Lammps Users Manual Vlcc

Summary

LAMMPS Users Manual
Large−scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov − Sandia National Laboratories
Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License

LAMMPS Users Manual
Table of Contents
LAMMPS Documentation.............................................................................................................................1
1. Introduction................................................................................................................................................3
1.1 What is LAMMPS.............................................................................................................................3
1.2 LAMMPS features.............................................................................................................................4
General features.......................................................................................................................................4
Particle and model types..........................................................................................................................4
Force fields..............................................................................................................................................4
Atom creation..........................................................................................................................................5
Ensembles, constraints, and boundary conditions...................................................................................5
Integrators................................................................................................................................................5
Diagnostics..............................................................................................................................................6
Output......................................................................................................................................................6
Multi−replica models...............................................................................................................................6
Pre− and post−processing........................................................................................................................6
Specialized features.................................................................................................................................6
1.3 LAMMPS non−features....................................................................................................................6
1.4 Open source distribution....................................................................................................................8
1.5 Acknowledgments and citations........................................................................................................9
2. Getting Started.........................................................................................................................................13
2.1 What's in the LAMMPS distribution...............................................................................................13
2.2 Making LAMMPS...........................................................................................................................13
2.3 Making LAMMPS with optional packages.....................................................................................18
2.4 Building LAMMPS as a library......................................................................................................21
2.5 Running LAMMPS.........................................................................................................................21
2.6 Command−line options...................................................................................................................23
2.7 LAMMPS screen output..................................................................................................................24
2.8 Running on GPUs............................................................................................................................26
GPU configuration.................................................................................................................................26
GPU input script....................................................................................................................................27
GPU asynchronous pair computation....................................................................................................27
GPU timing............................................................................................................................................27
GPU single vs double precision............................................................................................................27
2.9 Tips for users of previous LAMMPS versions................................................................................27
3. Commands...............................................................................................................................................29
3.1 LAMMPS input script.....................................................................................................................29
3.2 Parsing rules....................................................................................................................................30
3.3 Input script structure........................................................................................................................30
3.4 Commands listed by category.........................................................................................................32
3.5 Individual commands......................................................................................................................32
Fix styles................................................................................................................................................33
Compute styles......................................................................................................................................33
Pair_style potentials...............................................................................................................................34
Bond_style potentials............................................................................................................................34
Angle_style potentials...........................................................................................................................35
Dihedral_style potentials.......................................................................................................................35
Improper_style potentials......................................................................................................................35
Kspace solvers.......................................................................................................................................35
4. How−to discussions.................................................................................................................................36
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4.1 Restarting a simulation....................................................................................................................36
4.2 2d simulations..................................................................................................................................37
4.3 CHARMM, AMBER, and DREIDING force fields.......................................................................38
4.4 Running multiple simulations from one input script.......................................................................39
4.5 Multi−replica simulations................................................................................................................40
4.6 Granular models..............................................................................................................................41
4.7 TIP3P water model..........................................................................................................................42
4.8 TIP4P water model..........................................................................................................................43
4.9 SPC water model.............................................................................................................................44
4.10 Coupling LAMMPS to other codes...............................................................................................44
4.11 Visualizing LAMMPS snapshots..................................................................................................46
4.12 Triclinic (non−orthogonal) simulation boxes................................................................................46
4.13 NEMD simulations........................................................................................................................48
4.14 Extended spherical and aspherical particles..................................................................................49
4.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)..........................................51
4.16 Thermostatting, barostatting, and computing temperature............................................................55
4.17 Walls..............................................................................................................................................57
4.18 Elastic constants............................................................................................................................58
4.19 Library interface to LAMMPS......................................................................................................58
4.20 Calculating thermal conductivity..................................................................................................60
4.21 Calculating viscosity.....................................................................................................................60
5. Example problems....................................................................................................................................63
6. Performance &scalability.........................................................................................................................65
7. Additional tools........................................................................................................................................66
amber2lmp tool......................................................................................................................................66
binary2txt tool.......................................................................................................................................67
ch2lmp tool............................................................................................................................................67
chain tool...............................................................................................................................................67
createatoms tool.....................................................................................................................................67
data2xmovie tool...................................................................................................................................68
eam database tool..................................................................................................................................68
eam generate tool...................................................................................................................................68
eff tool...................................................................................................................................................68
emacs tool..............................................................................................................................................68
ipp tool...................................................................................................................................................68
lmp2arc tool...........................................................................................................................................69
lmp2cfg tool...........................................................................................................................................69
lmp2traj tool..........................................................................................................................................69
lmp2vmd tool.........................................................................................................................................69
matlab tool.............................................................................................................................................69
micelle2d tool........................................................................................................................................69
msi2lmp tool..........................................................................................................................................70
pymol_asphere tool...............................................................................................................................70
python tool.............................................................................................................................................70
reax tool.................................................................................................................................................70
restart2data tool.....................................................................................................................................70
thermo_extract tool................................................................................................................................71
vim tool..................................................................................................................................................71
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xmovie tool............................................................................................................................................71
8. Modifying &extending LAMMPS...........................................................................................................72
Atom styles............................................................................................................................................73
Bond, angle, dihedral, improper potentials...........................................................................................74
Compute styles......................................................................................................................................75
Dump styles...........................................................................................................................................75
Dump custom output options.................................................................................................................75
Fix styles................................................................................................................................................76
Input script commands..........................................................................................................................77
Kspace computations.............................................................................................................................77
Minimization solvers.............................................................................................................................78
Pairwise potentials.................................................................................................................................78
Region styles.........................................................................................................................................78
Thermodynamic output options.............................................................................................................79
Variable options.....................................................................................................................................79
Submitting new features to the developers to include in LAMMPS.....................................................80
10. Errors......................................................................................................................................................82
10.1 Common problems........................................................................................................................82
10.2 Reporting bugs...............................................................................................................................83
10.3 Error &warning messages.............................................................................................................83
Errors:....................................................................................................................................................83
Warnings:............................................................................................................................................135
11. Future and history................................................................................................................................140
11.1 Coming attractions.......................................................................................................................140
11.2 Past versions................................................................................................................................140
angle_style charmm command...................................................................................................................143
angle_style class2 command......................................................................................................................144
angle_style cg/cmm command...................................................................................................................146
angle_coeff command................................................................................................................................147
angle_style cosine command.....................................................................................................................149
angle_style cosine/delta command.............................................................................................................150
angle_style cosine/periodic command.......................................................................................................151
angle_style cosine/squared command........................................................................................................152
angle_style harmonic command.................................................................................................................153
angle_style hybrid command.....................................................................................................................154
angle_style none command........................................................................................................................155
angle_style command.................................................................................................................................156
angle_style table command........................................................................................................................158
atom_modify command.............................................................................................................................160
atom_style command.................................................................................................................................162
bond_style class2 command.......................................................................................................................164
bond_coeff command.................................................................................................................................165
bond_style fene command.........................................................................................................................167
bond_style fene/expand command.............................................................................................................168
bond_style harmonic command.................................................................................................................170
bond_style hybrid command......................................................................................................................171
bond_style morse command.......................................................................................................................172
bond_style none command.........................................................................................................................173
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bond_style nonlinear command.................................................................................................................174
bond_style quartic command.....................................................................................................................175
bond_style command.................................................................................................................................177
bond_style table command.........................................................................................................................179
boundary command....................................................................................................................................181
change_box command................................................................................................................................182
clear command...........................................................................................................................................183
communicate command.............................................................................................................................184
compute command.....................................................................................................................................186
compute ackland/atom command...............................................................................................................190
compute angle/local command...................................................................................................................192
compute atom/molecule command............................................................................................................194
compute bond/local command...................................................................................................................196
compute centro/atom command.................................................................................................................198
compute cna/atom command.....................................................................................................................200
compute com command.............................................................................................................................202
compute com/molecule command.............................................................................................................203
compute coord/atom command..................................................................................................................205
compute damage/atom command...............................................................................................................206
compute dihedral/local command..............................................................................................................207
compute displace/atom command..............................................................................................................208
compute erotate/asphere command............................................................................................................210
compute erotate/sphere command..............................................................................................................211
compute event/displace command.............................................................................................................212
compute group/group command................................................................................................................213
compute gyration command.......................................................................................................................214
compute gyration/molecule command.......................................................................................................215
compute heat/flux command......................................................................................................................217
compute improper/local command.............................................................................................................220
compute ke command................................................................................................................................221
compute ke/atom command.......................................................................................................................222
compute ke/atom/eff command..................................................................................................................223
compute ke/eff command...........................................................................................................................225
compute_modify command........................................................................................................................227
compute msd command.............................................................................................................................228
compute msd/molecule command..............................................................................................................230
compute pair command..............................................................................................................................232
compute pair/local command.....................................................................................................................234
compute pe command................................................................................................................................236
compute pe/atom command.......................................................................................................................238
compute pressure command.......................................................................................................................240
compute property/atom command.............................................................................................................242
compute property/local command..............................................................................................................244
compute property/molecule command.......................................................................................................246
compute rdf command...............................................................................................................................247
compute reduce command.........................................................................................................................249
compute reduce/region command..............................................................................................................249
compute stress/atom command..................................................................................................................252
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compute temp command............................................................................................................................254
compute temp/asphere command...............................................................................................................256
compute temp/com command....................................................................................................................258
compute temp/deform command...............................................................................................................260
compute temp/deform/eff command..........................................................................................................262
compute temp/eff command.......................................................................................................................263
compute temp/partial command.................................................................................................................265
compute temp/profile command................................................................................................................267
compute temp/ramp command...................................................................................................................269
compute temp/region command.................................................................................................................271
compute temp/region/eff command...........................................................................................................273
compute temp/sphere command.................................................................................................................274
compute ti command..................................................................................................................................276
create_atoms command..............................................................................................................................278
create_box command.................................................................................................................................281
delete_atoms command..............................................................................................................................283
delete_bonds command..............................................................................................................................285
dielectric command....................................................................................................................................287
dihedral_style charmm command..............................................................................................................288
dihedral_style class2 command.................................................................................................................290
dihedral_coeff command............................................................................................................................293
dihedral_style harmonic command............................................................................................................295
dihedral_style helix command...................................................................................................................296
dihedral_style hybrid command.................................................................................................................297
dihedral_style multi/harmonic command...................................................................................................298
dihedral_style none command...................................................................................................................299
dihedral_style opls command.....................................................................................................................300
dihedral_style command............................................................................................................................301
dimension command..................................................................................................................................303
dipole command.........................................................................................................................................304
displace_atoms command..........................................................................................................................305
displace_box command..............................................................................................................................307
dump command..........................................................................................................................................310
dump_modify command............................................................................................................................317
echo command...........................................................................................................................................321
fix command..............................................................................................................................................322
fix adapt command.....................................................................................................................................326
fix addforce command...............................................................................................................................330
fix atc command.........................................................................................................................................332
fix ave/atom command...............................................................................................................................336
fix ave/correlate command.........................................................................................................................338
fix ave/histo command...............................................................................................................................343
fix ave/spatial command............................................................................................................................348
fix ave/time command................................................................................................................................353
fix aveforce command................................................................................................................................358
fix bond/break command...........................................................................................................................360
fix bond/create command...........................................................................................................................363
fix bond/swap command............................................................................................................................366
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fix box/relax command..............................................................................................................................369
fix deform command..................................................................................................................................373
fix deposit command..................................................................................................................................379
fix drag command......................................................................................................................................382
fix dt/reset command..................................................................................................................................383
fix efield command....................................................................................................................................385
fix enforce2d command.............................................................................................................................386
fix evaporate command..............................................................................................................................387
fix external command.................................................................................................................................389
fix freeze command....................................................................................................................................391
fix gpu command.......................................................................................................................................392
fix gravity command..................................................................................................................................394
fix heat command.......................................................................................................................................396
fix imd command.......................................................................................................................................398
fix indent command...................................................................................................................................400
fix langevin command................................................................................................................................403
fix langevin/eff command..........................................................................................................................406
fix lineforce command...............................................................................................................................408
fix_modify command.................................................................................................................................409
fix momentum command...........................................................................................................................410
fix move command.....................................................................................................................................412
fix msst command.....................................................................................................................................415
fix neb command........................................................................................................................................418
fix nvt command........................................................................................................................................420
fix npt command........................................................................................................................................420
fix nph command.......................................................................................................................................420
fix nvt/eff command...................................................................................................................................427
fix npt/eff command...................................................................................................................................427
fix nph/eff command..................................................................................................................................427
fix nph/asphere command..........................................................................................................................430
fix nph/sphere command............................................................................................................................432
fix npt/asphere command...........................................................................................................................434
fix npt/sphere command.............................................................................................................................437
fix nve command........................................................................................................................................439
fix nve/asphere command..........................................................................................................................440
fix nve/eff command..................................................................................................................................441
fix nve/limit command...............................................................................................................................442
fix nve/noforce command..........................................................................................................................444
fix nve/sphere command............................................................................................................................445
fix nvt/asphere command...........................................................................................................................447
fix nvt/sllod command...............................................................................................................................449
fix nvt/sllod/eff command..........................................................................................................................451
fix nvt/sphere command.............................................................................................................................453
fix orient/fcc command..............................................................................................................................455
fix planeforce command.............................................................................................................................459
fix poems....................................................................................................................................................460
fix pour command......................................................................................................................................462
fix press/berendsen command....................................................................................................................464
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fix print command......................................................................................................................................467
fix qeq/comb command..............................................................................................................................469
fix qeq/reax command................................................................................................................................471
fix reax/bonds command............................................................................................................................473
fix recenter command.................................................................................................................................474
fix rigid command......................................................................................................................................476
fix rigid/nve command...............................................................................................................................476
fix rigid/nvt command................................................................................................................................476
fix setforce command.................................................................................................................................481
fix shake command....................................................................................................................................483
fix smd command.......................................................................................................................................485
fix spring command...................................................................................................................................488
fix spring/rg command...............................................................................................................................490
fix spring/self command.............................................................................................................................492
fix srd command.........................................................................................................................................493
fix store/force command............................................................................................................................498
fix store/state command.............................................................................................................................499
fix temp/berendsen command....................................................................................................................501
fix temp/rescale command.........................................................................................................................503
fix temp/rescale/eff command....................................................................................................................505
fix thermal/conductivity command............................................................................................................507
fix tmd command.......................................................................................................................................510
fix ttm command........................................................................................................................................512
fix viscosity command...............................................................................................................................515
fix viscous command.................................................................................................................................518
fix wall/lj93 command...............................................................................................................................520
fix wall/lj126 command.............................................................................................................................520
fix wall/colloid command..........................................................................................................................520
fix wall/harmonic command......................................................................................................................520
fix wall/gran command..............................................................................................................................524
fix wall/reflect command...........................................................................................................................527
fix wall/region command...........................................................................................................................530
fix wall/srd command.................................................................................................................................533
group command..........................................................................................................................................536
if command................................................................................................................................................538
improper_style class2 command................................................................................................................541
improper_coeff command..........................................................................................................................543
improper_style cvff command...................................................................................................................545
improper_style harmonic command...........................................................................................................546
improper_style hybrid command...............................................................................................................547
improper_style none command..................................................................................................................548
improper_style command...........................................................................................................................549
improper_style umbrella command...........................................................................................................551
include command.......................................................................................................................................553
jump command...........................................................................................................................................554
kspace_modify command..........................................................................................................................556
kspace_style command..............................................................................................................................558
label command...........................................................................................................................................560
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lattice command.........................................................................................................................................561
log command..............................................................................................................................................564
mass command...........................................................................................................................................565
min_modify command...............................................................................................................................567
min_style command...................................................................................................................................568
minimize command....................................................................................................................................570
neb command.............................................................................................................................................574
neigh_modify command............................................................................................................................579
neighbor command.....................................................................................................................................582
newton command.......................................................................................................................................584
next command............................................................................................................................................585
orient command..........................................................................................................................................587
origin command.........................................................................................................................................588
pair_style airebo command........................................................................................................................589
pair_style born command...........................................................................................................................592
pair_style born/coul/long command...........................................................................................................592
pair_style buck command..........................................................................................................................594
pair_style buck/coul/cut command............................................................................................................594
pair_style buck/coul/long command..........................................................................................................594
pair_style buck/coul command..................................................................................................................597
pair_style lj/charmm/coul/charmm command...........................................................................................600
pair_style lj/charmm/coul/charmm/implicit command..............................................................................600
pair_style lj/charmm/coul/long command.................................................................................................600
pair_style lj/charmm/coul/long/gpu command..........................................................................................600
pair_style lj/charmm/coul/long/opt command...........................................................................................600
pair_style lj/class2 command.....................................................................................................................604
pair_style lj/class2/coul/cut command.......................................................................................................604
pair_style lj/class2/coul/long command.....................................................................................................604
pair_style cg/cmm command.....................................................................................................................607
pair_style cg/cmm/gpu command..............................................................................................................607
pair_style cg/cmm/coul/cut command.......................................................................................................607
pair_style cg/cmm/coul/long command.....................................................................................................607
pair_style cg/cmm/coul/long/gpu command..............................................................................................607
pair_coeff command..................................................................................................................................611
pair_style colloid command.......................................................................................................................614
pair_style comb command.........................................................................................................................617
pair_style coul/cut command.....................................................................................................................621
pair_style coul/debye command.................................................................................................................621
pair_style coul/long command...................................................................................................................621
pair_style dipole/cut command..................................................................................................................623
pair_style dpd command............................................................................................................................626
pair_style dpd/tstat command....................................................................................................................626
pair_style dsmc command..........................................................................................................................629
pair_style eam command...........................................................................................................................631
pair_style eam/opt command.....................................................................................................................631
pair_style eam/alloy command..................................................................................................................631
pair_style eam/alloy/opt command............................................................................................................631
pair_style eam/cd command.......................................................................................................................631
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pair_style eam/fs command.......................................................................................................................631
pair_style eam/fs/opt command.................................................................................................................631
pair_style eff/cut command........................................................................................................................638
pair_style eim command............................................................................................................................642
pair_style gauss command.........................................................................................................................645
pair_style gayberne command...................................................................................................................647
pair_style gayberne/gpu command............................................................................................................647
pair_style gran/hooke command................................................................................................................651
pair_style gran/hooke/history command....................................................................................................651
pair_style gran/hertz/history command......................................................................................................651
pair_style lj/gromacs command.................................................................................................................655
pair_style lj/gromacs/coul/gromacs command...........................................................................................655
pair_style hbond/dreiding/lj command......................................................................................................657
pair_style hbond/dreiding/morse command...............................................................................................657
pair_style hybrid command........................................................................................................................661
pair_style hybrid/overlay command...........................................................................................................661
pair_style lj/cut command..........................................................................................................................665
pair_style lj/cut/gpu command...................................................................................................................665
pair_style lj/cut/opt command....................................................................................................................665
pair_style lj/cut/coul/cut command............................................................................................................665
pair_style lj/cut/coul/cut/gpu command.....................................................................................................665
pair_style lj/cut/coul/debye command.......................................................................................................665
pair_style lj/cut/coul/long command..........................................................................................................665
pair_style lj/cut/coul/long/gpu command...................................................................................................665
pair_style lj/cut/coul/long/tip4p command................................................................................................665
pair_style lj96/cut command......................................................................................................................670
pair_style lj96/cut/gpu command...............................................................................................................670
pair_style lj/coul command........................................................................................................................672
pair_style lj/expand command...................................................................................................................675
pair_style lj/smooth command...................................................................................................................677
pair_style lubricate command....................................................................................................................679
pair_style meam command........................................................................................................................682
pair_modify command...............................................................................................................................687
pair_style morse command........................................................................................................................690
pair_style morse/opt command..................................................................................................................690
pair_style none command..........................................................................................................................692
pair_style peri/pmb command....................................................................................................................693
pair_style peri/lps command......................................................................................................................693
pair_style reax command...........................................................................................................................695
pair_style reax/c command........................................................................................................................698
pair_style resquared command...................................................................................................................702
pair_style soft command............................................................................................................................705
pair_style command...................................................................................................................................707
pair_style sw command..............................................................................................................................710
pair_style table command..........................................................................................................................713
pair_style tersoff command........................................................................................................................716
pair_style tersoff/zbl command..................................................................................................................720
pair_write command..................................................................................................................................725
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pair_style yukawa command......................................................................................................................727
pair_style yukawa/colloid command.........................................................................................................729
prd command..............................................................................................................................................731
print command...........................................................................................................................................735
processors command..................................................................................................................................736
read_data command...................................................................................................................................737
read_restart command................................................................................................................................747
region command.........................................................................................................................................749
replicate command.....................................................................................................................................753
reset_timestep command............................................................................................................................754
restart command.........................................................................................................................................755
run command..............................................................................................................................................757
run_style command....................................................................................................................................760
set command..............................................................................................................................................763
shape command..........................................................................................................................................766
shell command...........................................................................................................................................768
special_bonds command............................................................................................................................770
tad command..............................................................................................................................................773
temper command........................................................................................................................................777
thermo command........................................................................................................................................779
thermo_modify command..........................................................................................................................780
thermo_style command..............................................................................................................................783
timestep command.....................................................................................................................................787
uncompute command.................................................................................................................................788
undump command......................................................................................................................................789
unfix command..........................................................................................................................................790
units command...........................................................................................................................................791
variable command......................................................................................................................................794
Math Operators....................................................................................................................................798
Math Functions....................................................................................................................................798
Group and Region Functions...............................................................................................................800
Special Functions.................................................................................................................................800
Atom Values and Vectors....................................................................................................................801
Compute References............................................................................................................................801
Fix References.....................................................................................................................................801
Variable References.............................................................................................................................802
velocity command......................................................................................................................................806
write_restart command...............................................................................................................................809
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LAMMPS Documentation
Version info:
The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated
continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on this page of
the WWW site. Each dated copy of LAMMPS contains all the features and bug−fixes up to and including that
version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the
file src/version.h and in the LAMMPS directory name created when you unpack a tarball

• If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most current
version of LAMMPS

• If you browse the HTML doc pages included in your tarball, they describe the version you have

• The PDF file on the WWW site or in the tarball is updated about once per month. This is because it is
large, and we don't want it to be part of very patch

LAMMPS stands for Large−scale Atomic/Molecular Massively Parallel Simulator

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It
was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE

It is an open−source code, distributed freely under the terms of the GNU Public License (GPL)

The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be
contacted at sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at http://lammps.sandia.gov has
more information about the code and its uses

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this
manual or have suggestions for useful information to add, please send an email to the developers so we can
improve the LAMMPS documentation

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm
since it gives quick access to documentation for all LAMMPS commands

PDF file of the entire manual, generated by htmldoc
1. Introduction
1.1 What is LAMMPS
1.2 LAMMPS features
1.3 LAMMPS non−features
1.4 Open source distribution
1.5 Acknowledgments and citations
2. Getting started
2.1 What's in the LAMMPS distribution
2.2 Making LAMMPS
2.3 Making LAMMPS with optional packages
2.4 Building LAMMPS as a library
2.5 Running LAMMPS
2.6 Command−line options
2.7 Screen output
2.8 Running on GPUs
2.9 Tips for users of previous versions
3. Commands
1

Table of Contents LAMMPS Documentation..1

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Frequently Asked Questions

What is the use of lammps_close function?

The lammps_close() function is used to shut down an instance of LAMMPS and free all its memory. The lammps_file() and lammps_command() functions are used to pass a file or string to LAMMPS as if it were an input script or single command in an input script.

Can lammps be coupled with other codes?

LAMMPS can be coupled to other codes in at least 3 ways. Each has advantages and disadvantages, which you'll have to think about in the context of your application. (1) Define a new fix command that calls the other code. In this scenario, LAMMPS is the driver code.

What are the output options for lammps?

See this section for an overview of LAMMPS output options. The output for dist will be in distance units. The output for eng will be in energy units. The output for force will be in force units.

How to use the values generated by a fix in lammps?

In LAMMPS, the values generated by a fix can be used in several ways: Global values can be output via the thermo_style custom or fix ave/time command. Or the values can be referenced in a variable equal or variable atom command. • Per−atom values can be output via the dump custom command or the fix ave/spatial command.