def _calc_directors(self, active_dim):
"""Calculate directors as the reciprocal lattice vectors. For
orthorombic and triclinic simulation boxes the reciprocal
lattice vectors are vectors perpendicular to each face of the
simulation cell.
Parameters
----------
active_dim : list of int
Active dimensions each intereger must be either 0 for off or
1 for on.
Returns
-------
directors : numpy array(=<3,3)
Directors along which to calculate the wave vector.
"""
# Get triclinic box vectors
box_edge_vectors = mdamath.triclinic_vectors(self.universe.dimensions)
# Calculate reciprocal lattice vectors
recip_lat_vecs = self._calc_reciprocal_lattice_vectors(
box_edge_vectors)
# Remove inactive dimensions
check_active_dim = [active_dim_i is 0 for active_dim_i in active_dim]
del_idx_active_dim = [i for i, x in enumerate(check_active_dim) if x]
directors = np.delete(recip_lat_vecs, del_idx_active_dim, axis=0)
return directors
def initialize_bm(self, box):
"""
Store box information and define direct and reciprocal box matrices.
Rows of the direct matrix are the components of the central cell
vectors. Rows of the reciprocal matrix are the components of the
normalized reciprocal lattice vectors. Each row of the reciprocal
matrix represents the vector normal to the unit cell face
associated to each axis.
For instance, in an orthorhombic cell the YZ-plane is associated to
the X-axis and its normal vector is (1, 0, 0). In a triclinic cell,
the plane associated to vector ``\vec{a}`` is perpendicular to the
normalized cross product of ``\vec{b}`` and ``\vec{c}``.
Parameters
----------
box : array-like or ``None``, optional, default ``None``
Simulation cell dimensions in the form of
:attr:`MDAnalysis.trajectory.base.Timestep.dimensions` when
periodic boundary conditions should be taken into account for
the calculation of contacts.
"""
box_type = _box_check(box)
if box_type == 'ortho':
a, b, c = box[:3]
dm = np.array([[a, 0, 0], [0, b, 0], [0, 0, c]], dtype=np.float32)
rm = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype=np.float32)
elif box_type in 'tri_box tri_vecs tri_vecs_bad':
if box_type == 'tri_box':
dm = triclinic_vectors(box)
elif box_type == 'tri_vecs':
dm = box.copy('C')
else: # case 'tri_vecs_bad'
dm = triclinic_vectors(triclinic_box(box[0], box[1], box[2]))
rm = np.zeros(9, dtype=np.float32).reshape(3, 3)
rm[0] = np.cross(dm[1], dm[2])
rm[1] = np.cross(dm[2], dm[0])
rm[2] = np.cross(dm[0], dm[1])
for i in range(self.dim):
rm[i] /= norm(rm[i]) # normalize
else:
raise ValueError('Failed to initialize direct/reciprocal matrices')
self.box = box
self._dm = dm
self._rm = rm
def __init__(self, dims):
assert len(dims) == 3 or len(
dims) == 6, "Invalid number of box dimensions"
if len(dims) == 3:
dims = [*dims, 90., 90., 90]
self.dims = np.array(dims)
self.h = triclinic_vectors(dims)
self.hinv = np.linalg.inv(self.h)
boxtype, box = check_box(self.dimensions)
self.boxtype = boxtype
def _write_dimensions(self, dimensions):
"""Convert dimensions to triclinic vectors, convert lengths to native
units and then write the dimensions section
"""
if self.convert_units:
triv = self.convert_pos_to_native(mdamath.triclinic_vectors(
dimensions),inplace=False)
self.f.write('\n')
self.f.write('{:f} {:f} xlo xhi\n'.format(0., triv[0][0]))
self.f.write('{:f} {:f} ylo yhi\n'.format(0., triv[1][1]))
self.f.write('{:f} {:f} zlo zhi\n'.format(0., triv[2][2]))
if any([triv[1][0], triv[2][0], triv[2][1]]):
self.f.write('{xy:f} {xz:f} {yz:f} xy xz yz\n'.format(
xy=triv[1][0], xz=triv[2][0], yz=triv[2][1]))
self.f.write('\n')
def count_counterions(u, ion_group, counterion_group, pore_group, framestart, nframes_per_window):
count = 0
for i, frame in enumerate(u.trajectory[framestart : framestart + nframes_per_window]):
box_vectors = np.mat(triclinic_vectors(u.trajectory.dimensions))
box_inv = linalg.inv(box_vectors)
reference_atom = pore_group[0].position
z_start = reference_atom
z_end = reference_atom
z_start_atom = pore_group[0]
z_end_atom = pore_group[0]
for atom in pore_group[1:]:
next_atom_minimum_disp = minimum_image_disp(box_vectors, reference_atom - atom.position, box_inv)
next_atom_pos = reference_atom - next_atom_minimum_disp
if next_atom_pos[2] < z_start[2]:
z_start = next_atom_pos
z_start_aotm = atom
if next_atom_pos[2] > z_end[2]:
z_end = next_atom_pos
z_end_atom = atom
z_center_of_pore = (z_start + z_end) / 2 # these two atoms' positions are in the same periodic image
print_ion = False
for cion in counterion_group:
z_pos = reference_atom - minimum_image_disp(box_vectors, reference_atom - cion.position, box_inv)
if z_pos[2] > z_start[2] and z_pos[2] < z_end[2]:
count += 1
print_ion = True
if print_ion:
ion_minimum_image_disp = minimum_image_disp(box_vectors, ion_group[0].position - z_center_of_pore, box_inv)
print(ion_minimum_image_disp[2])
return count
def test_set_triclinic_vectors(self):
ref_vec = triclinic_vectors(self.newbox)
self.ts.triclinic_dimensions = ref_vec
assert_equal(self.ts.dimensions, self.newbox)
assert_allclose(self.ts._unitcell, self.unitcell)
def test_triclinic_vectors(self):
assert_allclose(self.ts.triclinic_dimensions,
triclinic_vectors(self.ts.dimensions))
def test_set_triclinic_vectors(self, ts):
ref_vec = triclinic_vectors(self.newbox)
ts.triclinic_dimensions = ref_vec
assert_equal(ts.dimensions, self.newbox)
assert_equal(ts._unitcell, self.unitcell)
def test_set_triclinic_vectors(self):
ref_vec = triclinic_vectors(self.newbox)
self.ts.triclinic_dimensions = ref_vec
assert_equal(self.ts.dimensions, self.newbox)
assert_allclose(self.ts._unitcell, self.unitcell)
def test_triclinic_vectors(self):
assert_allclose(self.ts.triclinic_dimensions,
triclinic_vectors(self.ts.dimensions))
# Displacement vector subtraction with Periodic Boundary Conditions
def vector(posA, posB, boxvec):
vec = posA - posB
for i in range(3):
dot = np.dot(vec, boxvec[i]) / np.dot(boxvec[i], boxvec[i])
if dot > .5:
vec -= boxvec[i]
elif dot < -.5:
vec += boxvec[i]
return vec
fout = open(folder + 'cationpi.dat', 'w')
for ts in u.trajectory:
sys.stdout.write('\rTime = %d' % u.trajectory.time)
boxvec = mdamath.triclinic_vectors(u.dimensions)
for ipi in range(npigroup):
pigroup = pigroups[ipi]
picenter = pigroup.centroid(pbc=True)
for icat in range(ncat):
cation = cations[icat]
dist = distances.calc_bonds(coords1=cation.position,
coords2=picenter,
box=u.dimensions)
if dist < 7.0:
vec = vector(cation.position, picenter, boxvec)
v1 = vector(pigroup.positions[0], pigroup.positions[5], boxvec)
v2 = vector(pigroup.positions[1], pigroup.positions[4], boxvec)
v3 = vector(pigroup.positions[2], pigroup.positions[3], boxvec)
n1 = mdamath.normal(v1, v2)
n2 = mdamath.normal(v3, v1)
import pytest
import numpy as np
from numpy.testing import assert_equal, assert_almost_equal
from MDAnalysis.lib.pkdtree import PeriodicKDTree
from MDAnalysis.lib.mdamath import triclinic_vectors, triclinic_box
from MDAnalysis.lib.distances import (_box_check, transform_RtoS,
transform_StoR, apply_PBC)
#
# Testing initialization with different boxes.
#
boxes_1 = (np.array([1, 2, 3, 90, 90, 90], dtype=np.float32), # ortho
np.array([1, 2, 3, 30, 45, 60], dtype=np.float32), # tri_box
triclinic_vectors( # tri_vecs
np.array([1, 2, 3, 90, 90, 45], dtype=np.float32)),
np.array([[0.5, 0.9, 1.9], # tri_vecs_bad
[2.0, 0.4, 0.1],
[0.0, 0.6, 0.5]], dtype=np.float32)
)
rec_m = (np.array([[1, 0, 0],
[0, 1, 0],
[0, 0, 1]], dtype=np.float32),
np.array([[0.67044002, -0.38707867, -0.6329931],
[0, 0.54741204, -0.83686334],
[0, 0, 1]], dtype=np.float32),
np.array([[0.707106829, -0.707106829, 0],
[0, 1, 0],
[0, 0, 1]], dtype=np.float32),
np.array([[0.42783618, -0.16049984, -0.88949198],
[-0, 0.95654362, 0.29158944],
def test_set_triclinic_vectors(self, ts):
ref_vec = triclinic_vectors(self.newbox)
ts.triclinic_dimensions = ref_vec
assert_equal(ts.dimensions, self.newbox)
assert_equal(ts._unitcell, self.unitcell)