Mechanics

Workflow: friction on a layered 2D system

Pattern adapted from 31_Nanoribbon_friction. See assets/examples/friction/run.in.

potential   gr_bn_mos2.ilp
potential   nep.txt
velocity    300
time_step   1

# group 0: ghost driver layer (external spring)
# group 1: thermostatted layer
# group 2: production layer
# group 3: fixed bottom

ensemble    heat_lan 300 100 0 1 2      # Langevin only on group 1
fix         3                             # freeze group 3 completely
add_spring  ghost_atom 0 100.0 0.0 0.0 0.0 0 0.0005 0.0 0.0
dump_thermo 100
dump_exyz   10000 0 0
run         1000000

• potential — may be listed more than once to combine intralayer + interlayer potentials (e.g. nep.txt for the layers themselves and an ILP file for the interlayer term).
• heat_lan T tau groups...
  • Applies a Langevin thermostat only to the listed group(s).
• fix 3
  • Holds the atoms in group 3 at fixed positions.
• add_spring ghost_atom g k x0 y0 z0 axis v0 vx vy
  • Attaches a spring between the centre of mass of group g and a ghost atom that moves with velocity (vx, vy, vz). This drives shear motion.
• Group indices must match the group:I:M columns in model.xyz.

Post-process the spring force from thermo.out or a group-resolved dump to recover the friction coefficient.

Workflow: deposition

Pattern adapted from 16_Deposition and 27_Carbon_Cu111_deposition.

potential   nep.txt
velocity    300
time_step   1

# group 0: bottom fixed substrate
# group 1: thermostatted substrate
# group 2: free surface / deposition target
ensemble    heat_lan 300 100 0 1
fix         0
dump_thermo 100
dump_exyz   1000 0 0
run         100000

For actual deposition events the tutorial ships a deposition.py helper that repeatedly inserts atoms above the slab and resumes the GPUMD run. Expose it to the user rather than reinventing a deposition loop.

Key rules:

• the substrate's bottom layer must be fixed to prevent net drift under repeated deposition events
• the thermostat layer must be thick enough to absorb the impact energy of incoming atoms without heating the reactive region unphysically
• the incoming atoms should not overlap existing atoms when injected

Workflow: impact / collision

Use initial-velocity conditions on a group:

velocity    300
# after this point the user re-initializes a subset of atoms with a large
# directed velocity via a model.xyz vel:R:3 column, or with a second
# `velocity` call targeted at a group
ensemble    nve
dump_thermo 100
dump_exyz   100 0 0
run         20000

The tutorial example uses a prepared initial model.xyz with directed vel:R:3 columns on the projectile group, rather than modifying velocities mid-run.

Group bookkeeping rules

• Groups are declared by adding one or more group:I:M columns to the Properties header of model.xyz:

  Properties=species:S:1:pos:R:3:group:I:1
  

  Each group:I:M is a distinct grouping scheme. The M tells GPUMD how many columns make up this grouping.

• The upstream add_groups tool under GPUMD/tools/Analysis_and_Processing can assign groups automatically from spatial criteria.

Read first

• references/mechanics-deposition-friction.md

Read when needed:

• references/core-files-and-ensembles.md
• references/gpumd-keyword-cheatsheet.md
• references/tutorial-map.md

Bundled templates

• assets/examples/friction/run.in
• assets/examples/friction/model.xyz
• assets/examples/deposition/run.in
• assets/examples/deposition/model.xyz

Expected output

1. a group-resolved model.xyz that matches the intended physics
2. a run.in with explicit thermostat / fix / spring / driver blocks
3. a list of post-processing quantities (friction force, adsorbate count, penetration depth, …) and where they come from

References

• fix: https://gpumd.org/gpumd/input_parameters/fix.html
• add_spring: https://gpumd.org/gpumd/input_parameters/add_spring.html
• heat_lan: https://gpumd.org/gpumd/input_parameters/ensemble.html
• GPUMD-Tutorials: 16_Deposition, 20_Impact, 21_Fatigue, 27_Carbon_Cu111_deposition, 31_Nanoribbon_friction