def test_molecule_checkpoint_full():
mol1 = load_molecule_g03fchk(
pkg_resources.resource_filename(__name__, "../data/test/sterck/aa.fchk"))
mol1.set_default_graph()
mol1.unit_cell = UnitCell(np.identity(3, float)*25)
mol1.symbols = [periodic[n].symbol for n in mol1.numbers]
with tmpdir(__name__, 'test_molecule_checkpoint_full') as dn:
fn_out = os.path.join(dn, "molecule_checkpoint_full.chk")
mol1.write_to_file(fn_out)
mol2 = Molecule.read_from_file(fn_out)
assert mol1.numbers.shape == mol2.numbers.shape
assert abs(mol1.numbers - mol2.numbers).max() == 0
assert mol1.coordinates.shape == mol2.coordinates.shape
assert abs(mol1.coordinates - mol2.coordinates).max() < 1e-10
assert mol1.masses.shape == mol2.masses.shape
assert abs(mol1.masses - mol2.masses).max() < 1e-10
assert abs(mol1.energy - mol2.energy) < 1e-10
assert mol1.gradient.shape == mol2.gradient.shape
assert abs(mol1.gradient - mol2.gradient).max() < 1e-10
assert mol1.hessian.shape == mol2.hessian.shape
assert abs(mol1.hessian - mol2.hessian).max() < 1e-10
assert mol1.multiplicity == mol2.multiplicity
assert mol1.symmetry_number == mol2.symmetry_number
assert mol1.periodic == mol2.periodic
assert mol1.graph.edges == mol2.graph.edges
assert mol1.title == mol2.title
assert mol1.unit_cell.matrix.shape == mol2.unit_cell.matrix.shape
assert abs(mol1.unit_cell.matrix - mol2.unit_cell.matrix).max() < 1e-10
assert mol1.unit_cell.active.shape == mol2.unit_cell.active.shape
assert (mol1.unit_cell.active == mol2.unit_cell.active).all()
assert mol1.symbols == mol2.symbols
def fn():
from molmod import UnitCell
context.application.model.file_open("test/input/methane_box22_125.xyz")
universe = context.application.model.universe
context.application.action_manager.record_primitives = False
unit_cell = UnitCell(
numpy.identity(3, float) * 22 * angstrom, numpy.ones(3, bool))
primitive.SetProperty(universe, "cell", unit_cell)
context.application.main.select_nodes([universe])
AutoConnectPhysical = context.application.plugins.get_action(
"AutoConnectPhysical")
assert AutoConnectPhysical.analyze_selection()
AutoConnectPhysical()
context.application.main.select_nodes([universe])
FrameMolecules = context.application.plugins.get_action(
"FrameMolecules")
assert FrameMolecules.analyze_selection()
FrameMolecules()
Bond = context.application.plugins.get_node("Bond")
for frame in universe.children:
for bond in frame.children:
if isinstance(bond, Bond):
bond.calc_vector_dimensions()
assert bond.length < 2 * angstrom
def test_molecule_checkpoint_full():
mol1 = load_molecule_g03fchk("test/input/sterck/aa.fchk")
mol1.set_default_graph()
mol1.unit_cell = UnitCell(np.identity(3, float) * 25)
mol1.symbols = [periodic[n].symbol for n in mol1.numbers]
mol1.write_to_file("test/output/molecule_checkpoint_full.chk")
mol2 = Molecule.read_from_file("test/output/molecule_checkpoint_full.chk")
assert mol1.numbers.shape == mol2.numbers.shape
assert abs(mol1.numbers - mol2.numbers).max() == 0
assert mol1.coordinates.shape == mol2.coordinates.shape
assert abs(mol1.coordinates - mol2.coordinates).max() < 1e-10
assert mol1.masses.shape == mol2.masses.shape
assert abs(mol1.masses - mol2.masses).max() < 1e-10
assert abs(mol1.energy - mol2.energy) < 1e-10
assert mol1.gradient.shape == mol2.gradient.shape
assert abs(mol1.gradient - mol2.gradient).max() < 1e-10
assert mol1.hessian.shape == mol2.hessian.shape
assert abs(mol1.hessian - mol2.hessian).max() < 1e-10
assert mol1.multiplicity == mol2.multiplicity
assert mol1.symmetry_number == mol2.symmetry_number
assert mol1.periodic == mol2.periodic
assert mol1.graph.edges == mol2.graph.edges
assert mol1.title == mol2.title
assert mol1.unit_cell.matrix.shape == mol2.unit_cell.matrix.shape
assert abs(mol1.unit_cell.matrix - mol2.unit_cell.matrix).max() < 1e-10
assert mol1.unit_cell.active.shape == mol2.unit_cell.active.shape
assert (mol1.unit_cell.active == mol2.unit_cell.active).all()
assert mol1.symbols == mol2.symbols
def do(self):
universe = context.application.cache.node
# first make sure the cell is right handed
if numpy.linalg.det(
universe.cell.matrix) < 0 and universe.cell.active.sum() == 3:
new_matrix = universe.cell.matrix.copy()
temp = new_matrix[:, 0].copy()
new_matrix[:, 0] = new_matrix[:, 1]
new_matrix[:, 1] = temp
new_cell = UnitCell(new_matrix, universe.cell.active)
primitive.SetProperty(universe, "cell", new_cell)
# then rotate the unit cell box to the normalized frame:
rotation = universe.cell.alignment_a
for child in context.application.cache.transformed_children:
primitive.Transform(child, rotation)
new_cell = UnitCell(numpy.dot(rotation.r, universe.cell.matrix),
universe.cell.active)
primitive.SetProperty(universe, "cell", new_cell)
def create_pattern():
"Read the atom positions and transform them to the flat coordinates"
active, inactive = universe.cell.active_inactive
a = universe.cell.matrix[:, active[0]]
b = universe.cell.matrix[:, active[1]]
c = numpy.cross(a, b)
tmp_cell = UnitCell(numpy.array([a, b, c]).transpose())
rotation = tmp_cell.alignment_a
return [(atom.number, rotation * atom.get_absolute_frame().t)
for atom in iter_atoms([universe])]
def fn():
from molmod import UnitCell
context.application.model.file_open("test/input/core_objects.zml")
unit_cell = UnitCell(numpy.identity(3, float), numpy.ones(3, bool))
context.application.model.universe.cell = unit_cell
WrapCellContents = context.application.plugins.get_action("WrapCellContents")
assert WrapCellContents.analyze_selection()
WrapCellContents()
assert len(context.application.action_manager.undo_stack) == 1
WrapCellContents() # This should not result in an effective thing to happen:
assert len(context.application.action_manager.undo_stack) == 1
def __call__(self, f):
Universe = context.application.plugins.get_node("Universe")
universe = Universe()
Folder = context.application.plugins.get_node("Folder")
folder = Folder()
Atom = context.application.plugins.get_node("Atom")
counter = 1
atom_index = 0
for line in f:
#if len(line) != 81:
# raise FilterError("Each line in a PDB file must count 80 characters, error at line %i, len=%i" % (counter, len(line)-1))
if line.startswith("ATOM"):
extra = {"index": atom_index}
atom_info = periodic[line[76:78].strip()]
try:
t = numpy.array([
float(line[30:38].strip()),
float(line[38:46].strip()),
float(line[46:54].strip())
]) * angstrom
except ValueError:
raise FilterError(
"Error while reading PDB file: could not read coordinates at line %i."
% counter)
atom = Atom(name=line[12:16].strip(),
number=atom_info.number,
transformation=Translation(t),
extra=extra)
universe.add(atom)
atom_index += 1
elif line.startswith("CRYST1"):
space_group = line[55:66].strip().upper()
if space_group != "P 1":
raise FilterError(
"Error while reading PDB file: only unit cells with space group P 1 are supported."
)
a = float(line[6:15].strip()) * angstrom
b = float(line[15:24].strip()) * angstrom
c = float(line[24:33].strip()) * angstrom
alpha = float(line[33:40].strip()) * numpy.pi / 180
beta = float(line[40:47].strip()) * numpy.pi / 180
gamma = float(line[47:54].strip()) * numpy.pi / 180
universe.set_cell(
UnitCell.from_parameters3([a, b, c], [alpha, beta, gamma]))
counter += 1
return [universe, folder]
def __call__(self, f):
Universe = context.application.plugins.get_node("Universe")
universe = Universe()
Folder = context.application.plugins.get_node("Folder")
folder = Folder()
Atom = context.application.plugins.get_node("Atom")
counter = 1
atom_index = 0
for line in f:
#if len(line) != 81:
# raise FilterError("Each line in a PDB file must count 80 characters, error at line %i, len=%i" % (counter, len(line)-1))
if line.startswith("ATOM"):
extra = {"index": atom_index}
atom_info = periodic[line[76:78].strip()]
try:
t = numpy.array([
float(line[30:38].strip()),
float(line[38:46].strip()),
float(line[46:54].strip())
]) * angstrom
except ValueError:
raise FilterError("Error while reading PDB file: could not read coordinates at line %i." % counter)
atom = Atom(
name=line[12:16].strip(), number=atom_info.number,
transformation=Translation(t), extra=extra
)
universe.add(atom)
atom_index += 1
elif line.startswith("CRYST1"):
space_group = line[55:66].strip().upper()
if space_group != "P 1":
raise FilterError("Error while reading PDB file: only unit cells with space group P 1 are supported.")
a = float(line[6:15].strip())*angstrom
b = float(line[15:24].strip())*angstrom
c = float(line[24:33].strip())*angstrom
alpha = float(line[33:40].strip())*numpy.pi/180
beta = float(line[40:47].strip())*numpy.pi/180
gamma = float(line[47:54].strip())*numpy.pi/180
universe.set_cell(UnitCell.from_parameters3([a, b, c], [alpha, beta, gamma]))
counter += 1
return [universe, folder]
def read_from_file(cls, filename):
"""Construct a Molecule object from a previously saved checkpoint file
Arguments:
| ``filename`` -- the file to load from
Usage::
>>> mol = Molecule.read_from_file("mol.chk")
"""
from tamkin.io.internal import load_chk
# load the file
data = load_chk(filename)
# check the names of the fields:
mandatory_fields = set([
"numbers", "coordinates", "masses", "energy", "gradient", "hessian"
])
if not set(data.iterkeys()).issuperset(mandatory_fields):
raise IOError(
"The Checkpoint file does not contain the mandatory fields.")
# take the mandatory fields
constructor_args = {}
for mfield in mandatory_fields:
constructor_args[mfield] = data[mfield]
# take the optional arguments if present
opt_fields = [
"multiplicity", "symmetry_number", "periodic", "title", "symbols"
]
for ofield in opt_fields:
if ofield in data:
constructor_args[ofield] = data[ofield]
# take the special optional arguments that need conversion
if "edges" in data:
graph = MolecularGraph(data["edges"], data["numbers"])
constructor_args["graph"] = graph
if "cell_vectors" in data:
unit_cell = UnitCell(data["cell_vectors"], data.get("cell_active"))
constructor_args["unit_cell"] = unit_cell
# construct the molecule object
return Molecule(**constructor_args)
def __init__(self, filename):
"""
Arguments:
| ``filename`` -- The file to load.
"""
self.filename = filename
# auxiliary skip function
def skip_to(f, linestart):
while True:
line = f.readline()
if line.startswith(linestart):
return line
if len(line) == 0:
return
with open(filename) as f:
# Unit cell parameters
line = skip_to(f, ' DIRECT LATTICE VECTOR COMPONENTS (BOHR)')
if line is None:
raise FileFormatError('Could not find the lattice vectors')
f.readline()
f.readline()
vectors = []
for i in range(3):
line = f.readline()
vectors.append([float(word) for word in line.split()[1:]])
vectors = np.array(vectors)
self.unit_cell = UnitCell(vectors.transpose())
# Atomic numbers and coordinates
line = skip_to(f, ' ATOM CARTESIAN COORDINATES (BOHR)')
if line is None:
raise FileFormatError('Could not find the atomic coordinates')
f.readline()
f.readline()
f.readline()
numbers = []
symbols = []
coordinates = []
while True:
line = f.readline()
if line.startswith(' *****'):
break
words = line.split()
numbers.append(int(words[1]))
symbols.append(words[2])
coordinates.append(
[float(words[3]),
float(words[4]),
float(words[5])])
self.mol = Molecule(np.array(numbers),
np.array(coordinates),
symbols=symbols,
unit_cell=self.unit_cell)
# Basis set specification
line = skip_to(f, ' VARIATIONAL BASIS SET')
if line is None:
raise FileFormatError('Could not find the basis set')
f.readline()
f.readline()
f.readline()
f.readline()
f.readline()
f.readline()
self.basisset = {}
last_basis = None
last_contraction = None
while True:
line = f.readline()
if line.startswith(' *****'):
break
if line.startswith(' '):
# add info to the last atomic basis set
assert last_basis is not None
subshell = line[36:40].strip()
if len(subshell) == 0:
subshell = last_contraction[0]
# add a primitive to the contraction
exponent = float(line[40:50])
if subshell == 'S':
values = exponent, float(line[50:60])
elif subshell == 'SP':
values = exponent, float(line[50:60]), float(
line[60:70])
else:
values = exponent, float(line[70:80])
last_contraction[1].append(values)
else:
# define a new contraction
last_contraction = (subshell, [])
last_basis.append(last_contraction)
else:
# add new atoms
symbol = line.split()[1]
if symbol not in self.basisset:
last_basis = []
self.basisset[symbol] = last_basis
# Compute the total number of basis functions (and orbitals).
self.num_basis = 0
subshell_counts = {'S': 1, 'P': 3, 'SP': 4, 'D': 5, 'F': 7, 'G': 9}
for symbol, basis in self.basisset.items():
symbol_count = symbols.count(symbol)
for subshell, contraction in basis:
self.num_basis += symbol_count * subshell_counts[subshell]
# Density matrix.
line = skip_to(f, ' DENSITY MATRIX DIRECT LATTICE')
if line is None:
raise FileFormatError('Could not find the density matrix')
f.readline()
f.readline()
f.readline()
self.density_matrix = np.zeros((self.num_basis, self.num_basis),
float)
j0 = 0
while j0 < self.num_basis:
f.readline()
f.readline()
f.readline()
for i in range(self.num_basis):
line = f.readline()
words = line.split()[1:]
for j1, word in enumerate(words):
self.density_matrix[i, j0 + j1] = float(word)
j0 += 10
def do(self):
# the indices (n,m) that define the tube, see e.g. the wikipedia page
# about nanotubes for the interpretation of these indices:
# http://en.wikipedia.org/wiki/Carbon_nanotube
n = self.parameters.n
m = self.parameters.m
periodic_tube = isinstance(self.parameters.tube_length, Undefined)
universe = context.application.model.universe
def define_flat():
"Reads and converts the unit cell vectors from the current model."
# some parts of the algorithm have been arranged sub functions like
# these, to reduce the number of local variables in self.do. This
# should also clarify the code.
active, inactive = universe.cell.active_inactive
lengths, angles = universe.cell.parameters
a = lengths[active[0]]
b = lengths[active[1]]
theta = angles[inactive[0]]
return (numpy.array([a, 0], float),
numpy.array([b * numpy.cos(theta), b * numpy.sin(theta)],
float))
flat_a, flat_b = define_flat()
def create_pattern():
"Read the atom positions and transform them to the flat coordinates"
active, inactive = universe.cell.active_inactive
a = universe.cell.matrix[:, active[0]]
b = universe.cell.matrix[:, active[1]]
c = numpy.cross(a, b)
tmp_cell = UnitCell(numpy.array([a, b, c]).transpose())
rotation = tmp_cell.alignment_a
return [(atom.number, rotation * atom.get_absolute_frame().t)
for atom in iter_atoms([universe])]
pattern = create_pattern()
def define_big_periodic():
"Based on (n,m) calculate the size of the periodic sheet (that will be folded into a tube)."
big_a = n * flat_a - m * flat_b
norm_a = numpy.linalg.norm(big_a)
radius = norm_a / (2 * numpy.pi)
big_x = big_a / norm_a
big_y = numpy.array([-big_x[1], big_x[0]], float)
big_b = None
stack_vector = flat_b - flat_a * numpy.dot(
big_x, flat_b) / numpy.dot(big_x, flat_a)
stack_length = numpy.linalg.norm(stack_vector)
nominator = numpy.linalg.norm(stack_vector - flat_b)
denominator = numpy.linalg.norm(flat_a)
fraction = nominator / denominator
stack_size = 1
while True:
repeat = fraction * stack_size
if stack_length * stack_size > self.parameters.max_length:
break
if abs(repeat - round(repeat)
) * denominator < self.parameters.max_error:
big_b = stack_vector * stack_size
break
stack_size += 1
if big_b is None:
raise UserError(
"Could not create a periodic tube shorter than the given maximum length."
)
rotation = numpy.array([big_x, big_y], float)
return big_a, big_b, rotation, stack_vector, stack_size, radius
def define_big_not_periodic():
"Based on (n,m) calculate the size of the non-periodic sheet (that will be folded into a tube)."
big_a = n * flat_a - m * flat_b
norm_a = numpy.linalg.norm(big_a)
radius = norm_a / (2 * numpy.pi)
big_x = big_a / norm_a
big_y = numpy.array([-big_x[1], big_x[0]], float)
stack_vector = flat_b - flat_a * numpy.dot(
big_x, flat_b) / numpy.dot(big_x, flat_a)
stack_length = numpy.linalg.norm(stack_vector)
stack_size = int(self.parameters.tube_length / stack_length)
big_b = stack_vector * stack_size
rotation = numpy.array([big_x, big_y], float)
return big_a, big_b, rotation, stack_vector, stack_size, radius
if periodic_tube:
big_a, big_b, rotation, stack_vector, stack_size, radius = define_big_periodic(
)
else:
big_a, big_b, rotation, stack_vector, stack_size, radius = define_big_not_periodic(
)
def iter_translations():
"Yields the indices of the periodic images that are part of the tube."
to_fractional = numpy.linalg.inv(
numpy.array([big_a, big_b]).transpose())
col_len = int(
numpy.linalg.norm(big_a + m * stack_vector) /
numpy.linalg.norm(flat_a)) + 4
shift = numpy.dot(stack_vector - flat_b,
flat_a) / numpy.linalg.norm(flat_a)**2
for row in xrange(-m - 1, stack_size + 1):
col_start = int(numpy.floor(row * shift)) - 1
for col in xrange(col_start, col_start + col_len):
p = col * flat_a + row * flat_b
i = numpy.dot(to_fractional, p)
if (i >= 0).all() and (i < 1 - 1e-15).all():
yield p
#yield p, (i >= 0).all() and (i < 1).all()
def iter_pattern():
for number, coordinate in pattern:
yield number, coordinate.copy()
# first delete everything the universe:
while len(universe.children) > 0:
primitive.Delete(universe.children[0])
# add the new atoms
Atom = context.application.plugins.get_node("Atom")
if self.parameters.flat:
rot_a = numpy.dot(rotation, big_a)
rot_b = numpy.dot(rotation, big_b)
big_matrix = numpy.array([
[rot_a[0], rot_b[0], 0],
[rot_a[1], rot_b[1], 0],
[0, 0, 10 * angstrom],
], float)
big_cell = UnitCell(
big_matrix, numpy.array([True, periodic_tube, False], bool))
primitive.SetProperty(universe, "cell", big_cell)
for p in iter_translations():
for number, coordinate in iter_pattern():
coordinate[:2] += p
coordinate[:2] = numpy.dot(rotation, coordinate[:2])
translation = Translation(coordinate)
primitive.Add(
Atom(number=number, transformation=translation),
universe)
else:
tube_length = numpy.linalg.norm(big_b)
big_matrix = numpy.diag([radius * 2, radius * 2, tube_length])
big_cell = UnitCell(
big_matrix, numpy.array([False, False, periodic_tube], bool))
primitive.SetProperty(universe, "cell", big_cell)
for p in iter_translations():
for number, coordinate in iter_pattern():
coordinate[:2] += p
coordinate[:2] = numpy.dot(rotation, coordinate[:2])
translation = Translation(
numpy.array([
(radius + coordinate[2]) *
numpy.cos(coordinate[0] / radius),
(radius + coordinate[2]) *
numpy.sin(coordinate[0] / radius),
coordinate[1],
]))
primitive.Add(
Atom(number=number, transformation=translation),
universe)
from zeobuilder.nodes.reference import SpatialReference
from zeobuilder.nodes.vector import Vector
from zeobuilder.undefined import Undefined
from zeobuilder.gui.fields_dialogs import FieldsDialogSimple, DialogFieldInfo
from zeobuilder.zml import dump_to_file, load_from_file
import zeobuilder.actions.primitive as primitive
import zeobuilder.gui.fields as fields
import zeobuilder.authors as authors
from molmod import Translation, UnitCell, angstrom
import numpy, gtk
import StringIO
default_unit_cell = UnitCell(
numpy.identity(3, float) * 10 * angstrom, numpy.zeros(3, bool))
class GLPeriodicContainer(GLContainerBase):
#
# Properties
#
def update_vectors(self):
for node in self.children:
if isinstance(node, GLReferentBase):
node.invalidate_draw_list()
node.invalidate_boundingbox_list()
def set_cell(self, cell, init=False):
def convert_to_value(self, representation):
return UnitCell(self.fields[1].convert_to_value(representation[1]),
self.fields[0].convert_to_value(representation[0]))
def convert_to_value(self, representation):
lengths, angles = ComposedInTable.convert_to_value(
self, representation)
return UnitCell.from_parameters3(lengths, angles)
def endElement(self, name):
if name == "zml_file": return
# now that we have gatherd all information of this tag, create an appropriate object
# first find the tags involved in this operation
current_tag = self.hierarchy[-1][-1]
child_tags = []
if not current_tag.being_processed:
current_tag = self.hierarchy[-2][-1]
child_tags = self.hierarchy[-1]
# do it
if name == "str": current_tag.value = str(current_tag.content)
elif name == "float": current_tag.value = float(current_tag.content)
elif name == "int": current_tag.value = int(current_tag.content)
elif name == "bool":
temp = current_tag.content.lower().strip()
if temp == 'true': current_tag.value = True
else: current_tag.value = False
elif name == "list": current_tag.value = [tag.value for tag in child_tags]
elif name == "dict": current_tag.value = dict((tag.label, tag.value) for tag in child_tags)
elif name == "tuple": current_tag.value = tuple(tag.value for tag in child_tags)
elif name == "shape":
current_tag.value = tuple(int(item) for item in current_tag.content.split())
elif name == "cells":
current_tag.value = numpy.array([eval(item) for item in current_tag.content.split()])
elif name == "array":
child_dict = dict((tag.name, tag.value) for tag in child_tags)
current_tag.value = numpy.reshape(child_dict["cells"], child_dict["shape"])
elif name == "grid":
current_tag.value = numpy.reshape(numpy.array([eval(item) for item in current_tag.content.split()]), (int(current_tag.attributes["rows"]), int(current_tag.attributes["cols"]), -1))
elif name == "binary":
current_tag.value = StringIO.StringIO()
current_tag.content.seek(0)
base64.decode(current_tag.content, current_tag.value)
elif name == "translation":
current_tag.value = Translation(child_tags[0].value)
elif name == "rotation":
current_tag.value = Rotation(child_tags[0].value)
elif name == "transformation":
child_dict = dict((tag.label, tag.value) for tag in child_tags)
current_tag.value = Complete(
child_dict["rotation_matrix"],
child_dict["translation_vector"],
)
elif name == "unit_cell":
child_dict = dict((tag.label, tag.value) for tag in child_tags)
current_tag.value = UnitCell(
child_dict["matrix"],
child_dict["active"],
)
elif name == "expression":
current_tag.value = Expression(current_tag.content)
elif name == "reference":
current_tag.value = None
referent_tag = self.hierarchy[-3][-1]
target_ids = self.target_ids.get(referent_tag)
if target_ids is None:
target_ids = []
self.target_ids[referent_tag] = target_ids
target_ids.append(int(current_tag.attributes["to"]))
elif name == "model_object":
Class = context.application.plugins.get_node(str(current_tag.attributes["class"]))
current_tag.state = dict((tag.label, tag.value) for tag in child_tags)
current_tag.value = Class()
self.model_object_tags[int(current_tag.attributes["id"])] = current_tag
else: pass
# close the door
current_tag.content = None
current_tag.close()
if len(child_tags) > 0: self.hierarchy.pop()
def convert_to_value(self, representation):
lengths, angles = ComposedInTable.convert_to_value(self, representation)
return UnitCell.from_parameters3(lengths, angles)