Merge branch '1k_openmc_model' into 'master'

1k openmc model

See merge request !3

146_pebble/master.i

@@ -121,7 +121,7 @@
 [Outputs]
   exodus = true
   interval = 100
-  file_base = ../../../../../../../../scratch/gastdr/coe/146_pebbles/out
+  file_base = ./
 []
 
 [MultiApps]

146_pebble/openmc.i

@@ -27,7 +27,9 @@
 
 [Problem]
   type = OpenMCProblem
-  power = 146000 # 1000 per pebble
+  power = 1460 # 1000 per pebble
+  tally_type = 'cell'
+  mesh_template = 'sphere.e'
   centers = '-8.065973074285714972e+00 2.236820423458646623e+00 1.168503152842105308e+01
 -4.108761094736841812e+00 7.264663405714286704e+00 1.148013507969924873e+01
 -8.190250614135338836e+00 -1.669100062556391206e+00 1.174674951699248204e+01

146_pebble/openmc_master.i

@@ -237,10 +237,10 @@
 
 [Transfers]
   [./heat_source_from_openmc]
-    type = MultiAppUserObjectTransfer
+    type = MultiAppCopyTransfer
     direction = from_multiapp
     multi_app = openmc
-    user_object = heat_source
+    source_variable = heat_source
     variable = heat_source
   []
   [./average_temp_to_openmc]

146_pebble/plots.xml

 <?xml version='1.0' encoding='utf-8'?>
 <plots>
-  <plot basis="xy" color_by="material" filename="plot1" id="1" type="slice">
+  <plot color_by="material" filename="plotv1" id="5" type="voxel">
     <origin>0 0 0</origin>
-    <width>30.25 30.25</width>
-    <pixels>1000 1000</pixels>
-    <color id="1" rgb="165 42 42" />
-    <color id="2" rgb="176 196 222" />
-    <color id="3" rgb="0 0 255" />
-    <color id="4" rgb="255 165 0" />
-    <color id="5" rgb="0 255 255" />
-    <color id="6" rgb="0 191 255" />
-    <color id="7" rgb="0 0 128" />
-    <color id="8" rgb="255 255 0" />
-  </plot>
-  <plot basis="xy" color_by="material" filename="plot2" id="2" type="slice">
-    <origin>0 0 1</origin>
-    <width>30.25 30.25</width>
-    <pixels>1000 1000</pixels>
-    <color id="1" rgb="165 42 42" />
-    <color id="2" rgb="176 196 222" />
-    <color id="3" rgb="0 0 255" />
-    <color id="4" rgb="255 165 0" />
-    <color id="5" rgb="0 255 255" />
-    <color id="6" rgb="0 191 255" />
-    <color id="7" rgb="0 0 128" />
-    <color id="8" rgb="255 255 0" />
-  </plot>
-  <plot basis="xy" color_by="material" filename="plot3" id="3" type="slice">
-    <origin>0 0 1</origin>
-    <width>30.25 30.25</width>
-    <pixels>1000 1000</pixels>
-    <color id="1" rgb="165 42 42" />
-    <color id="2" rgb="176 196 222" />
-    <color id="3" rgb="0 0 255" />
-    <color id="4" rgb="255 165 0" />
-    <color id="5" rgb="0 255 255" />
-    <color id="6" rgb="0 191 255" />
-    <color id="7" rgb="0 0 128" />
-    <color id="8" rgb="255 255 0" />
-  </plot>
-  <plot basis="xz" color_by="material" filename="plot4" id="4" type="slice">
-    <origin>0 0 5.08</origin>
-    <width>31.49 31.49</width>
-    <pixels>1000 1000</pixels>
+    <width>20 20 20</width>
+    <pixels>400 400 400</pixels>
     <color id="1" rgb="165 42 42" />
     <color id="2" rgb="176 196 222" />
     <color id="3" rgb="0 0 255" />

146_pebble/settings.xml

@@ -5,7 +5,7 @@
   <batches>150</batches>
   <inactive>50</inactive>
   <source strength="1.0">
-    <space type="fission">
+    <space type="box">
       <parameters>-15.125 -15.125 -10.665 15.125 15.125 20.825</parameters>
     </space>
   </source>
@@ -18,7 +18,7 @@
     <domain_type>material</domain_type>
     <domain_ids>1</domain_ids>
     <samples>10000000</samples>
-    <lower_left>-1.4 -1.4 -1.4</lower_left>
-    <upper_right>1.4 1.4 1.4</upper_right>
+    <lower_left>-10 -10 -10</lower_left>
+    <upper_right>10 10 10</upper_right>
   </volume_calc>
 </settings>

1568_pebble_yuhsiang_E524k/NEKMOOSE

+      parameter (lsurf_m=170000)
+      common /point_cloudx/ pc_x(lsurf_m*4)
+      common /point_cloudy/ pc_y(lsurf_m*4)
+      common /point_cloudz/ pc_z(lsurf_m*4)
+      common /point_cloudt/ pc_t(lsurf_m*4)
+      common /point_cloudf/ pc_f(lsurf_m*4)
+      common /ref_element/  pc_flag(lsurf_m*4)
+      common /tot_surf/ nw_bdt       
+      common /data_reference/ plmask(lelt), pflmask(lelt), 
+     & pplist(lelt), offset, nw_bd1
+      common /test_passing/ flux_moose, temp_nek
+      real pc_x, pc_y, pc_z, pc_flag, pc_t, pc_f
+      integer plmask, pflmask, pllist, offset, nw_bd1, nw_bdt 
+

1568_pebble_yuhsiang_E524k/materials.xml

+<?xml version='1.0' encoding='utf-8'?>
+<materials>
+  <material depletable="true" id="1" name="m_fuel - uranium oxycarbide - triso partciles">
+    <density units="g/cm3" value="10.5" />
+    <nuclide name="U234" wo="0.03565284" />
+    <nuclide name="U235" wo="17.790767159999998" />
+    <nuclide name="U238" wo="71.75358" />
+    <nuclide name="C0" wo="1.8" />
+    <nuclide name="O16" wo="8.616527990092724" />
+    <nuclide name="O17" wo="0.003472009907274255" />
+  </material>
+  <material id="2" name="m_graphite_c_buffer - triso partciles">
+    <density units="g/cm3" value="1.0" />
+    <nuclide ao="1.0" name="C0" />
+    <sab name="c_Graphite" />
+  </material>
+  <material id="3" name="m_graphite_pyc - triso particles">
+    <density units="g/cm3" value="1.87" />
+    <nuclide ao="1.0" name="C0" />
+    <sab name="c_Graphite" />
+  </material>
+  <material id="4" name="sic - triso partciles">
+    <density units="g/cm3" value="3.2" />
+    <nuclide ao="1.0" name="C0" />
+    <nuclide ao="0.9222968" name="Si28" />
+    <nuclide ao="0.0468316" name="Si29" />
+    <nuclide ao="0.0308716" name="Si30" />
+  </material>
+  <material id="5" name="m_graphite_matrix - triso particles">
+    <density units="g/cm3" value="1.6" />
+    <nuclide ao="1.0" name="C0" />
+    <sab name="c_Graphite" />
+  </material>
+  <material id="6" name="m_graphite_inner - pebble inner zone">
+    <density units="g/cm3" value="1.59368" />
+    <nuclide ao="1.0" name="C0" />
+    <sab name="c_Graphite" />
+  </material>
+  <material id="7" name="m_graphite_outer - pebble outer zone">
+    <density units="g/cm3" value="1.74" />
+    <nuclide ao="1.0" name="C0" />
+    <sab name="c_Graphite" />
+  </material>
+  <material id="8" name="m_flibe - 2LiF-BeF2">
+    <density units="kg/m3" value="1962.13354" />
+    <nuclide ao="1.9999" name="Li7" />
+    <nuclide ao="9.999999999998899e-05" name="Li6" />
+    <nuclide ao="1.0" name="Be9" />
+    <nuclide ao="4.0" name="F19" />
+  </material>
+</materials>

1568_pebble_yuhsiang_E524k/nek.i

+[Mesh]
+  type = NekMesh
+[]
+
+[Variables]
+  [dummy]
+  []
+[]
+
+[AuxVariables]
+  [avg_flux]
+  []
+[]
+
+[Problem]
+  type = NekProblem
+[]
+
+[Executioner]
+  type = Transient
+  num_steps = 50000
+[]
+
+[Outputs]
+  [exo]
+    type = Exodus
+    output_dimension = 3
+    interval = 100
+    execute_on = 'timestep_end'
+  []
+[]
+
+[Postprocessors]
+  [total_flux]
+    type = Receiver
+    default = 0
+  []
+[]

1568_pebble_yuhsiang_E524k/nek_master.i

+[Mesh]
+  type = FileMesh
+  file = spheres_generator_in.e
+[]
+
+[Kernels]
+  [hc]
+    type = HeatConduction
+    variable = temp
+  []
+  [heat]
+    type = BodyForce
+    #value = 35.37
+    value = 70
+    variable = temp
+  []
+[]
+
+[BCs]
+  inactive = 'outside'
+  [outside]
+    type = DirichletBC
+    variable = temp
+    boundary = '1'
+    value = 300
+  []
+  [match_nek]
+    type = MatchedValueBC
+    variable = temp
+    boundary = '1'
+    v = 'nek_temp'
+  []
+[]
+
+[Materials]
+  [hc]
+    type = GenericConstantMaterial
+    prop_values = '0.2' # 20 W/mK -> 0.2 W/cmK
+    prop_names = 'thermal_conductivity'
+  []
+[]
+
+[Executioner]
+  type = Transient
+  petsc_options_iname = '-pc_type -pc_hypre_type'
+  num_steps = 50000
+  petsc_options_value = 'hypre boomeramg'
+  dt = 5e-4
+  nl_rel_tol = 1e-5
+[]
+
+[Variables]
+  [temp]
+  []
+[]
+
+[Outputs]
+  inteval = 100
+  exodus = true
+[]
+
+[MultiApps]
+  [nek]
+    type = TransientMultiApp
+    app_type = NekApp
+    input_files = 'nek.i'
+  []
+[]
+
+[Transfers]
+  [nek_temp]
+    type = MultiAppNearestNodeTransfer
+    source_variable = temp
+    direction = from_multiapp
+    multi_app = nek
+    variable = nek_temp
+    fixed_meshes = true
+  []
+  [avg_flux]
+    type = MultiAppNearestNodeTransfer
+    source_variable = avg_flux
+    direction = to_multiapp
+    multi_app = nek
+    variable = avg_flux
+    fixed_meshes = true
+  []
+  [total_flux_to_nek]
+    type = MultiAppPostprocessorTransfer
+    to_postprocessor = total_flux
+    direction = to_multiapp
+    from_postprocessor = total_flux
+    multi_app = nek
+  []
+[]
+
+[AuxVariables]
+  [nek_temp]
+  []
+  [avg_flux]
+    family = MONOMIAL
+    order = CONSTANT
+    initial_condition = 0
+  []
+[]
+
+[AuxKernels]
+  [avg_flux]
+    type = FluxAverageAux
+    coupled = 'temp'
+    diffusivity = thermal_conductivity
+    variable = avg_flux
+    boundary = '1'
+  []
+[]
+
+[Postprocessors]
+  [total_flux_check]
+    # Should add up to the same thing as total_flux
+    type = SideIntegralVariablePostprocessor
+    variable = avg_flux
+    boundary = 1
+  []
+
+  [total_flux]
+    type = SideFluxIntegral
+    diffusivity = thermal_conductivity
+    variable = 'temp'
+    boundary = '1'
+  []
+  [average_flux]
+    type = SideFluxAverage
+    diffusivity = thermal_conductivity
+    variable = 'temp'
+    boundary = '1'
+  []
+[]

1568_pebble_yuhsiang_E524k/peb1568.oudf

+// Boundary conditions
+void insVelocityDirichletConditions3D(bcData *bc)
+{                                                                        
+  bc->uP = 0.0;
+  bc->vP = 0.0;
+  bc->wP = 0.17;
+}
+
+void cdsDirichletConditions3D(bcData *bc)
+{
+  bc->sP = 573.0;
+}
+
+void cdsNeumannConditions3D(bcData *bc)
+{
+  bc->sF = bc->wrk[bc->idM];
+}
+
+// Stabilized outflow (Dong et al)
+void insPressureDirichletConditions3D(bcData *bc)
+{
+  const dfloat iU0delta = 10.0;
+  const dfloat un = bc->uM*bc->nx + bc->vM*bc->ny + bc->wM*bc->nz;
+  const dfloat s0 = 0.5 * (1.0 - tanh(un*iU0delta));
+  bc->pP = -0.5 * (bc->uM*bc->uM + bc->vM*bc->vM + bc->wM*bc->wM) * s0;
+}
+

1568_pebble_yuhsiang_E524k/peb1568.par

+[OCCA]
+backend = CUDA
+deviceNumber = 0
+
+[GENERAL]
+#verbose = true
+polynomialOrder = 7
+#startFrom = r5.fld
+stopAt = numSteps
+numSteps = 50000
+
+dt = 5.0e-4
+timeStepper = tombo2
+extrapolation = subCycling
+subCyclingSteps = 2
+
+writeControl = TIMESTEP
+writeInterval = 100 
+
+filtering = hpfrt
+filterWeight = 200
+filterModes = 2
+
+[PRESSURE]
+preconditioner = semg_amg
+amgSolver = parAlmond
+#galerkinCoarseOperator = yes
+residualTol = 1e-04
+
+[VELOCITY]
+#solver = pcg+block
+boundaryTypeMap = inlet, outlet, wall, wall
+density = 1.0
+viscosity = 0.0001
+residualTol = 1e-06
+
+[TEMPERATURE]
+#solver = none
+boundaryTypeMap = inlet, outlet, insulated, flux
+rhoCp = 45.0
+conductivity = 0.45
+residualTol = 1e-06
+
+#[SCALAR01]
+#solver = none
+
+#[BOOMERAMG]
+#coarsenType = 10
+#interpolationType = 6
+#smootherType = -1
+#iterations = 2 # testing
+#strongThreshold = 0.25
+#nonGalerkinTol = 0.1

1568_pebble_yuhsiang_E524k/peb1568.udf

+//
+// nekRS User Defined File
+//
+
+#include <math.h>
+#include "udf.hpp"
+#include <iostream>
+
+/* UDF Functions */                                                      
+
+void UDF_LoadKernels(ins_t *ins)
+{
+}
+
+void UDF_Setup(ins_t *ins)
+{
+  // get IC from nek
+  if (!ins->readRestartFile) nek_copyTo(ins->startTime);
+  ins->o_usrwrk.free(); free(ins->usrwrk);
+  ins->usrwrk   = (dfloat*) calloc(ins->mesh->Nelements*ins->mesh->Np, sizeof(dfloat));
+  ins->o_usrwrk = ins->mesh->device.malloc(ins->mesh->Nelements*ins->mesh->Np*sizeof(dfloat), ins->usrwrk);
+  ins->cds->o_usrwrk = ins->o_usrwrk;
+  // printf ("> Test %d \n", ins->mesh->Nelements*ins->mesh->Np*sizeof(dfloat));
+}
+
+void UDF_ExecuteStep(ins_t *ins, dfloat time, int tstep)
+{
+  nek_userchk();
+  //std::cout << "Finished userchk" << std::endl;
+
+  int nwbdt=nekData.cbscnrs[0];
+  auto *wrk1 =  nekData.cbscnrs; 
+  wrk1 = wrk1 + nwbdt*5*4 + 2; 
+  ins->o_usrwrk.copyFrom(wrk1,ins->mesh->Nelements*ins->mesh->Np*sizeof(dfloat));
+
+  //auto *ptr=nekData.cbscnrs;
+  //ins->o_usrwrk.copyFrom(wrk, mesh->Nelements*mesh->Np*sizeof(dfloat));
+  //std::cout << "Finished UDF_ExecuteStep" << std::endl;
+}

1568_pebble_yuhsiang_E524k/peb1568.usr

+      include 'nek_moose.f'
+c-----------------------------------------------------------------------
+      subroutine uservp(i,j,k,eg) ! set variable properties
+      include 'SIZE'
+      include 'TOTAL'
+      include 'NEKUSE'
+
+      integer i,j,k,e,eg
+     
+c     e = gllel(eg)
+
+      udiff  = 0.0
+      utrans = 0.0
+
+      return
+      end
+c-----------------------------------------------------------------------
+      subroutine userf(i,j,k,eg) ! set acceleration term
+c
+c     Note: this is an acceleration term, NOT a force!
+c     Thus, ffx will subsequently be multiplied by rho(x,t).
+c
+      include 'SIZE'
+      include 'TOTAL'
+      include 'NEKUSE'
+
+      integer i,j,k,e,eg
+
+c     e = gllel(eg)
+
+      ffx = 0.0
+      ffy = 0.0
+      ffz = 0.0
+
+      return
+      end
+c-----------------------------------------------------------------------
+      subroutine userq(i,j,k,eg) ! set source term
+      include 'SIZE'
+      include 'TOTAL'
+      include 'NEKUSE'
+
+      integer i,j,k,e,eg
+
+c     e = gllel(eg)
+
+      qvol   = 0.0
+
+      return
+      end
+c-----------------------------------------------------------------------
+      subroutine userbc(i,j,k,f,eg) ! set up boundary conditions
+c     NOTE ::: This routine MAY NOT be called by every process
+      include 'SIZE'
+      include 'TOTAL'
+      include 'NEKUSE'
+
+      integer i,j,k,f,e,eg
+      e=gllel(eg)
+
+      ux   = 0.0
+      uy   = 0.0
+      uz   = 1.0
+
+      if (cbu.eq.'o  ') then
+         U0 = 1.0                  ! characteristic velocity
+         delta = 0.1               ! small positive constant
+         pa = dongOutflow(i,j,k,e,f,U0,delta)
+      endif
+
+      flux = 0.0
+      temp = 0.0
+c     if (cbc(f,e,1).eq.'W  '.AND.cbc(f,e,2).eq.'t  ') temp=1.0
+      if (cbc(f,e,1).eq.'W  '.AND.cbc(f,e,2).eq.'f  ') flux=1.0
+
+      return
+      end
+c-----------------------------------------------------------------------
+      subroutine useric(i,j,k,eg) ! set up initial conditions
+      include 'SIZE'
+      include 'TOTAL'
+      include 'NEKUSE'
+      integer i,j,k,e,eg
+
+      ux   = 0.0
+      uy   = 0.0
+      uz   = 1.0
+      temp = 573.0
+
+      return
+      end
+c-----------------------------------------------------------------------
+      subroutine userchk
+      include 'SIZE'
+      include 'TOTAL'
+      include 'NEKMOOSE'
+c      implicit none
+      COMMON /SCNRS/ SC_NRS(LX1*LY1*LZ1*LELT*7*5)
+      real           SC_NRS
+      common /flux_reconstructed/flux_recon(lx1,ly1,lz1,lelt)
+
+      integer n_count
+      save n_count
+
+      n=lx1*ly1*lz1*nelt
+
+      if (istep.eq.0) then
+        xxmax = glmax(xm1,n)
+        yymax = glmax(ym1,n)
+        zzmax = glmax(zm1,n)
+        xxmin = glmin(xm1,n)
+        yymin = glmin(ym1,n)
+        zzmin = glmin(zm1,n)
+        if (nio.eq.0) then
+          write(6,18) xxmin,yymin,zzmin
+          write(6,19) xxmax,yymax,zzmax
+   18     format(' xyz min  ',5g13.5)
+   19     format(' xyz max  ',5g13.5)
+        endif
+        ifxyo=.true.
+c        call outpost(vx,vy,vz,t,pr,'   ')
+      endif
+
+c      if (mod(istep,500).eq.0) then
+c         umin=glmin(vx,n)
+c         umax=glmax(vx,n)
+c         vmin=glmin(vy,n)
+c         vmax=glmax(vy,n)
+c         wmin=glmin(vz,n)
+c         wmax=glmax(vz,n)
+c         tmin=glmin(t ,n)
+c         tmax=glmax(t ,n)
+c         if (nio.eq.0) write(6,1) 
+c     $    istep,time,umin,umax,vmin,vmax,wmin,wmax,tmin,tmax
+c    1    format(i9,1p9e11.3,' tmax')
+c
+c         call compute_cfl(cfl,vx,vy,vz,dt)
+c         call outpost(cflf,vy,vz,pr,t,'cfl')
+c      endif
+
+c      if (istep.gt.0) then
+c        ifield = 1 ! essential for lambda2 right now
+c        call lambda2(t(1,1,1,1,2))
+c          tmin=glmin(t(1,1,1,1,2) ,n)
+c          tmax=glmax(t(1,1,1,1,2) ,n)
+c          if (nio.eq.0) write(6,2)istep,time,tmin,tmax
+c    2     format(i9,1p3e11.3,' tmax2') 
+c
+c        ifxyo     = .true.
+c        ifvo      = .true.
+c        ifpro     = .true.
+c        ifto      = .true.
+c        ifpsco(1) = .true.
+cc       call outpost(vx,vy,vz,pr,t,'   ')
+c      endif
+c      call comp_Reynolds
+
+       n_count=n_count+1
+
+       ! The first call is at time step zero
+
+       if ((1+1+nw_bdt*4*5+n).gt.(7*5*n)) then
+          if (nid.eq.0) write(6,*) "> Insufficient scratch memory"
+          call exitt()
+       endif
+
+       if (n_count.gt.2) then
+       if (mod(n_count,2).eq.1) then
+          if (nid.eq.0) write(6,*) "> DOWNLOADING FLUX"
+          do i=1,nw_bdt*4
+             pc_f(i)=sc_nrs(1+i+nw_bdt*4*4)*1.5*1.5
+          enddo
+          flux_moose=sc_nrs(1+1+nw_bdt*4*5)
+          call flux_reconstruction()
+          do i=1,n
+            sc_nrs(1+1+nw_bdt*4*5+i)=flux_recon(i,1,1,1)
+          enddo
+       endif
+
+       if (mod(n_count,2).eq.0) then
+          if (nid.eq.0) write(6,*) "> LOADING TEMPERATURE"
+          tmin=glmin(t,n)
+          tmax=glmax(t,n)
+          if (nid.eq.0) then
+           write(6,*) "> Temperature: ", tmin," - ", tmax
+          endif
+          call nek_interpolation()
+          do i=1,nw_bdt*4
+             sc_nrs(1+i+nw_bdt*4*3)=pc_t(i)
+          enddo
+       endif
+      endif
+
+      return
+      end
+c-----------------------------------------------------------------------
+      subroutine usrdat   ! This routine to modify element vertices
+      include 'SIZE'
+      include 'TOTAL'
+
+      return
+      end
+c-----------------------------------------------------------------------
+      subroutine usrdat3
+      include 'SIZE'
+      include 'TOTAL'
+
+      return
+      end
+c-----------------------------------------------------------------------
+      subroutine usrdat2
+      include 'SIZE'
+      include 'TOTAL'
+      include 'NEKMOOSE'
+      COMMON /SCNRS/ SC_NRS(LX1*LY1*LZ1*LELT*7)
+      real           SC_NRS
+      common /flux_reconstructed/flux_recon(lx1,ly1,lz1,lelt)
+
+      integer f,e
+      n=lx1*ly1*lz1*nelt
+
+      nface = 2*ldim
+
+      do e=1,nelv
+      do f=1,nface
+        if(cbc(f,e,1).eq.'E  '.or.cbc(f,e,1).eq.'   ')then
+          cbc(f,e,1)='E  '
+          cbc(f,e,2)='E  '
+        elseif(cbc(f,e,1).eq.'v  ')then  ! z_bottom
+          boundaryID(f,e) = 1
+          cbc(f,e,2)='t  '
+        elseif(cbc(f,e,1).eq.'O  ')then  ! z_top
+          boundaryID(f,e) = 2
+          cbc(f,e,1)='o  ' ! Dong's outflow
+          cbc(f,e,2)='O  '