def outputFactory(name): """ Factory for material items. """ from pyre.inventory import facility from pylith.meshio.OutputSoln import OutputSoln return facility(name, family="output_manager", factory=OutputSoln)
class Inventory(Component.Inventory):
import pyre.inventory as inv
func = inv.facility('func', factory = Sin )
pass
class Inventory(Script.Inventory):
import pyre.inventory as inv
s = inv.str('s', default="abc")
i = inv.int('i', default=10)
f = inv.float('f', default=3.0)
func = inv.facility("func", factory=Sin)
pass
def faultFactory(name): """ Factory for fault items. """ from pyre.inventory import facility from pylith.faults.FaultCohesiveKin import FaultCohesiveKin return facility(name, family="fault", factory=FaultCohesiveKin)
def observerFactory(name):
"""
Factory for output items.
"""
from pyre.inventory import facility
from pylith.meshio.OutputConstraint import OutputConstraint
return facility(name, family="observer", factory=OutputConstraint)
def materialFactory(name): """ Factory for material items. """ from pyre.inventory import facility from pylith.materials.ElasticIsotropic3D import ElasticIsotropic3D return facility(name, family="material", factory=ElasticIsotropic3D)
def eqsrcFactory(name): """ Factory for earthquake source items. """ from pyre.inventory import facility from EqKinSrc import EqKinSrc return facility(name, family="eq_kinematic_src", factory=EqKinSrc)
def outputFactory(name): """ Factory for material items. """ from pyre.inventory import facility from pylith.meshio.OutputSoln import OutputSoln return facility(name, family="output_manager", factory=OutputSoln)
def materialFactory(name):
"""
Factory for material items.
"""
from pyre.inventory import facility
from pylith.materials.ElasticIsotropic3D import ElasticIsotropic3D
return facility(name, family="material", factory=ElasticIsotropic3D)
def faultFactory(name):
"""
Factory for fault items.
"""
from pyre.inventory import facility
from pylith.faults.FaultCohesiveKin import FaultCohesiveKin
return facility(name, family="fault", factory=FaultCohesiveKin)
def bcFactory(name):
"""
Factory for boundary condition items.
"""
from pyre.inventory import facility
from pylith.bc.DirichletBC import DirichletBC
return facility(name, family="boundary_condition", factory=DirichletBC)
def bcFactory(name): """ Factory for boundary condition items. """ from pyre.inventory import facility from pylith.bc.DirichletBC import DirichletBC return facility(name, family="boundary_condition", factory=DirichletBC)
def eqsrcFactory(name):
"""
Factory for earthquake source items.
"""
from pyre.inventory import facility
from EqKinSrc import EqKinSrc
return facility(name, family="eq_kinematic_src", factory=EqKinSrc)
class Inventory(Component.Inventory):
import pyre.inventory as inv
# component modules
import CitcomS.Components.Advection_diffusion as Advection_diffusion
import CitcomS.Components.Stokes_solver as Stokes_solver
# components
from CitcomS.Components.BC import BC
from CitcomS.Components.Const import Const
from CitcomS.Components.IC import IC
from CitcomS.Components.Output import Output
from CitcomS.Components.Param import Param
from CitcomS.Components.Phase import Phase
from CitcomS.Components.Tracer import Tracer
from CitcomS.Components.Visc import Visc
tsolver = inv.facility("tsolver",
factory=Advection_diffusion.temperature_diffadv)
vsolver = inv.facility("vsolver",
factory=Stokes_solver.incompressibleNewtonian)
bc = inv.facility("bc", factory=BC)
const = inv.facility("const", factory=Const)
ic = inv.facility("ic", factory=IC)
output = inv.facility("output", factory=Output)
param = inv.facility("param", factory=Param)
phase = inv.facility("phase", factory=Phase)
tracer = inv.facility("tracer", factory=Tracer)
visc = inv.facility("visc", factory=Visc)
datadir = inv.str("datadir", default=".")
datadir_old = inv.str("datadir_old", default=".")
rayleigh = inv.float("rayleigh", default=1e+05)
dissipation_number = inv.float("dissipation_number", default=0.0)
gruneisen = inv.float("gruneisen", default=0.0)
surfaceT = inv.float("surfaceT", default=0.1)
#adiabaticT0 = inv.float("adiabaticT0", default=0.4)
Q0 = inv.float("Q0", default=0.0)
stokes_flow_only = inv.bool("stokes_flow_only", default=False)
verbose = inv.bool("verbose", default=False)
see_convergence = inv.bool("see_convergence", default=True)
def vertexGroupFactory(name): """ Factory for vertex group items. """ from pyre.inventory import facility return facility(name, factory=VertexGroup)
def materialFactory(name): """ Factory for material items. """ from pyre.inventory import facility return facility(name, factory=Material)
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
from qchem.fireball.Fireball import Fireball
#from gamess.Gamess import Gamess #wait until Gamess is fully functional
from os import sep
from pyre.applications.Script import Script
from molDynamics.GeneralSettings import GeneralSettings
class QChemApp(Script):
'''Driver for the quantum chemistry engines'''
class Inventory(Script.Inventory):
import pyre.inventory as pinv
<<<<<<< .mine
quantumEngine = pinv.facility('quantumEngine', default=Fireball())
=======
quantumEngine = pinv.facility('quantumEngine', default=Fireball())
# quantumEngine = pinv.facility('quantumEngine', default='fireball')
>>>>>>> .r21
quantumEngine.meta['tip'] = 'which quantum engine to use'
<<<<<<< .mine
# quantumEngine.meta['known_plugins'] = ['fireball','gamess']
=======
# quantumEngine.meta['known_plugins'] = ['fireball','gamess']
generalSettings = pinv.facility('General Settings', default = GeneralSettings())
generalSettings.meta['tip'] = 'working directory, engine executable path, etc.'
>>>>>>> .r21
def __init__(self,name='QChemApp'):
Script.__init__(self, name)
class Inventory(Script.Inventory):
import pyre.inventory as inv
twoAtomInteraction = inv.facility('Two Atom Interaction Db', default=TwoAtomInteraction())
twoAtomInteraction.meta['tip'] = 'db of twoAtomsInteracting'
dbRetrieval = inv.facility('Two Atom Interaction Db', default=TwoAtomInteraction())
dbRetrieval.meta['tip'] = 'db of twoAtomsInteracting'
class Inventory(Component.Inventory):
import pyre.inventory as inv
barostatParameter = inv.float('Barostat Parameter', default=0.005)
barostatParameter.meta['tip'] = '''barostat parameter to keep
fluctuations relatively small'''
coordinateFormat = inv.str('Coordinate Format', default='cartesian')
coordinateFormat.meta['tip'] = 'what format the coordinates are in'
coordinateFormat.validator = inv.choice(['cartesian', 'fractional'])
constantPressureFit = inv.bool('Constant Pressure Fit', default=False)
constantPressureFit.meta[
'tip'] = '''keep pressure constant during fitting (fit
to irreducible cell coordinates and lattice lengths)'''
constantPressureOptimize = inv.bool('Constant Pressure Optimize',
default=False)
constantPressureOptimize.meta[
'tip'] = '''keep pressure constant during optimization'''
constantVolumeFit = inv.bool('Constant Volume Fit', default=False)
constantVolumeFit.meta[
'tip'] = '''keep volume constant during fitting (fit
to irreducible cell coordinates)'''
constantVolumeOptimize = inv.bool('Constant Volume Optimize',
default=False)
constantVolumeOptimize.meta[
'tip'] = '''keep volume constant during optimization'''
dispersionInRecipSpace = inv.bool(
'Calculate Dispersion in Reciprocal Space', default=False)
dispersionInRecipSpace.meta[
'tip'] = '''whether to calculate dispersion forces
partly in reciprocal space'''
dumpFrequency = inv.float('Dump Frequency', default=1.0)
dumpFrequency.meta[
'tip'] = '''frequency at which a restart file is written'''
engineExecutablePath = inv.str(
'Engine Executable Path', default='/home/brandon/gulp3.0/Src/gulp')
engineExecutablePath.meta[
'tip'] = '''path to the engine\'s executable'''
ensemble = inv.str('Thermodynamic Ensemble',
default='nve',
validator=inv.choice(["nve", "nvt", "npt"]))
ensemble.meta['tip'] = 'thermodynamic ensemble (nve, nvt, npt, ...)'
equilibrationTime = inv.float('Equilibration Time (ps)', default=0.1)
equilibrationTime.meta[
'tip'] = 'equilibration time of the simulation (ps)'
identifyMolecules = inv.bool('Indentify Molecules', default=False)
identifyMolecules.meta[
'tip'] = '''identify molecules based on covalent radii
and remove intramolecular coloumb interactions'''
integrator = inv.str('Integrator', default='velocity-verlet')
integrator.meta['tip'] = 'type of integrator'
inputDeckName = inv.str('Input Filename', default='gulp.gin')
inputDeckName.meta['tip'] = '''input file for executable'''
logFilename = inv.str('Log Filename', default='molDynamics.log')
logFilename.meta['tip'] = 'name of log file for md run'
optimizeCell = inv.bool('Optimize Cell', default=False)
optimizeCell.meta['tip'] = 'whether to optimize the unit cell'
optimizeCoordinates = inv.bool('Optimize Coordinates', default=False)
optimizeCoordinates.meta[
'tip'] = 'whether to optimize the coordinate positions'
productionTime = inv.float('Production Time (ps)', default=5.0)
productionTime.meta['tip'] = 'production time of the simulation'
computeMaterialProperties = inv.bool('Compute Material Properties',
default=False)
computeMaterialProperties.meta[
'tip'] = 'whether to print material properties'
restartFilename = inv.str('Restart Filename',
default='molDynamics.res')
restartFilename.meta['tip'] = '''restart file for md executable'''
runType = inv.str('Run Type',default='md',\
validator=inv.choice(['md', 'restart md', 'optimize', 'fit']))
runType.meta['tip'] = 'type of run'
sample = inv.facility('Sample', default=Component('sample', 'sample'))
sample.meta['importance'] = 10
sample.meta['tip'] = 'piece of material being measured/simulated'
sampleFrequency = inv.float('Sample Properties Frequency', default=5.0)
sampleFrequency.meta[
'tip'] = '''frequency at which sampled properties are
written to trajectory and log file'''
spaceGroup = inv.str('Space Group', default=None)
spaceGroup.meta['tip'] = 'specify space group symmetry'
thermostatParameter = inv.float('Thermostat Parameter', default=0.005)
thermostatParameter.meta['tip'] = '''thermostat parameter to keep
fluctuations relatively small'''
timeStep = inv.float('Time step (ps)', default=0.5)
timeStep.meta['tip'] = 'integration time step (ps)'
trajectoryFilename = inv.str('Trajectory Filename',
default='molDynamics.xyz')
trajectoryFilename.meta['tip'] = 'name of trajectory file'
#trajectoryType = inv.facility('Trajectory Type', default = TrajectoryType())
trajectoryType = inv.str('Trajectory Type', default='xyz (Gulp)')
trajectoryType.meta['tip'] = '''type of trajectory file'''
trajectoryType.validator = inv.choice([
'xyz (Gulp)', 'netcdf (Mmtk)', 'trajectory (Gulp)',
'history (Gulp)', 'phonon (Gulp)', 'arc (Gulp)'
])
workingDirectory = inv.str('Working Directory', default='$HOME')
workingDirectory.meta[
'tip'] = '''working directory where computation will
class Inventory(Script.Inventory):
import pyre.inventory as inv
translator = inv.facility('translator', default=Trajectory())
#translator = inv.facility('translator', default='trajectory')
translator.meta['tip'] = 'translate a file from one format to another'
translator.meta['known_plugins'] = ['trajectory']
class Inventory(Component.Inventory):
import pyre.inventory as pinv
cod = pinv.facility('cod', default=Cod())
sqlite = pinv.facility('sqlite', default=Sqlite)
