def _parse_yaml(adjacency, hopping, positions, nt=0, name="", comment=""):
"Parse a !lattice YAML node."
# turn hopping into a list if it isn't already
if not isinstance(hopping, list):
hopping = [hopping] * len(adjacency)
elif len(adjacency) != len(hopping):
raise RuntimeError(
"Lengths of adjacency matrix and list of hopping strengths do not match"
)
# create the lattice with partly empty sites
lat = Lattice(name=name, comment=comment, nt=nt)
lat.sites = [
Site(i, np.array(pos), [], []) for i, pos in enumerate(positions)
]
# fill in neighour and hopping lists
for (i, j), hop in zip(adjacency, hopping):
if i > len(hopping) or j > len(hopping):
raise RuntimeError("Site index out of range: [{}, {}]".format(
i, j))
_append_adj_hop(lat.sites[i], j, hop)
_append_adj_hop(lat.sites[j], i, hop)
return lat
class LatticeRunner(Thread):
def __init__(self, args):
Thread.__init__(self)
self.args = args
self.lattice = Lattice(size=args.size,
slider=args.slider,
onlyRedBlue=not args.any,
defKillers=args.defKillers,
density=args.density,
numRatio=args.numRatio,
redAdvantage=args.redAdvantage,
blueAdvantage=args.blueAdvantage,
redGrowth=args.redGrowth,
blueGrowth=args.blueGrowth,
deathRate=100000)
self.args = args
self.quit = False
def stop(self):
self.quit = True
def run(self):
for iteration in range(0, self.args.evolutions):
self.lattice.evolve(1)
if self.quit:
print("Aborting")
break
print("Generations: %d" % self.lattice.generation)
def _wnd_to_lattice(graph):
"Turn a graph read from a w3d or w2d file into a Lattice object."
lat = Lattice()
lat.sites = [
Site(idx, pos, neigh, [1] * len(neigh)) for idx, pos, neigh in graph
]
return lat
def __init__(self,datasetfilename):
"some codes, reserved rules, and average lift so far"
self.latt = Lattice(datasetfilename)
self.count = 0
self.DISCARD = -1
self.reserved = []
self.sumlifts = 0.0
self.numlifts = 0
def cleanup(self, preserve_last: bool = False):
'Delete all run directories'
n_lats = len(self.rholist) - 1
if preserve_last:
n_lats -= 1 # Save the last run
for i in range(n_lats):
mylat = Lattice(self.salt, self.sf, self.l, self.rholist[i][1])
mylat.cleanup()
def minimal_lattice(self, test, verbose=False, exclude=True):
print test
extent = copy.deepcopy(self.dataset)
for v in extent:
v.intent = v.intent & test.intent
if exclude and v.intent == test.intent:
v.intent = set()
lattice = Lattice(extent)
return lattice.score_lattice(verbose=verbose)
def __init__(self,
lattice,
positions,
atoms,
is_cartesian=False,
name=None):
"""
Create a Structure object.
Args:
lattice(Lattice or 3x3 Array): The lattice either as a Lattice object or as a 3x3 array of which each raw corresponds to a lattice vector.
frac_positions (List): A List of fractional coordinates of each atom.
atoms (List): A List of atoms either as atomic symbols or as atomic numbers or Element objects.
name (str): The name of the system. Default is None.
"""
if isinstance(lattice, Lattice):
self.__lattice = lattice
else:
self.__lattice = Lattice(lattice)
if is_cartesian:
self.__cart_positions = np.array(positions)
self.__frac_positions = self.__lattice.get_frac_coords(positions)
else:
self.__frac_positions = np.array(positions)
self.__cart_positions = self.__lattice.get_cart_coords(positions)
self.__atoms = []
for atom in atoms:
if isinstance(atom, Element):
element = atom
else:
element = Element(atom)
self.__atoms.append(element)
self.__element_species = []
self.__num_per_species = []
for species, atoms in itertools.groupby(self.__atoms):
self.__element_species.append(species)
self.__num_per_species.append(len(list(atoms)))
# tempt = None
# for atom in self.__atoms:
# if tempt != atom:
# self.__element_species.append(atom)
# self.__num_per_species.append(1)
# tempt = atom
# else:
# self.__num_per_species[-1] += 1
if name is None:
name = ''.join('{:s}{:d} '.format(element.atomic_symbol, num)
for element, num in zip(self.__element_species,
self.__num_per_species))
self.__name = name
def replace_QD_with_QDth_lattice(slices,k0,length,label,particle,aperture):
lattice = Lattice()
thinlen = length/slices
for nb in range(slices):
if FLAGS['express']:
instance = ELM.QDthx(k0=k0,length=thinlen,label=label,particle=particle,aperture=aperture)
else:
instance = ELM.QDth(k0=k0,length=thinlen,label=label,particle=particle,aperture=aperture)
lattice.add_element(instance)
return lattice
def main():
# Initialize lattice object:
l = Lattice(50)
# Initializing ojbect in the lattice (bacteria) and empty lattice:
x = int(0.99 * l.N)
x = l.N - 1
y = int(0.49 * l.N)
l.initial_lattice(int(x), y, 1, 1) # Top row = 1, object in lattice
epsilon = 10**-3
num_iterations = 0
start_time = time.time()
# Question 2.1
while (l.delta > epsilon):
l.SOR(omega=1)
l.grow_object(eta=1)
num_iterations += 1
print("--- %s seconds ---" % (time.time() - start_time))
print(">>>>", len(np.where(l.objects == 1)[0]))
print("Number of iterations needed to get here = ", num_iterations)
l.print_lattice()
def __init__(self, scale=0, depth=0):
"""
Initializes the instance with a DMERA with identity gates.
Args:
scales (int): Number of qubits = 2 ** scales
depth (int): Depth per scale
"""
self.D = depth
self.n = scale
self.lattice = Lattice()
def tagger_lattice(self, test):
extent = copy.deepcopy(self.dataset)
flag = False
for v in extent:
v.intent = v.intent & test.intent
if v.intent: flag = True
if flag:
lattice = Lattice(extent)
lattice.score_lattice()
return lattice.get_highest_outcome()
else:
return False
class MainWindow():
"""
Defines the main window for the envelope tool GUI
"""
def __init__(self):
"""Initialise the main window"""
self.window = Window(ROOT.gClient.GetRoot(), # pylint: disable=E1101
ROOT.gClient.GetRoot(), # pylint: disable=E1101
SHARE_DIR+"main_frame.json")
self.lattice = Lattice()
self.beam_setup = None
self.magnet_setup = None
self.plot_setup = None
self.plot_setup_options = [{"variable_type":0,
"first_var":0,
"plot_apertures":True}]
self.window.set_button_action("&Beam Setup", self.beam_button_action)
self.window.set_button_action("&Magnet Setup",
self.magnet_button_action)
self.window.set_button_action("&Plot Setup", self.plot_button_action)
self.window.set_button_action("E&xit", self.exit_button_action)
self.update_plot()
def beam_button_action(self):
"""Handle a Beam Setup button press"""
if self.beam_setup == None:
self.beam_setup = BeamSetup(self, self.window.main_frame)
ref, ellipse = self.lattice.get_beam()
self.beam_setup.set_reference(ref)
self.beam_setup.set_matrix(ellipse)
def magnet_button_action(self):
"""Handle a Magnet Setup button press"""
if self.magnet_setup == None:
self.magnet_setup = MagnetSetup(self, self.window.main_frame)
def plot_button_action(self):
"""Handle a Plot Setup button press"""
if self.plot_setup == None:
self.plot_setup = PlotSetup(self, self.window.main_frame,
self.plot_setup_options)
def exit_button_action(self):
"""Handle a Exit button press"""
self.window.close_window()
def update_plot(self):
"""Update the plot"""
canvas_frame = self.window.get_frame("main_canvas", "canvas")
canvas = canvas_frame.GetCanvas()
Plotter(self.plot_setup_options, canvas, self.lattice.ref_list,
self.lattice.ellipse_list, self.lattice.get_field_list())
def test_degree(self, test, verbose=False):
extent = copy.deepcopy(self.dataset)
for v in extent:
v.intent = v.intent & test.intent
lattice = Lattice(extent)
'''
try:
lattice = self.lattice
except AttributeError:
self.lattice = Lattice(copy.deepcopy(self.dataset), verbose)
lattice = self.lattice
'''
return lattice.score_similarity(verbose)
def getNodeEdgeList():
# Given the nodeDic, compute node list and edge list in Lattice.py, then return them as JS vars.
if str(request.form["jsonClean"]) == "true":
nodeDic = literal_eval(
json.loads(request.form['nodeDic'].replace(
'\n', '').decode('string_escape')))
else:
nodeDic = json.loads(request.form['nodeDic'])
G = Lattice()
node = G.generateNode(nodeDic)
edge = G.generateEdge(nodeDic)
return jsonify(edge, node)
def set_spec_G(self, G, preparsed=False):
"""
Take the spec G array for the psic geometry
and set all the relevant orientation info...
"""
if not preparsed:
(cell, or0, or1, n) = spec_psic_G(G)
else:
(cell, or0, or1, n) = G
self.n = n
self.or0 = or0
self.or1 = or1
self.lattice = Lattice(*cell)
self._calc_UB()
def main():
# begin_time = time.time()
parser = argparse.ArgumentParser()
parser.add_argument('--dict',
type=str,
default='./models/ipadic-vocab.txt.dict',
metavar='PATH',
help='double-array dictionary')
parser.add_argument('-q', '--query', type=str, help='query')
args = parser.parse_args()
da = DoubleArray()
print('Loading dic...')
da.load(args.dict)
print('Loaded!')
query = args.query
lattice = Lattice(query)
for idx in range(len(query)):
cps_q = query[idx:]
print('=====Search {}======'.format(cps_q))
cp_list = da.commonPrefixSearch(cps_q)
print('commonPrefixSearch("{}"): {}'.format(cps_q, cp_list))
for cp in cp_list:
lattice.insert(idx, idx + len(cp), cp)
# print('Process time: {:.1f}s'.format(time.time() - begin_time))
lattice.pprint()
lattice.plot()
def make_kagome(Lx, Ly, periodic, spacing, name, comment):
lat = Lattice(name, comment)
size = Lx * Ly
num_sites = size * 3
# translation vector
trans = list(np.array([1.0, np.sqrt(3)]) * spacing)
a, b, c, sites = position(Lx, Ly, trans)
site_pos = nearest_neighbours(size, a, b, c)
# boundary sites
boundary_sites_a = sites[0:Ly * 3:3] + sites[0::Ly * 3]
boundary_sites_b = sites[1::Ly * 3] + sites[Ly * 3 * (Lx - 1) + 1::3]
boundary_sites_c = sites[2:Ly * 3:3] + sites[(Ly * 3) - 1::(Ly * 3)]
boundary_ind_a = _finding_index(boundary_sites_a, sites)
boundary_ind_b = _finding_index(boundary_sites_b, sites)
boundary_ind_c = _finding_index(boundary_sites_c, sites)
neighbour_index, adjacency = adjacencyList(Lx, Ly, site_pos, sites,
boundary_ind_a, boundary_ind_b,
boundary_ind_c, periodic)
#hopping_matrix = np.ones(len(adjacency))
positions = np.zeros((num_sites, 3))
positions[:, :-1] = sites # making 3-dim
for i in range(len(sites)):
# hopping matrix of equal amplitude
hoppings = [1] * len(neighbour_index[i])
lat.sites.append(Site(i, positions[i], neighbour_index[i], hoppings))
return lat
def process_word(word):
lattice = Lattice(base_decompounder.get_decompound_lattice(word))
viterbi_path = vit.viterbi_decode(Compound(word, None, lattice))
return [
word.encode('utf-8'),
print_path(viterbi_path).encode('utf-8')
]
def test_generate_simple_exact_cover_solution2(self):
col_names = ['a', 'b', 'c', 'd']
matrix = [['0', '1', '1', '0'], ['1', '0', '0', '0'],
['1', '0', '1', '0'], ['0', '1', '0', '0']]
lattice = Lattice(matrix, col_names, delete_zeros=True)
solutions = generate_exact_cover_solutions(lattice)
self.assertEqual(0, len(solutions))
class DMERA1(Circuit):
"""
This is a DMERA circuit ansatz for quantum many-body systems in
one spatial dimension.
"""
def __init__(self, scale=0, depth=0):
"""
Initializes the instance with a DMERA with identity gates.
Args:
scales (int): Number of qubits = 2 ** scales
depth (int): Depth per scale
"""
self.D = depth
self.n = scale
self.lattice = Lattice()
def expand(self, factor):
"""
Expands the underlying lattice by a factor. Add preparation
gates for the newly introduced qubits.
"""
new_lattice = self.lattice.expand(factor)
pts_new = list(set(new_lattice.pts) - set(self.lattice.pts))
self.extend([Prepare(self.qubits[v]) for v in pts_new])
def entangle(self):
"""
def getJsonFromLattice():
# set up the tree example
G = Lattice()
v1 = vizObj(x=["Clinton", "Trump", "Others"],y="% of vote",filters=["All"],\
agg_func="SUM",tablename="election")
v1.setData([48, 46, 6])
root = vizNode(viz=v1, parents=None)
v2 = vizObj(x=["Clinton", "Trump", "Others"],y="% of vote",filters=["Race = White"],\
agg_func="SUM",tablename="election")
v2.setData([31, 62, 7])
W = vizNode(viz=v2, parents=[root])
v3 = vizObj(x=["Clinton", "Trump", "Others"],y="% of vote",filters=["Gender = F"],\
agg_func="SUM",tablename="election")
v3.setData([21, 70, 9])
F = vizNode(viz=v3, parents=[root])
v4 = vizObj(x=["Clinton", "Trump", "Others"], y="% of vote", filters=["Color = Blue"], \
agg_func="SUM", tablename="election")
v4.setData([21, 52, 27])
B = vizNode(viz=v4, parents=[W])
v5 = vizObj(x=["Clinton", "Trump", "Others"], y="% of vote", filters=["Job = Student"], \
agg_func="SUM", tablename="election")
v5.setData([20, 30, 50])
J = vizNode(viz=v5, parents=[W, B])
# set up the tree example
for nodes in G.getNodes():
for child in nodes.get_child():
G.addEdge(nodes, child)
G.addMultiNodes([root, W, F, B, J])
root.set_children([W, F])
W.set_children([B])
W.set_children([J])
B.set_children([J])
nodeDic = G.generateNodeDic()
#nodeDic = "{\"1\": [{ \"xAxis\": \"0\", \"yAxis\":43.40789274938343},{ \"xAxis\": \"1\", \"yAxis\":56.59210725061657},{\"childrenIndex\":[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12], \"populationSize\":492526704188, \"filter\":\"#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"2\": [{ \"xAxis\": \"0\", \"yAxis\":99.09927735409117},{ \"xAxis\": \"1\", \"yAxis\":0.9007226459088256},{\"childrenIndex\":[13, 28, 30, 34], \"populationSize\":65236316603, \"filter\":\"#is_profile_query$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"3\": [{ \"xAxis\": \"0\", \"yAxis\":99.09927735409117},{ \"xAxis\": \"1\", \"yAxis\":0.9007226459088256},{\"childrenIndex\":[17, 28, 38, 43], \"populationSize\":65236316603, \"filter\":\"#is_event_query$1#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"4\": [{ \"xAxis\": \"0\", \"yAxis\":98.84352038584385},{ \"xAxis\": \"1\", \"yAxis\":1.156479614156162},{\"childrenIndex\":[30, 38, 48], \"populationSize\":55050620539, \"filter\":\"#has_impressions_tbl$1#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"5\": [{ \"xAxis\": \"0\", \"yAxis\":87.72514337314605},{ \"xAxis\": \"1\", \"yAxis\":12.27485662685395},{\"childrenIndex\":[25, 35, 41, 46, 50, 52], \"populationSize\":115838325255, \"filter\":\"#has_distinct$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"6\": [{ \"xAxis\": \"0\", \"yAxis\":73.54175531539768},{ \"xAxis\": \"1\", \"yAxis\":26.458244684602324},{\"childrenIndex\":[64, 97, 102, 105, 107], \"populationSize\":53156154309, \"filter\":\"#is_profile_query$1#has_distinct$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"7\": [{ \"xAxis\": \"0\", \"yAxis\":73.54175531539768},{ \"xAxis\": \"1\", \"yAxis\":26.458244684602324},{\"childrenIndex\":[73, 97, 111, 115, 117], \"populationSize\":53156154309, \"filter\":\"#is_event_query$0#has_distinct$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"8\": [{ \"xAxis\": \"0\", \"yAxis\":29.77955596154781},{ \"xAxis\": \"1\", \"yAxis\":70.22044403845219},{\"childrenIndex\":[26, 27, 36, 42, 47, 51, 53], \"populationSize\":376688378933, \"filter\":\"#has_distinct$1#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"9\": [{ \"xAxis\": \"0\", \"yAxis\":30.47638712866313},{ \"xAxis\": \"1\", \"yAxis\":69.52361287133687},{\"childrenIndex\":[15, 18, 20, 22, 24, 27], \"populationSize\":82477942992, \"filter\":\"#is_multi_query$1#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"10\": [{ \"xAxis\": \"0\", \"yAxis\":19.748564939482314},{ \"xAxis\": \"1\", \"yAxis\":80.25143506051768},{\"childrenIndex\":[66, 76, 83, 88, 91], \"populationSize\":68383077780, \"filter\":\"#is_multi_query$1#has_distinct$1#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"11\": [{ \"xAxis\": \"0\", \"yAxis\":77.05061337960112},{ \"xAxis\": \"1\", \"yAxis\":22.949386620398883},{\"childrenIndex\":[81, 120, 122], \"populationSize\":61495053848, \"filter\":\"#has_impressions_tbl$0#has_distinct$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"12\": [{ \"xAxis\": \"0\", \"yAxis\":20.596887099254975},{ \"xAxis\": \"1\", \"yAxis\":79.40311290074501},{\"childrenIndex\":[56, 58, 60, 62], \"populationSize\":71779638383, \"filter\":\"#is_multi_query$1#is_profile_query$1#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"13\": [{ \"xAxis\": \"0\", \"yAxis\":20.596887099254975},{ \"xAxis\": \"1\", \"yAxis\":79.40311290074501},{\"childrenIndex\":[56, 68, 70, 72], \"populationSize\":71779638383, \"filter\":\"#is_multi_query$1#is_event_query$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"14\": [{ \"xAxis\": \"0\", \"yAxis\":21.13295807883538},{ \"xAxis\": \"1\", \"yAxis\":78.86704192116461},{\"childrenIndex\":[78, 80], \"populationSize\":72696207193, \"filter\":\"#is_multi_query$1#has_impressions_tbl$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"15\": [{ \"xAxis\": \"0\", \"yAxis\":21.933813158690548},{ \"xAxis\": \"1\", \"yAxis\":78.06618684130945},{\"childrenIndex\":[85], \"populationSize\":73168015971, \"filter\":\"#is_multi_query$1#has_clicks_tbl$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"16\": [{ \"xAxis\": \"0\", \"yAxis\":34.90524231845271},{ \"xAxis\": \"1\", \"yAxis\":65.09475768154729},{\"childrenIndex\":[14, 15, 29, 31, 32, 33], \"populationSize\":427290387585, \"filter\":\"#is_profile_query$1#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"17\": [{ \"xAxis\": \"0\", \"yAxis\":34.90524231845271},{ \"xAxis\": \"1\", \"yAxis\":65.09475768154729},{\"childrenIndex\":[16, 18, 29, 37, 39, 40], \"populationSize\":427290387585, \"filter\":\"#is_event_query$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"18\": [{ \"xAxis\": \"0\", \"yAxis\":79.8957702319091},{ \"xAxis\": \"1\", \"yAxis\":20.10422976809091},{\"childrenIndex\":[86, 124], \"populationSize\":70437357911, \"filter\":\"#has_clicks_tbl$0#has_distinct$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"19\": [{ \"xAxis\": \"0\", \"yAxis\":22.863232070479246},{ \"xAxis\": \"1\", \"yAxis\":77.13676792952076},{\"childrenIndex\":[], \"populationSize\":74047346293, \"filter\":\"#is_multi_query$1#has_actions_tbl$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}],\"20\": [{ \"xAxis\": \"0\", \"yAxis\":36.43204694793704},{ \"xAxis\": \"1\", \"yAxis\":63.56795305206296},{\"childrenIndex\":[19, 20, 44, 45], \"populationSize\":437476083649, \"filter\":\"#has_impressions_tbl$0#\",\"yName\":\"SUM(slots_millis_reduces)\"}]}"
#nodeDic = json.loads(nodeDic.replace('\n', '').decode('string_escape'))
print "nodeDic:"
print nodeDic
node = G.generateNode(nodeDic)
edge = G.generateEdge(nodeDic)
#print(ret)
ret2 = '<svg xmlns="http://www.w3.org/2000/svg" width="480" height="260"><g transform="translate(50,30)"><rect x="0" y="0" width="100%" height="100%" fill="#ffffff"></rect><rect x="14" y="0" width="105" height="200" fill="steelblue" class="Clinton" id="48"></rect><rect x="139" y="8.333333333333343" width="105" height="191.66666666666666" fill="steelblue" class="Trump" id="46"></rect><rect x="264" y="175" width="105" height="25" fill="steelblue" class="Others" id="6"></rect><g class="axis" transform="translate(-10, 0)"><g transform="translate(0,200)" style="opacity: 1;"><line class="tick" x2="-6" y2="0"></line><text x="-9" y="0" dy=".32em" style="text-anchor: end;">0</text></g><g transform="translate(0,158.33333333333334)" style="opacity: 1;"><line class="tick" x2="-6" y2="0"></line><text x="-9" y="0" dy=".32em" style="text-anchor: end;">10</text></g><g transform="translate(0,116.66666666666667)" style="opacity: 1;"><line class="tick" x2="-6" y2="0"></line><text x="-9" y="0" dy=".32em" style="text-anchor: end;">20</text></g><g transform="translate(0,75)" style="opacity: 1;"><line class="tick" x2="-6" y2="0"></line><text x="-9" y="0" dy=".32em" style="text-anchor: end;">30</text></g><g transform="translate(0,33.33333333333334)" style="opacity: 1;"><line class="tick" x2="-6" y2="0"></line><text x="-9" y="0" dy=".32em" style="text-anchor: end;">40</text></g><path class="domain" d="M-6,0H0V200H-6"></path></g><g class="axis" transform="translate(0,210)"><g transform="translate(70.5,0)" style="opacity: 1;"><line class="tick" y2="6" x2="0"></line><text y="9" x="0" dy=".71em" style="text-anchor: middle;">Clinton</text></g><g transform="translate(195.5,0)" style="opacity: 1;"><line class="tick" y2="6" x2="0"></line><text y="9" x="0" dy=".71em" style="text-anchor: middle;">Trump</text></g><g transform="translate(320.5,0)" style="opacity: 1;"><line class="tick" y2="6" x2="0"></line><text y="9" x="0" dy=".71em" style="text-anchor: middle;">Others</text></g><path class="domain" d="M0,6V0H390V6"></path></g><text transform="translate(-30, -20)">% of vote</text><text x="195" y="-8px" text-anchor="middle" style="font-size: 16px; text-decoration: underline;">All</text></g></svg>'
return (nodeDic, node, edge)
def getRSS(params, Na, Nb, blobs_by_point):
"""Return the sum of squared distances between all blobs and their lattice point"""
vax, vay, vbx, vby, ox, oy = params
lattice = Lattice(Na, Nb, [vax, vay], [vbx, vby], [ox, oy])
lattice_points = lattice.getLatticePoints()
sum = 0
for i, point in enumerate(blobs_by_point):
point_x, point_y = lattice_points[i]
for blob in point:
blob_y, blob_x, r = blob
square_dist = (point_x - blob_x)**2 + (point_y - blob_y)**2
sum += square_dist
return sum
def __init__(self, args):
Thread.__init__(self)
self.args = args
self.lattice = Lattice(size=args.size,
slider=args.slider,
onlyRedBlue=not args.any,
defKillers=args.defKillers,
density=args.density,
numRatio=args.numRatio,
redAdvantage=args.redAdvantage,
blueAdvantage=args.blueAdvantage,
redGrowth=args.redGrowth,
blueGrowth=args.blueGrowth,
deathRate=100000)
self.args = args
self.quit = False
def test_lattice_number_neigbors():
''' Test the number of neighbors in the lattice.'''
lattice = Lattice(3, 3)
for place in [(0, 0), (0, 1), (1, 1)]:
answer = lattice.find_neighbors(place)
assert len(answer) == 4, "Wrong number of neighbors"
assert (2, 1) in lattice.find_neighbors((1, 1))
try:
fail = True
lattice2 = Lattice(5, 1)
except AssertionError:
fail = False
assert not fail
def read_trj(trj_file):
"""
return: Simulation
parameters:
trj_file: string | name of trj file
"""
simulation = Simulation()
with open(trj_file, 'r') as trj:
while True:
line = trj.readline()
if not line:
break
lattice = Lattice()
lattice.set_a(np.array(line.split(), dtype=float))
lattice.set_b(np.array(trj.readline().split(), dtype=float))
lattice.set_c(np.array(trj.readline().split(), dtype=float))
configuration = Configuration(lattice=lattice)
atom_types = trj.readline().split()
atom_counts = np.array(trj.readline().split(), dtype=int)
natom = np.sum(atom_counts)
for i in xrange(natom):
atom_record = trj.readline().split()
atom_name = atom_record[0]
atom_position = np.array(atom_record[1:], dtype=float)
configuration.insert_atom(Atom(atom_name, atom_position))
simulation.insert_configuration(configuration)
return simulation
def add_bitext(self, src, tgt):
'''
Adds a training bitext.
Input:
src_data: filepath containing n-best list of src_data hypotheses
tgt_data: string containing translation
Postcondition:
A source word lattice is constructed from src_data, compiled into a weighted FSA.
A bitext containing the weighted source FSA and string tgt_data is stored.
'''
src_lattice = Lattice(syms=self.src_syms)
src_lattice.load_delimited(src)
# Weight the edges
src_lattice.forward_backward_weights()
# Add the NULL token at the front
src_lattice.prepend_epsilon()
self.src_data.append(src_lattice.fsa)
# TODO: Figure out how to extract vocabulary from FSA (src_lattice.sigma)
for arc in common.arcs(src_lattice.fsa):
self.src_vocab.add(arc.ilabel)
self.tgt_data.append(tgt)
self.tgt_vocab = self.tgt_vocab.union(set(tgt.split()))
def main():
time_size = int(os.getenv("TIME_SIZE"))
space_size = int(os.getenv("SPACE_SIZE"))
dimension = int(os.getenv("DIMENSION"))
beta = float(os.getenv("BETA"))
lattice = Lattice(
time_size,
space_size,
dimension,
beta,
SU3,
)
print "Lattice initialization complete! Beginning simulation..."
t0 = time.time()
for i in range(1000):
lattice.metropolisUpdate()
print time.time() - t0
def __init__(self):
"""Initialise the main window"""
self.window = Window(ROOT.gClient.GetRoot(), # pylint: disable=E1101
ROOT.gClient.GetRoot(), # pylint: disable=E1101
SHARE_DIR+"main_frame.json")
self.lattice = Lattice()
self.beam_setup = None
self.magnet_setup = None
self.plot_setup = None
self.plot_setup_options = [{"variable_type":0,
"first_var":0,
"plot_apertures":True}]
self.window.set_button_action("&Beam Setup", self.beam_button_action)
self.window.set_button_action("&Magnet Setup",
self.magnet_button_action)
self.window.set_button_action("&Plot Setup", self.plot_button_action)
self.window.set_button_action("E&xit", self.exit_button_action)
self.update_plot()
def test_entropy_equalsSumOfParts(self):
J = 1
gJ = 1
Tc = 123
Nm = 1
theta_D = 123
N = 1
F0 = 1
mc = Magnetocaloric(J, gJ, Tc, Nm, theta_D, N, F0)
mag = Magnetization(J, gJ, Tc, Nm)
lat = Lattice(theta_D, N)
temperature = 300
magnetic_field = 0
expected = mag.magnetic_entropy(
temperature, magnetic_field) + lat.lattice_entropy(temperature)
result = mc.entropy(temperature, magnetic_field)
assert result == expected
def main(opts):
opts = opts if opts is not None else argv
g = read_graph(opts[1:3])
levels_to_build = int(opts[opts.index('-l') + 1]) if '-l' in opts else None
start = time()
lattice = Lattice(g, levels_to_build)
elapsed = time() - start
lattice.save('lattice.txt')
print('Количество построенных уровней =', lattice.levels_count)
print('Построение заняло время =', elapsed)
print('Количество элементов решетки =', lattice.number_of_nodes())
if '-i' in opts:
filename = opts[opts.index('-fn') + 1] if '-fn' in opts else 'diagram.png'
draw_lattice(lattice, filename)
print(f'Диаграмма построена и сохранена в файл {filename}')
if '-it' in opts:
filename = opts[opts.index('-tfn') + 1] if '-fn' in opts else 'tree.png'
draw_tree(g, filename)
print(f'Изображение дерева построено и сохранено в файл {filename}')
def train(args):
# n_feature = 1 + (NUMBER_OF_POS + 2) ** (args.pos_lorder + args.pos_rorder + 1)
n_feature = (HIDDEN + NUMBER_OF_POS) * NUMBER_OF_POS
print('building CRF...')
model = HigherOrderCRF.build(n_feature, args.pos_lorder, args.pos_rorder,
args.posmodel, args.hoposmodel, args.lr,
args.train_alpha, args.l2, args.test_alpha)
model.init_weight()
print('build lattice')
l = Lattice(args.pos_lorder, args.pos_rorder, model)
print('done')
for epoch in range(args.epoch):
print('Start epoch {}'.format(epoch + 1))
s = time.time()
n_word = 0
n_corr = 0
sum_log_ll = 0
for [words, postags] in sent_tag_iter(args.train_data):
postags = [pos2id[pos] for pos in postags]
sufs = [sufvocab[suf] for suf in check_sufvocab(words)]
caps = [word2capf(word) for word in words]
words = [vocab[word] for word in check_vocab(words)]
features = [words, sufs, caps]
predtags = l.viterbe_decode_hocrf(features, train_flg=True)
assert len(postags) == len(predtags)
n_corr += sum(1 for i in range(len(postags))
if postags[i] == predtags[i])
n_word += len(words)
log_ll = l.update_hocrf(features, postags)
sum_log_ll += log_ll
print('Train accuracy : {} / {} = {}'.format(n_corr, n_word,
float(n_corr / n_word)))
print('Train Log Likelifood : {}'.format(sum_log_ll))
print('Running Time in this epoch : {} sec'.format(time.time() - s))
if args.valid_data:
valid_accuracy = validation(l, args.valid_data)
print('Valid accuracy : {}'.format(valid_accuracy))
if args.test_data:
test_accuracy = validation(l, args.test_data)
print('Test accuracy : {}'.format(test_accuracy))
def test_exact_cover(self):
base_shapes = get_base_shapes()
col_names = []
for shape in base_shapes:
col_names.append(shape.name)
for i in range(1, 60 + 1):
col_names.append(i)
binary_matrix = generate_all_orientations_with_encodings(base_shapes)
lattice = Lattice(binary_matrix, col_names)
c = lattice.head.east
while c is not lattice.head:
r = c.south
while r is not c:
if r.key is not None and r.key is 0:
lattice.delete(r)
r = r.south
c = c.east
solutions = generate_exact_cover_solutions(lattice)
print("Len solution: ", len(solutions))
self.assertIsNotNone(solutions)
def make_lattice(latticeList,in_data):
""" instanciate all elements from flattened node list"""
lattice = Lattice()
DEBUG_OFF('make_lattice for sollteilchen\n'+PARAMS['sollteilchen'].string())
elements = read_elements(in_data)
for ID in lattice_list:
element = elements[ID]
element = liofd2d(element)
elementClass = element['type']
elmItem = (elementClass,element)
# !!INSTANCIATE!!
(label,instance) = instanciate_element(elmItem)
section = instance.section if FLAGS['sections'] else '*'
DEBUG_MODULE('instance {} {} {}'.format(label,instance,section))
# add element instance to lattice
if isinstance(instance,ELM._Node):
lattice.add_element(instance)
# elif isinstance(instance,Lattice):
# lattice.concat(instance) # concatenate partial with lattice
return lattice # the complete lattice
def test_cover_col2(self):
col_names = ['a', 'b', 'c']
matrix = [['0', '1', '1'], ['1', '0', '0'], ['1', '1', '1']]
lattice = Lattice(matrix, col_names)
c = lattice.head.east
while c is not lattice.head:
r = c.south
while r is not c:
if r.key is not None and r.key is '0':
lattice.delete(r)
print("Deleting lattice node")
r = r.south
c = c.east
a = lattice.head.east
lattice = cover_col(lattice, a)
b = a.east
lattice = cover_col(lattice, b)
c = b.east
lattice = cover_col(lattice, c)
print(lattice)
def test__init__default():
lattice = Lattice()
assert isinstance(lattice.a0, float)
assert isinstance(lattice.H, np.ndarray)
assert isinstance(lattice.a1, np.ndarray)
assert isinstance(lattice.a2, np.ndarray)
assert isinstance(lattice.a3, np.ndarray)
assert lattice.H.shape == (3, 3)
assert lattice.a1.shape == (3, )
assert lattice.a2.shape == (3, )
assert lattice.a3.shape == (3, )
def import_from_vasp(filename):
"""
Import structure data from a VASP POSCAR or CONTCAR file.
Args:
filename (str): The file to import from.
Returns:
A Structure object.
"""
with open(filename) as f:
lines = f.readlines()
name = lines[0].strip('\n')
scale = float(lines[1])
vectors = []
for i in range(2, 5):
vector = [
float(coord) * scale for coord in lines[i].split()[:3]
]
vectors.append(vector)
lattice = Lattice(vectors)
num_per_species = []
for x in lines[6].split():
try:
num = int(x)
num_per_species.append(num)
except ValueError:
pass
element_species_symbols = lines[5].split()[:len(num_per_species)]
atoms = []
for symbol, num in zip(element_species_symbols, num_per_species):
atoms += [symbol] * num
if lines[7][0].lower() == 's':
index = 8
else:
index = 7
if (lines[index][0].lower() == 'c'
or lines[index][0].lower() == 'k'):
is_cartesian = True
else:
is_cartesian = False
index += 1
positions = []
for i in range(index, index + sum(num_per_species)):
position = [float(coord) for coord in lines[i].split()[:3]]
positions.append(position)
return Structure(lattice, positions, atoms, is_cartesian, name)
def test_energy_ferro():
''' Check the energy of the ferromagnetic state.'''
size = 4
coupling = 1.0
lattice = Lattice(size, size)
ham = Hamiltonian(lattice, coupling)
assert ham.energy(
ones((size, size), dtype=bool)
) == 2 * coupling * size * size, "Energy of ferromagnetic state is incorrect."
def __init__(\ self, dimX, dimY, energyScale, rate1, rate2, cat, \ monomerAppear, monomerVanish, dimerVanish, dimerBreak, \ monomerInitNum, dimer1InitNum, dimer2InitNum): MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2 self.lat = Lattice(dimX, dimY) self.energyScale = energyScale self.rate1 = rate1 self.rate2 = rate2 self.cat = cat self.monomerNum = monomerInitNum self.dimer1Num = dimer1InitNum self.dimer2Num = dimer2InitNum self.monomerAppear = monomerAppear self.monomerVanish = monomerVanish self.dimerVanish = dimerVanish self.dimerBreak = dimerBreak self.__initVars() self.lat.setAtomTypeNum(4) self.lat.setEnergyMatrix(array([\ [ 2, 2, 2, 0],\ [ 2, 2, 2, 0],\ [ 2, 2, 2, 0],\ [ 0, 0, 0, 0]]) * self.energyScale) self.lat.bindingEnergy = -1.0 * self.energyScale; mNum = monomerInitNum + dimer1InitNum + dimer2InitNum self.moleculeNum = mNum # initX = zeros(mNum) # initY = zeros(mNum) initX1 = randint(0, self.lat.dimX, self.monomerNum) initY1 = randint(0, self.lat.dimY, self.monomerNum) initX2 = randint(int(0.2*self.lat.dimX), int(0.4*self.lat.dimX), self.dimer1Num) initY2 = randint(int(0.2*self.lat.dimY), int(0.4*self.lat.dimY), self.dimer1Num) initX3 = randint(int(0.6*self.lat.dimX), int(0.8*self.lat.dimX), self.dimer2Num) initY3 = randint(int(0.6*self.lat.dimY), int(0.8*self.lat.dimY), self.dimer2Num) for n in range(self.monomerNum): self.lat.addMolecule(Molecule(MOL_MONOMER, initX1[n], initY1[n], self.moleculeTemp1)) for n in range(self.dimer1Num): self.lat.addMolecule(Molecule(MOL_DIMER1, initX2[n], initY2[n], self.moleculeTemp2)) for n in range(self.dimer2Num): self.lat.addMolecule(Molecule(MOL_DIMER2, initX3[n], initY3[n], self.moleculeTemp3))
def m_fodo(params):
kq = params['kq [1/m^2]']
lq = params['quad [m]']
ld = params['drift [m]']
particle = params['particle']
qf = elm.QF(k0=kq, length=lq/2., label='QF/2', particle=particle)
qd = elm.QD(k0=kq, length=lq, label='QD', particle=particle)
dr = elm.D( length=ld, label='D', particle=particle)
cell = Lattice()
cell.add_element(qf)
cell.add_element(dr)
cell.add_element(qd)
cell.add_element(dr)
cell.add_element(qf)
return cell
def __init__(\ self, dimX, dimY, energyScale, rate, \ monomerAppear, monomerVanish, dimerVanish, dimerBreak, \ monomerInitNum, dimer1InitNum, dimer2InitNum): MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2 self.lat = Lattice(dimX, dimY) self.energyScale = energyScale self.rate = rate self.monomerNum = monomerInitNum self.dimer1Num = dimer1InitNum self.dimer2Num = dimer2InitNum self.monomerAppear = monomerAppear self.monomerVanish = monomerVanish self.dimerVanish = dimerVanish self.dimerBreak = dimerBreak self.__initVars() self.lat.setAtomTypeNum(6) self.lat.setEnergyMatrix(array([\ [ 5, 5, 5, -3, 0, 0],\ [ 5, 5, 5, 0, 3, -3],\ [ 5, 5, 5, 0, 3, -3],\ [-3, 0, 0, 0, 0, 0],\ [ 0, 3, 3, 0, 0, 0],\ [ 0, -3, -3, 0, 0, 0]]) * self.energyScale) self.lat.bindingEnergy = -5.0 * self.energyScale; mNum = monomerInitNum + dimer1InitNum + dimer2InitNum self.moleculeNum = mNum initX = randint(0, self.lat.dimX, mNum) initY = randint(0, self.lat.dimY, mNum) for n in range(self.monomerNum): self.lat.addMolecule(Molecule(MOL_MONOMER, initX[n], initY[n], self.moleculeTemp1)) for n in range(self.dimer1Num): self.lat.addMolecule(Molecule(MOL_DIMER1, initX[n], initY[n], self.moleculeTemp2)) for n in range(self.dimer2Num): self.lat.addMolecule(Molecule(MOL_DIMER2, initX[n], initY[n], self.moleculeTemp3))
def make_thin (kf1,kf2,ld,anz=1,verbose=False):
kd1 = kf1 # k1 for qf1 & qd1
ld1 = lf1 = 0.4 # len qf1 & qd1
ff1 = kf1*lf1 # focal length qf1
fd1 = kd1*ld1 # focal length qd1
kf2 = kf2
kd2 = kf2 # same as above for qf2 & qd2
lf2 = ld2 = lf1
ff2 = kf2*lf2
fd2 = kd2*ld2
slices = 1 # present the quad by 1 thin-quads (bad!)
slices = 3 # present the quad by 3 thin-quads (better!)
slices = 6 # present the quad by 6 thin-quads (near perfect!)
DL = D(length=ld,label='L')
QF1 = QFth(k0=kf1,length=0.5*lf1/slices,label='QF1')
QF2 = QFth(k0=kf2,length=0.5*lf2/slices,label='QF2')
QD1 = QDth(k0=kd1,length=0.5*ld1/slices,label='QD1')
QD2 = QDth(k0=kd2,length=0.5*ld2/slices,label='QD2')
cell = Lattice()
for i in range(slices): cell.add_element(QD1)
for i in range(slices): cell.add_element(QF1)
cell.add_element(DL)
for i in range(slices): cell.add_element(QD2)
for i in range(slices): cell.add_element(QF2)
for i in range(slices): cell.add_element(QF2)
for i in range(slices): cell.add_element(QD2)
cell.add_element(DL)
for i in range(slices): cell.add_element(QF1)
for i in range(slices): cell.add_element(QD1)
lat = Lattice()
for i in range(anz):
lat.concat(cell)
lat.cell()
mcell = lat.accel
betax = lat.betax0
betay = lat.betay0
if verbose:
# {:.3f}
print('L= {:.3f}'.format(ld),end=' ')
print('triplet 1: kf= {:.3f}, kd={:.3f}'.format(kf1,kd1),end=' | ')
print('triplet 2: kf= {:.3f}, kd={:.3f}'.format(kf2,kd2),end=' | ')
print('betax= {:.3f}, betay= {:.3f}'.format(betax,betay))
return lat,betax,betay
from matplotlib import pyplot as plt
from lattice import Lattice
from matplotlib.patches import FancyBboxPatch
from matplotlib.transforms import Bbox
from mpl_toolkits.mplot3d import Axes3D
from numpy import sqrt, array
from numpy.linalg import norm
from fancyArrows import Arrow3D
lv = [[1, 0, 0],[.5, .5 * sqrt(3), 0],[.5, .5 * 1/sqrt(3), sqrt(2. / 3)]]
lb = [[0, 0, 0], [.5, 0, 0], [0, .5, 0], [0, 0, .5]]
pyro = Lattice(lv, lb)
h = {(1, 0, 0): array([[ 0., -1., 0., 0.],
[ 0., 0., 0., 0.],
[ 0., 0., 0., 0.],
[ 0., 0., 0., 0.]]),
(0, 0, 1): array([[ 0., 0., 0., -1.],
[ 0., 0., 0., 0.],
[ 0., 0., 0., 0.],
[ 0., 0., 0., 0.]]),
(0, -1, 1): array([[ 0., 0., 0., 0.],
[ 0., 0., 0., 0.],
[ 0., 0., 0., -1.],
[ 0., 0., 0., 0.]]),
(0, 0, 0): array([[ 0., -1., -1., -1.],
[-1., 0., -1., -1.],
[-1., -1., 0., -1.],
[-1., -1., -1., 0.]]),
(-1, 1, 0): array([[ 0., 0., 0., 0.],
[ 0., 0., -1., 0.],
[ 0., 0., 0., 0.],
def complete_lattice(self):
lattice = Lattice(self.dataset)
lattice.build_lattice()
return lattice
class Experiment:
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE = 0, 1, 2, 3
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = 0, 1, 2
# Monomer Temp
moleculeTemp1 = map(Atom.fromTuple, [\
(ATOM_MONOMER,0,0)])
# I Dimer
moleculeTemp2 = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, 1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, 1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, 1)])
# L Dimer
moleculeTemp3 = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, -1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, 0, 2)])
def __init__(\
self, dimX, dimY, energyScale, rate1, rate2, cat, \
monomerAppear, monomerVanish, dimerVanish, dimerBreak, \
monomerInitNum, dimer1InitNum, dimer2InitNum):
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
self.lat = Lattice(dimX, dimY)
self.energyScale = energyScale
self.rate1 = rate1
self.rate2 = rate2
self.cat = cat
self.monomerNum = monomerInitNum
self.dimer1Num = dimer1InitNum
self.dimer2Num = dimer2InitNum
self.monomerAppear = monomerAppear
self.monomerVanish = monomerVanish
self.dimerVanish = dimerVanish
self.dimerBreak = dimerBreak
self.__initVars()
self.lat.setAtomTypeNum(4)
self.lat.setEnergyMatrix(array([\
[ 2, 2, 2, 0],\
[ 2, 2, 2, 0],\
[ 2, 2, 2, 0],\
[ 0, 0, 0, 0]]) * self.energyScale)
self.lat.bindingEnergy = -1.0 * self.energyScale;
mNum = monomerInitNum + dimer1InitNum + dimer2InitNum
self.moleculeNum = mNum
initX = randint(0, self.lat.dimX, mNum)
initY = randint(0, self.lat.dimY, mNum)
for n in range(self.monomerNum):
self.lat.addMolecule(Molecule(MOL_MONOMER, initX[n], initY[n], self.moleculeTemp1))
for n in range(self.dimer1Num):
self.lat.addMolecule(Molecule(MOL_DIMER1, initX[n], initY[n], self.moleculeTemp2))
for n in range(self.dimer2Num):
self.lat.addMolecule(Molecule(MOL_DIMER2, initX[n], initY[n], self.moleculeTemp3))
def __initVars(self):
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE = \
self.ATOM_MONOMER, self.ATOM_DIMER1, self.ATOM_DIMER2, self.ATOM_SITE
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
self.newDimerTemp = range(8)
self.newDimerTemp[0] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 1, 0), \
(ATOM_SITE, 0, 1), (ATOM_SITE, 1, 1), \
(ATOM_SITE, 0, -1), (ATOM_SITE, 1, -1)] )
self.newDimerTemp[1] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, -1, 0), \
(ATOM_SITE, 0, 1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, -1), (ATOM_SITE, -1, -1)] )
self.newDimerTemp[2] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, 1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, 1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, 1)] )
self.newDimerTemp[3] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, -1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, -1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, -1)] )
self.newDimerTemp[4] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, 1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, 1), (ATOM_SITE, -1, -1),\
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[5] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, 1), (ATOM_DIMER2, 1, 0), \
(ATOM_SITE, -1, 1), (ATOM_SITE, 1, -1),\
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[6] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, 1, 0), \
(ATOM_SITE, -1, -1), (ATOM_SITE, 1, 1), \
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[7] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, -1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, 0, 2)])
self.reactDirMap = [[1,0],[-1,0],[0,1],[0,-1],[1,1],[-1,1],[-1,-1],[1,-1]]
colorScale = ( [
[0.20, 0.20, 0.20],\
[0.30, 0.00, 0.00],\
[0.00, 0.30, 0.00],\
[0.05, 0.05, 0.05]] )
def colorMap(self, lattice):
return clip(tensordot(lattice.atomNumMap, self.colorScale, axes=([0,0])), 0, 1)
def run(self, simulationTime, outputPeriod, display, outputFileName):
simTime = simulationTime
#display = display
#outputFileName = outputFileName
lat = self.lat
colorMap = self.colorMap
reactDirMap = self.reactDirMap
moleculeNum = self.moleculeNum
moleculeTemp1 = self.moleculeTemp1
newDimerTemp = self.newDimerTemp
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE = \
self.ATOM_MONOMER, self.ATOM_DIMER1, self.ATOM_DIMER2, self.ATOM_SITE
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
if outputFileName == None:
fileFlag = False
else:
fileFlag = True
file = open(outputFileName, 'w')
if display:
fig = figure()
img = imshow(self.colorMap(lat), interpolation='none')
ioff()
lat.newDimerNum = zeros((3,3), int)
tMoveMol = zeros(simTime, int)
tMoveDir = zeros(simTime, int)
tMoveDis = zeros(simTime, int)
tMoveProb = zeros(simTime)
rMoveMol = zeros(simTime, int)
rMoveDir = zeros(simTime, int)
rMoveProb = zeros(simTime)
reactMol = zeros(simTime, int)
reactDir = zeros(simTime, int)
reactAtom = zeros(simTime, int)
reactProb = rand(simTime)
degProb = rand(simTime)
newX = zeros(simTime, int)
newY = zeros(simTime, int)
newProb = rand(simTime)
bindProb = rand(simTime)
def expRandTime(rate=1.):
if rate > 0.:
return -log(rand())/rate
else:
return float('inf')
class Movement:
def reset(self):
newSpeed = float(self.speedFunc())
if newSpeed > 0.:
self.wait = self.timeFunc()/newSpeed
self.currentSpeed = newSpeed
else:
self.wait = float('inf')
self.currentSpeed = 0.
return self.wait
def updateParam(self):
newSpeed = float(self.speedFunc())
if newSpeed == self.currentSpeed:
pass
elif self.currentSpeed > 0.:
if newSpeed > 0.:
self.wait = self.wait * (self.currentSpeed/newSpeed)
self.currentSpeed = newSpeed
else:
self.wait = float('inf')
self.currentSpeed = 0.
else:
return self.reset()
def __call__(self):
return self.moveFunc(self)
def __init__(self,moveFunc,timeFunc,speedFunc):
self.moveFunc = moveFunc
self.timeFunc = timeFunc
self.speedFunc = speedFunc
self.currentSpeed = 0.
self.wait = 0.
def doTranslation(self):
# Translate one molecule
tMoveMol = randint(0, lat.moleculeNum)
tMoveDir = randint(0, 2)
tMoveDis = randint(0, 2) * 2 - 1
tMoveProb = rand()
dx = tMoveDis * tMoveDir
dy = tMoveDis * (1 - tMoveDir)
lat.translateMoleculeByIndex(tMoveMol, dx, dy, tMoveProb)
return False
def doRotation(self):
# Rotate one molecule
rMoveDir = randint(0, 2)
rMoveMol = randint(0, lat.moleculeNum)
rMoveProb = rand()
if lat.moleculeList[rMoveMol] != MOL_MONOMER:
if rMoveDir == 0:
lat.rotateMoleculeCWByIndex(rMoveMol, rMoveProb)
else:
lat.rotateMoleculeCCWByIndex(rMoveMol, rMoveProb)
return False
def subVacateMonomer(ra):
rm = ra.parent
rm.boundMonomer -= ra.copies
lat.raiseMolecule(rm)
ra.type = ATOM_SITE
lat.layMolecule(rm)
def subGetMonomer(ra):
rm = ra.parent
rm.boundMonomer += ra.copies
lat.raiseMolecule(rm)
ra.type = ATOM_MONOMER
lat.layMolecule(rm)
def doAttachDetach(self):
lm = lat.atomList[ATOM_MONOMER]
ra = lm[randint(0,len(lm))]
if ra.parent.type == MOL_MONOMER:
ls = filter(lambda a:a.type == ATOM_SITE,lat.getAtomListAt(ra.x, ra.y))
if len(ls) == 0:
return False
ra2 = ls[0]
subGetMonomer(ls[0])
lat.removeMolecule(ra.parent)
return True
else:
p = rand()
if p < exp(ra.copies*lat.bindingEnergy):
subVacateMonomer(ra)
lat.addMolecule(Molecule(MOL_MONOMER, ra.x, ra.y, moleculeTemp1))
return True
return False
def doMonomerBirth(self):
newX = randint(floor(lat.dimX*0.0), floor(lat.dimX*1.0))
newY = randint(floor(lat.dimY*0.0), floor(lat.dimY*1.0))
lat.addMolecule(Molecule(MOL_MONOMER, newX, newY, moleculeTemp1))
return True
def doMonomerBirth2(self):
newX = randint(floor(lat.dimX*0.4), floor(lat.dimX*0.6))
newY = randint(floor(lat.dimY*0.4), floor(lat.dimY*0.6))
lat.addMolecule(Molecule(MOL_MONOMER, newX, newY, moleculeTemp1))
return True
def doMonomerDeath(self):
al = lat.atomList[ATOM_MONOMER]
ra = al[randint(0,len(al))]
rm = ra.parent
if rm.type == MOL_MONOMER:
lat.removeMolecule(rm)
return True
else:
p = rand()
if p < exp(ra.copies*lat.bindingEnergy):
subVacateMonomer(ra)
return True
return False
def subRemoveDimer(rm):
for atom in rm.atomList:
if atom.type == ATOM_MONOMER:
lat.addMolecule(Molecule(MOL_MONOMER, atom.x, atom.y, moleculeTemp1))
lat.removeMolecule(rm)
def doDimerDeath(self):
a1,a2 = lat.atomList[ATOM_DIMER1],lat.atomList[ATOM_DIMER2]
n1,n2 = len(a1),len(a2)
m = randint(0,n1+n2)
if m < n1:
ra = a1[m]
else:
ra = a2[m-n1]
subRemoveDimer(ra.parent)
return True
def subMakeDimer(type,rd,ra,ra2):
# I-shaped dimer
if type == 0:
lat.addMolecule(Molecule(MOL_DIMER1, ra.x, ra.y, newDimerTemp[rd]))
# L-shaped dimer
else:
lat.addMolecule(Molecule(MOL_DIMER2, ra2.x, ra.y, newDimerTemp[rd]))
lat.newDimerNum[ra.parent.type, ra2.parent.type] += 1
# Remove the involved monomers
for atom in [ra, ra2]:
rm = atom.parent
if rm.type == MOL_MONOMER:
lat.removeMolecule(rm)
else:
subVacateMonomer(atom)
def doDimerization(self,type=0):
al = lat.atomList[ATOM_MONOMER]
ra = al[randint(0,len(al))]
rd = randint(0, 4) + type*4
x2 = ra.x + reactDirMap[rd][0]
y2 = ra.y + reactDirMap[rd][1]
if 0 < lat.getDataXY(lat.atomNumMap[ATOM_MONOMER], x2, y2):
for ra2 in lat.getAtomListAt(x2, y2):
if ra2.type == ATOM_MONOMER:
subMakeDimer(type,rd,ra,ra2)
return True
return False
doDimerizationI = lambda s: doDimerization(s,0)
doDimerizationL = lambda s: doDimerization(s,1)
def doCatDimerization(self,type=0):
al = lat.atomList[ATOM_MONOMER]
ra = al[randint(0,len(al))]
if ra.parent.type != MOL_MONOMER:
rd = randint(0, 4) + type*4
x2 = ra.x + reactDirMap[rd][0]
y2 = ra.y + reactDirMap[rd][1]
if 0 < lat.getDataXY(lat.atomNumMap[ATOM_MONOMER], x2, y2):
for ra2 in lat.getAtomListAt(x2, y2):
if ra2.type == ATOM_MONOMER and ra2.parent == ra.parent:
subMakeDimer(type,rd,ra,ra2)
return True
return False
doCatDimerizationI = lambda s: doCatDimerization(s,0)
doCatDimerizationL = lambda s: doCatDimerization(s,1)
def doAbsorbingBC(self):
i = randint(0, lat.moleculeNum)
rm = lat.moleculeList[i]
x = rm.x%lat.dimX
y = rm.y%lat.dimY
if 0 == x*y:
if rm.type == MOL_MONOMER:
lat.removeMolecule(rm)
else:
subRemoveDimer(rm)
return True
return False
def doDraw(self):
img.set_array(colorMap(lat))
draw()
return False
def doRecord(self):
newDimerNum = lat.newDimerNum
file.write('# New Dimer Num Per Interval\n')
for mt1 in newDimerNum:
file.write('# ')
for mt2 in mt1:
file.write('{} '.format(mt2))
file.write('\n')
file.write('# \n')
newDimerNum *= 0
for atomType in lat.atomNumMap:
for row in atomType:
for col in row:
file.write('{} '.format(col))
file.write('\n')
file.write('\n')
file.write('\n')
return False
mvList = [ \
Movement(doTranslation,expRandTime,lambda:lat.moleculeNum), \
Movement(doRotation,expRandTime,lambda:lat.moleculeNum), \
Movement(doAbsorbingBC,expRandTime,lambda:5. * lat.moleculeNum), \
Movement(doAttachDetach,expRandTime,lambda:5. * len(lat.atomList[ATOM_MONOMER])), \
#Movement(doDimerizationI,expRandTime,lambda:self.rate1 * len(lat.atomList[ATOM_MONOMER])), \
#Movement(doDimerizationL,expRandTime,lambda:self.rate2 * len(lat.atomList[ATOM_MONOMER])), \
Movement(doCatDimerizationI,expRandTime,lambda:self.cat * self.rate1 * len(lat.atomList[ATOM_MONOMER])), \
Movement(doCatDimerizationL,expRandTime,lambda:self.cat * self.rate2 * len(lat.atomList[ATOM_MONOMER])), \
Movement(doDimerDeath,expRandTime,lambda:self.dimerVanish * (len(lat.atomList[ATOM_DIMER1])+len(lat.atomList[ATOM_DIMER2]))/2), \
Movement(doMonomerBirth2,expRandTime,lambda:self.monomerAppear), \
Movement(doMonomerDeath,expRandTime,lambda:self.monomerVanish * len(lat.atomList[ATOM_MONOMER])) ]
if display:
mvList.append(Movement(doDraw,lambda:1,lambda:1./outputPeriod))
if fileFlag:
mv = Movement(doRecord,lambda:1,lambda:1./outputPeriod)
#mv.newDimerNum = newDimerNum
mvList.append(mv)
t = 0
for m in mvList:
m.reset()
mvList.sort(key=attrgetter('wait'))
wait = mvList[0].wait
t += wait
while t < simTime:
for m in mvList:
m.wait -= wait
isToUpdate = mvList[0]()
if isToUpdate:
for m in mvList:
m.updateParam()
mvList[0].reset()
mvList.sort(key=attrgetter('wait'))
wait = mvList[0].wait
t += wait
if fileFlag:
file.close()
return
class Experiment:
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE, ATOM_REP, ATOM_ATT = 0, 1, 2, 3, 4, 5
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = 0, 1, 2
# Monomer Temp
moleculeTemp1 = {'atomList': map(Atom.fromTuple, [\
(ATOM_MONOMER,0,0), \
(ATOM_REP,0,1),(ATOM_REP,1,0),(ATOM_REP,-1,0), \
(ATOM_REP,1,1),(ATOM_REP,-1,1)]), 'dir': (0,1)}
# I Dimer
moleculeTemp2 = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, 1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, 1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, 1)])
# L Dimer
moleculeTemp3 = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, -1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, 0 ),(ATOM_SITE, 0, 0)])
def __init__(\
self, dimX, dimY, energyScale, rate, \
monomerAppear, monomerVanish, dimerVanish, dimerBreak, \
monomerInitNum, dimer1InitNum, dimer2InitNum):
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
self.lat = Lattice(dimX, dimY)
self.energyScale = energyScale
self.rate = rate
self.monomerNum = monomerInitNum
self.dimer1Num = dimer1InitNum
self.dimer2Num = dimer2InitNum
self.monomerAppear = monomerAppear
self.monomerVanish = monomerVanish
self.dimerVanish = dimerVanish
self.dimerBreak = dimerBreak
self.__initVars()
self.lat.setAtomTypeNum(6)
self.lat.setEnergyMatrix(array([\
[ 5, 5, 5, -3, 0, 0],\
[ 5, 5, 5, 0, 3, -3],\
[ 5, 5, 5, 0, 3, -3],\
[-3, 0, 0, 0, 0, 0],\
[ 0, 3, 3, 0, 0, 0],\
[ 0, -3, -3, 0, 0, 0]]) * self.energyScale)
self.lat.bindingEnergy = -5.0 * self.energyScale;
mNum = monomerInitNum + dimer1InitNum + dimer2InitNum
self.moleculeNum = mNum
initX = randint(0, self.lat.dimX, mNum)
initY = randint(0, self.lat.dimY, mNum)
for n in range(self.monomerNum):
self.lat.addMolecule(Molecule(MOL_MONOMER, initX[n], initY[n], self.moleculeTemp1))
for n in range(self.dimer1Num):
self.lat.addMolecule(Molecule(MOL_DIMER1, initX[n], initY[n], self.moleculeTemp2))
for n in range(self.dimer2Num):
self.lat.addMolecule(Molecule(MOL_DIMER2, initX[n], initY[n], self.moleculeTemp3))
def __initVars(self):
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE, ATOM_REP, self.ATOM_ATT = \
self.ATOM_MONOMER, self.ATOM_DIMER1, self.ATOM_DIMER2, self.ATOM_SITE, self.ATOM_REP, self.ATOM_ATT
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
self.newDimerTemp = range(8)
self.newDimerTemp[0] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 1, 0), \
(ATOM_SITE, 0, 1), (ATOM_SITE, 1, 1), \
(ATOM_SITE, 0, -1), (ATOM_SITE, 1, -1)] )
self.newDimerTemp[1] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, -1, 0), \
(ATOM_SITE, 0, 1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, -1), (ATOM_SITE, -1, -1)] )
self.newDimerTemp[2] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, 1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, 1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, 1)] )
self.newDimerTemp[3] = map(Atom.fromTuple, [\
(ATOM_DIMER1, 0, 0), (ATOM_DIMER1, 0, -1), \
(ATOM_SITE, 1, 0), (ATOM_SITE, 1, -1), \
(ATOM_SITE, -1, 0), (ATOM_SITE, -1, -1)] )
self.newDimerTemp[4] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, 1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, 1), (ATOM_SITE, -1, -1),\
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[5] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, 1), (ATOM_DIMER2, 1, 0), \
(ATOM_SITE, -1, 1), (ATOM_SITE, 1, -1),\
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[6] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, 1, 0), \
(ATOM_SITE, -1, -1), (ATOM_SITE, 1, 1), \
(ATOM_SITE, 0, 0, 2)])
self.newDimerTemp[7] = map(Atom.fromTuple, [\
(ATOM_DIMER2, 0, -1), (ATOM_DIMER2, -1, 0), \
(ATOM_SITE, 1, -1), (ATOM_SITE, -1, 1), \
(ATOM_SITE, 0, 0, 2)])
self.reactDirMap = [[1,0],[-1,0],[0,1],[0,-1],[1,1],[-1,1],[-1,-1],[1,-1]]
colorScale = ( [
[0.20, 0.20, 0.20],\
[0.30, 0.00, 0.00],\
[0.00, 0.30, 0.00],\
[0.00, 0.00, 0.00],\
[0.05, 0.05, 0.05],\
[0.05, 0.05, 0.05]] )
def colorMap(self, lattice):
return clip(tensordot(lattice.atomNumMap, self.colorScale, axes=([0,0])), 0, 1)
def run(self, simulationTime, outputPeriod, display, outputFileName):
simTime = simulationTime
#display = display
#outputFileName = outputFileName
lat = self.lat
reactDirMap = self.reactDirMap
moleculeNum = self.moleculeNum
moleculeTemp1 = self.moleculeTemp1
newDimerTemp = self.newDimerTemp
ATOM_MONOMER, ATOM_DIMER1, ATOM_DIMER2, ATOM_SITE, ATOM_REP = \
self.ATOM_MONOMER, self.ATOM_DIMER1, self.ATOM_DIMER2, self.ATOM_SITE, self.ATOM_REP
MOL_MONOMER, MOL_DIMER1, MOL_DIMER2 = self.MOL_MONOMER, self.MOL_DIMER1, self.MOL_DIMER2
if outputFileName == None:
fileFlag = False
else:
fileFlag = True
file = open(outputFileName, 'w')
if display:
fig = figure()
img = imshow(self.colorMap(lat), interpolation='none')
ioff()
newDimerNum = zeros((3,3), int)
tMoveMol = zeros(simTime, int)
tMoveDir = zeros(simTime, int)
tMoveDis = zeros(simTime, int)
tMoveProb = zeros(simTime)
rMoveMol = zeros(simTime, int)
rMoveDir = zeros(simTime, int)
rMoveProb = zeros(simTime)
reactMol = zeros(simTime, int)
reactDir = zeros(simTime, int)
reactAtom = zeros(simTime, int)
reactProb = rand(simTime)
degProb = rand(simTime)
newX = zeros(simTime, int)
newY = zeros(simTime, int)
newProb = rand(simTime)
bindProb = rand(simTime)
for t in range(simTime):
# Translate one molecule
tMoveMol[t] = randint(0, lat.moleculeNum)
tMoveDir[t] = randint(0, 2)
tMoveDis[t] = randint(0, 2) * 2 - 1
tMoveProb[t] = rand()
dx = tMoveDis[t] * tMoveDir[t]
dy = tMoveDis[t] * (1 - tMoveDir[t])
lat.translateMoleculeByIndex(tMoveMol[t], dx, dy, tMoveProb[t])
# Rotate one molecule
rMoveDir[t] = randint(0, 2)
rMoveMol[t] = randint(0, lat.moleculeNum)
rMoveProb[t] = rand()
if lat.moleculeList[rMoveMol[t]] != MOL_MONOMER:
if rMoveDir[t] == 0:
lat.rotateMoleculeCWByIndex(rMoveMol[t], rMoveProb[t])
else:
lat.rotateMoleculeCCWByIndex(rMoveMol[t], rMoveProb[t])
if reactProb[t] < self.rate:
# Pick one monomer atom and see if a dimer can be formed
molN = len(lat.atomList[ATOM_MONOMER]) + len(lat.atomList[ATOM_DIMER1])/2 + len(lat.atomList[ATOM_DIMER2])/2;
reactAtom[t] = randint(0, molN)
if reactAtom[t] < len(lat.atomList[ATOM_MONOMER]):
ra = lat.atomList[ATOM_MONOMER][reactAtom[t]]
rd = reactDir[t] = randint(0, 8)
x2 = ra.x + reactDirMap[rd][0]
y2 = ra.y + reactDirMap[rd][1]
#anl = lat.getAtomNumAt(x2, y2)
if 0 < lat.getDataXY(lat.atomNumMap[ATOM_MONOMER], x2, y2):
for ra2 in lat.getAtomListAt(x2, y2):
if ra2.type == ATOM_MONOMER and ra.parent.dir == ra2.parent.dir:
# I-shaped dimer
if rd < 4:
lat.addMolecule(Molecule(MOL_DIMER1, ra.x, ra.y, newDimerTemp[rd]))
# L-shaped dimer
else:
lat.addMolecule(Molecule(MOL_DIMER2, ra2.x, ra.y, newDimerTemp[rd]))
newDimerNum[ra.parent.type, ra2.parent.type] = newDimerNum[ra.parent.type, ra2.parent.type] + 1
# Remove the involved monomers
for atom in [ra, ra2]:
rm = atom.parent
if rm.type == MOL_MONOMER:
lat.removeMolecule(rm)
else:
lat.raiseMolecule(rm)
atom.type = ATOM_SITE
lat.layMolecule(rm)
break
reactMol[t] = randint(0, lat.moleculeNum)
rm = lat.moleculeList[reactMol[t]]
# Death of monomer
if rm.type == MOL_MONOMER:
if degProb[t] < self.monomerVanish:
lat.removeMolecule(rm)
elif (rm.type == MOL_DIMER1 or rm.type == MOL_DIMER2):
# Death of dimer
if degProb[t] < self.dimerVanish:
for atom in rm.atomList:
if atom.type == ATOM_MONOMER:
lat.addMolecule(Molecule(MOL_MONOMER, atom.x, atom.y, moleculeTemp1))
lat.removeMolecule(rm)
moleculeNum -= 1
# Degradation of dimer into monomers
elif degProb[t] > (1-self.dimerBreak):
for atom in rm.atomList:
if atom.type != ATOM_SITE:
lat.addMolecule(Molecule(MOL_MONOMER, atom.x, atom.y, moleculeTemp1))
lat.removeMolecule(rm)
else:
pass
#for atom in rm.atomList:
# # Attach monomer to adsorption site of dimer
# if atom.type == ATOM_SITE:
# aL1 = lat.getAtomListAt(atom.x, atom.y)
# for atom1 in filter(lambda x: x.parent.type == MOL_MONOMER, aL1):
# lat.raiseMolecule(rm)
# atom.type = ATOM_MONOMER
# lat.layMolecule(rm)
# lat.removeMolecule(atom1.parent)
# break
# # Detach monomer from adsorption site of dimer
# elif atom.type == ATOM_MONOMER:
# if bindProb[t] < min(1,exp(atom.copies*lat.bindingEnergy)):
# lat.raiseMolecule(rm)
# atom.type = ATOM_SITE
# lat.layMolecule(rm)
# lat.addMolecule(Molecule(MOL_MONOMER, atom.x, atom.y, moleculeTemp1))
# Add monomers randomly to the system
if newProb[t] < self.monomerAppear/lat.moleculeNum:
newX[t] = randint(floor(lat.dimX*0.0), floor(lat.dimX*1.0))
newY[t] = randint(floor(lat.dimY*0.0), floor(lat.dimY*1.0))
lat.addMolecule(Molecule(MOL_MONOMER, newX[t], newY[t], moleculeTemp1))
# Update the animation per ## moves
if (t+1)%(outputPeriod) == 0:
if display:
img.set_array(self.colorMap(lat))
draw()
if fileFlag:
file.write('# New Dimer Num Per Interval\n')
for mt1 in newDimerNum:
file.write('# ')
for mt2 in mt1:
file.write('{} '.format(mt2))
file.write('\n')
file.write('# \n')
newDimerNum = newDimerNum * 0;
for atomType in lat.atomNumMap:
for row in atomType:
for col in row:
file.write('{} '.format(col))
file.write('\n')
file.write('\n')
file.write('\n')
if fileFlag:
file.close()
def make_thick(kf1,kf2,ld,anz=1,verbose=False):
kf1 = kf1
kd1 = kf1
lf1 = 0.4
ld1 = lf1
ff1 = kf1*lf1
fd1 = kd1*ld1
kf2 = kf2
kd2 = kf2
lf2 = lf1
ld2 = lf2
ff2 = kf2*lf2
fd2 = kd2*ld2
ld = ld
DL = D(length=ld,label='L')
QF1 = QF(k0=kf1,length=0.5*lf1,label='QF1')
QF2 = QF(k0=kf2,length=0.5*lf2,label='QF2')
QD1 = QD(k0=kd1,length=0.5*ld1,label='QD1')
QD2 = QD(k0=kd2,length=0.5*ld2,label='QD2')
cell = Lattice()
cell.add_element(QD1)
cell.add_element(QF1)
cell.add_element(DL)
cell.add_element(QD2)
cell.add_element(QF2)
cell.add_element(QF2)
cell.add_element(QD2)
cell.add_element(DL)
cell.add_element(QF1)
cell.add_element(QD1)
lat = Lattice()
for i in range(anz):
lat.concat(cell)
lat.cell()
mcell = lat.accel
betax = lat.betax0
betay = lat.betay0
if verbose:
# {:.3f}
print('L= {:.3f}'.format(ld),end=' ')
print('triplet 1: kf= {:.3f}, kd={:.3f}'.format(kf1,kd1),end=' | ')
print('triplet 2: kf= {:.3f}, kd={:.3f}'.format(kf2,kd2),end=' | ')
print('betax= {:.3f}, betay= {:.3f}'.format(betax,betay))
return lat,betax,betay
file.write(s)
elif (j+1)%p==0:
s = '%-5s %7.5f %7.5f %7.5f %5i\n' % (el_name[j],xyz[j,0],xyz[j,1],xyz[j,2],p)
file.write(s)
file.close()
##########################################################################
##########################################################################
if __name__ == "__main__":
# define cell and hkl:
#cell = [a,b,c,alpha,beta,gam]
#hkl = [h,k,l]
cell = [10.223, 5.992, 4.761,90,90,90]
hkl = [1.,0.,1.]
lat = Lattice(*cell)
# calculate d spacing in Angstroms
d_space = lat.d(hkl)
# calculate vector d in bulk real space basis
d = lat.dvec(hkl)
# calculate inplane vectors to choose Va and Vb
Vs,Vr = surface_vectors(hkl,lat)
#################
# choose basis vectors for surface system
Va = [1.,0.,-1.]
Vb = [0.,1.,0.]
Vc = 5*d
and filename[-len(output_suffix):] == output_suffix)+1
except Exception as e:
counter = 1
opt.output = os.path.join(output_dir, (output_prefix+'{:05d}'+
output_suffix).format(counter))
fd = open(opt.output, 'w', buffer_size)
fd.write('# N={:d}\n'.format(N))
fd.write('# beta={:f}\n'.format(opt.beta))
# Write RNG seed and commit hash so this run can be repeated after the code has
# changed
fd.write('# seed={:d}\n'.format(seed))
fd.write('# commit='+check_output(['git', 'log', '--pretty=format:%H', '-n',
'1' ])+'\n')
lattice = Lattice(sp.random.random_integers(0, 1, size=(opt.length,
opt.length)))
print 'Simulating {:d} steps of a {:d}x{:d} lattice at beta={:f}'.format(
opt.steps, opt.length, opt.length, opt.beta)
print 'Writing run data to ' + opt.output
if opt.movie:
if opt.movie != True:
video_filename = opt.movie
else:
if opt.output[-4] == '.':
video_filename = opt.output[:-3] + 'avi'
else:
video_filename = opt.output + '.avi'
from cv import FOURCC
from cv2 import VideoWriter
movieWriter = VideoWriter(video_filename, FOURCC('U','2','6','3'),
def main():
l = Lattice(20,20)
answer = l.count_lattice_paths()
sys.stdout.write("%s\n" %answer)
import scipy as sp
from lattice import Lattice
from sys import stdout
length = 512
fps = 20
from cv import FOURCC
from cv2 import VideoWriter
movieWriter = VideoWriter('freeze.avi', FOURCC('U','2','6','3'),
fps, (length, length), False)
lattice = Lattice(sp.random.random(size=(length, length)))
samples = fps*60
x = samples/10
for beta in sp.linspace(.01, 10, samples):
movieWriter.write((128*lattice.state).astype(sp.uint8))
lattice.step(beta)
samples -= 1
if samples % x == 0:
stdout.write('-')
stdout.flush()