Esempio n. 1
0
def test(xyz):
    a = rotate(xyz)
    ixyz = '%sx,%sy,%sz' % irotate(a)
    a2 = rotate(ixyz)
    print(xyz)
    print(ixyz)
    assert abs(a - a2).max() < 1e-10
Esempio n. 2
0
 def test(xyz):
     a = rotate(xyz)
     ixyz = '%sx,%sy,%sz' % irotate(a)
     a2 = rotate(ixyz)
     print(xyz)
     print(ixyz)
     assert abs(a - a2).max() < 1e-10
Esempio n. 3
0
def test(xyz):
    a = rotate(xyz)
    ixyz = '%sx,%sy,%sz' % irotate(a)
    a2 = rotate(ixyz)
    #print xyz
    #print ixyz
    #print np.around(a-a2, 5)
    assert abs(a-a2).max() < 1e-10
Esempio n. 4
0
File: rotate.py Progetto: lqcata/ase
def test(xyz):
    a = rotate(xyz)
    ixyz = '%sx,%sy,%sz' % irotate(a)
    a2 = rotate(ixyz)
    print xyz
    print ixyz
    #print np.around(a-a2, 5)
    assert abs(a - a2).max() < 1e-10
Esempio n. 5
0
File: view.py Progetto: btodac/ase
    def __init__(self, rotations):
        self.colormode = 'jmol'  # The default colors
        self.nselected = 0
        self.labels = None
        self.axes = rotate(rotations)
        self.configured = False
        self.frame = None

        # XXX
        self.colormode = 'jmol'
        self.colors = {}

        for i, rgb in enumerate(jmol_colors):
            self.colors[i] = ('#{0:02X}{1:02X}{2:02X}'.format(*(int(x * 255)
                                                                for x in rgb)))

        # scaling factors for vectors
        self.force_vector_scale = self.config['force_vector_scale']
        self.velocity_vector_scale = self.config['velocity_vector_scale']

        # buttons
        self.b1 = 1  # left
        self.b3 = 3  # right
        if self.config['swap_mouse']:
            self.b1 = 3
            self.b3 = 1
Esempio n. 6
0
 def __init__(self, rotations):
     self.colormode = 'jmol'  # The default colors
     self.nselected = 0
     self.labels = None
     self.axes = rotate(rotations)
     self.configured = False
     self.frame = None
Esempio n. 7
0
File: view.py Progetto: gjuhasz/ase
 def __init__(self, vbox, rotations):
     self.colormode = 'jmol'  # The default colors
     self.nselected = 0
     self.light_green_markings = 0
     self.axes = rotate(rotations)
     # this is a hack, in order to be able to toggle menu actions off/on
     # without getting into an infinte loop
     self.menu_change = 0
 
     self.atoms_to_rotate = None
     
     self.drawing_area = gtk.DrawingArea()
     self.drawing_area.set_size_request(450, 450)
     self.drawing_area.connect('button_press_event', self.press)
     self.drawing_area.connect('button_release_event', self.release)
     self.drawing_area.connect('motion-notify-event', self.move)
     # Signals used to handle backing pixmap:
     self.drawing_area.connect('expose_event', self.expose_event)
     self.drawing_area.connect('configure_event', self.configure_event)
     self.drawing_area.set_events(gtk.gdk.BUTTON_PRESS_MASK |
                                  gtk.gdk.BUTTON_RELEASE_MASK |
                                  gtk.gdk.BUTTON_MOTION_MASK |
                                  gtk.gdk.POINTER_MOTION_HINT_MASK)
     vbox.pack_start(self.drawing_area)
     self.drawing_area.show()
     self.configured = False
     self.frame = None
Esempio n. 8
0
    def __init__(self, vbox, rotations):
        self.colormode = 'jmol'  # The default colors
        self.nselected = 0
        self.light_green_markings = 0
        self.axes = rotate(rotations)
        # this is a hack, in order to be able to toggle menu actions off/on
        # without getting into an infinte loop
        self.menu_change = 0

        self.atoms_to_rotate = None

        self.drawing_area = gtk.DrawingArea()
        self.drawing_area.set_size_request(450, 450)
        self.drawing_area.connect('button_press_event', self.press)
        self.drawing_area.connect('button_release_event', self.release)
        self.drawing_area.connect('motion-notify-event', self.move)
        # Signals used to handle backing pixmap:
        self.drawing_area.connect('expose_event', self.expose_event)
        self.drawing_area.connect('configure_event', self.configure_event)
        self.drawing_area.set_events(gtk.gdk.BUTTON_PRESS_MASK
                                     | gtk.gdk.BUTTON_RELEASE_MASK
                                     | gtk.gdk.BUTTON_MOTION_MASK
                                     | gtk.gdk.POINTER_MOTION_HINT_MASK)
        vbox.pack_start(self.drawing_area)
        self.drawing_area.show()
        self.configured = False
        self.config = None
        self.frame = None
Esempio n. 9
0
    def __init__(self, rotations):
        self.colormode = 'jmol'  # The default colors
        self.nselected = 0
        self.labels = None
        self.axes = rotate(rotations)
        self.configured = False
        self.frame = None

        # XXX
        self.colormode = 'jmol'
        self.colors = {}

        for i, rgb in enumerate(jmol_colors):
            self.colors[i] = ('#{0:02X}{1:02X}{2:02X}'.format(*(int(x * 255)
                                                                for x in rgb)))
Esempio n. 10
0
    def __init__(self, rotations):
        self.colormode = 'jmol'  # The default colors
        self.nselected = 0
        self.labels = None
        self.axes = rotate(rotations)
        self.configured = False
        self.frame = None

        # XXX
        self.colormode = 'jmol'
        self.colors = {}

        for i, rgb in enumerate(jmol_colors):
            self.colors[i] = ('#{0:02X}{1:02X}{2:02X}'
                              .format(*(int(x * 255) for x in rgb)))
Esempio n. 11
0
    def calculate_plotting_offset(self, rotation, scale, maxwidth):
        # from ase.visualize.plot and ase.io.utils
        R = np.dot(self.atoms.get_positions(), rotate(rotation))
        radii = covalent_radii[self.atoms.numbers]

        X1 = (R - radii[:, None]).min(0)
        X2 = (R + radii[:, None]).max(0)
        if show_unit_cell == 2:
            X1 = np.minimum(X1, cell_vertices.min(0))
            X2 = np.maximum(X2, cell_vertices.max(0))
        M = (X1 + X2) / 2
        S = 1.05 * (X2 - X1)
        w = scale * S[0]
        if w > maxwidth:
            w = maxwidth
            scale = w / S[0]
        h = scale * S[1]
        offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])

        return offset
Esempio n. 12
0
 def __init__(self, vbox, rotations):
     self.colors = [None] * (len(jmol_colors) + 1)
     self.nselected = 0
     self.rotation = rotate(rotations)
     
     self.drawing_area = gtk.DrawingArea()
     self.drawing_area.set_size_request(450, 450)
     self.drawing_area.connect('button_press_event', self.press)
     self.drawing_area.connect('button_release_event', self.release)
     self.drawing_area.connect('motion-notify-event', self.move)
     # Signals used to handle backing pixmap:
     self.drawing_area.connect('expose_event', self.expose_event)
     self.drawing_area.connect('configure_event', self.configure_event)
     self.drawing_area.set_events(gtk.gdk.BUTTON_PRESS_MASK |
                                  gtk.gdk.BUTTON_RELEASE_MASK |
                                  gtk.gdk.BUTTON_MOTION_MASK |
                                  gtk.gdk.POINTER_MOTION_HINT_MASK)
     vbox.pack_start(self.drawing_area)
     self.drawing_area.show()
     self.configured = False
     self.frame = None
Esempio n. 13
0
    def set_view(self, menuitem):
        plane_rotation = menuitem.get_name()

        if plane_rotation == 'xyPlane':
            self.axes = rotate('0.0x,0.0y,0.0z')
        elif plane_rotation == 'yzPlane':
            self.axes = rotate('-90.0x,-90.0y,0.0z')
        elif plane_rotation == 'zxPlane':
            self.axes = rotate('90.0x,0.0y,90.0z')
        elif plane_rotation == 'yxPlane':
            self.axes = rotate('180.0x,0.0y,90.0z')
        elif plane_rotation == 'zyPlane':
            self.axes = rotate('0.0x,90.0y,0.0z')
        elif plane_rotation == 'xzPlane':
            self.axes = rotate('-90.0x,0.0y,0.0z')
        else:
            if plane_rotation == 'a1a2Plane':
                i, j = 0, 1
            elif plane_rotation == 'a2a3Plane':
                i, j = 1, 2
            elif plane_rotation == 'a3a1Plane':
                i, j = 2, 0
            elif plane_rotation == 'a2a1Plane':
                i, j = 1, 0
            elif plane_rotation == 'a3a2Plane':
                i, j = 2, 1
            elif plane_rotation == 'a1a3Plane':
                i, j = 0, 2

            x1 = self.images.A[self.frame, i]
            x2 = self.images.A[self.frame, j]

            norm = np.linalg.norm

            x1 = x1 / norm(x1)
            x2 = x2 - x1 * np.dot(x1, x2)
            x2 /= norm(x2)
            x3 = np.cross(x1, x2)

            self.axes = np.array([x1, x2, x3]).T

        self.set_coordinates()
Esempio n. 14
0
    def set_view(self, menuitem):
        plane_rotation = menuitem.get_name()

        if plane_rotation == 'xyPlane':
            self.axes = rotate('0.0x,0.0y,0.0z')
        elif plane_rotation == 'yzPlane':
            self.axes = rotate('-90.0x,-90.0y,0.0z')
        elif plane_rotation == 'zxPlane':
            self.axes = rotate('90.0x,0.0y,90.0z')
        elif plane_rotation == 'yxPlane':
            self.axes = rotate('180.0x,0.0y,90.0z')
        elif plane_rotation == 'zyPlane':
            self.axes = rotate('0.0x,90.0y,0.0z')
        elif plane_rotation == 'xzPlane':
            self.axes = rotate('-90.0x,0.0y,0.0z')
        else:
            if plane_rotation == 'a1a2Plane':
                i, j = 0, 1
            elif plane_rotation == 'a2a3Plane':
                i, j = 1, 2
            elif plane_rotation == 'a3a1Plane':
                i, j = 2, 0
            elif plane_rotation == 'a2a1Plane':
                i, j = 1, 0
            elif plane_rotation == 'a3a2Plane':
                i, j = 2, 1
            elif plane_rotation == 'a1a3Plane':
                i, j = 0, 2

            x1 = self.images.A[self.frame, i]
            x2 = self.images.A[self.frame, j]

            norm = np.linalg.norm

            x1 = x1 / norm(x1)
            x2 = x2 - x1 * np.dot(x1, x2)
            x2 /= norm(x2)
            x3 = np.cross(x1, x2)

            self.axes = np.array([x1, x2, x3]).T

        self.set_coordinates()
Esempio n. 15
0
    def set_view(self, key):
        if key == 'Z':
            self.axes = rotate('0.0x,0.0y,0.0z')
        elif key == 'X':
            self.axes = rotate('-90.0x,-90.0y,0.0z')
        elif key == 'Y':
            self.axes = rotate('90.0x,0.0y,90.0z')
        elif key == 'Alt+Z':
            self.axes = rotate('180.0x,0.0y,90.0z')
        elif key == 'Alt+X':
            self.axes = rotate('0.0x,90.0y,0.0z')
        elif key == 'Alt+Y':
            self.axes = rotate('-90.0x,0.0y,0.0z')
        else:
            if key == '3':
                i, j = 0, 1
            elif key == '1':
                i, j = 1, 2
            elif key == '2':
                i, j = 2, 0
            elif key == 'Alt+3':
                i, j = 1, 0
            elif key == 'Alt+1':
                i, j = 2, 1
            elif key == 'Alt+2':
                i, j = 0, 2

            A = complete_cell(self.atoms.cell)
            x1 = A[i]
            x2 = A[j]

            norm = np.linalg.norm

            x1 = x1 / norm(x1)
            x2 = x2 - x1 * np.dot(x1, x2)
            x2 /= norm(x2)
            x3 = np.cross(x1, x2)

            self.axes = np.array([x1, x2, x3]).T

        self.set_frame()
Esempio n. 16
0
File: view.py Progetto: btodac/ase
    def set_view(self, key):
        if key == 'Z':
            self.axes = rotate('0.0x,0.0y,0.0z')
        elif key == 'X':
            self.axes = rotate('-90.0x,-90.0y,0.0z')
        elif key == 'Y':
            self.axes = rotate('90.0x,0.0y,90.0z')
        elif key == 'Alt+Z':
            self.axes = rotate('180.0x,0.0y,90.0z')
        elif key == 'Alt+X':
            self.axes = rotate('0.0x,90.0y,0.0z')
        elif key == 'Alt+Y':
            self.axes = rotate('-90.0x,0.0y,0.0z')
        else:
            if key == '3':
                i, j = 0, 1
            elif key == '1':
                i, j = 1, 2
            elif key == '2':
                i, j = 2, 0
            elif key == 'Alt+3':
                i, j = 1, 0
            elif key == 'Alt+1':
                i, j = 2, 1
            elif key == 'Alt+2':
                i, j = 0, 2

            A = complete_cell(self.atoms.cell)
            x1 = A[i]
            x2 = A[j]

            norm = np.linalg.norm

            x1 = x1 / norm(x1)
            x2 = x2 - x1 * np.dot(x1, x2)
            x2 /= norm(x2)
            x3 = np.cross(x1, x2)

            self.axes = np.array([x1, x2, x3]).T

        self.set_frame()
Esempio n. 17
0
    def __init__(self, atoms, rotation='', show_unit_cell=2,
                              radii=None, bbox=None, colors=None, scale=20,
                              maxwidth=500, extra_offset=(0., 0.)):
        self.numbers = atoms.get_atomic_numbers()
        self.colors = colors
        if colors is None:
            self.colors = jmol_colors[self.numbers]

        if radii is None:
            radii = covalent_radii[self.numbers]
        elif isinstance(radii, float):
            radii = covalent_radii[self.numbers] * radii
        else:
            radii = np.array(radii)

        natoms = len(atoms)

        if isinstance(rotation, basestring):
            rotation = rotate(rotation)

        cell = atoms.get_cell()
        disp = atoms.get_celldisp().flatten()

        if show_unit_cell > 0:
            L, T, D = cell_to_lines(self, cell)
            cell_vertices = np.empty((2, 2, 2, 3))
            for c1 in range(2):
                for c2 in range(2):
                    for c3 in range(2):
                        cell_vertices[c1, c2, c3] = np.dot([c1, c2, c3],
                                                           cell) + disp
            cell_vertices.shape = (8, 3)
            cell_vertices = np.dot(cell_vertices, rotation)
        else:
            L = np.empty((0, 3))
            T = None
            D = None
            cell_vertices = None

        nlines = len(L)

        positions = np.empty((natoms + nlines, 3))
        R = atoms.get_positions()
        positions[:natoms] = R
        positions[natoms:] = L

        r2 = radii**2
        for n in range(nlines):
            d = D[T[n]]
            if ((((R - L[n] - d)**2).sum(1) < r2) &
                (((R - L[n] + d)**2).sum(1) < r2)).any():
                T[n] = -1

        positions = np.dot(positions, rotation)
        R = positions[:natoms]

        if bbox is None:
            X1 = (R - radii[:, None]).min(0)
            X2 = (R + radii[:, None]).max(0)
            if show_unit_cell == 2:
                X1 = np.minimum(X1, cell_vertices.min(0))
                X2 = np.maximum(X2, cell_vertices.max(0))
            M = (X1 + X2) / 2
            S = 1.05 * (X2 - X1)
            w = scale * S[0]
            if w > maxwidth:
                w = maxwidth
                scale = w / S[0]
            h = scale * S[1]
            offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
        else:
            w = (bbox[2] - bbox[0]) * scale
            h = (bbox[3] - bbox[1]) * scale
            offset = np.array([bbox[0], bbox[1], 0]) * scale

        offset[0] = offset[0] - extra_offset[0]
        offset[1] = offset[1] - extra_offset[1]
        self.w = w + extra_offset[0]
        self.h = h + extra_offset[1]

        positions *= scale
        positions -= offset

        if nlines > 0:
            D = np.dot(D, rotation)[:, :2] * scale

        if cell_vertices is not None:
            cell_vertices *= scale
            cell_vertices -= offset

        cell = np.dot(cell, rotation)
        cell *= scale

        self.cell = cell
        self.positions = positions
        self.D = D
        self.T = T
        self.cell_vertices = cell_vertices
        self.natoms = natoms
        self.d = 2 * scale * radii

        # extension for partial occupancies
        self.frac_occ = False
        self.tags = None
        self.occs = None

        try:
            self.occs = atoms.info['occupancy']
            self.tags = atoms.get_tags()
            self.frac_occ = True
        except KeyError:
            pass
Esempio n. 18
0
 def change(self, adjustment):
     if self.update:
         x, y, z = [float(a.value) for a in self.rotate]
         self.gui.axes = rotate('%fx,%fy,%fz' % (x, y, z))
         self.gui.set_coordinates()
     return True
Esempio n. 19
0
    def __init__(self, atoms,
                 rotation='', show_unit_cell=False, radii=None,
                 bbox=None, colors=None, scale=20):
        self.numbers = atoms.get_atomic_numbers()
        self.colors = colors
        if colors is None:
            self.colors = jmol_colors[self.numbers]

        if radii is None:
            radii = covalent_radii[self.numbers]
        elif type(radii) is float:
            radii = covalent_radii[self.numbers] * radii
        else:
            radii = np.array(radii)

        natoms = len(atoms)

        if isinstance(rotation, str):
            rotation = rotate(rotation)

        A = atoms.get_cell()
        if show_unit_cell > 0:
            L, T, D = self.cell_to_lines(A)
            C = np.empty((2, 2, 2, 3))
            for c1 in range(2):
                for c2 in range(2):
                    for c3 in range(2):
                        C[c1, c2, c3] = np.dot([c1, c2, c3], A)
            C.shape = (8, 3)
            C = np.dot(C, rotation)  # Unit cell vertices
        else:
            L = np.empty((0, 3))
            T = None
            D = None
            C = None

        nlines = len(L)

        X = np.empty((natoms + nlines, 3))
        R = atoms.get_positions()
        X[:natoms] = R
        X[natoms:] = L

        r2 = radii**2
        for n in range(nlines):
            d = D[T[n]]
            if ((((R - L[n] - d)**2).sum(1) < r2) &
                (((R - L[n] + d)**2).sum(1) < r2)).any():
                T[n] = -1

        X = np.dot(X, rotation)
        R = X[:natoms]

        if bbox is None:
            X1 = (R - radii[:, None]).min(0)
            X2 = (R + radii[:, None]).max(0)
            if show_unit_cell == 2:
                X1 = np.minimum(X1, C.min(0))
                X2 = np.maximum(X2, C.max(0))
            M = (X1 + X2) / 2
            S = 1.05 * (X2 - X1)
            w = scale * S[0]
            if w > 500:
                w = 500
                scale = w / S[0]
            h = scale * S[1]
            offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
        else:
            w = (bbox[2] - bbox[0]) * scale
            h = (bbox[3] - bbox[1]) * scale
            offset = np.array([bbox[0], bbox[1], 0]) * scale

        self.w = w
        self.h = h

        X *= scale
        X -= offset

        if nlines > 0:
            D = np.dot(D, rotation)[:, :2] * scale

        if C is not None:
            C *= scale
            C -= offset

        A = np.dot(A, rotation)
        A *= scale

        self.A = A
        self.X = X
        self.D = D
        self.T = T
        self.C = C
        self.natoms = natoms
        self.d = 2 * scale * radii
Esempio n. 20
0
 def reset_view(self, menuitem):
     self.axes = rotate('0.0x,0.0y,0.0z')
     self.set_coordinates()
     self.focus(self)
Esempio n. 21
0
 def change(self):
     x, y, z = [float(a.value) for a in self.rotate]
     self.gui.axes = rotate('%fx,%fy,%fz' % (x, y, z))
     self.gui.set_frame()
Esempio n. 22
0
File: view.py Progetto: gjuhasz/ase
 def reset_view(self, menuitem):
     self.axes = rotate('0.0x,0.0y,0.0z')
     self.set_coordinates()
     self.focus(self)
Esempio n. 23
0
 def change(self, adjustment):
     if self.update:
         x, y, z = [float(a.value) for a in self.rotate]
         self.gui.axes = rotate('%fx,%fy,%fz' % (x, y, z))
         self.gui.set_coordinates()
     return True
Esempio n. 24
0
def generate_writer_variables(writer,
                              atoms,
                              rotation='',
                              show_unit_cell=0,
                              radii=None,
                              bbox=None,
                              colors=None,
                              scale=20,
                              maxwidth=500,
                              extra_offset=(0., 0.)):
    writer.numbers = atoms.get_atomic_numbers()
    writer.colors = colors
    if colors is None:
        writer.colors = jmol_colors[writer.numbers]

    if radii is None:
        radii = covalent_radii[writer.numbers]
    elif isinstance(radii, float):
        radii = covalent_radii[writer.numbers] * radii
    else:
        radii = np.array(radii)

    natoms = len(atoms)

    if isinstance(rotation, basestring):
        rotation = rotate(rotation)

    cell = atoms.get_cell()
    disp = atoms.get_celldisp().flatten()

    if show_unit_cell > 0:
        L, T, D = cell_to_lines(writer, cell)
        cell_vertices = np.empty((2, 2, 2, 3))
        for c1 in range(2):
            for c2 in range(2):
                for c3 in range(2):
                    cell_vertices[c1, c2,
                                  c3] = np.dot([c1, c2, c3], cell) + disp
        cell_vertices.shape = (8, 3)
        cell_vertices = np.dot(cell_vertices, rotation)
    else:
        L = np.empty((0, 3))
        T = None
        D = None
        cell_vertices = None

    nlines = len(L)

    positions = np.empty((natoms + nlines, 3))
    R = atoms.get_positions()
    positions[:natoms] = R
    positions[natoms:] = L

    r2 = radii**2
    for n in range(nlines):
        d = D[T[n]]
        if ((((R - L[n] - d)**2).sum(1) < r2) &
            (((R - L[n] + d)**2).sum(1) < r2)).any():
            T[n] = -1

    positions = np.dot(positions, rotation)
    R = positions[:natoms]

    if bbox is None:
        X1 = (R - radii[:, None]).min(0)
        X2 = (R + radii[:, None]).max(0)
        if show_unit_cell == 2:
            X1 = np.minimum(X1, cell_vertices.min(0))
            X2 = np.maximum(X2, cell_vertices.max(0))
        M = (X1 + X2) / 2
        S = 1.05 * (X2 - X1)
        w = scale * S[0]
        if w > maxwidth:
            w = maxwidth
            scale = w / S[0]
        h = scale * S[1]
        offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
    else:
        w = (bbox[2] - bbox[0]) * scale
        h = (bbox[3] - bbox[1]) * scale
        offset = np.array([bbox[0], bbox[1], 0]) * scale

    offset[0] = offset[0] - extra_offset[0]
    offset[1] = offset[1] - extra_offset[1]
    writer.w = w + extra_offset[0]
    writer.h = h + extra_offset[1]

    positions *= scale
    positions -= offset

    if nlines > 0:
        D = np.dot(D, rotation)[:, :2] * scale

    if cell_vertices is not None:
        cell_vertices *= scale
        cell_vertices -= offset

    cell = np.dot(cell, rotation)
    cell *= scale

    writer.cell = cell
    writer.positions = positions
    writer.D = D
    writer.T = T
    writer.cell_vertices = cell_vertices
    writer.natoms = natoms
    writer.d = 2 * scale * radii
Esempio n. 25
0
 def change(self):
     x, y, z = [float(a.value) for a in self.rotate]
     self.gui.axes = rotate('%fx,%fy,%fz' % (x, y, z))
     self.gui.set_frame()
Esempio n. 26
0
 def reset_view(self, menuitem):
     self.axes = rotate('0.0x,0.0y,0.0z')
     self.set_frame()
     self.focus(self)
Esempio n. 27
0
File: view.py Progetto: btodac/ase
 def reset_view(self, menuitem):
     self.axes = rotate('0.0x,0.0y,0.0z')
     self.set_frame()
     self.focus(self)