Table of Contents
USER-ATC package.......................................................................................................................45
USER-AWPMD package................................................................................................................45
USER-COLVARS package............................................................................................................45
USER-CG-CMM package..............................................................................................................46
USER-CUDA package....................................................................................................................46
USER-EFF package........................................................................................................................47
USER-OMP package......................................................................................................................47
USER-REAXC package.................................................................................................................47
USER-SPH package........................................................................................................................48
5. Accelerating LAMMPS performance................................................................................................49
5.1 Measuring performance............................................................................................................49
5.2 General strategies......................................................................................................................50
5.3 Packages with optimized styles................................................................................................50
5.4 OPT package.............................................................................................................................51
5.5 USER-OMP package................................................................................................................51
5.6 GPU package............................................................................................................................53
5.7 USER-CUDA package..............................................................................................................55
5.8 Comparison of GPU and USER-CUDA packages...................................................................57
6. How-to discussions............................................................................................................................59
6.1 Restarting a simulation.............................................................................................................59
6.2 2d simulations...........................................................................................................................61
6.3 CHARMM, AMBER, and DREIDING force fields.................................................................61
6.4 Running multiple simulations from one input script................................................................62
6.5 Multi-replica simulations..........................................................................................................64
6.6 Granular models........................................................................................................................64
6.7 TIP3P water model...................................................................................................................65
6.8 TIP4P water model...................................................................................................................66
6.9 SPC water model.......................................................................................................................68
6.10 Coupling LAMMPS to other codes........................................................................................68
6.11 Visualizing LAMMPS snapshots............................................................................................69
6.12 Triclinic (non-orthogonal) simulation boxes..........................................................................70
6.13 NEMD simulations.................................................................................................................74
6.14 Finite-size spherical and aspherical particles..........................................................................74
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)....................................78
6.16 Thermostatting, barostatting, and computing temperature.....................................................82
6.17 Walls.......................................................................................................................................84
6.18 Elastic constants......................................................................................................................85
6.19 Library interface to LAMMPS................................................................................................85
6.20 Calculating thermal conductivity............................................................................................86
6.21 Calculating viscosity...............................................................................................................87
7. Example problems.............................................................................................................................90
8. Performance & scalability.................................................................................................................92
9. Additional tools.................................................................................................................................93
amber2lmp tool...............................................................................................................................94
binary2txt tool.................................................................................................................................94
ch2lmp tool.....................................................................................................................................94
chain tool.........................................................................................................................................94
createatoms tool..............................................................................................................................94
LAMMPS Users Manual
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