC and AP)\n"
        filestring += "%5i%5i" % (self.cell.spacegroupnr,
                                  Number2AP[self.cell.spacegroupnr])+"\n"
        filestring += "structure type\n"
        filestring += "UNKNOWN\n"
        filestring += "lattice parameter A  [a.u.]\n"
        filestring += "%18.12f\n" % self.cell.lengthscale
        filestring += "ratio of lattice parameters  b/a  c/a\n"
        filestring += "%18.12f%18.12f\n" % (self.cell.boa, self.cell.coa)
        filestring += "lattice parameters  a b c  [a.u.]\n"
        a = self.cell.lengthscale
        b = self.cell.b * self.cell.lengthscale / self.cell.a
        c = self.cell.c * self.cell.lengthscale / self.cell.a
        filestring += "%18.12f%18.12f%18.12f\n" % (a, b, c)
        filestring += "lattice angles  alpha beta gamma  [deg]\n"
        filestring += "%18.12f%18.12f%18.12f\n" % (
            self.cell.alpha, self.cell.beta, self.cell.gamma)
        filestring += "primitive vectors     (cart. coord.) [A]\n"
        for vec in self.cell.latticevectors:
            for p in vec:
                filestring += "%18.12f" % p
            filestring += "\n"
        # Get number of sites and fill out with empty spheres if the sites are not fully filled
        filestring += "number of sites NQ\n"
        nq = 0
        for a in self.cell.atomdata:
            nq += len(a)
        self.cell.fill_out_empty(label="Vc")
        filestring += "%3i\n" % nq
        filestring += " IQ ICL     basis vectors     (cart. coord.) [A]                      RWS [a.u.]  NLQ  NOQ ITOQ\n"
        # Average Wigner-Seitz radius
        rws = pow(3*self.cell.volume()/(4*pi*len(self.cell.atomset)),
                  1.0/3.0)*self.cell.lengthscale
        iq = 0
        icl = 0
        itoq = 0
        for a in self.cell.atomdata:
            icl += 1
            itoqs = []
            for sp in a[0].species:
                itoq += 1
                itoqs.append(itoq)
            for b in a:
                iq += 1
                if self.minangmom:
                    angmom = max(max([ed.angularmomentum[ed.elementblock[spcs]]
                                      for spcs in b.species])+1, self.minangmom)
                else:
                    angmom = max([ed.angularmomentum[ed.elementblock[spcs]]
                                  for spcs in b.species])+1
                v = mvmult3(self.cell.latticevectors, b.position)
                filestring += "%3i%4i%18.12f%18.12f%18.12f  %18.12f%4i%5i " % (
                    iq, icl, v[0], v[1], v[2], rws, angmom, len(a[0].species))
                for i in itoqs:
                    filestring += "%3i" % i
                filestring += "\n"
        filestring += "number of sites classes NCL\n"
        filestring += "%3i\n" % len(self.cell.atomdata)
        filestring += "ICL WYCK NQCL IQECL (equivalent sites)\n"
        iq = 0
        icl = 0
        for a in self.cell.atomdata:
            icl += 1
            filestring += "%3i   %1s%5i" % (icl, '-', len(a))
            for b in a:
                iq += 1
                filestring += "%3i" % iq
            filestring += "\n"
        filestring += "number of atom types NT\n"
        nt = 0
        for a in self.cell.atomdata:
            nt += len(a[0].species)
        filestring += "%3i\n" % nt
        filestring += " IT  ZT  TXTT  NAT  CONC  IQAT (sites occupied)\n"
        iq = 0
        it = 0
        for a in self.cell.atomdata:
            corr = 0
            for sp, conc in a[0].species.items():
                it += 1
                filestring += " %2i%4i  %8s%5i%6.3f" % (
                    it, ed.elementnr[sp], sp, len(a), conc)
                iq -= corr*len(a)
                for b in a:
                    iq += 1
                    filestring += "%3i" % iq
                corr = 1
                filestring += "\n"
        return filestring


class SPCFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed in a [filename].dat file for the SPC program
    and the method __str__ that outputs the contents of the .dat file as a string.
    """

    def __init__(self, crystalstructure, string):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.jobnam = "default"
        self.latticenr = 1
        self.compoundname = ""
        self.a = 1
        self.b = 1
        self.c = 1
        self.alpha = 90
        self.beta = 90
        self.gamma = 90
        self.iprim = 0
        #
        self.supercell = [1, 1, 1]
        self.pairs = 6
        self.triplets = 4
        self.quartets = 2
        # To be put on the first line
        self.programdoc = ""

    def __str__(self):
        import datetime
        now = datetime.datetime.now()
        datestring = now.strftime("%d %b %y")
        filestring = "SPC       HP......=N                                         "+datestring+"\n"
        filestring += "JOBNAM...="+self.jobnam.ljust(10)+" MSGL.=  1 \n"
        if os.path.isdir('spc'):
            dirname = 'spc/'
        else:
            dirname = './'
        filestring += "FOR001="+dirname+"\n"
        filestring += "FOR002="+dirname+"\n"
        filestring += "FOR004="+dirname+"\n"
        filestring += "FOR006=\n"
        filestring += "FOR008="+dirname+"\n"
        filestring += "FOR009="+dirname+"\n"
        filestring += self.docstring
        filestring += "Supercell, "+self.compoundname+"\n"
        filestring += "NPRN..=  0 TEST.=  0 NCOL.=  0 STAT.=  1 TCLIM=  0 nsho.= 10\n"
        filestring += "NQ3...=%3i LAT..=%3i IPRIM=%3i HIGH.=  0 NSHC.= 10 NL...=  4 NLH..=  7\n" % (
            self.cell.natoms(), self.latticenr, self.iprim)
        self.a = self.cell.latticevectors[0].length()*self.cell.lengthscale
        self.b = self.cell.latticevectors[1].length()*self.cell.lengthscale
        self.c = self.cell.latticevectors[2].length()*self.cell.lengthscale
        # Renormalized lattice vectors
        lv = []
        for i in range(3):
            lv.append([])
            for j in range(3):
                lv[i].append(self.cell.latticevectors[i][j]
                             * self.cell.lengthscale/self.a)
        filestring += "A........=%10f B.......=%10f C.......=%10f\n" % (
            self.a, self.b, self.c)
        tmpstring = ""
        if self.iprim == 0:
            for i in range(3):
                tmpstring += "BSX......=%10f BSY.....=%10f BSZ.....=%10f\n" % (
                    lv[i][0], lv[i][1], lv[i][2])
        else:
            tmpstring += "ALPHA....=%10f BETA....=%10f GAMMA...=%10f\n" % (
                self.alpha, self.beta, self.gamma)
        filestring += tmpstring
        for a in self.cell.atomdata:
            for b in a:
                v = mvmult3(lv, b.position)
                filestring += "QX.......=%10f QY......=%10f QZ......=%10f" % (
                    v[0], v[1], v[2])
                filestring += "      "+b.spcstring()+"\n"
        filestring += "LAMDA....=    2.5000 AMAX....=    4.5000 BMAX....=    4.5000\n"
        filestring += "Size of the super cell\n"
        filestring += "NA.......=%4i NB.......=%4i NC.......=%4i  Dmax     4.5\n" % (
            self.supercell[0], self.supercell[1], self.supercell[2])
        filestring += "NSDC.....=  20 NSDS.....=   1 NSDM.....=   1\n"
        filestring += "NMAXMX...=   3 TMLIM....= 1.0\n"
        filestring += "NT.......=%4i\n" % (len(self.cell.atomdata))
        filestring += "NTA(IQ)..="
        i = 0
        nat = 0
        for a in self.cell.atomdata:
            i += 1
            for b in a:
                nat += 1
                filestring += "%4i" % i
                if nat % 15 == 0:
                    filestring += "\n          "
        filestring = filestring.rstrip(" ")
        if self.cell.natoms() % 15 != 0:
            filestring += "\n"
        #
        filestring += "NTO......=%4i\n" % (len(self.cell.atomdata))
        filestring += "NTAO(IQ).="
        i = 0
        nat = 0
        for a in self.cell.atomdata:
            i += 1
            for b in a:
                nat += 1
                filestring += "%4i" % i
                if nat % 15 == 0:
                    filestring += "\n          "
        filestring = filestring.rstrip(" ")
        if self.cell.natoms() % 15 != 0:
            filestring += "\n"
        #
        filestring += "NQ3O.....=%4i\n" % (len(self.cell.atomdata))
        filestring += "IQO(IQ)..="
        i = 0
        nat = 0
        for a in self.cell.atomdata:
            i += 1
            for b in a:
                nat += 1
                filestring += "%4i" % i
                if nat % 15 == 0:
                    filestring += "\n          "
        filestring = filestring.rstrip(" ")
        if self.cell.natoms() % 15 != 0:
            filestring += "\n"
        conc = []
        ascii = string.ascii_uppercase+string.ascii_lowercase
        i = 0
        for b in self.cell.atomdata:
            natom = 0
            conc.append([])
            for a in self.cell.atomdata:
                for k, v in a[0].species.items():
                    if a == b:
                        conc[i].append((ascii[natom], v))
                    else:
                        conc[i].append((ascii[natom], 0.0))
                    natom += 1
            i += 1
        filestring += "NATOM....=%4i\n" % natom
        filestring += "SMB(IAT).="
        for a in conc[0]:
            filestring += "%4s" % a[0]
        filestring += "\n"
        filestring += "Concentrations on sublattices:\n"
        for a in conc:
            for c in a:
                filestring += "%f " % c[1]
            filestring += "\n"
        filestring += "Correlation functions and weights for each pairs of elem. (A-B, A-C, ... )\n"
        i = 0
        for a in self.cell.atomdata:
            i += 1
            filestring += "Sublattice\n"
            filestring += "%i\n" % i
            if len(a[0].species) == 1:
                continue
            filestring += "nc2  r_max\n"
            if len(a[0].species) == 1:
                filestring += "0     3.0\n"
                filestring += "i    alpha           weight\n"
            else:
                filestring += "%i     3.0\n" % self.pairs
                filestring += "i    alpha           weight\n"
                for p in range(self.pairs):
                    if p < 3:
                        filestring += "%i     0.0               1.0\n" % (p+1)
                    else:
                        filestring += "%i     0.0               0.0\n" % (p+1)
            filestring += "nc3\n"
            filestring += "0\n"
            filestring += "i   i1  i2  i3           <sss>          weight\n"
            filestring += "nc4\n"
            filestring += "0\n"
            filestring += "i   i1 i2 i3 i4 i5 i6    <ssss>         weight\n"
            filestring += "T_i,   T_f,  delt_T\n"
            filestring += "10.0   0.0   1.0\n"
            filestring += "100                   nsteps\n"
        return filestring

################################################################################################
# MOPAC FILE


class MOPACFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting a MOPAC file
    and the method __str__ that outputs the contents of the MOPAC file as a string.
    """

    def __init__(self, crystalstructure, string, setupall=False, firstline="", secondline="", thirdline="", freeze=-1):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        self.cell.newunit(newunit="angstrom")
        self.setupall = setupall
        self.firstline = firstline
        self.secondline = secondline
        self.thirdline = thirdline
        self.freeze = freeze
        # Make sure the docstring has comment form
        self.docstring = self.docstring.rstrip("\n")
        tmpstrings = self.docstring.split("\n")
        t = True
        for s in tmpstrings:
            t = t and (s[0] == '*')
        if t:
            self.docstring += "\n"
        else:
            self.docstring = ""
            for string in tmpstrings:
                string = string.lstrip("*")
                string = "*"+string+"\n"
                self.docstring += string

    def __str__(self):
        filestring = self.docstring
        if self.setupall:
            if self.firstline == "":
                filestring += " BZ \n"
            else:
                filestring += self.firstline.rstrip("\n")+"\n"
            filestring += self.secondline.rstrip("\n")+"\n"
            filestring += self.thirdline.rstrip("\n")+"\n"
        # Set up lattice vectors
        lv = []
        for i in range(3):
            lv.append(Vector(
                [self.cell.lengthscale*self.cell.latticevectors[i][j] for j in range(3)]))
        # Print sites
        if self.freeze == 0:
            freezestring = " 0"
        elif self.freeze == 1:
            freezestring = " 1"
        else:
            freezestring = ""
        for a in self.cell.atomdata:
            for b in a:
                t = Vector(mvmult3(lv, b.position))
                filestring += str(b).split()[0]+"  "+str(t)+freezestring+"\n"
        # Print lattice vectors
        for l in lv:
            filestring += "Tv  "+str(l)+"\n"
        return filestring

################################################################################################
# GNXAS CRYMOL FILE

class CRYMOLFile(GeometryOutputFile):
    """
    Class for storing the geometrical data needed for outputting an input file
    for crymol program of the GNXAS package and the method __str__ that outputs
    the contents of the file as a string.
    """

    def __init__(self, crystalstructure, string, compound):
        GeometryOutputFile.__init__(self, crystalstructure, string)
        # Document string on last line after
        self.programdoc = ""
        self.compound = compound

    def __str__(self):
        filestring = "CRY\n"
        filestring += self.compound+"\n"
        if self.cell.crystal_system() == 'cubic':
            filestring += "C\n"+str(self.cell.a)+"\n"
        elif self.cell.crystal_system() == 'hexagonal':
            filestring += "H\n"+str(self.cell.a)+", "+str(self.cell.c)+"\n"
        elif self.cell.crystal_system() == 'tetragonal':
            filestring += "E\n"+str(self.cell.a)+", "+str(self.cell.c)+"\n"
        elif self.cell.crystal_system() == 'orthorhombic':
            filestring += "O\n"+str(self.cell.a)+", "+str(self.cell.b)+", "+str(self.cell.c)+"\n"
        elif self.cell.crystal_system() == 'trigonal':
            filestring += "R\n"+str(self.cell.a)+"\n"+str(self.cell.alpha)+"\n"
        elif self.cell.crystal_system() == 'monoclinic':
            filestring += "M\n"+str(self.cell.a)+", "+str(self.cell.b)+", " \
                          +str(self.cell.c)+"\n"+str(self.cell.beta)+"\n"
        elif self.cell.crystal_system() == 'triclinic':
            filestring += "T\n"+str(self.cell.a)+", "+str(self.cell.b)+", "+str(self.cell.c)+"\n"\
                          +str(self.cell.alpha)+", "+str(self.cell.beta)+", "+str(self.cell.gamma)+"\n"
        else:
            raise SetupError("No support for " +
                  self.crystal_system()+" crystal systems in crymol.")

        filestring += "%i\n" % (self.cell.natoms())
        index = 1
        width = 2
        for a in self.cell.atomdata:
            for b in a:
                filestring += str(index).rjust(width)+"  '"+b.spcstring().rjust(width)\
                             +"'  "+str(b.position)+" 12 0.0 0.0\n"
                index += 1
        filestring += "NNY\n"
        filestring += "1\n"
        filestring += "'*' '*' [cut-off distance for first neighbors]\n"
        filestring += "7.0\n"
        filestring += "[3 letters name for output files]\n"
        filestring += "1,[index of photo-absorbing atom]\n"
        filestring += "0.10\n"
        filestring += "[photo-absorption process: 1 for K-edge, 2 for L1-edge, etc.]\n"
        filestring += "1\n"
        filestring += "[Core ionization energy in Ry],0.\n"
        filestring += "3,-0.2,120.0,0.04\n"
        filestring += "5,-1\n"
        filestring += "'S',1,50.,15.,'S',' ','S'\n\n"
        filestring += self.docstring
        filestring += "! Remember to insert missing parameters (indicated by []) !"

        return filestring
