The Helsinki Discrete Element Model (HiDEM)
Developers: Jan Åström & Joe Todd
This is HiDEM, the Helsinki Discrete Element Model, a particle model for simulating elastic behaviour, fracture and calving at marine terminating glaciers. Due to its computational demands, this code is designed to be run on parallel HPC facilities.
Configuration, compilation and installation is handled by CMake. Example installation scripts for Cray and Ubuntu systems are located in scripts/compilation. These scripts invoke cmake with toolchain files located in scripts/toolchains, which set default compilers etc.
By default, compilation produces a single binary 'HiDEM' in the top level of the 'build' directory.
If you generate your own toolchain/compilation scripts for different systems, please get in touch or make a pull request!
On starting, HiDEM reads the name of an input file from HIDEM_STARTINFO (e.g. 'inp.dat').
inp.dat - defines various parameters for the simulation
The user must also supply the initial geometry in gridded format: X,Y,SURF,BASE,BED,FRICTION
This initial geometry file is specified in the input file as 'Geometry File':
Geometry File = "mass3.dat"
Head of a sample mass3.dat file:
15851 0.000000000000000000e+00 0.000000000000000000e+00 9.248271630519999462e+02 9.248271630519999462e+02 9.248271630519999462e+02 1.833796257881020755e+07 5.000000000000000000e+01 0.000000000000000000e+00 9.248386672000000317e+02 9.248386672000000317e+02 9.248386672000000317e+02 2.784068307483682781e+07 1.000000000000000000e+02 0.000000000000000000e+00 9.248503686919999609e+02 9.248503686919999609e+02 9.248503686919999609e+02 4.768270480512356758e+07
Note: To avoid spurious single particles appearing at the edge of the domain, interpolation of
particle locations is not permitted where not all 4 supporting points have valid surface and bed
values. To permit this, set
Strict Domain Interpolation = False.
Typical simulation domains:
- 100m x 100m * 100m - typical particle size 2-10m
- 100km x 100km * 1km - typical particle size 30-100m
- Domain in x-y plane
- Main flow in y-direction
- Forces acting on edge should be defined
- Should have at least 10 particles in thickness direction (preferably 20-30).
- Maximum ~10 million particles
- Max timestep size scales with particle size:
- Too long timestep => instability
- Too short timestep => long execution times
Getting data ready
Replace no data with zero
Adjust the waterline (lowest point in domain must be non-negative)
Choose the number of cores
Do something to the restitution coefficient
Point to the input file (e.g. testinp.dat) using HIDEM_STARTINFO
A test case is provided in the
test directory. This is a simple rectangular domain with a sloping upper surface. This simulation will produce fracturing behaviour within a 6 hour simulation on 130 CPUs. The user should edit
example.job to provide a valid PBS budget account, and the correct number of nodes and cores (currently 6, 130) depending on system architecture (cores per node).
The behaviour of the test case can be changed by modifying
Max Load and
Friction Scale in inp.dat.
Running the model
The model runs in parallel using MPI, so the simulation should be started using
mpirun -n 70 HiDEM
An example PBS job script is provided in example.job
The user may specify a run name which is preprended on all output files:
Run Name = Example_Simulation
It is possible to restart one run from another:
Restart = 1
If the run name has changed, specify the run from which to restart:
Run Name = Example_Simulation_Part2 Restart from Run Name = Example_Simulation
If the simulation explodes (particles moving too far):
Set a higher
Rotational Dampingin the input file - multiply by two? Very high values for damping might be e.g. 16E4 and 8E4
Fracture After Time = 50.0or so, to allow the simulation to settle before permitting fracture
friction scalein input - this scales the bed friction
Smooth gradients in basal friction or geometry (in
Kill all motion every x timesteps
Files, Variables and Parameters
Structure of the repository
src- all the code required to compile the HiDEM binary.
- Within the
analysis- various fortran and python scripts for post-processing
compilation- example compilation scripts
job_scripts- example PBS scripts
io- fortran programs for modifying input
paraview- macros for working with HiDEM data in Paraview
HiDEM Source Code
These are part of the compiled code:
|wave2.f90||The main program|
|dist.f||Efficiently finding neighbouring particles which may interact|
|circ.f||Confirms which particles are in contact and computes forces|
|effload.f||Computes elastic forces in particle beams|
|amat.f||Called by effload, does integration|
|tmat.f, ttmat.f||Rotation matrices|
|kmat.f||Stiffness matrix computation|
|glas.f90||Computing the FCC lattice, dense packing|
|ranmar.f||Random number generator|
|dt.f90||Called by glas.f90, finds and write connections to FSfiles|
ave*.f - these compute averages of various outputs
rc2.f90, rc3.f90 - compute the calved size distrib
|Run Name||RUNNAME||The name of the simulation (prepended to output filenames)|
|Work Directory||wrkdir||The subdirectory in which to store working files (directory must exist!)|
|Results Directory||resdir||The subdirectory in which to store result files (directory must exist!)|
|Geometry File||geomfile||The name of the file which defines the geometry (see above)|
|Density||RHO||The density of the material (ice)|
|Water Density||RHOW||The density of the water in which the ice floats|
|Gravity||GRAV||Magnitude of gravity (positive!)|
|Backwall Pressure||PRESS||optional backwall/water pressure (not yet properly implemented!)|
|Submarine Melt||MELT||optional basal melt rate passed to fibg3 for altering domain shape|
|UC||UC||optional frontal melt rate|
|Width||S||beam width (relative to unit particle)|
|Youngs Modulus||EF0||particle bond young's mod, describes interaction between connected particles|
|Size||LS||Something to do with the fcc lattice 'box size'|
|Domain Inclination||SUB||Angle of the domain vs gravity vector, not used|
|Water Line||WL||Sea level for buoyancy calc|
|Grounding Line||GL||'grounding line' - not used|
|Shear Line||SLIN||A distance below the surface where all bonds are broken?|
|No Timesteps||STEPS0||The number of steps|
|Max Load||MLOAD||Maximum load on bond - bonds break beyond this|
|Friction Scale||FRIC||Scale factor for friction input|
|Restart||REST||1 = restart from prev, 0 = new run|
|Restart From Run Name||restname||Specifies the name of the run from which to restart (defaults to same as 'Run Name')|
|Scale||SCL||Scale factor for particle and beam size|
|Grid||GRID||Resolution of mass3.dat input grid|
|Porosity||POR||The proportion of initially broken bonds|
|Random Seed||SEEDI||Seed for random number generator|
|Translational Damping||DAMP1||The damping coefficient for translation|
|Rotational Damping||DAMP2||The damping coefficient for rotation|
|Drag Coefficient||DRAG||The drag coefficient|
|Output Interval||OUTINT||The output interval (every OUTINT steps, write out CSV)|
|Restart Output Interval||RESOUTINT||The restart output interval (every RESOUTINT, write out restart files) <- Joe's addition|
|Maximum Displacement||MAXUT||The maximum displacement of particles - default 1.0e6 metres (particles further than this are frozen)|
|Fracture After Time||FRACTIME||Fracture is permitted after this time.|
|Bed Stiffness Constant||BedIntConst||The stiffness constant of the bed|
|Bed Z Only||BedZOnly||Whether to consider only the z component of bed interaction (rather than normal)|
|Strict Domain Interpolation||StrictDomain||Determines limit of interpolation w.r.t geometry input file. See note above|
|CSV Output||CSVOutput||If true, produce output in .csv format rather than binary (uses more disk space! Default false)|
|Double Precision Output||DoublePrec||If true, output data will be Float64 (as opposed to Float32). (doubles output filesize..., Default false)|
|Geometry File Has Mask||GeomMasked||Specifies whether the geometry file includes a mask column (required for 'Fixed Lateral Margins'|
|Fixed Lateral Margins||FixLat||If true, particles near the lateral margins are not permitted to move in XY plane|
|Fixed Inflow Margin||FixBack||If true, particles near the inflow margin are not permitted to move in XY plane|
mass3.dat is the input configuration, in format:
x, y, surface, base, bed. friction (Newton seconds per metre)
x and y must start at zero, must have a (0,0) corner.
output transformation matrix which takes from Elmer domain to HiDEM domain.
make sure the bed is buffered beyond the edge of the ice, and define these regions by setting surf and base equal to bed.
User may optionally specify a 'mask' column in geometry input file, which tells the model which regions are ice (=1), fjord (=2), bedrock(=0). This is required for imposing lateral boundary conditions (Fixed Lateral Margins).
|YN||the number of partitions in the Y direction.|
|NTOT||the total number of partitions in the model|
|GRID||The grid size of the mass3.dat data, make sure it matches|
|SCL||diameter of each particle|
|RESTART||1 = true|
|FRZ (FRY,FRX)||contact forces (particle-particle, particle-bed)|
|BOYZ, BOYY||buoyant forces|
|WSX,WSY||wall contact forces?|
|MN||mass of particles|
|MFIL||mass of particles - per particle|
|JS||moment of rotational inertia|
|NAN||list of connections between particles e.g. NAN(1:2,1) lists the two particle numbers which make up connection 1|
|NRXF%M,%F||initial position of the particles|
Output - JYR and STR files
By default the model produces particle information in .vtu format (readable in Paraview (v5.5) - use HiDEM_load.py macro) and bond strain information in binary format (readable by the python script rh.py). For CSV output, use the 'CSV Output' option in the inp.dat (beware this produces much larger files which make visualisation time consuming).
JYR files list the position of all particles in x,y,z, every 2 seconds.
Read this in paraview quite easily.
STR file list the midpoint position and strain of each bond between two particles, for each node connection in initial geometry (including broken bonds)
dtop* files - these show the total energy in the system for different parts
dtop00 - T,WENS,ENMS+ENMS0,KINS,MGHS-MGH0
dtop01 - T,DPES,DMPENS,PSUMS,GSUMS
dtopr - T,system energy, damping energy?
WENS - elastic energy of the spheres - imagine the particles overlap and are deformed against each other. Then they might bounce back apart.
ENMS+ENMS0 - elastic deformation energy - the energy held in a deformed/bent system
MGHS-MGH0 - potential energy
Kins - translational kinetic energy
Kins2 - rotational kinetic energy
DPES,DMPENS - guess energy lost to drag and damping?
PSUMS - something like pressure
GSUMS - energy of bed interaction
rc2.f90 computes the size distribution of calved blocks
1 452000 2 4560 3 985 ... largest_block 1
'maxi' is the same as jyr but for the largest intact block (e.g. the remaining glacier)
rh2.f90 - computes velocity
rh.f - computes strain
INFI1 - first JYR
INFI2 - second JYR
N - wc -l JYR0001.csv
max - 10?
First simply load csv, with blank space delimiter, merge delimiters, has no header
Then apply table to points filter
Then ensure enable ospray and shadows, and pick point size that makes them touch
For the sea: add a box, set size and centrepoints
For the bed: get bed.csv, read it in same as other CSVs
then apply Delaunay2D filter.
Changes made by Jan since commit
Got rid of: UTPP, VELO, D, MAXDT,XIND,YIND
The change means BEDZONLY=TRUE is implicit
Using lbound,rbound fib00,tbed files, but NOT dtmax
Changed ice density
lots of things involving SCL seem to have changed power
some change to setting porisity/predamage - no longer considers proximity to bed/base?
EFLOAD1,2 -> EFFLOAD: Only EFFLOAD exists, and its passed more stuff
Seems to get rid of UTP prediction, damping
Improve the partitioning scheme
Get rid of redundant code using pointers
Translate & Rotate input
Domain needs to be orientated in XY because:
Boundary conditions are applied in WSY (, WSX?) components (need to compute normal? Ask