class Inventory(CitcomComponent.Inventory):
import pyre.inventory as inv
tracer = inv.bool("tracer", default=False)
# tracer_ic_method=0 (random generated array)
# tracer_ic_method=1 (all proc read the same file)
# tracer_ic_method=2 (each proc reads its own file)
tracer_ic_method = inv.int("tracer_ic_method", default=0)
# (tracer_ic_method == 0)
tracers_per_element = inv.int("tracers_per_element", default=10)
# (tracer_ic_method == 1)
tracer_file = inv.str("tracer_file", default="tracer.dat")
# How many flavors of tracers
# If tracer_flavors > 0, each element will report the number of
# tracers of each flavor inside it. This information can be used
# later for many purposes. One of it is to compute composition,
# either using absolute method or ratio method.
tracer_flavors = inv.int("tracer_flavors", default=0)
# How to initialize tracer flavors
ic_method_for_flavors = inv.int("ic_method_for_flavors", default=0)
z_interface = inv.list("z_interface", default=[0.7])
ictracer_grd_file = inv.str("ictracer_grd_file", default="")
ictracer_grd_layers = inv.int("ictracer_grd_layers", default=2)
# Warning level
itracer_warnings = inv.bool("itracer_warnings", default=True)
# Enriched internal heat production
tracer_enriched = inv.bool("tracer_enriched", default=False)
Q0_enriched = inv.float("Q0_enriched", default=0.0)
# Regular grid parameters
regular_grid_deltheta = inv.float("regular_grid_deltheta", default=1.0)
regular_grid_delphi = inv.float("regular_grid_delphi", default=1.0)
# Analytical Test Function
#analytical_tracer_test = inv.int("analytical_tracer_test", default=0)
chemical_buoyancy = inv.bool("chemical_buoyancy", default=True)
# ibuoy_type=0 (absolute method, not implemented)
# ibuoy_type=1 (ratio method)
buoy_type = inv.int("buoy_type", default=1)
buoyancy_ratio = inv.list("buoyancy_ratio", default=[1.0])
# DJB
hybrid_method = inv.int("hybrid_method", default=0)
# This is not used anymore and is left here for backward compatibility
reset_initial_composition = inv.bool("reset_initial_composition",
default=False)
class Inventory(CitcomComponent.Inventory):
import pyre.inventory as prop
ADV = prop.bool("ADV", default=True)
filter_temp = prop.bool("filter_temp", default=False)
monitor_max_T = prop.bool("monitor_max_T", default=True)
fixed_timestep = prop.float("fixed_timestep", default=0.0)
finetunedt = prop.float("finetunedt", default=0.9)
adv_gamma = prop.float("adv_gamma", default=0.5)
adv_sub_iterations = prop.int("adv_sub_iterations", default=2)
inputdiffusivity = prop.float("inputdiffusivity", default=1)
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
class Inventory(Component.Inventory):
a = inv.str('a', default='abc')
b = inv.float('b', default=3.0, validator=inv.greater(0))
pass
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)
class Inventory(AbstractComponent.Inventory):
import pyre.inventory as pinv
radius1 = pinv.float("radius1", default=0.3)
radius2 = pinv.float("radius2", default=0.5)
height1 = pinv.float("height1", default=0.5)
height2 = pinv.float("height2", default=0.5)
theta1 = pinv.float("theta1", default=0)
theta2 = pinv.float("theta2", default=180)
dtheta = pinv.float("dtheta", default=1)
oscillation = pinv.float("oscillation", default=1)
pass
class Inventory(CitcomComponent.Inventory):
import pyre.inventory as prop
Solver = prop.str("Solver", default="cgrad",
validator=prop.choice(["cgrad",
"multigrid"]))
node_assemble = prop.bool("node_assemble", default=True)
precond = prop.bool("precond", default=True)
accuracy = prop.float("accuracy", default=1.0e-4)
inner_accuracy_scale = prop.float("inner_accuracy_scale", default=1.0)
check_continuity_convergence = prop.bool("check_continuity_convergence", default=True)
check_pressure_convergence = prop.bool("check_pressure_convergence", default=True)
mg_cycle = prop.int("mg_cycle", default=1)
down_heavy = prop.int("down_heavy", default=3)
up_heavy = prop.int("up_heavy", default=3)
vlowstep = prop.int("vlowstep", default=1000)
vhighstep = prop.int("vhighstep", default=3)
max_mg_cycles = prop.int("max_mg_cycles", default=50)
piterations = prop.int("piterations", default=1000)
aug_lagr = prop.bool("aug_lagr", default=True)
aug_number = prop.float("aug_number", default=2.0e3)
uzawa = prop.str("uzawa", default="cg",
validator=prop.choice(["cg", "bicg"]))
compress_iter_maxstep = prop.int("compress_iter_maxstep", default=100)
inner_remove_rigid_rotation = prop.bool("inner_remove_rigid_rotation", default=False)
remove_rigid_rotation = prop.bool("remove_rigid_rotation", default=True)
remove_angular_momentum = prop.bool("remove_angular_momentum", default=True)
only_check_vel_convergence = prop.bool("only_check_vel_convergence", default=False)
# Not used. Retained here for backward compatibility.
tole_compressibility = prop.float("tole_compressibility", default=1.0e-7)
relative_err_accuracy = prop.float("relative_err_accuracy", default=0.001)
class Inventory( AbstractComponent.Inventory ):
import pyre.inventory as pinv
tofmin = pinv.float( 'tofmin', default = 0 )
tofmin.meta['tip'] = 'tof min'
tofmax = pinv.float( 'tofmax', default = 0.01 )
tofmax.meta['tip'] = 'tof max'
ntof = pinv.int( 'ntof', default = 100 )
ntof.meta['tip'] = 'number of tof channels'
xmin = pinv.float( 'xmin', default = -0.1 )
xmin.meta['tip'] = 'x min'
xmax = pinv.float( 'xmax', default = 0.1 )
xmax.meta['tip'] = 'x max'
nx = pinv.int( 'nx', default = 100 )
nx.meta['tip'] = 'number of x bins'
ymin = pinv.float( 'ymin', default = -0.1 )
ymin.meta['tip'] = 'y min'
ymax = pinv.float( 'ymax', default = 0.1 )
ymax.meta['tip'] = 'y max'
ny = pinv.int( 'ny', default = 100 )
ny.meta['tip'] = 'number of y bins'
eventsdat = pinv.str( 'eventsdat', default = 'events.dat' )
eventsdat.meta['tip'] = 'output event data file'
pass
class Inventory(MultiMonitors.Inventory):
from mcni.pyre_support import facility
m1 = facility('m1', default="monitors/NDMonitor(t)")
m2 = facility('m2', default="monitors/NDMonitor(w)")
m3 = facility('m3', default="monitors/NDMonitor(t)")
m4 = facility('m4', default="monitors/NDMonitor(w)")
m5 = facility('m5', default="monitors/NDMonitor(t)")
m6 = facility('m6', default="monitors/NDMonitor(w)")
import pyre.inventory as inv
xwidth = inv.float(name='xwidth', default=0.77)
yheight = inv.float(name='yheight', default=0.385)
tmin = inv.float(name='tmin', default=0.)
tmax = inv.float(name='tmax', default=0.1)
nt = inv.int(name='nt', default=100)
wmin = inv.float(name='wmin', default=0.)
wmax = inv.float(name='wmax', default=10)
nw = inv.int(name='nw', default=100)
class Inventory(AbstractComponent.Inventory):
import pyre.inventory as pinv
energy = pinv.float('energy', default=0) # meV
energy.meta['tip'] = (
'energy of the neutron. if "energy" is given, '
'the neutron velocity will be computed so that '
'the energy of the neutron will be the given value of energy,'
'and the moving direction will be determined by the "velocity" vector'
)
energy_width = pinv.float('energy-width', default=0)
energy_width.meta['tip'] = (
"energy spread. if positive, there will be a normal distribution",
"of neutron energies around the central energy.",
"the energy_width is the standard deviation of the normal",
"distribution.",
)
velocity = pinv.array('velocity', default='0,0,3000') # m/s
velocity.meta[
'tip'] = 'velocity of neutrons. unit: m/s. Note: if energy is nonzero, the magnitude of the velocity is set by energy'
position = pinv.array('position', default='0,0,0')
position.meta['tip'] = 'position of neutrons. unit: m'
width = pinv.float('width', default=0)
width.meta['tip'] = 'width of source. unit:m'
height = pinv.float('height', default=0)
height.meta['tip'] = 'height of source. unit:m'
time = pinv.float('time', default=0)
time.meta['tip'] = 'time of flight for neutrons. unit: s'
probability = pinv.float('probability', default=1.)
probability.meta['tip'] = 'probabliity of neutrons. unit: 1'
pass
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(Component.Inventory):
import pyre.inventory as pyre_inventory
A = pyre_inventory.float("A", default=1.0)
B = pyre_inventory.float("B", default=2.0)
class Inventory(Component.Inventory):
import pyre.inventory as inv
a = inv.str('a', default='abc')
a.meta['known_alternatives'] = ['def', 'ghi']
b = inv.float('b', default=3.0)
