def __init__(self, name, facility="solver"): Component.__init__(self, name, facility) self.all_variables = None self.communicator = None self.start_cpu_time = 0 return
def __init__(self, name): if name is None: name = "user-manager" Component.__init__(self, name, facility="userManager") # public data self.home = "" self.passwd = None self.method = None self._users = {} self._reload = True self._encoder = None self._decoder = None # encoders self._encoders = { 'md5': self._md5Encoder, 'sha': self._shaEncoder, 'crypt': self._cryptEncoder, } # decoders self._decoders = { 'md5': self._md5Decoder, 'sha': self._shaDecoder, 'crypt': self._cryptDecoder, } return
def __init__(self, name="quadrature2dquadratic"): """ Constructor. """ Component.__init__(self, name, facility="quadrature") # These are just approximate points used to test the quadrature routine self.quadPtsRef = numpy.array( [[-0.75, -0.75], [0.75, -0.75], [-0.75, 0.75], [0, -0.75], [-0.75, 0], [0.25, 0.25]], dtype=numpy.float64) self.quadWts = numpy.array( [1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0], dtype=numpy.float64) #self.quadPtsRef = numpy.array( [[-0.64288254347276719, -0.68989794855663567], # [-0.84993777955478378, 0.28989794855663559], # [0.33278049202940285, -0.68989794855663567], # [-0.43996016900185175, 0.28989794855663559]], # dtype=numpy.float64) #self.quadWts = numpy.array([0.63608276, 0.36391724, 0.63608276, 0.36391724], # dtype=numpy.float64) self.numBasis = 6 self.numQuadPts = 6 self.spaceDim = 2 self.cellDim = 2 return
def __init__(self, name="values"): """ Constructor. """ Component.__init__(self, name, facility="database_values") self.values = [] return
def __init__(self, name="mesh2din3dquadratic"): """ Constructor. """ Component.__init__(self, name, facility="mesh") self.spaceDim = 3 self.cellDim = 2 self.numVertices = 6 self.numCells = 1 self.gravityVec = numpy.array( [0.0, 0.0, -1.0e8], dtype=numpy.float64) self.vertices = numpy.array( [[ 2.0, -0.5, -0.5], [ 0.5, 3.0, 0.0], [-0.5, 0.0, 2.0], [ 0.0, 1.5, 1.0], [ 0.75, -0.25, 0.75], [ 1.25, 1.25, -0.25]], dtype=numpy.float64) self.cells = numpy.array( [[0, 1, 2, 3, 4, 5]], dtype=numpy.int32) self.verticesRef = numpy.array( [[-1.0, -1.0], [+1.0, -1.0], [-1.0, +1.0], [ 0.0, 0.0], [-1.0, 0.0], [ 0.0, -1.0]], dtype=numpy.float64) return
def __init__(self, name="spatialdb"): """ Constructor. """ Component.__init__(self, name, facility="spatial_database") self._createModuleObj() return
def __init__(self, name="coordsys"): """ Constructor. """ Component.__init__(self, name, facility="coordsys") self._createModuleObj() return
def __init__(self, name): if name is None: name = 'evaluator' Component.__init__(self, name, facility='serviceRequestEvaluator') return
def __init__(self, name='phonIsoSurfaceCalcor', unitcell=None, phonondatasource=None, tau=None, plotter=None, slicer=None, Ei=50, Etransfer=20): #branchtoplot=None, atomtoplot=None, energies=None): Component.__init__(self, name, facility='facility') self._uc = unitcell if phonondatasource is not None: self._phonondatasource = phonondatasource self._nkpts = None self._tau = tau self._phonondata = None self._kptGrid = None self._energyGrid = None self._polarizationGrid = None self._intensityGrid = None try: self._numatoms = unitcell.getNumAtoms() except: raise ValueError, "Unit cell is not valid: invalid number of atoms." #self._branchtoplot = branchtoplot #self._atomtoplot = atomtoplot #self._energies = energies if plotter is None: plotter = VTKIsoSurfacePlotter() self._plotter = plotter if slicer is None: slicer = VTKPlaneSlicer() self._slicer = slicer # neutron scattering parameters: self.Ei = Ei self.Etransfer = Etransfer
def __init__(self, name="petsc"): """ Constructor. """ Component.__init__(self, name, facility="petsc_manager") self.options = [] return
def __init__(self, name=None): if name is None: name = 'Urea Forcefield' Component.__init__(self, name, facility='facility') self.i=self.inventory self.i.CAndOBond.assignInteraction('morseGulpEx10') self.i.CAndOBond.i.interIntra = 'intramolecular' self.i.CAndNBond.assignInteraction('morseGulpEx10') self.i.CAndNBond.i.interIntra = 'intramolecular' self.i.HAndNBond.assignInteraction('morseGulpEx10') self.i.HAndNBond.i.interIntra = 'intramolecular' self.i.CAndO.assignInteraction('lennardGulpEx10') self.i.CAndO.i.interIntra = 'intermolecular' self.i.CAndN.assignInteraction('lennardGulpEx10') self.i.CAndN.i.interIntra = 'intermolecular' self.i.OAndO.assignInteraction('lennardGulpEx10') self.i.OAndO.i.interIntra = 'intermolecular' self.i.NAndO.assignInteraction('lennardGulpEx10') self.i.NAndO.i.interIntra = 'intermolecular' self.i.NAndN.assignInteraction('lennardGulpEx10') self.i.NAndN.i.interIntra = 'intermolecular' self.i.CAndC.assignInteraction('lennardGulpEx10') self.i.CAndC.i.interIntra = 'intermolecular' self.i.NAndCAndO.assignInteraction('threeBodyGulpEx10') self.i.HAndNAndC.assignInteraction('threeBodyGulpEx10') self.i.HAndNAndH.assignInteraction('threeBodyGulpEx10') self.i.NAndCAndN.assignInteraction('threeBodyGulpEx10') self.i.OAndCAndNAndH.assignInteraction('torsionGulpEx10') self.i.NAndCAndNAndH.assignInteraction('torsionGulpEx10') self.i.OAndCAndNAndN.assignInteraction('torsionGulpEx10')
def __init__(self, name="nondimensional"): """ Constructor. """ Component.__init__(self, name, facility="nondimensional") self._createModuleObj() return
def __init__(self, name="timehistory"): """ Constructor. """ Component.__init__(self, name, facility="temporal_database") self._createModuleObj() return
def __init__(self, name="shapers"): """ Constructor. """ Component.__init__(self, name, facility="shapers") self.shapers = [] return
def __init__(self, name="geometry"): """ Constructor. """ Component.__init__(self, name, facility="geometry") self.vertices = None return
def _fini(self): Component._fini(self) import sys if self.logstream != sys.stdout: self.logstream.close() if self.errlogstream != sys.stderr and self.errlogstream != self.logstream: self.errlogstream.close() return
def _init(self): base._init(self) # connect to the database import pyre.db dbkwds = DbAddressResolver().resolve(self.inventory.db) self.db = pyre.db.connect(wrapper=self.inventory.dbwrapper, **dbkwds)
def _configure(self): Component._configure(self) self.logfile = self.inventory.logfile errlogfile = self.inventory.errlogfile if errlogfile == '': errlogfile = self.logfile self.errlogfile = errlogfile return
def __init__(self, name="simpleio"): """ Constructor. """ Component.__init__(self, name, facility="simpledb_io") self._createModuleObj() return
def __init__(self): Component.__init__(self, "lm3drun", "solver") print "" print "Hello from lm3drun.__init__!" return
def __init__(self, name="solution2dquadratic"): """ Constructor. """ Component.__init__(self, name, facility="solution") # Input fields self.dt = 0.01 self.fieldTIncr = numpy.array([ -0.4, -0.6, +0.7, +0.8, +0.0, +0.2, -0.5, -0.4, +0.3, +0.9, -0.3, -0.9 ], dtype=numpy.float64) self.fieldT = numpy.array([ -0.3, -0.4, +0.5, +0.6, +0.0, +0.1, -0.2, -0.3, +0.2, +0.3, -0.1, -0.2 ], dtype=numpy.float64) self.fieldTmdt = numpy.array([ -0.2, -0.3, +0.3, +0.4, +0.0, -0.1, -0.3, -0.2, +0.1, +0.4, -0.2, -0.6 ], dtype=numpy.float64) return
def __init__(self, name, facility=None): if facility is None: facility = "service" Component.__init__(self, name, facility) # number of idle seconds before onTimeout gets called self.timeout = 0 # the event loop and dispatcher self.selector = None # the monitor of my servcie port that gets me network connections self.monitor = None # the object repsonsible for extracting service requests from the network stream self.marshaller = None # the object repsonsible for translating service requests into method calls self.evaluator = None # someone must supply a weaver for rendering my current state in _storeConfiguration() # this is typically done by my parent self.weaver = None return
def __init__(self, name = 'geometer'): Component.__init__(self, name, 'geometer') base.__init__(self) import journal self._warning = journal.warning( 'mcni.pyre_support.geometer' ) return
def __init__(self, name="quadrature2dquadratic"): """ Constructor. """ Component.__init__(self, name, facility="quadrature") # These are just approximate points used to test the quadrature routine self.quadPtsRef = numpy.array( [[-0.75,-0.75], [0.75,-0.75], [-0.75,0.75], [0,-0.75], [-0.75,0], [0.25,0.25]], dtype=numpy.float64) self.quadWts = numpy.array([1.0/3.0, 1.0/3.0, 1.0/3.0, 1.0/3.0, 1.0/3.0, 1.0/3.0], dtype=numpy.float64) #self.quadPtsRef = numpy.array( [[-0.64288254347276719, -0.68989794855663567], # [-0.84993777955478378, 0.28989794855663559], # [0.33278049202940285, -0.68989794855663567], # [-0.43996016900185175, 0.28989794855663559]], # dtype=numpy.float64) #self.quadWts = numpy.array([0.63608276, 0.36391724, 0.63608276, 0.36391724], # dtype=numpy.float64) self.numBasis = 6 self.numQuadPts = 6 self.spaceDim = 2 self.cellDim = 2 return
def __init__(self, name='convertdata'): """Constructor.""" Component.__init__(self, name, facility='convertdata') self._fileSrc = None self._fileDest = None self._command = None return
def __init__(self, name="mesh2dquadratic"): """ Constructor. """ Component.__init__(self, name, facility="mesh") self.spaceDim = 2 self.cellDim = 2 self.numVertices = 6 self.numCells = 1 self.gravityVec = numpy.array( [0.0, -1.0e8], dtype=numpy.float64) self.vertices = numpy.array( [[-1.0, -1.0], [+1.0, +0.2], [-1.5, +0.5], [-0.25, +0.35], [-1.25, -0.25], [0.0, -0.4]], dtype=numpy.float64) self.cells = numpy.array( [[0, 1, 2, 3, 4, 5]], dtype=numpy.int32) self.verticesRef = numpy.array( [[-1.0, -1.0], [+1.0, -1.0], [-1.0, +1.0], [ 0.0, 0.0], [-1.0, 0.0], [ 0.0, -1.0]], dtype=numpy.float64) a = (2.0**2 + 1.2**2)**0.5 b = (2.5**2 + 0.3**2)**0.5 c = (0.5**2 + 1.5**2)**0.5 k = 0.5 * (a + b + c) r = (k*(k-a)*(k-b)*(k-c))**0.5 / k self.minCellWidth = min(a, b, c, 3.0*r) return
def _configure(self): Component._configure(self) self.host = self.inventory.host self.port = self.inventory.port return
def __init__(self, name='geometer'): Component.__init__(self, name, 'geometer') base.__init__(self) import journal self._warning = journal.warning('mcni.pyre_support.geometer') return
def __init__(self): Component.__init__(self, "tabulator", "tabulator") self.low = 0.0 self.high = 1.0 self.step = 0.1 self.functor = None return
def _configure(self): """ Set attributes based on inventory. """ Component._configure(self) ModuleSpatialDB.label(self, self.inventory.label) return
def __init__(self, name="solution3dquadratic"): """ Constructor. """ Component.__init__(self, name, facility="solution") # Input fields self.dt = 0.01 self.fieldTIncr = numpy.array([ +0.3, -0.4, -0.4, -0.6, +0.8, +0.2, +0.5, +0.5, +0.7, -0.7, -0.5, -0.7, -0.6, -0.3, +0.8, -0.4, -0.8, -0.5, +0.7, +0.8, -0.5, -0.5, -0.5, -0.7, -0.3, -0.9, +0.8, -0.1, +0.5, -0.9 ], dtype=numpy.float64) self.fieldT = numpy.array([ +0.1, -0.2, -0.6, -0.3, +0.4, +0.9, +0.6, +0.8, +0.5, -0.8, -0.6, -0.8, -0.0, -0.2, +0.6, -0.4, -0.7, -0.2, +0.7, +0.6, -0.1, -0.4, -0.3, -0.3, -0.7, -0.6, +0.1, -0.9, +0.3, -0.8 ], dtype=numpy.float64) self.fieldTmdt = numpy.array([ +0.2, -0.3, -0.1, -0.4, +0.2, +0.3, -0.5, +0.2, +0.2, -0.3, -0.8, -0.3, -0.5, -0.9, +0.4, -0.3, -0.6, -0.8, +0.9, +0.5, -0.2, -0.7, -0.2, -0.9, -0.5, -0.8, +0.4, -0.4, +0.5, -0.7 ], dtype=numpy.float64) return
def _configure(self): """ Setup members using inventory. """ Component._configure(self) pylith.perf.Material.Material.__init__(self, self.inventory.label, self.inventory.size) return
def __init__(self, name="mesh2din3dlinearxy"): """ Constructor. """ Component.__init__(self, name, facility="mesh") self.spaceDim = 3 self.cellDim = 2 self.numVertices = 3 self.numCells = 1 self.gravityVec = numpy.array([0.0, 0.0, -1.0e8], dtype=numpy.float64) self.vertices = numpy.array( [[0.0, 0.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], dtype=numpy.float64) self.cells = numpy.array([[0, 1, 2]], dtype=numpy.int32) self.verticesRef = numpy.array( [[-1.0, -1.0], [+1.0, -1.0], [-1.0, +1.0]], dtype=numpy.float64) a = (1.0**2 + 0.0**2 + 0.0**2)**0.5 b = (1.0**2 + 0.0**2 + 1.0**2)**0.5 c = (0.0**2 + 0.0**2 + 1.0**2)**0.5 k = 0.5 * (a + b + c) r = (k * (k - a) * (k - b) * (k - c))**0.5 / k self.minCellWidth = r return
def __init__(self, name="mesh2din3dlinearyz"): """ Constructor. """ Component.__init__(self, name, facility="mesh") self.spaceDim = 3 self.cellDim = 2 self.numVertices = 3 self.numCells = 1 self.gravityVec = numpy.array( [0.0, 0.0, -1.0e8], dtype=numpy.float64) self.vertices = numpy.array( [[ 0.0, 0.0, 0.0], [ 0.0, 1.0, 0.0], [ 0.0, 0.0, 1.0]], dtype=numpy.float64) self.cells = numpy.array( [[0, 1, 2]], dtype=numpy.int32) self.verticesRef = numpy.array( [[-1.0, -1.0], [+1.0, -1.0], [-1.0, +1.0]], dtype=numpy.float64) a = (0.0**2 + 1.0**2 + 0.0**2)**0.5 b = (0.0**2 + 1.0**2 + 0.0**2)**0.5 c = (0.0**2 + 0.0**2 + 1.0**2)**0.5 k = 0.5 * (a + b + c) r = (k*(k-a)*(k-b)*(k-c))**0.5 / k self.minCellWidth = r return
def __init__(self): Component.__init__(self, "locator", facility="recordLocator") self._alphabet = None self._base = None self._hashtable = None return
def _init(self): Component._init(self) # connect to the database import pyre.db dbkwds = DbAddressResolver().resolve(self.inventory.db) self.db = pyre.db.connect(wrapper=self.inventory.dbwrapper, **dbkwds)
def __init__(self, name="dumpparameters"): """ Constructor. """ Component.__init__(self, name="dumpparamters", facility="dumpparameters") self.info = None return
def __init__(self, name="mesh3dlinear"): """ Constructor. """ Component.__init__(self, name, facility="mesh") self.spaceDim = 3 self.cellDim = 3 self.numVertices = 4 self.numCells = 1 self.gravityVec = numpy.array([0.0, 0.0, -1.0e8], dtype=numpy.float64) self.vertices = numpy.array([[-0.5, -1.0, -0.5], [1.0, -0.1, -0.3], [2.0, -0.5, -0.4], [-0.2, 0.5, 2.0]], dtype=numpy.float64) self.cells = numpy.array([[0, 1, 2, 3]], dtype=numpy.int32) self.verticesRef = numpy.array( [[-1.0, -1.0, -1.0], [-1.0, +1.0, -1.0], [+1.0, -1.0, -1.0], [-1.0, -1.0, +1.0]], dtype=numpy.float64) v0 = self.vertices[0, :] v1 = self.vertices[1, :] v2 = self.vertices[2, :] v3 = self.vertices[3, :] e01 = ((v0[0] - v1[0])**2 + (v0[1] - v1[1])**2 + (v0[2] - v1[2])**2)**0.5 e12 = ((v1[0] - v2[0])**2 + (v1[1] - v2[1])**2 + (v1[2] - v2[2])**2)**0.5 e20 = ((v2[0] - v0[0])**2 + (v2[1] - v0[1])**2 + (v2[2] - v0[2])**2)**0.5 e03 = ((v0[0] - v3[0])**2 + (v0[1] - v3[1])**2 + (v0[2] - v3[2])**2)**0.5 e13 = ((v1[0] - v3[0])**2 + (v1[1] - v3[1])**2 + (v1[2] - v3[2])**2)**0.5 e23 = ((v2[0] - v3[0])**2 + (v2[1] - v3[1])**2 + (v2[2] - v3[2])**2)**0.5 vol = 1.0 / 6.0 * numpy.linalg.det( numpy.array( [[1.0, v0[0], v0[1], v0[2]], [1.0, v2[0], v2[1], v2[2]], [1.0, v1[0], v1[1], v1[2]], [1.0, v3[0], v3[1], v3[2]]], dtype=numpy.float64)) cross012 = numpy.cross(v1 - v0, v2 - v0) area012 = 0.5 * (numpy.dot(cross012, cross012))**0.5 cross013 = numpy.cross(v1 - v0, v3 - v0) area013 = 0.5 * (numpy.dot(cross013, cross013))**0.5 cross123 = numpy.cross(v2 - v1, v3 - v1) area123 = 0.5 * (numpy.dot(cross123, cross123))**0.5 cross203 = numpy.cross(v0 - v2, v3 - v2) area203 = 0.5 * (numpy.dot(cross203, cross203))**0.5 area = area012 + area013 + area123 + area203 r = 3.0 * vol / area self.minCellWidth = min(e01, e12, e20, e03, e13, e23, 6.38 * r) return
def _init(self): Component._init(self) self._alphabet = list(self.inventory.alphabet) self._base = len(self._alphabet) self._hashtable = self._hash(self._alphabet) return