def __init__(self, app, system, freq=30):
self.system = system
self.on_update_gui = Signal()
self.frq = freq
self.app = app
self.on_run_started = Signal()
self.on_run_finished = Signal()
def __init__(self, parent=None):
super(NEBWidget, self).__init__(parent=parent)
self.ui = ui.nebbrowser.Ui_Form()
self.ui.setupUi(self)
self.plw = self.ui.widget
# self.plw.axes.set_ylabel("NEB image energy")
# pl.xlabel("distance along the path")
# self.system = system
# self.min1 = min1
# self.min2 = min2
# self.minimum_selected = Signal()
# self.minimum_selected(minim)
#the function which tells the eventloop to continue processing events
#if this is not set, the plots will stall and not show until the end of the NEB run.
#ideally it is the function app.processEvents where app is returned by
#app = QApplication(sys.argv)
self.process_events = Signal()
self.on_neb_pick = Signal()
self.on_neb_pick.connect(self.on_pick)
def __init__(self,
system,
database,
min1,
min2,
outstream=None,
return_smoothed_path=True,
daemon=True):
QtCore.QObject.__init__(self)
self.system = system
self.database = database
self.min1, self.min2 = min1, min2
self.return_smoothed_path = return_smoothed_path
self.daemon = daemon
self.outstream = outstream
self.on_finished = Signal()
self.decprocess = None
self.newminima = set()
self.newtransition_states = set()
self.success = False
self.killed_early = False
self.is_running = False
def __init__(self, database, graph=None, params=None, parent=None):
if params is None: params = dict()
super(DGraphWidget, self).__init__(parent=parent)
self.database = database
self.graph = graph
self.ui = dgraph_browser.Ui_Form()
self.ui.setupUi(self)
self.canvas = self.ui.widget.canvas
# self.ui.wgt_mpl_toolbar = NavigationToolbar()
# self.toolbar = self.
self.input_params = params.copy()
self.params = {}
self.set_defaults()
self.minimum_selected = Signal()
# self.minimum_selected(minim)
self._selected_minimum = None
# self.rebuild_disconnectivity_graph()
self.colour_tree = []
self.tree_selected = None
self._tree_cid = None
self._minima_cid = None
self._minima_labels = dict()
def __init__(self, plw, axes, neb=None, frq=30, nplots=3):
self.count = 0
self.nplots = nplots
self.data = deque()
self.frq = frq
self.process_events = Signal()
self.plw = plw
self.axes = axes
self.neb = neb
self.on_coords_select = Signal()
self.points_list = []
def on_pick_tmp(event):
self.on_pick(event)
return
self.plw.mpl_connect('pick_event', on_pick_tmp)
def __init__(self, app, systemtype, parent=None):
QtGui.QWidget.__init__(self)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.systemtype = systemtype
self.transition = None
self.app = app
self.double_ended_connect_runs = []
self.pick_count = 0
self.minima_selection = MySelection()
self.on_minimum_1_selected = Signal()
self.on_minimum_2_selected = Signal()
# set up the list manager
self.list_manager = ListViewManager(self)
# define the system
self.NewSystem()
# finish setting up the list manager (this must be done after NewSystem() is called)
self.list_manager.finish_setup()
# try to load the pymol viewer.
try:
self.usepymol = self.system.params.gui.use_pymol
except (KeyError, AttributeError):
self.usepymol = config.getboolean("gui", "use_pymol")
if self.usepymol:
try:
from .pymol_viewer import PymolViewer
self.pymolviewer = PymolViewer(self.system.load_coords_pymol)
except (ImportError or NotImplementedError):
self.usepymol = False
if not self.usepymol:
# note: glutInit() must be called exactly once. pymol calls it
# during pymol.finish_launching(), so if we call it again it will
# give an error. On the other hand, if we're not using pymol we
# must call it.
from OpenGL.GLUT import glutInit
glutInit()
self.bhmanager = None
def __init__(self,
potential,
coords1,
coords2,
k=100.,
max_images=50,
image_density=10.,
iter_density=10.,
verbose=0,
factor=1.05,
NEBquenchParams=None,
adjustk_freq=0,
adjustk_tol=0.1,
adjustk_factor=1.05,
dneb=True,
reinterpolate_tol=0.1,
reinterpolate=0,
adaptive_nimages=False,
adaptive_niter=False,
interpolator=interpolate_linear,
distance=distance_cart,
**kwargs):
self.potential = potential
self.interpolator = interpolator
self.verbose = verbose
self.distance = distance
self.factor = factor
self.max_images = max_images
self.min_images = 3
self.image_density = image_density
self.iter_density = iter_density
self.update_event = Signal()
self.coords1 = coords1
self.coords2 = coords2
self.reinterpolate = reinterpolate
self.reinterpolate_tol = reinterpolate_tol
self._nebclass = NEB
self._kwargs = kwargs.copy()
self.k = k
self.adaptive_images = adaptive_nimages
self.adaptive_niter = adaptive_niter
self._kwargs["adjustk_freq"] = adjustk_freq
self._kwargs["adjustk_tol"] = adjustk_tol
self._kwargs["adjustk_factor"] = adjustk_factor
self._kwargs["dneb"] = dneb
if NEBquenchParams is None:
NEBquenchParams = {'tol': 1e-2, 'maxErise': 100.0}
self.quenchParams = NEBquenchParams
self.prepared = False
def __init__(self,
db=":memory:",
accuracy=1e-3,
connect_string='sqlite:///%s',
compareMinima=None,
createdb=True):
self.accuracy = accuracy
self.compareMinima = compareMinima
if not os.path.isfile(db) or db == ":memory:":
newfile = True
if not createdb:
raise IOError(
"createdb is False, but database does not exist (%s)" % db)
else:
newfile = False
# set up the engine which will manage the backend connection to the database
self.engine = create_engine(connect_string % db, echo=verbose)
if not newfile and not self._is_pele_database():
raise IOError("existing file (%s) is not a pele database." % db)
# set up the tables and check the schema version
if newfile:
self._set_schema_version()
self._check_schema_version()
self._update_schema()
# self._check_schema_version_and_create_tables(newfile)
# set up the session which will manage the frontend connection to the database
Session = sessionmaker(bind=self.engine)
self.session = Session()
# these functions will be called when a minimum or transition state is
# added or removed
self.on_minimum_added = Signal()
self.on_minimum_removed = Signal()
self.on_ts_added = Signal()
self.on_ts_removed = Signal()
self.lock = threading.Lock()
self.connection = self.engine.connect()
def __init__(self, system, database, on_number_alive_changed=None):
self.system = system
self.database = database
self.workers = []
self._old_nalive = -1
self.on_number_alive_changed = Signal()
if on_number_alive_changed is not None:
self.on_number_alive_changed.connect(on_number_alive_changed)
self.refresh_timer = QtCore.QTimer()
self.refresh_timer.timeout.connect(self._check_number)
def __init__(self, system, database, nsteps=None, on_finish=None):
QtCore.QObject.__init__(self)
self.system = system
self.database = database
self.daemon = True
self.nsteps = nsteps
#child_conn = self
self.bhprocess = None
self.on_finish = Signal()
if on_finish is not None:
self.on_finish.connect(on_finish)
def __init__(self, database=None, parent=None, app=None, minima=None):
QWidget.__init__(self, parent=parent)
self.ui = Ui_Form()
self.ui.setupUi(self)
self.database = database
self.minima = minima
self.app = app
self.canvas = self.ui.canvas.canvas
self.axes = self.canvas.axes
self.fig = self.canvas.fig
self.on_minima_picked = Signal()
self.from_minima = set()
self.positions = dict()
self.boundary_nodes = set()
self._selected_minimum = None
self._mpl_cid = None
self._minima_color_value = None
def __init__(self, *args, **kwargs):
super(Show3DWithSlider, self).__init__(*args, **kwargs)
self.setMinimumSize(200, 200)
self.ui = Ui_show3d_with_slider()
self.ui.setupUi(self)
self.label = self.ui.label
self.label.hide()
self.ui.btn_animate.hide()
self.ui.btn_animate.setCheckable(True)
self.oglwgt = self.ui.oglwgt
self.slider = self.ui.slider
self.on_frame_updated = Signal()
self.animate = False
self._animate_dir = 1
def __init__(self, parent=None, nplots=3):
MPLWidget.__init__(self, parent=parent)
self.nplots = nplots
self.on_neb_pick = Signal()
self.mpl_connect('pick_event', self.on_pick)
def __init__(self, value):
self.__value = value
self.changed = Signal()
def __init__(self, *args, **kwargs):
super(GetThermodynamicInfoParallelQT, self).__init__(*args, **kwargs)
self.on_finish = Signal()