test gkeyll

showvalues.py

import h5py
import numpy
numpy.set_printoptions(precision=16)

def printValues(fname):
    fp = h5py.File(fname)
    field = fp["StructGridField"][...]
    print(field)
    fp.close()

for fname in ["gem_qBeforeSrc.h5", "gem_qAfterSrc.h5", "gem_qSweep.h5"]:
    print(fname)
    printValues(fname)
    print("\n")

test_gkeyll.lua

-- GEM-challenge problem

Pi = Lucee.Pi
log = Lucee.logInfo

-- physical parameters
gasGamma = 5./3.
elcCharge = -1.0
ionCharge = 1.0
ionMass = 1.0
elcMass = 0.25
lightSpeed = 1.0
epsilon0 = 1.0
mgnErrorSpeedFactor = 1.0

Lx = 25.6
Ly = 12.8
n0 = 1.0
VAe = 0.5
plasmaBeta = 1.0
lambda = 0.5
TiOverTe = 5.0
nbOverN0 = 0.2
pert = 0.1

Valf = VAe*math.sqrt(elcMass/ionMass)
B0 = Valf*math.sqrt(n0*ionMass)
OmegaCi0 = ionCharge*B0/ionMass
psi0 = pert*B0

-- resolution and time-stepping
NX = 64
NY = 32
NX = 2
NY = 2
cfl = 1.
tStart = 0.0
tEnd = 1
nFrames = 1

log(string.format("elcMass/ionMass=1/%g",ionMass/elcMass))
log(string.format("Lx=%gdi=%gde", Lx,Lx*math.sqrt(ionMass/elcMass)))
log(string.format("plasmaBeta=%g", plasmaBeta))
log(string.format("Valf/c=%g", Valf))
log(string.format("lambda/di=%g", lambda))
log(string.format("TiOverTe=%g", TiOverTe))
log(string.format("nbOverN0=%g", nbOverN0))
log(string.format("pert=%g", pert))
log(string.format("tEnd=%g,  nFrames=%d",tEnd,nFrames))
log(string.format("NX=%d,dx=%gdi=%gde,cfl=%g\n", NX,Lx/NX,Lx/NX*math.sqrt(ionMass/elcMass),cfl))


------------------------------------------------
-- COMPUTATIONAL DOMAIN, DATA STRUCTURE, ETC. --
------------------------------------------------
-- decomposition object
decomp = DecompRegionCalc2D.CartGeneral {}
-- computational domain
grid = Grid.RectCart2D {
   lower = {0, 0},
   upper = {1., 1.},
   cells = {4, 1,},
   decomposition = decomp,
   periodicDirs = {0,1},
}

-- solution
q = DataStruct.Field2D {
   onGrid = grid,
   numComponents = 18,
   ghost = {2, 2},
}
-- solution after update along X (ds algorithm)
qX = DataStruct.Field2D {
   onGrid = grid,
   numComponents = 18,
   ghost = {2, 2},
}
-- final updated solution
qNew = DataStruct.Field2D {
   onGrid = grid,
   numComponents = 18,
   ghost = {2, 2},
}
-- duplicate copy in case we need to take the step again
qDup = DataStruct.Field2D {
   onGrid = grid,
   numComponents = 18,
   ghost = {2, 2},
}
qNewDup = DataStruct.Field2D {
   onGrid = grid,
   numComponents = 18,
   ghost = {2, 2},
}

-- aliases to various sub-systems
elcFluid = q:alias(0, 5)
ionFluid = q:alias(5, 10)
emField = q:alias(10, 18)

elcFluidX = qX:alias(0, 5)
ionFluidX = qX:alias(5, 10)
emFieldX = qX:alias(10, 18)

elcFluidNew = qNew:alias(0, 5)
ionFluidNew = qNew:alias(5, 10)
emFieldNew = qNew:alias(10, 18)

-----------------------
-- INITIAL CONDITION --
-----------------------
-- initial conditions
function init(x,y,z)
         local n = 1 + .3 * x
         print(x, n)
         local rhoe = 1 + .3 * x
         local rhovxe = 2 + .3 * x
         local rhovye = 3 + .3 * x
         local rhovze = 4 + .3 * x
         local pe = 5 + .3 * x
         local ue = pe / (gasGamma-1) + 0.5 * (rhovxe^2 + rhovye^2 + rhovze^2) / rhoe

         local n = 1.4
         local rhoi = 1.4
         local rhovxi = 2.4
         local rhovyi = 3.4
         local rhovzi = 4.4
         local pi = 5.4
         local ui = pi / (gasGamma-1) + 0.5 * (rhovxi^2 + rhovyi^2 + rhovzi^2) / rhoi

         local Ex = 1 + .1 * x
         local Ey = 1 + .2 * x
         local Ez = 1 + .3 * x
         local Bx = 2 + .1 * x
         local By = 2 + .2 * x
         local Bz = 2 + .3 * x

         return rhoe, rhovxe, rhovye, rhovze, ue,
                rhoi, rhovxi, rhovyi, rhovzi, ui,
                Ex, Ey, Ez, Bx, By, Bz, 0., 0.
end


------------------------
-- Boundary Condition --
------------------------
-- boundary applicator objects for fluids and fields

bcElcCopy = BoundaryCondition.Copy { components = {0, 4} }
bcElcWall = BoundaryCondition.ZeroNormal { components = {1, 2, 3} }
bcIonCopy = BoundaryCondition.Copy { components = {5, 9} }
bcIonWall = BoundaryCondition.ZeroNormal { components = {6, 7, 8} }
bcElcFld = BoundaryCondition.ZeroTangent { components = {10, 11, 12} }
bcMgnFld = BoundaryCondition.ZeroNormal { components = {13, 14, 15} }
bcPot = BoundaryCondition.Copy { components = {16, 17} }
--FIXME: fact in bcPot

-- create boundary condition object
function createBc(myDir, myEdge)
   local bc = Updater.Bc2D {
      onGrid = grid,
      -- boundary conditions to apply
      boundaryConditions = {
   bcElcCopy, bcElcWall, 
   bcIonCopy, bcIonWall,
   bcElcFld, bcMgnFld, bcPot,
      },
      -- direction to apply
      dir = myDir,
      -- edge to apply on
      edge = myEdge,
   }
   return bc
end

-- create updaters to apply boundary conditions
bcBottom = createBc(1, "lower")
bcTop = createBc(1, "upper")

-- function to apply boundary conditions to specified field
function applyBc(fld, tCurr, myDt)
   -- for i,bc in ipairs({bcBottom, bcTop}) do
   --    bc:setOut( {fld} )
   --    bc:advance(tCurr+myDt)
   -- end
   -- sync ghost cells
   fld:sync()
end

----------------------
-- EQUATION SOLVERS --
----------------------
-- regular Euler equations
elcEulerEqn = HyperEquation.Euler {
   gasGamma = gasGamma,
}
ionEulerEqn = HyperEquation.Euler {
   gasGamma = gasGamma,
}
-- (Lax equations are used to fix negative pressure/density)
elcEulerLaxEqn = HyperEquation.Euler {
   gasGamma = gasGamma,
   numericalFlux = "lax",   
}
ionEulerLaxEqn = HyperEquation.Euler {
   gasGamma = gasGamma,
   numericalFlux = "lax",
}
maxwellEqn = HyperEquation.PhMaxwell {
   lightSpeed = lightSpeed,
   elcErrorSpeedFactor = 0.0,
   mgnErrorSpeedFactor = mgnErrorSpeedFactor
}

-- ds solvers for regular Euler equations along X
elcFluidSlvrDir0 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = elcEulerEqn,
   -- one of no-limiter, min-mod, superbee, 
   -- van-leer, monotonized-centered, beam-warming
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {0} -- directions to update
}
ionFluidSlvrDir0 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = ionEulerEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {0}
}
maxSlvrDir0 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = maxwellEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {0}
}

-- ds solvers for regular Euler equations along Y
elcFluidSlvrDir1 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = elcEulerEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {1}
}
ionFluidSlvrDir1 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = ionEulerEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {1}
}
maxSlvrDir1 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = maxwellEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {1}
}

-- ds solvers for Lax Euler equations along X
elcLaxSlvrDir0 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = elcEulerLaxEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {0}
}
ionLaxSlvrDir0 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = ionEulerLaxEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {0}
}
maxLaxSlvrDir0 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = maxwellEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {0}
}

-- ds solvers for Lax Euler equations along Y
elcLaxSlvrDir1 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = elcEulerLaxEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {1}
}
ionLaxSlvrDir1 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = ionEulerLaxEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {1}
}
maxLaxSlvrDir1 = Updater.WavePropagation2D {
   onGrid = grid,
   equation = maxwellEqn,
   limiter = "van-leer",
   cfl = cfl,
   cflm = 1.1*cfl,
   updateDirections = {1}
}

-- updater for source terms
sourceSlvr = Updater.ImplicitFiveMomentSrc2D {
   onGrid = grid,
   numFluids = 2,
   charge = {elcCharge, ionCharge},
   mass = {elcMass, ionMass},
   epsilon0 = epsilon0,
   -- linear solver to use: one of partialPivLu or colPivHouseholderQr
   linearSolver = "partialPivLu",
   hasStaticField = false,
}

-- function to update source terms
function updateSource(elcIn, ionIn, emIn, tCurr, t)
  print("updateSource dt", t-tCurr)
   sourceSlvr:setOut( {elcIn, ionIn, emIn} )
   sourceSlvr:setCurrTime(tCurr)
   sourceSlvr:advance(t)

   -- momentum drag relaxation
end

-- function to update the fluid and field using dimensional splitting
function updateFluidsAndField(tCurr, t)
   local myStatus = true
   local myDtSuggested = 1e3*math.abs(t-tCurr)
   local useLaxSolver = False
   -- X-direction updates
   applyBc(q, tCurr, t-tCurr)
   for i,slvr in ipairs({elcFluidSlvrDir0, ionFluidSlvrDir0, maxSlvrDir0}) do
      slvr:setCurrTime(tCurr)
      local status, dtSuggested = slvr:advance(t)
      myStatus = status and myStatus
      myDtSuggested = math.min(myDtSuggested, dtSuggested)
   end

   if ((elcEulerEqn:checkInvariantDomain(elcFluidX) == false)
    or (ionEulerEqn:checkInvariantDomain(ionFluidX) == false)) then
      useLaxSolver = true
   end

   if ((myStatus == false) or (useLaxSolver == true)) then
      return myStatus, myDtSuggested, useLaxSolver
   end

   -- apply BCs to intermediate update after X sweep
   applyBc(qX, tCurr, t-tCurr)

   -- Y-direction updates
   for i,slvr in ipairs({elcFluidSlvrDir1, ionFluidSlvrDir1, maxSlvrDir1}) do
      slvr:setCurrTime(tCurr)
      local status, dtSuggested = slvr:advance(t)
      myStatus = status and myStatus
      myDtSuggested = math.min(myDtSuggested, dtSuggested)
   end

   if ((elcEulerEqn:checkInvariantDomain(elcFluidNew) == false)
    or (ionEulerEqn:checkInvariantDomain(ionFluidNew) == false)) then
       useLaxSolver = true
   end

   return myStatus, myDtSuggested, useLaxSolver
end

write = true
-- function to take one time-step with Euler solver
function solveTwoFluidSystem(tCurr, t)
   local dthalf = 0.5*(t-tCurr)

   -- update source terms
   if write then
      q:write("qBeforeSrc.h5", 0)
   end
   updateSource(elcFluid, ionFluid, emField, tCurr, tCurr+dthalf)
   applyBc(q, tCurr, t-tCurr)
   if write then
      q:write("qAfterSrc.h5", 0)
   end

   -- update fluids and fields
   local status, dtSuggested, useLaxSolver = updateFluidsAndField(tCurr, t)
   if write then
      q:write("qSweep.h5", 0)
   end

   -- update source terms
   updateSource(elcFluidNew, ionFluidNew, emFieldNew, tCurr, tCurr+dthalf)
   applyBc(qNew, tCurr, t-tCurr)

   if write then
     write = false
   end
   os.exit()

   return status, dtSuggested,useLaxSolver
end

-- function to update the fluid and field using dimensional splitting Lax scheme
function updateFluidsAndFieldLax(tCurr, t)
   local myStatus = true
   local myDtSuggested = 1e3*math.abs(t-tCurr)
   applyBc(q, tCurr, t-tCurr)
   for i,slvr in ipairs({elcLaxSlvrDir0, ionLaxSlvrDir0, maxLaxSlvrDir0}) do
      slvr:setCurrTime(tCurr)
      local status, dtSuggested = slvr:advance(t)
      myStatus = status and myStatus
      myDtSuggested = math.min(myDtSuggested, dtSuggested)
   end

   applyBc(qX, tCurr, t-tCurr)

   -- Y-direction updates
   for i,slvr in ipairs({elcLaxSlvrDir1, ionLaxSlvrDir1, maxLaxSlvrDir1}) do
      slvr:setCurrTime(tCurr)
      local status, dtSuggested = slvr:advance(t)
      myStatus = status and myStatus
      myDtSuggested = math.min(myDtSuggested, dtSuggested)
   end

   return myStatus, myDtSuggested
end

-- function to take one time-step with Lax Euler solver
function solveTwoFluidLaxSystem(tCurr, t)
   local dthalf = 0.5*(t-tCurr)

   -- update source terms
   updateSource(elcFluid, ionFluid, emField, tCurr, tCurr+dthalf)
   applyBc(q, tCurr, t-tCurr)

   -- update fluids and fields
   local status, dtSuggested = updateFluidsAndFieldLax(tCurr, t)

   -- update source terms
   updateSource(elcFluidNew, ionFluidNew, emFieldNew, tCurr, tCurr+dthalf)
   applyBc(qNew, tCurr, t-tCurr)

   return status, dtSuggested
end

----------------------------
-- DIAGNOSIS AND DATA I/O --
----------------------------
-- dynvector to store integrated flux
byAlias = qNew:alias(14, 15)
byFlux = DataStruct.DynVector { numComponents = 1 }
byFluxCalc = Updater.IntegrateFieldAlongLine2D {
   onGrid = grid,
   -- start cell
   startCell = {0, NY/2},
   -- direction to integrate in
   dir = 0,
   -- number of cells to integrate
   numCells = NX,
   -- integrand
   integrand = function (by)
		  return math.abs(by)
	       end,
}
byFluxCalc:setIn( {byAlias} )
byFluxCalc:setOut( {byFlux} )

-- dynvector to store Ez at X-point
ezAlias = qNew:alias(12, 13)
xpointEz = DataStruct.DynVector { numComponents = 1 }
xpointEzRec = Updater.RecordFieldInCell2D {
   onGrid = grid,
   -- index of cell to record
   cellIndex = {(NX-1)/2, (NY-1)/2},
}
xpointEzRec:setIn( {ezAlias} )
xpointEzRec:setOut( {xpointEz} )

-- dynvector to store number density at X-point
neAlias = qNew:alias(0, 1)
xpointNe = DataStruct.DynVector { numComponents = 1 }
xpointNeRec = Updater.RecordFieldInCell2D {
   onGrid = grid,
   -- index of cell to record
   cellIndex = {(NX-1)/2, (NY-1)/2},
}
xpointNeRec:setIn( {neAlias} )
xpointNeRec:setOut( {xpointNe} )

-- dynvector to store electron uz at X-point
uzeAlias = qNew:alias(3, 4)
xpointUze = DataStruct.DynVector { numComponents = 1 }
xpointUzeRec = Updater.RecordFieldInCell2D {
   onGrid = grid,
   -- index of cell to record
   cellIndex = {(NX-1)/2, (NY-1)/2},
}
xpointUzeRec:setIn( {uzeAlias} )
xpointUzeRec:setOut( {xpointUze} )

-- dynvector to store ion uz at X-point
uziAlias = qNew:alias(8, 9)
xpointUzi = DataStruct.DynVector { numComponents = 1 }
xpointUziRec = Updater.RecordFieldInCell2D {
   onGrid = grid,
   -- index of cell to record
   cellIndex = {(NX-1)/2, (NY-1)/2},
}
xpointUziRec:setIn( {uziAlias} )
xpointUziRec:setOut( {xpointUzi} )

-- compute diagnostic
function calcDiagnostics(tCurr, dt)
   for i,diag in ipairs({byFluxCalc, xpointEzRec, xpointNeRec, xpointUzeRec, xpointUziRec}) do
      diag:setCurrTime(tCurr)
      diag:advance(tCurr+dt)
   end
end

-- write data to H5 files
function writeFields(frame, t)
   qNew:write( string.format("q_%d.h5", frame), t )
   byFlux:write( string.format("byFlux_%d.h5", frame) )
   xpointEz:write(string.format("xpointEz_%d.h5", frame) )
   xpointNe:write(string.format("xpointNe_%d.h5", frame) )
   xpointUze:write(string.format("xpointUze_%d.h5", frame) )
   xpointUzi:write(string.format("xpointUzi_%d.h5", frame) )
end

Fluids = qNew:alias(0, 10)
function writeFieldsBwd(frame, t)
   Fluids:write( string.format("Fluids_%d_bwd.h5", frame), t )
end
function writeFieldsFwd(frame, t)
   Fluids:write( string.format("Fluids_%d_fwd.h5", frame), t )
end

----------------------------
-- TIME-STEPPING FUNCTION --
----------------------------
function runSimulation(tStart, tEnd, nFrames, initDt)

   local frame = 1
   local tFrame = (tEnd-tStart)/nFrames
   local nextIOt = tFrame
   local step = 1
   local tCurr = tStart
   local myDt = initDt
   local status, dtSuggested
   local useLaxSolver = false
   local doWriteFieldsFwd = false

   -- the grand loop 
   while true do
      -- copy q and qNew in case we need to take this step again
      qDup:copy(q)
      qNewDup:copy(qNew)

      -- if needed adjust dt to hit tEnd exactly
      if (tCurr+myDt > tEnd) then
        myDt = tEnd-tCurr
      end

      -- advance fluids and fields
      if (useLaxSolver) then
        -- call Lax solver if positivity violated
        log (string.format(" Taking step %5d at time %6g with dt %g (using Lax solvers)", step, tCurr, myDt))
        status, dtSuggested = solveTwoFluidLaxSystem(tCurr, tCurr+myDt)
        useLaxSolver = false
      else
        log (string.format(" Taking step %5d at time %6g with dt %g", step, tCurr, myDt))
        status, dtSuggested, useLaxSolver = solveTwoFluidSystem(tCurr, tCurr+myDt)
      end

      if (status == false) then
        -- time-step too large
        log (string.format(" ** Time step %g too large! Will retake with dt %g", myDt, dtSuggested))
        myDt = dtSuggested
        qNew:copy(qNewDup)
        q:copy(qDup)
      elseif (useLaxSolver == true) then
        -- negative density/pressure occured
        log (string.format(" ** Negative pressure or density at %8g! Will retake step with Lax fluxes", tCurr+myDt))
        q:copy(qDup)
        qNew:copy(qNewDup)
      else
        -- check if a nan occured
        if (qNew:hasNan()) then
           log (string.format(" ** NaN occured at %g! Stopping simulation", tCurr))
           break
        end

        -- compute diagnostics
        calcDiagnostics(tCurr, myDt)
        -- copy updated solution back
        q:copy(qNew)
  
         if (tCurr+myDt <= nextIOt and tCurr+myDt+dtSuggested > nextIOt) then
           log (string.format(" Writing electron data (bwd) at time %g (frame %d) ...", tCurr+myDt, frame))
           writeFieldsBwd(frame, tCurr+myDt)
        end    
        if doWriteFieldsFwd then
           log (string.format(" Writing electron data (fwd) at time %g (frame %d) ...", tCurr+myDt, frame-1))
           writeFieldsFwd(frame-1, tCurr+myDt)
           doWriteFieldsFwd = false
        end    
        -- write out data
        if (tCurr+myDt > nextIOt or tCurr+myDt >= tEnd) then
           log (string.format(" Writing data at time %g (frame %d) ...\n", tCurr+myDt, frame))
           writeFields(frame, tCurr+myDt)
           frame = frame + 1
           nextIOt = nextIOt + tFrame
           step = 0
           doWriteFieldsFwd = true
        end
     
        tCurr = tCurr + myDt
        myDt = dtSuggested
        step = step + 1

        -- check if done
        if (tCurr >= tEnd) then
           break
        end
      end 
   end -- end of time-step loop
   
   return dtSuggested
end


----------------------------
-- RUNNING THE SIMULATION --
----------------------------
-- setup initial condition
q:set(init)
q:sync()
qNew:copy(q)

-- set input/output arrays for various solvers
elcFluidSlvrDir0:setIn( {elcFluid} )
elcFluidSlvrDir0:setOut( {elcFluidX} )
ionFluidSlvrDir0:setIn( {ionFluid} )
ionFluidSlvrDir0:setOut( {ionFluidX} )
maxSlvrDir0:setIn( {emField} )
maxSlvrDir0:setOut( {emFieldX} )

elcFluidSlvrDir1:setIn( {elcFluidX} )
elcFluidSlvrDir1:setOut( {elcFluidNew} )
ionFluidSlvrDir1:setIn( {ionFluidX} )
ionFluidSlvrDir1:setOut( {ionFluidNew} )
maxSlvrDir1:setIn( {emFieldX} )
maxSlvrDir1:setOut( {emFieldNew} )

elcLaxSlvrDir0:setIn( {elcFluid} )
elcLaxSlvrDir0:setOut( {elcFluidX} )
ionLaxSlvrDir0:setIn( {ionFluid} )
ionLaxSlvrDir0:setOut( {ionFluidX} )
maxLaxSlvrDir0:setIn( {emField} )
maxLaxSlvrDir0:setOut( {emFieldX} )

elcLaxSlvrDir1:setIn( {elcFluidX} )
elcLaxSlvrDir1:setOut( {elcFluidNew} )
ionLaxSlvrDir1:setIn( {ionFluidX} )
ionLaxSlvrDir1:setOut( {ionFluidNew} )
maxLaxSlvrDir1:setIn( {emFieldX} )
maxLaxSlvrDir1:setOut( {emFieldNew} )

-- apply BCs on initial conditions
-- applyBc(q, 0.0, 0.0)
-- applyBc(qNew, 0.0, 0.0)

-- write initial conditions
calcDiagnostics(0.0, 0.0)
writeFields(0, 0.0)

initDt = 100.0
runSimulation(tStart, tEnd, nFrames, initDt)