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src/m/a/matter-0.8-r960-20110308/matter/StrukturberichtDesignationFinder.py   matter(Download)
    def testA1(self):
        import matter
        struct = matter.Structure(
            lattice = matter.Lattice(a=1,b=1,c=1,alpha=60,beta=60,gamma=60),
            sgid = 225,
    def testA2(self):
        import matter
        struct = matter.Structure(
            lattice = matter.Lattice(a=1,b=1,c=1,alpha=acos1_3,beta=acos1_3,gamma=acos1_3),
            sgid = 229,
 
        struct = matter.Structure(
            lattice = matter.Lattice(a=1,b=1,c=1,alpha=90,beta=90,gamma=90),
            sgid = 229,
            atoms = [matter.Atom('Cu', xyz=[0,0,0]), matter.Atom('Cu', xyz=[0.5,0.5,0.5])],
    def testAh(self):
        import matter
        struct = matter.Structure(
            lattice = matter.Lattice(a=1,b=1,c=1,alpha=90,beta=90,gamma=90),
            sgid = 221,
    def testB1(self):
        import matter
        struct = matter.Structure(
            lattice = matter.Lattice(a=1,b=1,c=1,alpha=60,beta=60,gamma=60),
            sgid = 225,

src/m/a/matter-0.8-r960-20110308/matter/Parsers/P_xyz.py   matter(Download)
import sys
 
from matter import Structure, Lattice, Atom
from matter import StructureFormatError
from matter.Parsers import StructureParser
        linefields = [l.split() for l in lines]
        # prepare output structure
        stru = Structure()
        # find first valid record
        start = 0
        lattice = matter.Lattice(2*a, 2*a, 2*a, 90,90,90)
        atoms = [matter.Atom('Ni'), matter.Atom('Ni', (0.5,0.5,0.5))]
        struct = Structure(lattice=lattice, atoms=atoms, sgid=229)
 
        print 'original unitcell, cartesian coords'

src/m/a/matter-0.8-r960-20110308/matter/expansion/supercell_mod.py   matter(Download)
 
import numpy
from matter import Structure, Atom
 
 
 
    # create return instance
    newS = Structure(S)
    if mno == (1, 1, 1):
        return newS

src/m/a/matter-0.8-r960-20110308/tests/TestParsers.py   matter(Download)
import re
 
from matter import Structure, StructureFormatError
from matter import Lattice
from matter import Atom
    def setUp(self):
        self.stru = Structure()
        self.format = 'xyz'
        import tempfile
        handle, self.tmpname = tempfile.mkstemp()
        at3 = Atom('Al', [0.5, 0.0, 0.5])
        at4 = Atom('Al', [0.5, 0.5, 0.0])
        self.stru4 = Structure( [ at1, at2, at3, at4], 
                        lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
                        sgid = 225 )
    def setUp(self):
        self.stru = Structure()
        self.format = 'forces'
        import tempfile
        handle, self.tmpname = tempfile.mkstemp()
    def setUp(self):
        self.stru = Structure()
        self.format = "rawxyz"
 
    def test_read_plainxyz(self):

src/m/a/matter-0.8-r960-20110308/matter/Parsers/P_rawxyz.py   matter(Download)
import sys
 
from matter import Structure, Lattice, Atom
from matter import StructureFormatError
from matter.Parsers import StructureParser
        linefields = [l.split() for l in lines]
        # prepare output structure
        stru = Structure()
        # find first valid record
        start = 0

src/m/a/matter-0.8-r960-20110308/matter/expansion/makeEllipsoid.py   matter(Download)
from math import ceil
from numpy import array
from matter import Structure, Atom
from matter.expansion.shapeUtils import findCenter
 
    import os.path
    datadir = "../../tests/testdata"
    S = Structure()
    S.read(os.path.join(datadir, "CdSe_bulk.stru"), "pdffit")
    newS = makeEllipsoid(S, 12)
    newS.write("CdSe_d24.stru", "pdffit")
    newS = makeEllipsoid(S, 20, 10, 10)
    newS.write("CdSe_a20_b10_c10.stru", "pdffit")
    newS = makeEllipsoid(S, 20, 15, 10)

src/m/a/matter-0.8-r960-20110308/matter/Parsers/P_xcfg.py   matter(Download)
import numpy
 
from matter import Structure, Lattice, Atom
from matter import StructureFormatError
from matter.Parsers import StructureParser
        p_auxiliary = {}
        try:
            stru = Structure()
            # ignore trailing blank lines
            stop = len(lines)

src/m/a/matter-0.8-r960-20110308/matter/Parsers/P_pdb.py   matter(Download)
from numpy import pi
 
from matter import Structure, Lattice, Atom
from matter import StructureFormatError
from matter.Parsers import StructureParser
        """
        try:
            stru = Structure()
            scale = numpy.identity(3, dtype=float)
            scaleU = numpy.zeros(3, dtype=float)

src/m/a/matter-0.8-r960-20110308/matter/Parsers/P_cif.py   matter(Download)
import numpy
 
from matter import Structure, Lattice, Atom
from matter import StructureFormatError
from matter.Parsers import StructureParser
        if not block.has_key('_atom_site_label'):   return
        # here block contains structure, initialize output data
        self.stru = Structure()
        self.labelindex.clear()
        # execute specialized block parsers

src/m/a/matter-0.8-r960-20110308/tests/TestSuperCell.py   matter(Download)
testdata_dir = os.path.join(tests_dir, 'testdata')
 
from matter import Structure
from matter.Lattice import Lattice
from matter.Atom import  Atom
    def setUp(self):
        # load test structures once
        if TestSuperCell.stru_cdse is None:
            cdsefile = os.path.join(testdata_dir, "CdSe_bulk.stru")
            TestSuperCell.stru_cdse = Structure(filename=cdsefile)
        if TestSuperCell.stru_ni is None:
            nifile = os.path.join(testdata_dir, "Ni.stru")
            TestSuperCell.stru_ni = Structure(filename=nifile)
        at3 = Atom('Al', [0.5, 0.0, 0.5])
        at4 = Atom('Al', [0.5, 0.5, 0.0])
        self.stru4 = Structure( [ at1, at2, at3, at4], 
                               lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
                               sgid = 225 )
        at7 = Atom('I', [0.0, 0.5, 0.0])
        at8 = Atom('I', [0.5, 0.0, 0.0])
        naI = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8], 
                               lattice = Lattice(6.482, 6.482, 6.482, 90, 90, 90),
                               sgid = 225 )

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