def mouseReleaseEvent(self, event):
button = event.button()
self.setCursor(Qt.arrowCursor)
if button == Qt.LeftButton:
try:
dx = event.x() - self.click1x
dy = event.y() - self.click1y
except AttributeError:
return
if dx != 0 or dy != 0:
normal = Vector(self.axis)
move = Vector(-dx*self.plane[:,0]+dy*self.plane[:,1])
axis = normal.cross(move) / \
N.minimum.reduce(N.fabs(self.plotbox_size))
rot = Rotation(axis.normal(), axis.length())
self.axis = rot(normal).array
self.plane[:,0] = rot(Vector(self.plane[:,0])).array
self.plane[:,1] = rot(Vector(self.plane[:,1])).array
elif button == Qt.MidButton:
try:
dx = event.x() - self.click2x
dy = event.y() - self.click2y
except AttributeError:
return
if dx != 0 or dy != 0:
self.translate = self.translate + N.array([dx, dy])
else:
try:
dy = event.y() - self.click3y
except AttributeError:
return
if dy != 0:
ratio = -dy/self.plotbox_size[1]
self.scale = self.scale * (1.+ratio)
self.update()
def evaluationPoints(object, n, smallest=0.3, largest=0.5):
"""Returns a list of |n| points suitable for the evaluation of
the electrostatic potential around |object|. The points are chosen
at random and uniformly in a shell around the object such that
no point has a distance larger than |largest| from any atom or
smaller than |smallest| from any non-hydrogen atom.
"""
atoms = object.atomList()
p1, p2 = object.boundingBox()
margin = Vector(largest, largest, largest)
p1 = p1 - margin
p2 = p2 + margin
a, b, c = tuple(p2 - p1)
offset = 0.5 * Vector(a, b, c)
points = []
while len(points) < n:
p = p1 + Random.randomPointInBox(a, b, c) + offset
m = 2 * largest
ok = 1
for atom in atoms:
d = (p - atom.position()).length()
m = min(m, d)
if d < smallest and atom.symbol != 'H':
ok = 0
if not ok: break
if ok and m <= largest:
points.append(p)
return points
def _userdefined_qvectors(self):
hkls = self._generate_hkls()
if self.universe.reciprocalBasisVectors() is None:
qVects = [Vector(v) for v in hkls]
else:
qVects = [self.transRecBasis * Vector(hkl) for hkl in hkls]
qVectsDict = {}
for i in range(len(qVects)):
qVect = qVects[i]
hkl = Vector(hkls[i])
qLength = round(qVect.length(), 3)
if qVectsDict.has_key(qLength):
qVectsDict[qLength]["qvect"].append(qVect)
qVectsDict[qLength]["hkl"].append(hkl)
else:
qVectsDict[qLength] = {"qvect": [qVect], "hkl": [hkl]}
for q in sorted(qVectsDict.keys()):
self.qRadii.append(q)
self.qVectors.append(qVectsDict[q]["qvect"])
self.hkls.append(qVectsDict[q]["hkl"])
def _explicit_qvectors(self, qMin, qMax, indRange):
qVects = []
hkls = []
dimen = len(self.qDirections)
for ind in indRange:
qVect = Vector()
for i in range(dimen):
qVect += ind[i] * self.qDirections[i]
if qMin < qVect.length() <= qMax:
if not qVect in qVects:
qVects.append(qVect)
hkl = Vector([0, 0, 0])
for i in range(dimen):
hkl += ind[i] * self.hkl_dir[i]
hkls.append(hkl)
if len(qVects) >= self.qVectorsPerShell:
break
LogMessage(
'info', '%d explicit Q vectors generated for shell [%s,%s].' %
(len(qVects), qMin, qMax), ['file', 'console'])
return qVects, hkls
def __init__(self, cellsize, cells, function=None, base=None):
"""
@param cellsize: the edge length of the cubic elementary cell
@type cellsize: C{float}
@param cells: a tuple of three integers, indicating how often the
elementary cell should be replicated along each
lattice vector
@param cells: C{tuple} of C{int}
@param function: the function to be applied to each point in the
lattice in order to obtain the value stored in the
lattice. If no function is specified, the point
itself becomes the value stored in the lattice.
@type function: callable
@param base: an offset added to all lattice points
@type base: L{Scientific.Geometry.Vector}
"""
lattice_vectors = (cellsize * Vector(1., 0., 0.),
cellsize * Vector(0., 1., 0.),
cellsize * Vector(0., 0., 1.))
if type(cells) != type(()):
cells = 3 * (cells, )
BravaisLattice.__init__(self, lattice_vectors, cells, function, base)
def __init__(self, cellsize, cells, function=None, base=None):
lattice_vectors = (cellsize*Vector(1., 0., 0.),
cellsize*Vector(0., 1., 0.),
cellsize*Vector(0., 0., 1.))
if type(cells) != type(()):
cells = 3*(cells,)
BravaisLattice.__init__(self, lattice_vectors, cells, function, base)
def basisVectors(parameters):
"""Returns the basis vectors for the simulation cell from the six crystallographic parameters.
@param parameters: the a, b, c, alpha, bete and gamma of the simulation cell.
@type: parameters: list of 6 floats
@return: a list of three Scientific.Geometry.Vector objects representing respectively a, b and c
basis vectors.
@rtype: list
"""
# The simulation cell parameters.
a, b, c, alpha, beta, gamma = parameters
# By construction the a vector is aligned with the x axis.
e1 = Vector(a, 0.0, 0.0)
# By construction the b vector is in the xy plane.
e2 = b * Vector(N.cos(gamma), N.sin(gamma), 0.0)
e3_x = N.cos(beta)
e3_y = (N.cos(alpha) - N.cos(beta) * N.cos(gamma)) / N.sin(gamma)
e3_z = N.sqrt(1.0 - e3_x**2 - e3_y**2)
e3 = c * Vector(e3_x, e3_y, e3_z)
return (e1, e2, e3)
def asuToUnitCell(self, asu_contents, compact=True):
"""
:param asu_contents: the molecules in the asymmetric unit, usually
obtained from :func:~MMTK.PDB.PDBConfiguration.createAll().
:param compact: if True, all molecules images are shifted such that
their centers of mass lie inside the unit cell.
:type compact: bool
:returns: a collection containing all molecules in the unit cell,
obtained by copying and moving the molecules from the
asymmetric unit according to the crystallographic
symmetry operations.
:rtype: :class:~MMTK.Collections.Collection
"""
unit_cell_contents = Collections.Collection()
for symop in self.cs_transformations:
transformation = symop.asLinearTransformation()
rotation = transformation.tensor
translation = transformation.vector
image = copy.deepcopy(asu_contents)
for atom in image.atomList():
atom.setPosition(symop(atom.position()))
if compact:
cm = image.centerOfMass()
cm_fr = self.to_fractional(cm)
cm_fr = Vector(cm_fr[0] % 1., cm_fr[1] % 1., cm_fr[2] % 1.) \
- Vector(0.5, 0.5, 0.5)
cm = self.from_fractional(cm_fr)
image.translateTo(cm)
unit_cell_contents.addObject(image)
return unit_cell_contents
def anchor(universe): """Anchor a universe""" if(universe.numberOfAtoms() >=3): #set anchor atoms indexes a1i = 0 for i in range(len(universe.atomList()[a1i].bondedTo())): for j in range(len(universe.atomList()[a1i].bondedTo()[i].bondedTo())): if universe.atomList()[a1i] is not \ universe.atomList()[a1i].bondedTo()[i].bondedTo()[j] : a2i = i; a3i = j; break print 'anchor using: ', a1i, a2i, a3i v1 = universe.atomList()[a1i].position(); v2 = universe.atomList()[a1i].bondedTo()[a2i].position(); v3 = universe.atomList()[a1i].bondedTo()[a2i].bondedTo()[a3i].position(); vT01 = -v1; tra01 = Translation(vT01); universe.applyTransformation(tra01); x = universe.atomList()[a1i].bondedTo()[a2i].position().x(); y = 0; z = universe.atomList()[a1i].bondedTo()[a2i].position().z(); vR01 = Vector(x,y,z); vR02 = Vector(1,0,0); sign = 1.0 if ((z > 0) and (x > 0)) or ((z < 0) and (x < 0)): sign = -1.0 rot01 = Rotation(Vector(0,1,0), sign*vR01.angle(vR02)); universe.applyTransformation(rot01); v4 = universe.atomList()[a1i].bondedTo()[a2i].position(); sign = -1.0 if ((x > 0) and (y > 0)) or ((x < 0) and (y < 0)): sign = 1.0 rot02 = Rotation(Vector(0,0,1), sign*v4.angle(Vector(1,0,0))); universe.applyTransformation(rot02); x = 0; y = universe.atomList()[a1i].bondedTo()[a2i].bondedTo()[a3i].position().y(); z = universe.atomList()[a1i].bondedTo()[a2i].bondedTo()[a3i].position().z(); sign = 1.0 if ((z > 0) and (y > 0)) or ((z < 0) and (y < 0)): sign = -1.0 vR03 = Vector(x,y,z); vR04 = Vector(0,1,0); rot03 = Rotation(Vector(1,0,0), sign*vR03.angle(vR04)); universe.applyTransformation(rot03); else: print "Molecule too little to be anchored";
def superpositionFit(confs):
"""
:param confs: the weight, reference position, and alternate
position for each atom
:type confs: sequence of (float, Vector, Vector)
:returns: the quaternion representing the rotation,
the center of mass in the reference configuration,
the center of mass in the alternate configuraton,
and the RMS distance after the optimal superposition
"""
w_sum = 0.
wr_sum = N.zeros((3, ), N.Float)
for w, r_ref, r in confs:
w_sum += w
wr_sum += w * r_ref.array
ref_cms = wr_sum / w_sum
pos = N.zeros((3, ), N.Float)
possq = 0.
cross = N.zeros((3, 3), N.Float)
for w, r_ref, r in confs:
w = w / w_sum
r_ref = r_ref.array - ref_cms
r = r.array
pos = pos + w * r
possq = possq + w*N.add.reduce(r*r) \
+ w*N.add.reduce(r_ref*r_ref)
cross = cross + w * r[:, N.NewAxis] * r_ref[N.NewAxis, :]
k = N.zeros((4, 4), N.Float)
k[0, 0] = -cross[0, 0] - cross[1, 1] - cross[2, 2]
k[0, 1] = cross[1, 2] - cross[2, 1]
k[0, 2] = cross[2, 0] - cross[0, 2]
k[0, 3] = cross[0, 1] - cross[1, 0]
k[1, 1] = -cross[0, 0] + cross[1, 1] + cross[2, 2]
k[1, 2] = -cross[0, 1] - cross[1, 0]
k[1, 3] = -cross[0, 2] - cross[2, 0]
k[2, 2] = cross[0, 0] - cross[1, 1] + cross[2, 2]
k[2, 3] = -cross[1, 2] - cross[2, 1]
k[3, 3] = cross[0, 0] + cross[1, 1] - cross[2, 2]
for i in range(1, 4):
for j in range(i):
k[i, j] = k[j, i]
k = 2. * k
for i in range(4):
k[i, i] = k[i, i] + possq - N.add.reduce(pos * pos)
from Scientific import LA
e, v = LA.eigenvectors(k)
i = N.argmin(e)
v = v[i]
if v[0] < 0: v = -v
if e[i] <= 0.:
rms = 0.
else:
rms = N.sqrt(e[i])
from Scientific.Geometry import Quaternion
return Quaternion.Quaternion(v), Vector(ref_cms), \
Vector(pos), rms
def partitions(self):
"""Returns a list of cubic partitions. Each partition is specified
by a tuple containing two vectors (describing the diagonally
opposite corners) and the list of objects in the partition."""
list = []
for index, objects in self.partition.items():
min = Vector(index) * self.partition_size
max = min + Vector(3 * [self.partition_size])
list.append((min, max, objects))
return list
def findTransformationAsQuaternion(self, conf1, conf2=None):
universe = self.universe()
if conf1.universe != universe:
raise ValueError("conformation is for a different universe")
if conf2 is None:
conf1, conf2 = conf2, conf1
else:
if conf2.universe != universe:
raise ValueError("conformation is for a different universe")
ref = conf1
conf = conf2
weights = universe.masses()
weights = weights / self.mass()
ref_cms = self.centerOfMass(ref).array
pos = Numeric.zeros((3, ), Numeric.Float)
possq = 0.
cross = Numeric.zeros((3, 3), Numeric.Float)
for a in self.atomList():
r = a.position(conf).array
r_ref = a.position(ref).array - ref_cms
w = weights[a]
pos = pos + w * r
possq = possq + w*Numeric.add.reduce(r*r) \
+ w*Numeric.add.reduce(r_ref*r_ref)
cross = cross + w * r[:,
Numeric.NewAxis] * r_ref[Numeric.NewAxis, :]
k = Numeric.zeros((4, 4), Numeric.Float)
k[0, 0] = -cross[0, 0] - cross[1, 1] - cross[2, 2]
k[0, 1] = cross[1, 2] - cross[2, 1]
k[0, 2] = cross[2, 0] - cross[0, 2]
k[0, 3] = cross[0, 1] - cross[1, 0]
k[1, 1] = -cross[0, 0] + cross[1, 1] + cross[2, 2]
k[1, 2] = -cross[0, 1] - cross[1, 0]
k[1, 3] = -cross[0, 2] - cross[2, 0]
k[2, 2] = cross[0, 0] - cross[1, 1] + cross[2, 2]
k[2, 3] = -cross[1, 2] - cross[2, 1]
k[3, 3] = cross[0, 0] + cross[1, 1] - cross[2, 2]
for i in range(1, 4):
for j in range(i):
k[i, j] = k[j, i]
k = 2. * k
for i in range(4):
k[i, i] = k[i, i] + possq - Numeric.add.reduce(pos * pos)
from Scientific import LA
e, v = LA.eigenvectors(k)
i = Numeric.argmin(e)
v = v[i]
if v[0] < 0: v = -v
if e[i] <= 0.:
rms = 0.
else:
rms = Numeric.sqrt(e[i])
return Quaternion.Quaternion(v), Vector(ref_cms), \
Vector(pos), rms
def rigidMovement(atoms, vector):
a = N.zeros((len(atoms), 3, 2, 3), N.Float)
b = N.zeros((len(atoms), 3), N.Float)
for i in range(len(atoms)):
a[i, :, 0, :] = delta.array
a[i, :, 1, :] = (epsilon * atoms[i].position()).array
b[i] = vector[atoms[i]].array
a.shape = (3 * len(atoms), 6)
b.shape = (3 * len(atoms), )
vo = N.dot(LA.generalized_inverse(a), b)
return Vector(vo[:3]), Vector(vo[3:])
def __init__(self,atoms,outfile=None):
unitcell = atoms.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length()#*angstroms2bohr
b = B.length()#*angstroms2bohr
c = C.length()#*angstroms2bohr
# angles between the vectors
rad2deg = 360./(2.*math.pi)
alpha = B.angle(C)*rad2deg
beta = A.angle(C)*rad2deg
gamma = A.angle(B)*rad2deg
scaledpositions = atoms.get_scaled_positions()
chemicalsymbols = [atom.get_symbol() for atom in atoms]
input = ''
input += 'title \n'
input += '0 tolerance\n'
input += '2 lattice parameters in lengths and angles\n'
input += '%1.3f %1.3f %1.3f %1.3f %1.3f %1.3f\n' % (a,b,c,
alpha,beta,gamma)
input += '1 3 basis vectors for unit cell\n'
input += '1.00 0.00 0.00\n'
input += '0.00 1.00 0.00\n'
input += '0.00 0.00 1.00\n'
input += '%i number of atoms\n' % len(atoms)
types = ''
for atom in atoms:
types += str(atom.get_atomic_number()) + ' '
input += types + '\n'
for i,atom in enumerate(atoms):
input += '%1.3f %1.3f %1.3f\n' % tuple(scaledpositions[i])
pin,pout = os.popen2('findsym')
pin.writelines(input)
pin.close()
self.output = pout.readlines()
pout.close()
if outfile:
f = open(outfile,'w')
f.writelines(self.output)
f.close()
if os.path.exists('findsym.log'):
os.remove('findsym.log')
def boundingBox(self, conf=None):
"""Returns two opposite corners of a bounding box around the
object. The bounding box is the smallest rectangular bounding box
with edges parallel to the coordinate axes."""
atoms = self.atomList()
min = atoms[0].position(conf).array
max = min
for a in atoms[1:]:
r = a.position(conf).array
min = Numeric.minimum(min, r)
max = Numeric.maximum(max, r)
return Vector(min), Vector(max)
def evaluatorParameters(self, universe, subset1, subset2, global_data):
rsum = not self.options.get('no_reciprocal_sum', 0)
if not universe.is_periodic and rsum:
raise ValueError("Ewald method accepts only periodic universes")
if not universe.is_orthogonal and rsum:
raise ValueError("Ewald method implemented only for orthogonal universes")
n = universe.numberOfPoints()
charge = N.zeros((n,), N.Float)
for o in universe:
for a in o.atomList():
charge[a.index] = self._charge(o, a, global_data)
charge = charge*N.sqrt(self.scale_factor)
precision = self.options.get('ewald_precision', 1.e-6)
p = N.sqrt(-N.log(precision))
if rsum:
beta_opt = N.sqrt(N.pi) * \
(5.*universe.numberOfAtoms()/universe.cellVolume()**2)**(1./6.)
max_cutoff = universe.largestDistance()
beta_opt = max(p/max_cutoff, beta_opt)
else:
beta_opt = 0.01
options = {}
options['beta'] = beta_opt
options['real_cutoff'] = p/beta_opt
options['reciprocal_cutoff'] = N.pi/(beta_opt*p)
options['no_reciprocal_sum'] = 0
for key, value in self.options.items():
options[key] = value
lx = universe.boxToRealCoordinates(Vector(1., 0., 0.)).length()
ly = universe.boxToRealCoordinates(Vector(0., 1., 0.)).length()
lz = universe.boxToRealCoordinates(Vector(0., 0., 1.)).length()
kmax = N.array([lx,ly,lz])/options['reciprocal_cutoff']
kmax = N.ceil(kmax).astype(N.Int)
excluded_pairs, one_four_pairs, atom_subset = \
self.excludedPairs(subset1, subset2, global_data)
if atom_subset is not None:
raise ValueError("Ewald summation not available for subsets")
if options['no_reciprocal_sum']:
kcutoff = 0.
else:
kcutoff = (2.*N.pi/options['reciprocal_cutoff'])**2
return {'electrostatic': {'algorithm': 'ewald',
'charge': charge,
'real_cutoff': options['real_cutoff'],
'reciprocal_cutoff': kcutoff,
'beta': options['beta'],
'k_max': kmax,
'one_four_factor': self.es_14_factor},
'nonbonded': {'excluded_pairs': excluded_pairs,
'one_four_pairs': one_four_pairs,
'atom_subset': atom_subset}
}
def _convertUnits(self):
for residue in self.residues:
for atom in residue:
atom.position = atom.position * Units.Ang
try:
b = atom.properties['temperature_factor']
atom.properties['temperature_factor'] = b * Units.Ang**2
except KeyError:
pass
try:
u = atom.properties['u']
atom.properties['u'] = u * Units.Ang**2
except KeyError:
pass
# All these attributes exist only if ScientificPython >= 2.7.5 is used.
# The Scaling transformation was introduced with the same version,
# so if it exists, the rest should work as well.
try:
from Scientific.Geometry.Transformation import Scaling
except ImportError:
return
for attribute in ['a', 'b', 'c']:
value = getattr(self, attribute)
if value is not None:
setattr(self, attribute, value * Units.Ang)
for attribute in ['alpha', 'beta', 'gamma']:
value = getattr(self, attribute)
if value is not None:
setattr(self, attribute, value * Units.deg)
if self.to_fractional is not None:
self.to_fractional = self.to_fractional * Scaling(1. / Units.Ang)
v1 = self.to_fractional(Vector(1., 0., 0.))
v2 = self.to_fractional(Vector(0., 1., 0.))
v3 = self.to_fractional(Vector(0., 0., 1.))
self.reciprocal_basis = (Vector(v1[0], v2[0], v3[0]),
Vector(v1[1], v2[1], v3[1]),
Vector(v1[2], v2[2], v3[2]))
else:
self.reciprocal_basis = None
if self.from_fractional is not None:
self.from_fractional = Scaling(Units.Ang) * self.from_fractional
self.basis = (self.from_fractional(Vector(1., 0., 0.)),
self.from_fractional(Vector(0., 1., 0.)),
self.from_fractional(Vector(0., 0., 1.)))
else:
self.basis = None
for i in range(len(self.ncs_transformations)):
tr = self.ncs_transformations[i]
tr_new = Scaling(Units.Ang) * tr * Scaling(1. / Units.Ang)
tr_new.given = tr.given
tr_new.serial = tr.serial
self.ncs_transformations[i] = tr_new
for i in range(len(self.cs_transformations)):
tr = self.cs_transformations[i]
tr_new = Scaling(Units.Ang) * tr * Scaling(1. / Units.Ang)
self.cs_transformations[i] = tr_new
def findPositions(self):
# First atom at origin
self.coordinates[self.data[0][0]] = Vector(0, 0, 0)
# Second atom along x-axis
self.coordinates[self.data[1][0]] = Vector(self.data[1][2], 0, 0)
# Third atom in xy-plane
try:
pos1 = self.coordinates[self.data[2][1]]
except KeyError:
raise ValueError("atom %d has no defined position" %
self.data[2][1].number)
try:
pos2 = self.coordinates[self.data[2][3]]
except KeyError:
raise ValueError("atom %d has no defined position" %
self.data[2][3].number)
sphere = Sphere(pos1, self.data[2][2])
cone = Cone(pos1, pos2 - pos1, self.data[2][4])
plane = Plane(Vector(0, 0, 0), Vector(0, 0, 1))
points = sphere.intersectWith(cone).intersectWith(plane)
self.coordinates[self.data[2][0]] = points[0]
# All following atoms defined by distance + angle + dihedral
for entry in self.data[3:]:
try:
pos1 = self.coordinates[entry[1]]
except KeyError:
raise ValueError("atom %d has no defined position" %
entry[1].number)
try:
pos2 = self.coordinates[entry[3]]
except KeyError:
raise ValueError("atom %d has no defined position" %
entry[3].number)
try:
pos3 = self.coordinates[entry[5]]
except KeyError:
raise ValueError("atom %d has no defined position" %
entry[5].number)
distance = entry[2]
angle = entry[4]
dihedral = entry[6]
sphere = Sphere(pos1, distance)
cone = Cone(pos1, pos2 - pos1, angle)
plane123 = Plane(pos3, pos2, pos1)
points = sphere.intersectWith(cone).intersectWith(plane123)
for p in points:
if Plane(pos2, pos1, p).normal * plane123.normal > 0:
break
p = rotatePoint(p, Line(pos1, pos2 - pos1), dihedral)
self.coordinates[entry[0]] = p
def test_P1(self):
cell = UnitCell(Vector(1., 0., 0.), Vector(0., 1., 0.),
Vector(0., 0., 1.))
res_max = 0.5
res_min = 10.
reflections = ReflectionSet(cell,
space_groups['P 1'],
res_max,
res_min,
compact=self.compact)
self.assert_(reflections.isComplete())
nr = sum([r.n_symmetry_equivalents for r in reflections]) + \
sum([r.n_symmetry_equivalents
for r in reflections.systematic_absences])
self.assertEqual(reflections.totalReflectionCount(), nr)
self.assert_(reflections.totalReflectionCount() == 2 *
len(reflections.minimal_reflection_list))
for r in reflections:
self.assert_(len(r.symmetryEquivalents()) == 2)
self.assert_(res_max <= r.resolution() <= res_min)
self.assert_(not r.isCentric())
self.assert_(r.symmetryFactor() == 1)
self._shellTest(reflections)
self._subsetTest(reflections)
self._symmetryTest(reflections)
self._intersectionTest(reflections)
self._equalityTest(reflections)
frozen = reflections.freeze()
self.assert_(frozen is reflections.freeze())
self.assert_(frozen is frozen.freeze())
self.assert_(frozen.isComplete())
self.assert_(frozen.totalReflectionCount() == 2 *
len(frozen._reflections))
for r in frozen:
self.assert_(reflections.hasReflection(r.h, r.k, r.l))
self.assert_(len(r.symmetryEquivalents()) == 2)
self.assert_(res_max <= r.resolution() <= res_min)
self.assert_(not r.isCentric())
self.assert_(r.symmetryFactor() == 1)
for r in reflections:
self.assert_(frozen.hasReflection(r.h, r.k, r.l))
self.assert_(r.index == frozen[(r.h, r.k, r.l)].index)
self._shellTest(frozen)
self._subsetTest(frozen)
self._symmetryTest(frozen)
self._intersectionTest(frozen)
self._equalityTest(frozen)
def __init__(self, universe, rigid_bodies):
"""
:param universe: the universe for which the subspace is created
:type universe: :class:~MMTK.Universe.Universe
:param rigid_bodies: a list or set of rigid bodies
with some common atoms
"""
ex_ey_ez = [Vector(1.,0.,0.), Vector(0.,1.,0.), Vector(0.,0.,1.)]
# Constructs
# 1) a list of vectors describing the rigid-body motions of each
# rigid body as if it were independent.
# 2) a list of pair-distance constraint vectors for all pairs of
# atoms inside a rigid body.
# The LRB subspace is constructed from the projections of the
# first set of vectors onto the orthogonal complement of the
# subspace generated by the second set of vectors.
vectors = []
c_vectors = []
for rb in rigid_bodies:
atoms = rb.atomList()
for d in ex_ey_ez:
v = ParticleProperties.ParticleVector(universe)
for a in atoms:
v[a] = d
vectors.append(v)
if len(atoms) > 1:
center = rb.centerOfMass()
iv = len(vectors)-3
for d in ex_ey_ez:
v = ParticleProperties.ParticleVector(universe)
for a in atoms:
v[a] = d.cross(a.position()-center)
for vt in vectors[iv:]:
v -= v.dotProduct(vt)*vt
if v.dotProduct(v) > 0.:
vectors.append(v)
for a1, a2 in Utility.pairs(atoms):
distance = universe.distanceVector(a1.position(),
a2.position())
v = ParticleProperties.ParticleVector(universe)
v[a1] = distance
v[a2] = -distance
c_vectors.append(v)
if c_vectors:
constraints = Subspace(universe, c_vectors)
vectors = [constraints.projectionComplementOf(v)
for v in vectors]
Subspace.__init__(self, universe, vectors)
def getPosition(self, atom_id):
"""
:param atom_id: id of the atom whose position is requested
:return: the position of the atom
:rtype: Scientific.Geometry.Vector
"""
return Vector(self.positions[self.id_dict[atom_id]])
def initialize(self):
"""Initializes the analysis (e.g. parses and checks input parameters, set some variables ...).
"""
# The input parameters are parsed.
self.interpreteInputParameters()
self.bondNames = {}
for aIndexes in self.group:
for at in self.universe.atomList():
if at.index == aIndexes[0]:
if isinstance(at.topLevelChemicalObject(),
(Protein, PeptideChain, NucleotideChain)):
self.bondNames[tuple(
aIndexes)] = at.parent.parent.sequence_number
else:
self.bondNames[tuple(aIndexes)] = at.index
break
self.referenceDirection = Vector(0.0, 0.0, 1.0)
# The results are stored in dictionnary because the order in which the bonds are treated does not
# always follow the structure.
self.P2 = {}
self.S2 = {}
def writeSpecification(self, file):
d = 0.5 * self.edge
semi_diag = Vector(d, d, d)
file.writeString('.box')
file.writeVector((self.center - semi_diag) * file.scale)
file.writeVector((self.center + semi_diag) * file.scale)
file.writeString('\n')
def __init__(self,
elementary_cell,
lattice_vectors,
cells,
function=None,
base=None):
"""
:param elementary_cell: a list of points in the elementary cell
:param lattice_vectors: a list of lattice vectors. Each lattice
vector defines a lattice dimension (only
values from one to three make sense) and
indicates the displacement along this
dimension from one cell to the next.
:param cells: a list of integers, whose length must equal the number
of dimensions. Each entry specifies how often a cell is
repeated along this dimension.
:param function: a function that is called for every lattice point with
the vector describing the point as argument. The return
value of this function is stored in the lattice object.
If the function is 'None', the vector is directly
stored in the lattice object.
"""
if len(lattice_vectors) != len(cells):
raise TypeError('Inconsistent dimension specification')
if base is None:
base = Vector(0, 0, 0)
self.dimension = len(lattice_vectors)
self.elements = []
self.makeLattice(elementary_cell, lattice_vectors, cells, base)
Lattice.__init__(self, function)
def cell_parameters(atoms, weight=1.0, cells=None):
'''
adds entries to CELL PARAMETERS for the unit cell geometry of the
atoms object.
'''
description = reax_hash(atoms)
# get all the parameters needed for a cell parameters block
uc = atoms.get_cell()
a, b, c = [Vector(x) for x in uc]
A = a.length()
B = b.length()
C = c.length()
rad2deg = 360. / (2 * math.pi)
alpha = b.angle(c) * rad2deg
beta = a.angle(c) * rad2deg
gamma = a.angle(b) * rad2deg
cells['CELL PARAMETERS'].append('# created by reax.trainset')
# this is an org-link to the geo file
#cells['CELL PARAMETERS'].append('# file:geo::%s' % description)
for key, val in [('a', A), ('b', B), ('c', C), ('alpha', alpha),
('beta', beta), ('gamma', gamma)]:
s = '%(description)s %(weight)f %(key)s %(val)s' % locals()
if s not in cells['CELL PARAMETERS']:
cells['CELL PARAMETERS'].append(s)
return cells
def gradientTest(universe, atoms=None, delta=0.0001):
"""
Test gradients by comparing to numerical derivatives of the energy.
:param universe: the universe on which the test is performed
:type universe: :class:`~MMTK.Universe.Universe`
:param atoms: the atoms of the universe for which the gradient
is tested (default: all atoms)
:type atoms: list
:param delta: the step size used in calculating the numerical derivatives
:type delta: float
"""
e0, grad = universe.energyAndGradients()
print 'Energy: ', e0
if atoms is None:
atoms = universe.atomList()
for a in atoms:
print a
print grad[a]
num_grad = []
for v in [ex, ey, ez]:
x = a.position()
a.setPosition(x + delta * v)
eplus = universe.energy()
a.setPosition(x - delta * v)
eminus = universe.energy()
a.setPosition(x)
num_grad.append(0.5 * (eplus - eminus) / delta)
print Vector(num_grad)
def parseAtom(self, element):
atom_spec = {
'atom_id':
element.get('id', None),
'element':
element.find(self.prefix + 'type_symbol').text,
'name':
element.find(self.prefix + 'label_atom_id').text,
'alt_id':
element.find(self.prefix + 'label_alt_id').text,
'model':
int(element.find(self.prefix + 'pdbx_PDB_model_num').text),
'comp_id':
element.find(self.prefix + 'label_comp_id').text,
'asym_id':
element.find(self.prefix + 'label_asym_id').text,
'entity_id':
element.find(self.prefix + 'label_entity_id').text,
'position':
Vector(float(element.find(self.prefix + 'Cartn_x').text),
float(element.find(self.prefix + 'Cartn_y').text),
float(element.find(self.prefix + 'Cartn_z').text)),
'occupancy':
float(element.find(self.prefix + 'occupancy').text),
'beta':
float(element.find(self.prefix + 'B_iso_or_equiv').text),
}
seq_id = element.find(self.prefix + 'label_seq_id').text
if seq_id is None:
atom_spec['seq_id'] = None
else:
atom_spec['seq_id'] = int(seq_id)
return atom_spec
def __init__(self,
elementary_cell,
lattice_vectors,
cells,
function=None,
base=None):
"""
@param elementary_cell: a list of the points in the elementary cell
@type elementary_cell: C{list} of L{Scientific.Geometry.Vector}
@param lattice_vectors: the edges of the elementary cell
@type lattice_vectors: C{tuple} of three L{Scientific.Geometry.Vector}
@param cells: a tuple of three integers, indicating how often the
elementary cell should be replicated along each
lattice vector
@param cells: C{tuple} of C{int}
@param function: the function to be applied to each point in the
lattice in order to obtain the value stored in the
lattice. If no function is specified, the point
itself becomes the value stored in the lattice.
@type function: callable
@param base: an offset added to all lattice points
@type base: L{Scientific.Geometry.Vector}
"""
if len(lattice_vectors) != len(cells):
raise TypeError('Inconsistent dimension specification')
if base is None:
base = Vector(0, 0, 0)
self.dimension = len(lattice_vectors)
self.elements = []
self.makeLattice(elementary_cell, lattice_vectors, cells, base)
Lattice.__init__(self, function)
def centerAndMomentOfInertia(self, conf=None):
"""
:param conf: a configuration object, or None for the
current configuration
:type conf: :class:~MMTK.ParticleProperties.Configuration or NoneType
:returns: the center of mass and the moment of inertia tensor
in the given configuration
"""
from Scientific.Geometry import delta
offset = None
universe = self.universe()
if universe is not None:
offset = universe.contiguousObjectOffset([self], conf)
m = 0.
mr = Vector(0., 0., 0.)
t = Tensor(3 * [3 * [0.]])
for a in self.atomIterator():
ma = a._mass
if offset is None:
r = a.position(conf)
else:
r = a.position(conf) + offset[a]
m += ma
mr += ma * r
t += ma * r.dyadicProduct(r)
cm = mr / m
t -= m * cm.dyadicProduct(cm)
t = t.trace() * delta - t
return cm, t
def __init__(self, universe, cutoff):
"""
:param universe: the universe for which the basis will be used
:type universe: :class:~MMTK.Universe.Universe
:param cutoff: the wavelength cutoff. A smaller value yields
a larger basis.
:type cutoff: float
"""
p1, p2 = universe.boundingBox()
p2 = p2 + Vector(cutoff, cutoff, cutoff)
l = (p2 - p1).array
n_max = (0.5 * l / cutoff + 0.5).astype(N.Int)
wave_numbers = [(nx, ny, nz)
for nx in range(-n_max[0], n_max[0]+1)
for ny in range(-n_max[1], n_max[1]+1)
for nz in range(-n_max[2], n_max[2]+1)
if (nx/l[0])**2 + (ny/l[1])**2 + (nz/l[2])**2 \
< 0.25/cutoff**2]
atoms = universe.atomList()
natoms = len(atoms)
basis = N.zeros((3 * len(wave_numbers) + 3, natoms, 3), N.Float)
cm = universe.centerOfMass()
i = 0
for rotation in [
Vector(1., 0., 0.),
Vector(0., 1., 0.),
Vector(0., 0., 1.)
]:
v = ParticleProperties.ParticleVector(universe, basis[i])
for a in atoms:
v[a] = rotation.cross(a.position() - cm)
i += i
conf = universe.configuration().array - p1.array
for n in wave_numbers:
k = 2. * N.pi * N.array(n) / l
w = self._w(conf[:, 0], k[0]) * self._w(conf[:, 1], k[1]) * \
self._w(conf[:, 2], k[2])
basis[i, :, 0] = w
basis[i + 1, :, 1] = w
basis[i + 2, :, 2] = w
i += 3
self.array = basis
self.universe = universe
def momentum(self, velocities=None):
"Returns the momentum."
if velocities is None:
velocities = self.atomList()[0].universe().velocities()
p = Vector(0., 0., 0.)
for a in self.atomList():
p = p + a._mass * velocities[a]
return p
def __init__(self, points, **attr):
"""
@param points: a sequence of points to be connected by lines
@type points: sequence of L{Scientific.Geometry.Vector}
@param attr: graphics attributes as keyword parameters
"""
self.points = points
ShapeObject.__init__(self, attr, None, None, Vector(0., 0., 0.))
def randomPointInSphere(r):
"""Returns a vector drawn from a uniform distribution within
a sphere of radius |r|."""
rsq = r * r
while 1:
x = N.array([uniform(-r, r), uniform(-r, r), uniform(-r, r)])
if N.dot(x, x) < rsq: break
return Vector(x)
def __init__(self,atoms,outfile=None):
unitcell = atoms.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length()#*angstroms2bohr
b = B.length()#*angstroms2bohr
c = C.length()#*angstroms2bohr
# angles between the vectors
rad2deg = 360./(2.*math.pi)
alpha = B.angle(C)*rad2deg
beta = A.angle(C)*rad2deg
gamma = A.angle(B)*rad2deg
scaledpositions = atoms.get_scaled_positions()
chemicalsymbols = [atom.get_symbol() for atom in atoms]
input = ''
input += '%1.3f %1.3f %1.3f %1.3f %1.3f %1.3f\n' % (a,b,c,
alpha,beta,gamma)
input += '1 1 0.1 0.1\n'
for atom in atoms:
sym = atom.get_symbol()
group = 1
x,y,z = atom.get_position()
#format(a6,i2,6f9.5)
input += str(FortranLine((sym,
group,
x,y,z),
FortranFormat('a6,i2,3f9.5')))+'\n'
pin,pout = os.popen2('symmol')
pin.writelines(input)
pin.close()
self.output = pout.readlines()
pout.close()
if outfile:
f = open(outfile,'w')
f.writelines(self.output)
f.close()
if os.path.exists('symmol.log'):
os.remove('symmol.log')
def releasehandler1(self, event):
self.configure(cursor='top_left_arrow')
self.update_idletasks()
try:
dx = event.x - self.click1x
dy = event.y - self.click1y
except AttributeError:
return
if dx != 0 or dy != 0:
normal = Vector(self.axis)
move = Vector(-dx*self.plane[:,0]+dy*self.plane[:,1])
axis = normal.cross(move) / \
Numeric.minimum.reduce(Numeric.fabs(self.plotbox_size))
rot = Rotation(axis.normal(), axis.length())
self.axis = rot(normal).array
self.plane[:,0] = rot(Vector(self.plane[:,0])).array
self.plane[:,1] = rot(Vector(self.plane[:,1])).array
self.clear(1)
self.redraw()
def set_axis(self, axis):
try:
self._axis = Vector(axis)
except (TypeError,ValueError):
raise ProjectorError('Wrong axis definition: must be a sequence of 3 floats')
try:
self._axis = self._axis.normal()
except ZeroDivisionError:
raise ProjectorError('The axis vector can not be the null vector')
self._projectionMatrix = numpy.identity(3) - numpy.outer(self._axis, self._axis)
class PlanarProjector(IProjector):
type = 'planar'
def set_axis(self, axis):
try:
self._axis = Vector(axis)
except (TypeError,ValueError):
raise ProjectorError('Wrong axis definition: must be a sequence of 3 floats')
try:
self._axis = self._axis.normal()
except ZeroDivisionError:
raise ProjectorError('The axis vector can not be the null vector')
self._projectionMatrix = numpy.identity(3) - numpy.outer(self._axis, self._axis)
def __call__(self, value):
try:
return numpy.dot(value,self._projectionMatrix.T)
except (TypeError,ValueError):
raise ProjectorError("Invalid data to apply projection on")
'''
Gstar = np.dot(G, G.T)
id2 = np.dot(hkl, np.dot(Gstar, hkl))
print('d_111 spacing (method 2) =',np.sqrt(1 / id2))
# http://books.google.com/books?id=nJHSqEseuIUC&lpg=PA118&ots=YA9TBldoVH
# &dq=reciprocal%20metric%20tensor&pg=PA119#v=onepage
# &q=reciprocal%20metric%20tensor&f=false
'''Finally, many text books on crystallography use long algebraic
formulas for computing the d-spacing with sin and cos, vector lengths,
and angles. Below we compute these and use them in the general
triclinic structure formula which applies to all the structures.
'''
from Scientific.Geometry import Vector
import math
unitcell = ag.get_cell()
A = Vector(unitcell[0])
B = Vector(unitcell[1])
C = Vector(unitcell[2])
# lengths of the vectors
a = A.length()#*angstroms2bohr
b = B.length()#*angstroms2bohr
c = C.length()#*angstroms2bohr
# angles between the vectors in radians
alpha = B.angle(C)
beta = A.angle(C)
gamma = A.angle(B)
print('')
print('a b c alpha beta gamma')
print('{0:1.3f} {1:1.3f} {2:1.3f} {3:1.3f} {4:1.3f} {5:1.3f}\n'.format(a,b,c, alpha,beta,gamma))
h, k, l = (1, 1, 1)
from math import sin, cos
import numpy as np from Scientific.Geometry import Vector A = Vector([1,1,1]) #Scientfic a = np.array([1,1,1]) #numpy B = Vector([0.0,1.0,0.0]) print '|A| = ',A.length() #Scientific Python way print '|a| = ',np.sum(a**2)**0.5 #numpy way print '|a| = ',np.linalg.norm(a) #numpy way 2 print 'ScientificPython angle = ',A.angle(B) #in radians print 'numpy angle = ',np.arccos(np.dot(a/np.linalg.norm(a),B/np.linalg.norm(B))) #cross products print 'Scientific A .cross. B = ',A.cross(B) print 'numpy A .cross. B = ',np.cross(A,B) #you can use Vectors in numpy
def pretty_print(self):
'''
__str__ function to print the calculator with a nice summary, e.g. jaspsum
'''
# special case for neb calculations
if self.int_params['images'] is not None:
# we have an neb.
s = []
s.append(': -----------------------------')
s.append(' VASP NEB calculation from %s' % os.getcwd())
try:
images, energies = self.get_neb()
for i,e in enumerate(energies):
s += ['image {0}: {1: 1.3f}'.format(i,e)]
except (VaspQueued):
s += ['Job is in queue']
return '\n'.join(s)
s = []
s.append(': -----------------------------')
s.append(' VASP calculation from %s' % os.getcwd())
if hasattr(self,'converged'):
s.append(' converged: %s' % self.converged)
try:
atoms = self.get_atoms()
uc = atoms.get_cell()
try:
self.converged = self.read_convergence()
except IOError:
# eg no outcar
self.converged = False
if not self.converged:
try:
print self.read_relaxed()
except IOError:
print False
if self.converged:
energy = atoms.get_potential_energy()
forces = atoms.get_forces()
else:
energy = np.nan
forces = [np.array([np.nan, np.nan, np.nan]) for atom in atoms]
if self.converged:
if hasattr(self,'stress'):
stress = self.stress
else:
stress = None
else:
stress = None
# get a,b,c,alpha,beta, gamma
from Scientific.Geometry import Vector
A = Vector(uc[0,:])
B = Vector(uc[1,:])
C = Vector(uc[2,:])
a = A.length()
b = B.length()
c = C.length()
alpha = B.angle(C)*180/np.pi
beta = A.angle(C)*180/np.pi
gamma = B.angle(C)*180/np.pi
volume = atoms.get_volume()
s.append(' Energy = %f eV' % energy)
s.append('\n Unit cell vectors (angstroms)')
s.append(' x y z length')
s.append(' a0 [% 3.3f % 3.3f % 3.3f] %3.3f' % (uc[0][0],
uc[0][1],
uc[0][2],
A.length()))
s.append(' a1 [% 3.3f % 3.3f % 3.3f] %3.3f' % (uc[1][0],
uc[1][1],
uc[1][2],
B.length()))
s.append(' a2 [% 3.3f % 3.3f % 3.3f] %3.3f' % (uc[2][0],
uc[2][1],
uc[2][2],
C.length()))
s.append(' a,b,c,alpha,beta,gamma (deg): %1.3f %1.3f %1.3f %1.1f %1.1f %1.1f' % (a,
b,
c,
alpha,
beta,gamma))
s.append(' Unit cell volume = {0:1.3f} Ang^3'.format(volume))
if stress is not None:
s.append(' Stress (GPa):xx, yy, zz, yz, xz, xy')
s.append(' % 1.3f % 1.3f % 1.3f % 1.3f % 1.3f % 1.3f' % tuple(stress))
else:
s += [' Stress was not computed']
constraints = None
if hasattr(atoms, 'constraints'):
from ase.constraints import FixAtoms, FixScaled
constraints = [[None, None, None] for atom in atoms]
for constraint in atoms.constraints:
if isinstance(constraint, FixAtoms):
for i, constrained in enumerate(constraint.index):
if constrained:
constraints[i] = [True, True, True]
if isinstance(constraint, FixScaled):
constraints[constraint.a] = constraint.mask.tolist()
if constraints is None:
s.append(' Atom# sym position [x,y,z] tag rmsForce')
else:
s.append(' Atom# sym position [x,y,z] tag rmsForce constraints')
for i,atom in enumerate(atoms):
rms_f = np.sum(forces[i]**2)**0.5
ts = ' {0:^4d} {1:^4s} [{2:<9.3f}{3:^9.3f}{4:9.3f}] {5:^6d}{6:1.2f}'.format(i,
atom.symbol,
atom.x,
atom.y,
atom.z,
atom.tag,
rms_f)
# VASP has the opposite convention of constrained
# Think: F = frozen
if constraints is not None:
ts += ' {0} {1} {2}'.format('F' if constraints[i][0] is True else 'T',
'F' if constraints[i][1] is True else 'T',
'F' if constraints[i][2] is True else 'T')
s.append(ts)
s.append('--------------------------------------------------')
if self.get_spin_polarized() and self.converged:
s.append('Spin polarized: Magnetic moment = %1.2f' % self.get_magnetic_moment(atoms))
except AttributeError:
# no atoms
pass
if os.path.exists('INCAR'):
# print all parameters that are set
self.read_incar()
ppp_list = self.get_pseudopotentials()
else:
ppp_list=[(None, None, None)]
s += ['\nINCAR Parameters:']
s += ['-----------------']
for d in [self.int_params,
self.float_params,
self.exp_params,
self.bool_params,
self.list_params,
self.dict_params,
self.string_params,
self.special_params,
self.input_params]:
for key in d:
if key is 'magmom':
np.set_printoptions(precision=3)
value = textwrap.fill(str(d[key]),
width=56,
subsequent_indent=' '*17)
s.append(' %12s: %s' % (key, value))
elif d[key] is not None:
value = textwrap.fill(str(d[key]),
width=56,
subsequent_indent=' '*17)
s.append(' %12s: %s' % (key, value))
s += ['\nPseudopotentials used:']
s += ['----------------------']
for sym,ppp,hash in ppp_list:
s += ['{0}: {1} (git-hash: {2})'.format(sym,ppp,hash)]
# if ibrion in [5,6,7,8] print frequencies
if self.int_params['ibrion'] in [5,6,7,8]:
freq,modes = self.get_vibrational_modes()
s += ['\nVibrational frequencies']
s += ['mode frequency']
s += ['------------------']
for i,f in enumerate(freq):
if isinstance(f, float):
s += ['{0:4d}{1: 10.3f} eV'.format(i,f)]
elif isinstance(f, complex):
s += ['{0:4d}{1: 10.3f} eV'.format(i,-f.real)]
return '\n'.join(s)
natoms = len(atoms)
try:
x, V0, e0, B = analyze_eos()
except TypeError:
x, V0, e0, B = None, None, None, None
magmom = atoms.get_magnetic_moment()
# now we want to write out a row of
data = [id1, composition, spacegroup, natoms, formation_energy, B, magmom]
for i, d in enumerate(data):
sh0.write(NROWS0, i, d)
# now for sheet 1 - unit cell parameters
uc = atoms.get_cell()
A = Vector(uc[0, :])
B = Vector(uc[1, :])
C = Vector(uc[2, :])
a = A.length()
b = B.length()
c = C.length()
alpha = B.angle(C) * 180.0 / np.pi
beta = A.angle(C) * 180.0 / np.pi
gamma = B.angle(C) * 180.0 / np.pi
volume = atoms.get_volume()
stress = atoms.get_stress()
if stress is not None:
sxx, syy, szz, sxy, syz, sxz = stress
else:
sxx, syy, szz, sxy, syz, sxz = [None, None, None, None, None, None]
"""testing to see in what order the points in sketchup are given
Results: Right hand corkscrew in the direction of the normal"""
from Scientific.Geometry import Vector
import readsketchup
import geometry
txt = open('e.txt', 'r').read()
dct = readsketchup.readsketchup(txt)
for key in dct.keys():
plane = dct[key]['points']
normal = Vector(dct[key]['normal'])
calcnormal = geometry.facenormal(plane)
# print normal
# print calcnormal
print normal.angle(calcnormal)
print