Index

A

angle\_coeff angle\_style angle\_style charmm angle\_style class2 angle\_style cosine angle\_style cosine/delta angle\_style cosine/periodic angle\_style cosine/shift angle\_style cosine/shift/exp angle\_style cosine/squared angle\_style dipole

angle\_style fourier angle\_style fourier/simple angle\_style harmonic angle\_style hybrid angle\_style none angle\_style quartic angle\_style sdk angle\_style table angle\_style zero atom\_modify atom\_style

B

balance bond\_coeff bond\_style bond\_style class2 bond\_style fene bond\_style fene/expand bond\_style harmonic bond\_style harmonic/shift bond\_style harmonic/shift/cut bond\_style hybrid

bond\_style morse bond\_style none bond\_style nonlinear bond\_style oxdna/fene bond\_style quartic bond\_style table bond\_style zero bond\_write boundary box

C

change\_box clear comm\_modify comm\_style compute compute ackland/atom compute angle compute angle/local compute angmom/chunk compute basal/atom compute body/local compute bond compute bond/local compute centro/atom compute chunk/atom compute cluster/atom compute cna/atom compute com compute com/chunk compute contact/atom compute coord/atom compute damage/atom compute dihedral compute dihedral/local compute dilatation/atom compute dipole/chunk compute displace/atom compute dpd compute dpd/atom compute erotate/asphere compute erotate/rigid compute erotate/sphere compute erotate/sphere/atom compute event/displace compute fep compute force/tally compute global/atom compute group/group compute gyration compute gyration/chunk compute heat/flux compute hexorder/atom compute improper compute improper/local compute inertia/chunk compute ke compute ke/atom compute ke/atom/eff compute ke/eff compute ke/rigid compute meso/e/atom compute meso/rho/atom compute meso/t/atom compute msd compute msd/chunk compute msd/nongauss compute omega/chunk compute orientorder/atom compute pair compute pair/local

compute pe compute pe/atom compute plasticity/atom compute pressure compute property/atom compute property/chunk compute property/local compute rdf compute reduce compute rigid/local compute saed compute slice compute smd/contact/radius compute smd/damage compute smd/hourglass/error compute smd/internal/energy compute smd/plastic/strain compute smd/plastic/strain/rate compute smd/rho compute smd/tlsph/defgrad compute smd/tlsph/dt compute smd/tlsph/num/neighs compute smd/tlsph/shape compute smd/tlsph/strain compute smd/tlsph/strain/rate compute smd/tlsph/stress compute smd/ulsph/num/neighs compute smd/ulsph/strain compute smd/ulsph/strain/rate compute smd/ulsph/stress compute smd/vol compute sna/atom compute stress/atom compute temp compute temp/asphere compute temp/body compute temp/chunk compute temp/com compute temp/cs compute temp/deform compute temp/deform/eff compute temp/drude compute temp/eff compute temp/partial compute temp/profile compute temp/ramp compute temp/region compute temp/region/eff compute temp/rotate compute temp/sphere compute ti compute torque/chunk compute vacf compute vcm/chunk compute voronoi/atom compute xrd compute\_modify create\_atoms create\_bonds create\_box

D

delete\_atoms delete\_bonds dielectric dihedral\_coeff dihedral\_style dihedral\_style charmm dihedral\_style class2 dihedral\_style cosine/shift/exp dihedral\_style fourier dihedral\_style harmonic dihedral\_style helix dihedral\_style hybrid dihedral\_style multi/harmonic dihedral\_style nharmonic dihedral\_style none

dihedral\_style opls dihedral\_style quadratic dihedral\_style spherical dihedral\_style table dihedral\_style zero dimension displace\_atoms dump dump custom/vtk dump h5md dump image dump molfile dump nc dump\_modify

E

echo

F

fix fix adapt fix adapt/fep fix addforce fix addtorque fix append/atoms fix atc fix atom/swap fix ave/atom fix ave/chunk fix ave/correlate fix ave/correlate/long fix ave/histo fix ave/time fix aveforce fix balance fix bond/break fix bond/create fix bond/swap fix box/relax fix cmap fix colvars fix controller fix deform fix deposit fix dpd/energy fix drag fix drude fix drude/transform/direct fix dt/reset fix efield fix ehex fix enforce2d fix eos/cv fix eos/table fix eos/table/rx fix evaporate fix external fix filter/corotate fix flow/gauss fix freeze fix gcmc fix gld fix gle fix gravity fix grem fix halt fix heat fix imd fix indent fix ipi fix langevin fix langevin/drude fix langevin/eff fix lb/fluid fix lb/momentum fix lb/pc fix lb/rigid/pc/sphere fix lb/viscous fix lineforce fix manifoldforce fix meso fix meso/stationary fix momentum fix move fix mscg fix msst fix neb fix nph/asphere fix nph/body fix nph/sphere fix nphug fix npt/asphere fix npt/body fix npt/sphere fix nve fix nve/asphere fix nve/asphere/noforce fix nve/body

fix nve/dot fix nve/dotc/langevin fix nve/eff fix nve/limit fix nve/line fix nve/manifold/rattle fix nve/noforce fix nve/sphere fix nve/tri fix nvk fix nvt fix nvt/asphere fix nvt/body fix nvt/eff fix nvt/manifold/rattle fix nvt/sllod fix nvt/sllod/eff fix nvt/sphere fix oneway fix orient/fcc fix phonon fix pimd fix planeforce fix pour fix press/berendsen fix print fix property/atom fix qbmsst fix qeq/comb fix qeq/point fix qeq/reax fix qmmm fix qtb fix reax/bonds fix reax/c/species fix recenter fix restrain fix rigid fix rx fix saed/vtk fix setforce fix shake fix shardlow fix smd fix smd/adjust\_dt fix smd/integrate\_tlsph fix smd/integrate\_ulsph fix smd/move\_tri\_surf fix smd/setvel fix smd/wall\_surface fix spring fix spring/chunk fix spring/rg fix spring/self fix srd fix store/force fix store/state fix temp/berendsen fix temp/csvr fix temp/rescale fix temp/rescale/eff fix tfmc fix thermal/conductivity fix ti/spring fix tmd fix ttm fix tune/kspace fix vector fix viscosity fix viscous fix wall/gran fix wall/gran/region fix wall/lj93 fix wall/piston fix wall/reflect fix wall/region fix wall/srd fix\_modify

G

group

group2ndx

I

if improper\_coeff improper\_style improper\_style class2 improper\_style cossq improper\_style cvff improper\_style distance improper\_style fourier

improper\_style harmonic improper\_style hybrid improper\_style none improper\_style ring improper\_style umbrella improper\_style zero include info

J

jump

K

kspace\_modify

kspace\_style

L

label lattice

log

M

mass min\_modify min\_style

minimize molecule

N

neb neigh\_modify neighbor

newton next

P

package pair\_coeff pair\_modify pair\_style pair\_style adp pair\_style agni pair\_style airebo pair\_style awpmd/cut pair\_style beck pair\_style body pair\_style bop pair\_style born pair\_style born/coul/long/cs pair\_style brownian pair\_style buck pair\_style buck/long/coul/long pair\_style colloid pair\_style comb pair\_style coul/cut pair\_style coul/diel pair\_style dpd pair\_style dpd/fdt pair\_style dsmc pair\_style eam pair\_style edip pair\_style eff/cut pair\_style eim pair\_style exp6/rx pair\_style gauss pair\_style gayberne pair\_style gran/hooke pair\_style hbond/dreiding/lj pair\_style hybrid pair\_style kim pair\_style kolmogorov/crespi/z pair\_style lcbop pair\_style line/lj pair\_style list pair\_style lj/charmm/coul/charmm pair\_style lj/class2 pair\_style lj/cubic pair\_style lj/cut pair\_style lj/cut/dipole/cut pair\_style lj/cut/soft pair\_style lj/expand pair\_style lj/gromacs pair\_style lj/long/coul/long pair\_style lj/mdf pair\_style lj/sdk pair\_style lj/sf pair\_style lj/smooth pair\_style lj/smooth/linear pair\_style lj96/cut

pair\_style lubricate pair\_style lubricateU pair\_style meam pair\_style mgpt pair\_style mie/cut pair\_style momb pair\_style morse pair\_style multi/lucy pair\_style multi/lucy/rx pair\_style nb3b/harmonic pair\_style nm/cut pair\_style none pair\_style oxdna/excv pair\_style oxdna2/excv pair\_style peri/pmb pair\_style polymorphic pair\_style quip pair\_style reax pair\_style reax/c pair\_style resquared pair\_style smd/hertz pair\_style smd/tlsph pair\_style smd/tri\_surface pair\_style smd/ulsph pair\_style smtbq pair\_style snap pair\_style soft pair\_style sph/heatconduction pair\_style sph/idealgas pair\_style sph/lj pair\_style sph/rhosum pair\_style sph/taitwater pair\_style sph/taitwater/morris pair\_style srp pair\_style sw pair\_style table pair\_style table/rx pair\_style tersoff pair\_style tersoff/mod pair\_style tersoff/zbl pair\_style thole pair\_style tri/lj pair\_style vashishta pair\_style yukawa pair\_style yukawa/colloid pair\_style zbl pair\_style zero pair\_write partition prd print processors python

Q

quit

R

read\_data read\_dump read\_restart region replicate

rerun reset\_timestep restart run run\_style

S

set shell

special\_bonds suffix

T

tad temper temper/grem thermo

thermo\_modify thermo\_style timer timestep

U

uncompute undump

unfix units

V

variable

velocity

W

write\_coeff write\_data

write\_dump write\_restart