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LAMMPS Users Manual

24 Jan 2013 version

http://lammps.sandia.gov - Sandia National Laboratories

Table of Contents

LAMMPS Documentation.............................................................................................................................1

7 Jun 2013 version...................................................................................................................................1

Version info:.....................................................................................................................................1

1. Introduction.........................................................................................................................................4

1.1 What is LAMMPS......................................................................................................................4

1.2 LAMMPS features......................................................................................................................5

General features................................................................................................................................5

Particle and model types...................................................................................................................5

Force fields........................................................................................................................................5

Atom creation....................................................................................................................................6

Ensembles, constraints, and boundary conditions............................................................................6

Integrators.........................................................................................................................................7

Diagnostics........................................................................................................................................7

Output...............................................................................................................................................7

Multi-replica models.........................................................................................................................7

Pre- and post-processing...................................................................................................................7

Specialized features..........................................................................................................................7

1.3 LAMMPS non-features...............................................................................................................8

1.4 Open source distribution.............................................................................................................9

1.5 Acknowledgments and citations...............................................................................................10

2. Getting Started...................................................................................................................................12

2.1 What's in the LAMMPS distribution........................................................................................12

2.2 Making LAMMPS....................................................................................................................13

2.3 Making LAMMPS with optional packages..............................................................................19

2.4 Building LAMMPS via the Make.py script..............................................................................21

2.5 Building LAMMPS as a library................................................................................................22

2.6 Running LAMMPS...................................................................................................................24

2.7 Command-line options..............................................................................................................25

2.8 LAMMPS screen output...........................................................................................................29

2.9 Tips for users of previous LAMMPS versions.........................................................................30

3. Commands.........................................................................................................................................32

3.1 LAMMPS input script...............................................................................................................32

3.2 Parsing rules..............................................................................................................................33

3.3 Input script structure.................................................................................................................34

3.4 Commands listed by category...................................................................................................35

3.5 Individual commands................................................................................................................36

Fix styles.........................................................................................................................................37

Compute styles................................................................................................................................37

Pair_style potentials........................................................................................................................38

Bond_style potentials......................................................................................................................39

Angle_style potentials.....................................................................................................................40

Dihedral_style potentials................................................................................................................40

Improper_style potentials................................................................................................................41

Kspace solvers................................................................................................................................41

4. Packages............................................................................................................................................42

4.1 Standard packages.....................................................................................................................42

4.2 User packages...........................................................................................................................43

USER-MISC package.....................................................................................................................44

LAMMPS Users Manual

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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data2xmovie tool.............................................................................................................................95

eam database tool............................................................................................................................95

eam generate tool............................................................................................................................95

eff tool.............................................................................................................................................95

emacs tool.......................................................................................................................................95

ipp tool............................................................................................................................................95

kate tool...........................................................................................................................................96

lmp2arc tool....................................................................................................................................96

lmp2cfg tool....................................................................................................................................96

lmp2vmd tool..................................................................................................................................96

matlab tool......................................................................................................................................96

micelle2d tool..................................................................................................................................96

moltemplate tool.............................................................................................................................97

msi2lmp tool...................................................................................................................................97

phonon tool.....................................................................................................................................97

pymol_asphere tool.........................................................................................................................97

python tool......................................................................................................................................97

reax tool..........................................................................................................................................98

restart2data tool...............................................................................................................................98

thermo_extract tool.........................................................................................................................98

vim tool...........................................................................................................................................98

xmovie tool.....................................................................................................................................99

10. Modifying & extending LAMMPS...............................................................................................100

10.1 Atom styles...........................................................................................................................101

10.2 Bond, angle, dihedral, improper potentials...........................................................................102

10.3 Compute styles......................................................................................................................103

10.4 Dump styles..........................................................................................................................104

10.5 Dump custom output options................................................................................................104

10.6 Fix styles...............................................................................................................................104

10.7 Input script commands..........................................................................................................106

10.8 Kspace computations............................................................................................................106

10.9 Minimization styles...............................................................................................................107

10.10 Pairwise potentials..............................................................................................................107

10.11 Region styles.......................................................................................................................107

10.11 Body styles..........................................................................................................................108

10.13 Thermodynamic output options..........................................................................................108

10.14 Variable options..................................................................................................................109

10.15 Submitting new features for inclusion in LAMMPS..........................................................109

11. Python interface to LAMMPS.......................................................................................................111

11.1 Building LAMMPS as a shared library................................................................................112

11.2 Installing the Python wrapper into Python............................................................................112

11.3 Extending Python with MPI to run in parallel......................................................................113

11.4 Testing the Python-LAMMPS interface...............................................................................114

11.5 Using LAMMPS from Python..............................................................................................116

11.6 Example Python scripts that use LAMMPS.........................................................................119

12. Errors.............................................................................................................................................121

12.1 Common problems................................................................................................................121

12.2 Reporting bugs......................................................................................................................122

LAMMPS Users Manual

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12.3 Error & warning messages....................................................................................................122

Errors:...........................................................................................................................................123

Warnings:......................................................................................................................................197

13. Future and history..........................................................................................................................204

13.1 Coming attractions................................................................................................................204

13.2 Past versions..........................................................................................................................204

angle_style charmm command............................................................................................................206

angle_style charmm/omp command....................................................................................................206

angle_style class2 command...............................................................................................................208

angle_style class2/omp command.......................................................................................................208

angle_coeff command.........................................................................................................................210

angle_style cosine command...............................................................................................................212

angle_style cosine/omp command.......................................................................................................212

angle_style cosine/delta command......................................................................................................214

angle_style cosine/delta/omp command..............................................................................................214

angle_style cosine/periodic command.................................................................................................216

angle_style cosine/periodic/omp command........................................................................................216

angle_style cosine/shift command.......................................................................................................218

angle_style cosine/shift/omp command..............................................................................................218

angle_style cosine/shift/exp command................................................................................................220

angle_style cosine/shift/exp/omp command........................................................................................220

angle_style cosine/squared command.................................................................................................222

angle_style cosine/squared/omp command.........................................................................................222

angle_style dipole command...............................................................................................................224

angle_style dipole/omp command.......................................................................................................224

angle_style fourier command..............................................................................................................226

angle_style fourier/omp command......................................................................................................226

angle_style fourier/simple command..................................................................................................228

angle_style fourier/simple/omp command..........................................................................................228

angle_style harmonic command..........................................................................................................230

angle_style harmonic/omp command..................................................................................................230

angle_style hybrid command...............................................................................................................232

angle_style none command.................................................................................................................234

angle_style quartic command..............................................................................................................235

angle_style quartic/omp command......................................................................................................235

angle_style sdk command....................................................................................................................237

angle_style command..........................................................................................................................238

angle_style table command.................................................................................................................240

angle_style table/omp command.........................................................................................................240

atom_modify command.......................................................................................................................243

atom_style command...........................................................................................................................245

balance command................................................................................................................................248

Body particles......................................................................................................................................252

bond_style class2 command................................................................................................................255

bond_style class2/omp command........................................................................................................255

bond_coeff command..........................................................................................................................257

bond_style fene command...................................................................................................................259

bond_style fene/omp command...........................................................................................................259

LAMMPS Users Manual