ERROR: Please increase the number of atom types in the 'create_box' command to match the number of atom types you use in the sim

Dear All,

I am trying to perform a simulation similar to the ErgunTestMPI test, but with a different geometry than the cylinder showed in the tutorial. My geometry comes from three STL files. created with a CAD. From the STL files (inlet.stl, outlet.stl, wall.stl) I generated a volumetric mesh, employing the "snappyHexMesh", and I run successfully the CFD part. The inlet gas is also moving the DEM particles, which means that the CFDEM coupling is working. During the simulations I have noticed that I forgot to delete the walls in the DEM, I mean the cylinder's walls from the tutorial (I modified the ErgunTestMPI tutorial scripts). Therefore I added the three stl files, as here showed:

--------------------------------------------------------------------------
fix zwalls1 all mesh/surface file ../DEM/meshes/inlet.stl type 2 scale 0.001
fix zwalls2 all mesh/surface file ../DEM/meshes/outlet.stl type 2 scale 0.001
fix cylwalls all mesh/surface file ../DEM/meshes/wall.stl type 2 scale 0.001
--------------------------------------------------------------------------

Once I added the new STL walls inside the scripts "in.liggghts_run" and "in.liggghts_run" in the "DEM" folder, I got the following error message during the simulation run "./Allrun.sh":

--------------------------------------------------------------------------
Resetting global state of Fix contacthistory Style contacthistory from restart file info
Resetting per-atom state of Fix contacthistory Style contacthistory from restart file info
ERROR: Please increase the number of atom types in the 'create_box' command to match the number of atom types you use in the simulation (../properties.cpp:122)
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[189,1],1]
Exit code: 1
simulation finished? ...press enter to proceed
--------------------------------------------------------------------------

Any suggestion ??

I just remind that the CFD-DEM coupling (and therefore the command "./Allrun.sh") works correctly if I keep the walls of the tutorial, which are not STL files. For further information here following I reported all the "./Allrun.sh" output (the error message is at the end).

Thank you All for your help.
Best,
Limone

[user@limone ErgunTestMPI2c]$ ./Allrun.sh
mesh was built before - using old mesh
LIGGGHTS init was run before - using existing restart file
************************************
using userdefined CFDEM_SRC_DIR = /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/src
using userdefined CFDEM_SOLVER_DIR = /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/applications/solvers
using userdefined CFDEM_DOC_DIR = /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/doc
using userdefined CFDEM_UT_DIR = /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/applications/utilities
using userdefined CFDEM_TUT_DIR = /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/tutorials
using userdefined CFDEM_LAMMPS_LIB_DIR = /home/cfdemuser/LIGGGHTS/LIGGGHTS-PUBLIC/src/../lib
using userdefined CFDEM_LIGGGHTS_LIB_PATH = /home/cfdemuser/LIGGGHTS/LIGGGHTS-PUBLIC/src
using userdefined CFDEM_ADD_LIBS_DIR = /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/src/lagrangian/cfdemParticle/etc/addLibs_universal
using userdefined CFDEM_ADD_LIBS_NAME = additionalLibs_3.0.x
using userdefined CFDEM_LIB_DIR = /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/platforms/linux64GccDPInt32Opt/lib
using userdefined CFDEM_USER_LIB_DIR = /home/cfdemuser/CFDEM/cfdemuser-PUBLIC-3.0.x/platforms/linux64GccDPInt32Opt/lib
using userdefined CFDEM_APP_DIR = /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/platforms/linux64GccDPInt32Opt/bin
using userdefined CFDEM_USER_APP_DIR = /home/cfdemuser/CFDEM/cfdemuser-PUBLIC-3.0.x/platforms/linux64GccDPInt32Opt/bin
************************************
Decomposing case.
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 3.0.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 3.0.x-ac3f6c67e02f
Exec : decomposePar -force
Date : Aug 30 2017
Time : 11:35:15
Host :
PID :
Case : /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/tutorials_LO/cfdemSolverPiso/ErgunTestMPI2c/CFD
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Decomposing mesh region0

Removing 4 existing processor directories
Create mesh

Calculating distribution of cells
Selecting decompositionMethod simple

Finished decomposition in 4.56 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes

Processor 0
Number of cells = 1621277
Number of faces shared with processor 1 = 17733
Number of faces shared with processor 2 = 18089
Number of processor patches = 2
Number of processor faces = 35822
Number of boundary faces = 52304

Processor 1
Number of cells = 1618763
Number of faces shared with processor 0 = 17733
Number of faces shared with processor 3 = 18058
Number of processor patches = 2
Number of processor faces = 35791
Number of boundary faces = 52053

Processor 2
Number of cells = 1618763
Number of faces shared with processor 0 = 18089
Number of faces shared with processor 3 = 17782
Number of processor patches = 2
Number of processor faces = 35871
Number of boundary faces = 52189

Processor 3
Number of cells = 1621277
Number of faces shared with processor 1 = 18058
Number of faces shared with processor 2 = 17782
Number of processor patches = 2
Number of processor faces = 35840
Number of boundary faces = 52182

Number of processor faces = 71662
Max number of cells = 1621277 (0.0775916% above average 1.62002e+06)
Max number of processor patches = 2 (0% above average 2)
Max number of faces between processors = 35871 (0.111635% above average 35831)

Time = 0

Processor 0: field transfer
Processor 1: field transfer
Processor 2: field transfer
Processor 3: field transfer

End

do nothing.

// run_parallel_cfdemSolverPiso_ErgunTestMPI_CFDDEM //

/home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/tutorials_LO/cfdemSolverPiso/ErgunTestMPI2c/CFD

rm: cannot remove ‘couplingFiles/*’: No such file or directory
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 3.0.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 3.0.x-ac3f6c67e02f
Exec : cfdemSolverPiso -parallel
Date : Aug 30 2017
Time : 11:35:28
Host :
PID :
Case : /home/cfdemuser/CFDEM/CFDEMcoupling-PUBLIC-3.0.x/tutorials_LO/cfdemSolverPiso/ErgunTestMPI2c/CFD
nProcs : 4
Slaves :
3
(
)

Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

PISO: Operating solver in PISO mode

Reading field p

Reading physical velocity field U
Note: only if voidfraction at boundary is 1, U is superficial velocity!!!

Reading momentum exchange field Ksl

Reading voidfraction field voidfraction = (Vgas/Vparticle)

Creating density field rho

Reading particle velocity field Us

Reading/calculating face flux field phi

Generating interstitial face flux field phiByVoidfraction

Selecting incompressible transport model Newtonian
Selecting turbulence model type laminar
No finite volume options present

Reading g
Selecting locateModel engine
Selecting dataExchangeModel twoWayMPI
Starting up LIGGGHTS for first time execution
Executing input script '../DEM/in.liggghts_run'
LIGGGHTS (Version LIGGGHTS-PUBLIC 3.7.0, compiled 2017-08-14-11:14:06 by cfdemuser, git commit c449f30b63c5eec5c8053a67dccd892fe2c5cef2)
log ../DEM/log.liggghts
thermo_log ../DEM/post/thermo.txt

atom_style granular
atom_modify map array
communicate single vel yes

boundary m m m
newton off

units si
processors 2 2 1

# read the restart file
read_restart ../DEM/post/restart/liggghts.restart
version 3 7
version 3 7
version 3 7
Reading restart file ...
WARNING: Restart file version does not match LIGGGHTS version (../read_restart.cpp:507)
--> restart file = Version LIGGGHTS-PUBLIC 3.7.0, compiled 2017-08-14-11:07:09 by cfdemuser, git commit c449f30b63c5eec5c8053a67dccd892fe2c5cef2
--> LIGGGHTS = Version LIGGGHTS-PUBLIC 3.7.0, compiled 2017-08-14-11:14:06 by cfdemuser, git commit c449f30b63c5eec5c8053a67dccd892fe2c5cef2
version 3 7
WARNING: Restart file used different 3d processor grid (../read_restart.cpp:587)
orthogonal box = (-0.015 -0.015 -0.001) to (0.015 0.015 0.0554)
2 by 2 by 1 MPI processor grid
10000 atoms

neighbor 0.0005 bin
neigh_modify delay 0

# Material properties required for granular pair styles

fix m1 all property/global youngsModulus peratomtype 5.e6
fix m2 all property/global poissonsRatio peratomtype 0.45
fix m3 all property/global coefficientRestitution peratomtypepair 1 0.3
fix m4 all property/global coefficientFriction peratomtypepair 1 0.5

# pair style
pair_style gran model hertz tangential history # Hertzian without cohesion
pair_coeff * *

# timestep, gravity
timestep 0.00001
fix gravi all gravity 9.81 vector 0.0 0.0 -1.0

# walls
# fix zwalls1 all wall/gran model hertz tangential history primitive type 1 zplane 0.0
# fix zwalls2 all wall/gran model hertz tangential history primitive type 1 zplane 0.0553
# fix cylwalls all wall/gran model hertz tangential history primitive type 1 zcylinder 0.01385 0. 0.

# Import STL file from CAD
fix zwalls1 all mesh/surface file ../DEM/meshes/inlet.stl type 2 scale 0.001

Reading STL file '../DEM/meshes/inlet.stl' (mesh processing step 1/3)
fix zwalls2 all mesh/surface file ../DEM/meshes/outlet.stl type 2 scale 0.001

Reading STL file '../DEM/meshes/outlet.stl' (mesh processing step 1/3)
fix cylwalls all mesh/surface file ../DEM/meshes/wall.stl type 2 scale 0.001

Reading STL file '../DEM/meshes/wall.stl' (mesh processing step 1/3)

# Use the imported mesh as granular wall
fix geometry all wall/gran model hertz tangential history mesh n_meshes 3 meshes zwalls1 zwalls2 cylwalls

# cfd coupling
fix cfd all couple/cfd couple_every 100 mpi
nevery as specified in LIGGGHTS is overriden by calling external program (../cfd_datacoupling_mpi.cpp:77)
fix cfd2 all couple/cfd/force/implicit
#fix cfd2 all couple/cfd/force/accumulator RongDrag 10 1.5e-3
#fix cfd2 all couple/cfd/force/implicit/accumulated #CrankNicolson 0.5

# apply nve integration to all particles that are inserted as single particles
fix integr all nve/sphere

# center of mass
compute centerOfMass all com

# compute explicit dragforce
compute explDrag all reduce update_on_run_end yes sum f_dragforce[1] f_dragforce[2] f_dragforce[3]

# sum of explicit and implicit drag force given from CFD to DEM
variable totalDragX equal f_cfd2[1]
variable totalDragY equal f_cfd2[2]
variable totalDragZ equal f_cfd2[3]

# explicit drag force given from CFD to DEM
variable explicitDragX equal c_explDrag[1]
variable explicitDragY equal c_explDrag[2]
variable explicitDragZ equal c_explDrag[3]

variable time equal step*dt
fix extra all print 10 "${time} ${explicitDragX} ${explicitDragY} ${explicitDragZ} ${totalDragX} ${totalDragY} ${totalDragZ}" file ../DEM/post/forces.txt title "# time expDrag(X Y Z) totDrag(X Y Z)"

# screen output
compute rke all erotate/sphere
thermo_style custom step atoms ke c_rke vol c_centerOfMass[3] c_explDrag[1] c_explDrag[2] c_explDrag[3] f_cfd2[1] f_cfd2[2] f_cfd2[3]
thermo 10
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:159)

# dump dmp all custom 5000 ../DEM/post/dump*.liggghts_run id type x y z vx vy vz fx fy fz f_dragforce[1] f_dragforce[2] f_dragforce[3] radius
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:159)
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:159)
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:159)
# #dump dmp all custom/vtk 5000 ../DEM/post/dump_liggghts_run.*.vtk id type x y z vx vy vz fx fy fz f_dragforce[1] f_dragforce[2] f_dragforce[3] radius

# Create imaging information
dump dumpstl all stl 1000 ../DEM/post/dump*.stl
dump dmp all custom 1000 ../DEM/post/dump*.liggghts_run id type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius
#dump dmp all custom/vtk 1000 ../DEM/post/dump_liggghts_run.*.vtk id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius
undump dumpstl

run 0
Resetting global state of Fix contacthistory Style contacthistory from restart file info
Resetting per-atom state of Fix contacthistory Style contacthistory from restart file info
ERROR: Please increase the number of atom types in the 'create_box' command to match the number of atom types you use in the simulation (../properties.cpp:122)
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[189,1],1]
Exit code: 1
--------------------------------------------------------------------------
simulation finished? ...press enter to proceed