Esempio n. 1
0
def read_dynmat(path='.', natoms=None, filename='dynmat.out', axsf='dynmat.axsf'):
    """Read ``dynmat.x`` output.

    `freqs` are parsed from `filename` and `vecs` from `axsf`. `qpoints` is
    alawys Gamma, i.e. [0,0,0].     

    Output format is the same as in :func:`read_dyn`.

    Parameters
    ----------
    path : str
        path where output files are
    natoms : int
    filename : str
        Text output from dynmat.x, where the frequencies are printed, relative
        to `path`.
    axsf : str
        AXSF file (``filxsf`` in input) with mode vectors as forces.
    
    Returns
    -------
    qpoints, freqs, vecs
    qpoints : 1d array (3,)
        The qpoint, which is Gamma, i.e. [0,0,0]
    freqs : 1d array, (nmodes,) where nmodes = 3*natoms
        3*natoms phonon frequencies in [cm^-1] at the q-point.
    vecs : 3d real array (nmodes, natoms, 3)
        Real parts (???) if the eigenvectors of the dynamical matrix for the
        q-point.
    
    Notes
    -----
    We assume the output to be generated with ``dynmat.x < dynmat.in >
    dynmat.out``. 
    """
    assert natoms is not None, ("natoms is None")
    nmodes = 3*natoms
    out_fn = pj(path, filename)
    axsf_fn = pj(path, axsf)
    cmd = "grep -A{0} PRIMCO {1} | sed -re '/PRIMCO.*/{{N;d;}}' | \
            awk '{{print $5\" \"$6\" \"$7}}'".format(natoms+1, axsf_fn)
    qpoints = np.zeros((3,))
    vecs = np.fromstring(common.backtick(cmd), sep=' ').reshape(nmodes,natoms,3)
    cmd = "grep -A{0} 'mode.*cm-1' {1} | grep -v mode | \
           awk '{{print $2}}'".format(nmodes, out_fn)
    freqs = np.fromstring(common.backtick(cmd), sep=' ')
    return qpoints,freqs,vecs
Esempio n. 2
0
def read_dynmat(path='.', natoms=None, filename='dynmat.out', axsf='dynmat.axsf'):
    """Read ``dynmat.x`` output.

    `freqs` are parsed from `filename` and `vecs` from `axsf`. `qpoints` is
    alawys Gamma, i.e. [0,0,0].     

    Output format is the same as in :func:`read_dyn`.

    Parameters
    ----------
    path : str
        path where output files are
    natoms : int
    filename : str
        Text output from dynmat.x, where the frequencies are printed, relative
        to `path`.
    axsf : str
        AXSF file (``filxsf`` in input) with mode vectors as forces.
    
    Returns
    -------
    qpoints, freqs, vecs
    qpoints : 1d array (3,)
        The qpoint, which is Gamma, i.e. [0,0,0]
    freqs : 1d array, (nmodes,) where nmodes = 3*natoms
        3*natoms phonon frequencies in [cm^-1] at the q-point.
    vecs : 3d real array (nmodes, natoms, 3)
        Real parts (???) if the eigenvectors of the dynamical matrix for the
        q-point.
    
    Notes
    -----
    We assume the output to be generated with ``dynmat.x < dynmat.in >
    dynmat.out``. 
    """
    assert natoms is not None, ("natoms is None")
    nmodes = 3*natoms
    out_fn = pj(path, filename)
    axsf_fn = pj(path, axsf)
    cmd = "grep -A{0} PRIMCO {1} | sed -re '/PRIMCO.*/{{N;d;}}' | \
            awk '{{print $5\" \"$6\" \"$7}}'".format(natoms+1, axsf_fn)
    qpoints = np.zeros((3,))
    vecs = np.fromstring(common.backtick(cmd), sep=' ').reshape(nmodes,natoms,3)
    cmd = "grep -A{0} 'mode.*cm-1' {1} | grep -v mode | \
           awk '{{print $2}}'".format(nmodes, out_fn)
    freqs = np.fromstring(common.backtick(cmd), sep=' ')
    return qpoints,freqs,vecs
Esempio n. 3
0
def test_write_lammps():
    st = crys.Structure(coords_frac=rand(20, 3),
                        cell=rand(3, 3),
                        symbols=['Al'] * 10 + ['N'] * 10)
    # align cell to lammps standard [[x,0,0],...]
    st.coords = None
    st.cell = None
    st.set_all()
    st_fn = common.pj(testdir, 'lmp.struct')
    io.write_lammps(st_fn, st)
    symbols = common.file_read(st_fn + '.symbols').split()
    assert st.symbols == symbols
    cmd = r"grep -A22 Atoms %s | grep '^[0-9]'" % st_fn
    arr = parse.arr2d_from_txt(common.backtick(cmd))
    assert arr.shape == (20, 5)
    assert np.allclose(st.coords, arr[:, 2:])
Esempio n. 4
0
def test_write_lammps():
    st = crys.Structure(coords_frac=rand(20,3),
                        cell=rand(3,3),
                        symbols=['Al']*10+['N']*10)
    # align cell to lammps standard [[x,0,0],...]
    st.coords = None  
    st.cell = None
    st.set_all()
    st_fn = common.pj(testdir, 'lmp.struct')
    io.write_lammps(st_fn, st)
    symbols = common.file_read(st_fn + '.symbols').split()
    assert st.symbols == symbols
    cmd = r"grep -A22 Atoms %s | grep '^[0-9]'" %st_fn
    arr = parse.arr2d_from_txt(common.backtick(cmd))
    assert arr.shape == (20,5)
    assert np.allclose(st.coords, arr[:,2:])
Esempio n. 5
0
def test_dcd():
    # nstep = 101
    # natoms = 16
    dir_lmp = tools.unpack_compressed('files/lammps/md-npt.tgz')
    fn_lmp = pj(dir_lmp, 'lmp.out.dcd')

    # nstep = 16
    # natoms = 57
    dir_cp2k = tools.unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
    fn_cp2k = pj(dir_cp2k, 'PROJECT-pos-1.dcd')

    # read headers
    hdr_lmp = dcd.read_dcd_header(fn_lmp)
    hdr_cp2k = dcd.read_dcd_header(fn_cp2k)

    print(">>> comparing headers")
    for ref, dct in [(hdr_cp2k_ref, hdr_cp2k), (hdr_lmp_ref, hdr_lmp)]:
        tools.assert_dict_with_all_types_equal(ref,
                                               dct,
                                               keys=list(ref.keys()),
                                               strict=True)

    # compare data read by python (dcd.py) and fortran (dcd.f90, _dcd)
    # implementations
    # cc = cryst_const
    # co = coords
    print(">>> comparing data")
    for fn, convang, nstephdr, nstep, natoms in [
        (fn_lmp, True, True, 101, 16), (fn_lmp, True, False, 101, 16),
        (fn_cp2k, False, False, 16, 57)
    ]:
        cc_py, co_py = dcd.read_dcd_data(fn, convang=convang)
        cc_f, co_f = dcd.read_dcd_data_f(fn,
                                         convang=convang,
                                         nstephdr=nstephdr)
        print(">>> ... cryst_const")
        tools.assert_array_equal(cc_py, cc_f)
        print(">>> ... coords")
        tools.assert_array_equal(co_py, co_f)
        print(">>> ... shapes")
        assert cc_f.shape == (nstep, 6)
        assert co_f.shape == (nstep, natoms, 3)
        # lmp angles are around 60, cp2k around 90 degree, cosines are between
        # -1 and 1, make sure the angle conversion works
        print(">>> ... angles")
        assert (cc_py[:, 3:] > 50).all()

    # compare slow and fast python versions
    # cc = cryst_const
    # co = coords
    print(">>> comparing data")
    for fn, convang, nstep, natoms in [(fn_lmp, True, 101, 16),
                                       (fn_lmp, True, 101, 16),
                                       (fn_cp2k, False, 16, 57)]:
        cc_py_fast, co_py_fast = dcd.read_dcd_data(fn, convang=convang)
        cc_py_ref, co_py_ref = dcd.read_dcd_data_ref(fn, convang=convang)
        print(">>> ... cryst_const")
        tools.assert_array_equal(cc_py_fast, cc_py_ref)
        print(">>> ... coords")
        tools.assert_array_equal(co_py_fast, co_py_ref)
        print(">>> ... shapes")
        assert cc_py_ref.shape == (nstep, 6)
        assert co_py_ref.shape == (nstep, natoms, 3)
        # lmp angles are around 60, cp2k around 90 degree, cosines are between
        # -1 and 1, make sure the angle conversion works
        print(">>> ... angles")
        assert (cc_py_fast[:, 3:] > 50).all()
Esempio n. 6
0
def test_dcd():
    # nstep = 101
    # natoms = 16
    dir_lmp = tools.unpack_compressed('files/lammps/md-npt.tgz')
    fn_lmp = pj(dir_lmp, 'lmp.out.dcd') 

    # nstep = 16
    # natoms = 57
    dir_cp2k = tools.unpack_compressed('files/cp2k/dcd/npt_dcd.tgz')
    fn_cp2k = pj(dir_cp2k, 'PROJECT-pos-1.dcd')
    
    # read headers
    hdr_lmp = dcd.read_dcd_header(fn_lmp)
    hdr_cp2k = dcd.read_dcd_header(fn_cp2k)
    
    print ">>> comparing headers"
    for ref, dct in [(hdr_cp2k_ref, hdr_cp2k), (hdr_lmp_ref, hdr_lmp)]:
        tools.assert_dict_with_all_types_equal(ref, dct, keys=ref.keys(),
                                               strict=True)
    
    # compare data read by python (dcd.py) and fortran (dcd.f90, _dcd)
    # implementations
    # cc = cryst_const
    # co = coords
    print ">>> comparing data"
    for fn,convang,nstephdr,nstep,natoms in [(fn_lmp,True,True,101,16), 
                                             (fn_lmp,True,False,101,16),
                                             (fn_cp2k,False,False,16,57)]:
        cc_py, co_py = dcd.read_dcd_data(fn, convang=convang)
        cc_f, co_f = dcd.read_dcd_data_f(fn, convang=convang, nstephdr=nstephdr)
        print ">>> ... cryst_const"
        tools.assert_array_equal(cc_py, cc_f)
        print ">>> ... coords"
        tools.assert_array_equal(co_py, co_f)
        print ">>> ... shapes"
        assert cc_f.shape == (nstep,6)
        assert co_f.shape == (nstep,natoms,3)
        # lmp angles are around 60, cp2k around 90 degree, cosines are between
        # -1 and 1, make sure the angle conversion works
        print ">>> ... angles"
        assert (cc_py[:,3:] > 50).all()

    # compare slow and fast python versions
    # cc = cryst_const
    # co = coords
    print ">>> comparing data"
    for fn,convang,nstep,natoms in [(fn_lmp,True,101,16), 
                                    (fn_lmp,True,101,16),
                                    (fn_cp2k,False,16,57)]:
        cc_py_fast, co_py_fast = dcd.read_dcd_data(fn, convang=convang)
        cc_py_ref, co_py_ref = dcd.read_dcd_data_ref(fn, convang=convang)
        print ">>> ... cryst_const"
        tools.assert_array_equal(cc_py_fast, cc_py_ref)
        print ">>> ... coords"
        tools.assert_array_equal(co_py_fast, co_py_ref)
        print ">>> ... shapes"
        assert cc_py_ref.shape == (nstep,6)
        assert co_py_ref.shape == (nstep,natoms,3)
        # lmp angles are around 60, cp2k around 90 degree, cosines are between
        # -1 and 1, make sure the angle conversion works
        print ">>> ... angles"
        assert (cc_py_fast[:,3:] > 50).all()