Example #1
0
def test_velocity_traj():
    # Test Trajectory.get_velocity() against velocities output from CP2K. The
    # agreement is very good. Works only for fixed-cell MDs, however!
    dr = 'files/cp2k/md/nvt_print_low'
    base = os.path.dirname(dr) 
    fn = '%s/cp2k.out' %dr
    print common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr))
    tr = io.read_cp2k_md(fn)
    # read from data file
    v1 = tr.velocity.copy()
    # If tr.velocity != None, then get_velocity() doesn't calculate it. Then,
    # it simply returns tr.velocity, which is what we of course usually want.
    tr.velocity = None
    # calculate from coords + time step, b/c of central diffs, only steps 1:-1
    # are the same
    v2 = tr.get_velocity()
    print ">>>> np.abs(v1).max()", np.abs(v1).max()
    print ">>>> np.abs(v1).min()", np.abs(v1).min()
    print ">>>> np.abs(v2).max()", np.abs(v2).max()
    print ">>>> np.abs(v2).min()", np.abs(v2).min()
    print ">>>> np.abs(v1-v2).max()", np.abs(v1-v2).max()
    print ">>>> np.abs(v1-v2).min()", np.abs(v1-v2).min()
    assert np.allclose(v1[1:-1,...], v2[1:-1,...], atol=1e-4)
    
    ##from pwtools import mpl
    ##fig,ax = mpl.fig_ax()
    ##ax.plot(v1[1:-1,:,0], 'b')
    ##ax.plot(v2[1:-1,:,0], 'r')
    ##mpl.plt.show()
    
    shape = (100,10,3)
    arr = np.random.rand(*shape)
    assert crys.velocity_traj(arr, axis=0).shape == shape
    assert crys.velocity_traj(arr, axis=0, endpoints=False).shape == (98,10,3)
Example #2
0
def test_velocity_traj():
    # Test Trajectory.get_velocity() against velocities output from CP2K. The
    # agreement is very good. Works only for fixed-cell MDs, however!
    dr = 'files/cp2k/md/nvt_print_low'
    base = os.path.dirname(dr) 
    fn = '%s/cp2k.out' %dr
    print(common.backtick('tar -C {0} -xzf {1}.tgz'.format(base,dr)))
    tr = io.read_cp2k_md(fn)
    # read from data file
    v1 = tr.velocity.copy()
    # If tr.velocity != None, then get_velocity() doesn't calculate it. Then,
    # it simply returns tr.velocity, which is what we of course usually want.
    tr.velocity = None
    # calculate from coords + time step, b/c of central diffs, only steps 1:-1
    # are the same
    v2 = tr.get_velocity()
    print(">>>> np.abs(v1).max()", np.abs(v1).max())
    print(">>>> np.abs(v1).min()", np.abs(v1).min())
    print(">>>> np.abs(v2).max()", np.abs(v2).max())
    print(">>>> np.abs(v2).min()", np.abs(v2).min())
    print(">>>> np.abs(v1-v2).max()", np.abs(v1-v2).max())
    print(">>>> np.abs(v1-v2).min()", np.abs(v1-v2).min())
    assert np.allclose(v1[1:-1,...], v2[1:-1,...], atol=1e-4)
    
    ##from pwtools import mpl
    ##fig,ax = mpl.fig_ax()
    ##ax.plot(v1[1:-1,:,0], 'b')
    ##ax.plot(v2[1:-1,:,0], 'r')
    ##mpl.plt.show()
    
    shape = (100,10,3)
    arr = np.random.rand(*shape)
    assert crys.velocity_traj(arr, axis=0).shape == shape
    assert crys.velocity_traj(arr, axis=0, endpoints=False).shape == (98,10,3)
Example #3
0
def pdos(coords_arr_3d, axis=0):
    f, d = pd.direct_pdos(velocity_traj(coords_arr_3d, axis=axis))
    return d
Example #4
0
# Use most settings (nfreq, ...) from above. Create random array of x,y,z time
# traces for `natoms` atoms. Each x,y,z trajectory is a sum of sin's (`coords`
# in the 1d case).
natoms = 5
coords = np.empty((nstep, natoms, 3))
# `nfreq` frequencies for each x,y,z component of each atom
freqs = rand(natoms, 3, nfreq) * fmax
for i in range(natoms):
    for k in range(3):
        # vector w/ frequencies: freqs[i,k,:] <=> f_j, j=0, ..., nfreq-1
        # sum_j sin(2*pi*f_j*t)
        coords[:, i, k] = np.sin(2 * pi * freqs[i, k, :][:, None] *
                                 taxis).sum(axis=0)

##arr = coords
arr = crys.velocity_traj(coords)
massvec = rand(natoms)

# no mass weighting
M = None
f4, y4n = pydos.vacf_pdos(arr, dt=dt, m=M, mirr=True)
f5, y5n = pydos.direct_pdos(arr, dt=dt, m=M)

# with mass weighting
M = massvec
f6, y6nm = pydos.vacf_pdos(arr, dt=dt, m=M, mirr=True)
f7, y7nm = pydos.direct_pdos(arr, dt=dt, m=M)

if use_fourier:
    # For each atom, write an array (time.shape[0], 3) with coords at all time
    # steps, run fourier.x on that, sum up the power spectra. No mass
Example #5
0
def pdos(coords_arr_3d, axis=0):
    f, d = pd.direct_pdos(velocity_traj(coords_arr_3d, axis=axis))
    return d
Example #6
0
# Use most settings (nfreq, ...) from above. Create random array of x,y,z time
# traces for `natoms` atoms. Each x,y,z trajectory is a sum of sin's (`coords`
# in the 1d case).
natoms = 5
coords = np.empty((nstep, natoms, 3))
# `nfreq` frequencies for each x,y,z component of each atom
freqs = rand(natoms, 3, nfreq)*fmax
for i in range(natoms):
    for k in range(3):
        # vector w/ frequencies: freqs[i,k,:] <=> f_j, j=0, ..., nfreq-1
        # sum_j sin(2*pi*f_j*t)
        coords[:,i,k] = np.sin(2*pi*freqs[i,k,:][:,None]*taxis).sum(axis=0)

##arr = coords
arr = crys.velocity_traj(coords)
massvec = rand(natoms)

# no mass weighting
M = None
f4, y4n = pydos.vacf_pdos(arr, dt=dt, m=M, mirr=True)
f5, y5n = pydos.direct_pdos(arr, dt=dt, m=M)

# with mass weighting
M = massvec
f6, y6nm = pydos.vacf_pdos(arr, dt=dt, m=M, mirr=True)
f7, y7nm = pydos.direct_pdos(arr, dt=dt, m=M)

if use_fourier:
    # For each atom, write an array (time.shape[0], 3) with coords at all time
    # steps, run fourier.x on that, sum up the power spectra. No mass