Table of Contents
USER-AWPMD package................................................................................................................44
USER-COLVARS package............................................................................................................44
USER-CG-CMM package..............................................................................................................45
USER-CUDA package....................................................................................................................45
USER-EFF package........................................................................................................................45
USER-EWALDN package..............................................................................................................46
USER-OMP package......................................................................................................................46
USER-REAXC package.................................................................................................................47
USER-SPH package........................................................................................................................47
5. Accelerating LAMMPS performance................................................................................................48
5.1 Measuring performance............................................................................................................48
5.2 General strategies......................................................................................................................49
5.3 Packages with optimized styles................................................................................................49
5.4 OPT package.............................................................................................................................50
5.5 USER-OMP package................................................................................................................50
5.6 GPU package............................................................................................................................52
5.7 USER-CUDA package..............................................................................................................54
5.8 Comparison of GPU and USER-CUDA packages...................................................................56
6. How-to discussions............................................................................................................................58
6.1 Restarting a simulation.............................................................................................................58
6.2 2d simulations...........................................................................................................................60
6.3 CHARMM, AMBER, and DREIDING force fields.................................................................60
6.4 Running multiple simulations from one input script................................................................61
6.5 Multi-replica simulations..........................................................................................................63
6.6 Granular models........................................................................................................................63
6.7 TIP3P water model...................................................................................................................64
6.8 TIP4P water model...................................................................................................................65
6.9 SPC water model.......................................................................................................................66
6.10 Coupling LAMMPS to other codes........................................................................................67
6.11 Visualizing LAMMPS snapshots............................................................................................68
6.12 Triclinic (non-orthogonal) simulation boxes..........................................................................69
6.13 NEMD simulations.................................................................................................................73
6.14 Extended spherical and aspherical particles...........................................................................73
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)....................................76
6.16 Thermostatting, barostatting, and computing temperature.....................................................80
6.17 Walls.......................................................................................................................................82
6.18 Elastic constants......................................................................................................................83
6.19 Library interface to LAMMPS................................................................................................84
6.20 Calculating thermal conductivity............................................................................................85
6.21 Calculating viscosity...............................................................................................................86
7. Example problems.............................................................................................................................89
8. Performance & scalability.................................................................................................................91
9. Additional tools.................................................................................................................................92
amber2lmp tool...............................................................................................................................92
binary2txt tool.................................................................................................................................93
ch2lmp tool.....................................................................................................................................93
chain tool.........................................................................................................................................93
createatoms tool..............................................................................................................................93
LAMMPS Users Manual
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