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Merge pull request #202 from akohlmey/doc-formatting-fixes

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collected documentation updates and corrections from LAMMPS-ICMS
This commit is contained in:
sjplimp
2016-10-06 15:49:44 -06:00
committed by GitHub
parent 54fc194e5b 0b5d71537a
commit e9fed80928
73 changed files with 230 additions and 227 deletions
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22
doc/src/Section_example.txt
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@ -54,30 +54,30 @@ accelerate: run with various acceleration options (OpenMP, GPU, Phi)
balance: dynamic load balancing, 2d system
body: body particles, 2d system
colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
comb: models using the COMB potential
coreshell: core/shell model using CORESHELL package
crack: crack propagation in a 2d solid
crack: crack propagation in a 2d solid
deposit: deposit atoms and molecules on a surface
dipole: point dipolar particles, 2d system
dreiding: methanol via Dreiding FF
eim: NaCl using the EIM potential
ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel
flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
hugoniostat: Hugoniostat shock dynamics
indent: spherical indenter into a 2d solid
indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
msst: MSST shock dynamics
min: energy minimization of 2d LJ melt
msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamic model of cylinder impacted by indenter
peri: Peridynamic model of cylinder impacted by indenter
pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: using embedded Python in a LAMMPS input script

2
doc/src/Section_history.txt
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@ -37,7 +37,7 @@ pitfalls or alternatives.
Please see some of the closed issues for examples of how to
suggest code enhancements, submit proposed changes, or report
elated issues and how they are resoved.
possible bugs and how they are resoved.
As an alternative to using GitHub, you may e-mail the
"core developers"_http://lammps.sandia.gov/authors.html or send

46
doc/src/Section_howto.txt
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@ -68,7 +68,7 @@ Look at the {in.chain} input script provided in the {bench} directory
of the LAMMPS distribution to see the original script that these 2
scripts are based on. If that script had the line
restart 50 tmp.restart :pre
restart 50 tmp.restart :pre
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
@ -76,17 +76,17 @@ and tmp.restart.100) as it ran.
This script could be used to read the 1st restart file and re-run the
last 50 timesteps:
read_restart tmp.restart.50 :pre
read_restart tmp.restart.50 :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
timestep 0.012 :pre
timestep 0.012 :pre
run 50 :pre
run 50 :pre
Note that the following commands do not need to be repeated because
their settings are included in the restart file: {units, atom_style,
@ -107,25 +107,25 @@ lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
Then, this script could be used to re-run the last 50 steps:
units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
units lj
atom_style bond
pair_style lj/cut 1.12
pair_modify shift yes
bond_style fene
special_bonds 0.0 1.0 1.0 :pre
read_data tmp.restart.data :pre
read_data tmp.restart.data :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
neighbor 0.4 bin
neigh_modify every 1 delay 1 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297 :pre
timestep 0.012 :pre
timestep 0.012 :pre
reset_timestep 50
run 50 :pre
reset_timestep 50
run 50 :pre
Note that nearly all the settings specified in the original {in.chain}
script must be repeated, except the {pair_coeff} and {bond_coeff}
@ -2092,11 +2092,11 @@ lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 39.948
mass 1 39.948
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep $\{dt\}
thermo $d :pre
thermo $d :pre
# equilibration and thermalization :pre

34
doc/src/Section_python.txt
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@ -552,32 +552,32 @@ lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre
xlo = lmp.extract_global(name,type) # extract a global quantity
# name = "boxxlo", "nlocal", etc
# type = 0 = int
# 1 = double :pre
# type = 0 = int
# 1 = double :pre
coords = lmp.extract_atom(name,type) # extract a per-atom quantity
# name = "x", "type", etc
# type = 0 = vector of ints
# 1 = array of ints
# 2 = vector of doubles
# 3 = array of doubles :pre
# type = 0 = vector of ints
# 1 = array of ints
# 2 = vector of doubles
# 3 = array of doubles :pre
eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
# id = ID of compute or fix
# style = 0 = global data
# 1 = per-atom data
# 2 = local data
# type = 0 = scalar
# 1 = vector
# 2 = array
# i,j = indices of value in global vector or array :pre
# style = 0 = global data
# 1 = per-atom data
# 2 = local data
# type = 0 = scalar
# 1 = vector
# 2 = array
# i,j = indices of value in global vector or array :pre
var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
# name = name of variable
# group = group ID (ignored for equal-style variables)
# flag = 0 = equal-style variable
# 1 = atom-style variable :pre
# name = name of variable
# group = group ID (ignored for equal-style variables)
# flag = 0 = equal-style variable
# 1 = atom-style variable :pre
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
natoms = lmp.get_natoms() # total # of atoms as int

2
doc/src/atom_style.txt
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@ -14,7 +14,7 @@ atom_style style args :pre
style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
{dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \
{molecular} or {peri} or {smd} or {sphere} or {tri} or \
{molecular} or {peri} or {smd} or {sphere} or {tri} or \
{template} or {hybrid} :ulb,l
args = none for any style except the following
{body} args = bstyle bstyle-args

2
doc/src/comm_modify.txt
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@ -135,7 +135,7 @@ and angular momentum of a particle. If the {vel} option is set to
{yes}, then ghost atoms store these quantities; if {no} then they do
not. The {yes} setting is needed by some pair styles which require
the velocity state of both the I and J particles to compute a pairwise
I,J interaction.
I,J interaction, as well as by some compute and fix commands.
Note that if the "fix deform"_fix_deform.html command is being used
with its "remap v" option enabled, then the velocities for ghost atoms

4
doc/src/compute_heat_flux.txt
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@ -152,11 +152,11 @@ lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 39.948
mass 1 39.948
pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep $\{dt\}
thermo $d :pre
thermo $d :pre
# equilibration and thermalization :pre

8
doc/src/compute_pe_atom.txt
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@ -52,7 +52,7 @@ The KSpace contribution is calculated using the method in
"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
as specified by the "kspace_style pppm"_kspace_style.html command.
For PPPM, the calcluation requires 1 extra FFT each timestep that
per-atom energy is calculated. Thie "document"_PDF/kspace.pdf
per-atom energy is calculated. This "document"_PDF/kspace.pdf
describes how the long-range per-atom energy calculation is performed.
Various fixes can contribute to the per-atom potential energy of the
@ -68,9 +68,9 @@ As an example of per-atom potential energy compared to total potential
energy, these lines in an input script should yield the same result
in the last 2 columns of thermo output:
compute peratom all pe/atom
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe :pre
compute peratom all pe/atom
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe :pre
NOTE: The per-atom energy does not any Lennard-Jones tail corrections
invoked by the "pair_modify tail yes"_pair_modify.html command, since

22
doc/src/compute_property_atom.txt
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@ -16,20 +16,20 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
property/atom = style name of this compute command :l
input = one or more atom attributes :l
possible attributes = id, mol, proc, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
vfrac, s0,
spin, eradius, ervel, erforce,
spin, eradius, ervel, erforce,
rho, drho, e, de, cv,
i_name, d_name :pre
id = atom ID

14
doc/src/compute_property_local.txt
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@ -15,12 +15,12 @@ compute ID group-ID property/local attribute1 attribute2 ... keyword args ... :p
ID, group-ID are documented in "compute"_compute.html command :ulb,l
property/local = style name of this compute command :l
one or more attributes may be appended :l
possible attributes = natom1 natom2 ntype1 ntype2
patom1 patom2 ptype1 ptype2
batom1 batom2 btype
aatom1 aatom2 aatom3 atype
datom1 datom2 datom3 dtype
iatom1 iatom2 iatom3 itype :pre
possible attributes = natom1 natom2 ntype1 ntype2
patom1 patom2 ptype1 ptype2
batom1 batom2 btype
aatom1 aatom2 aatom3 atype
datom1 datom2 datom3 dtype
iatom1 iatom2 iatom3 itype :pre
natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
@ -129,8 +129,6 @@ The attributes that start with "a", "d", "i", refer to similar values
for "angles"_angle_style.html, "dihedrals"_dihedral_style.html, and
"impropers"_improper_style.html.
The optional {cutoff} keyword
[Output info:]
This compute calculates a local vector or local array depending on the

4
doc/src/compute_reduce.txt
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@ -155,8 +155,8 @@ Thus, for example, if you wish to use this compute to find the bond
with maximum stretch, you can do it as follows:
compute 1 all property/local batom1 batom2
compute 2 all bond/local dist
compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
compute 2 all bond/local dist
compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre
The first two input values in the compute reduce command are vectors

8
doc/src/compute_rigid_local.txt
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@ -17,11 +17,11 @@ rigid/local = style name of this compute command :l
rigidID = ID of fix rigid/small command or one of its variants :l
input = one or more rigid body attributes :l
possible attributes = id, mol, mass,
x, y, z, xu, yu, zu, ix, iy, iz
vx, vy, vz, fx, fy, fz,
x, y, z, xu, yu, zu, ix, iy, iz
vx, vy, vz, fx, fy, fz,
omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk,
tqx, tqy, tqz,
inertiax, inertiay, inertiaz
id = atom ID of atom within body which owns body properties

8
doc/src/compute_stress_atom.txt
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@ -128,10 +128,10 @@ d = dimension and V is the volume of the system, the result should be
These lines in an input script for a 3d system should yield that
result. I.e. the last 2 columns of thermo output will be the same:
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
thermo_style custom step temp etotal press v_press :pre
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
thermo_style custom step temp etotal press v_press :pre
[Output info:]

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doc/src/compute_temp_asphere.txt Executable file → Normal file
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doc/src/compute_temp_sphere.txt Executable file → Normal file
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8
doc/src/create_atoms.txt
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@ -218,14 +218,14 @@ larger version.
variable x equal 100
variable y equal 25
lattice hex 0.8442
region box block 0 $x 0 $y -0.5 0.5
create_box 1 box :pre
lattice hex 0.8442
region box block 0 $x 0 $y -0.5 0.5
create_box 1 box :pre
variable xx equal 0.0
variable yy equal 0.0
variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
create_atoms 1 box var v set x xx set y yy :pre
create_atoms 1 box var v set x xx set y yy :pre
:c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)

10
doc/src/dump.txt
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@ -55,13 +55,13 @@ args = list of arguments for a particular style :l
{custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
possible attributes = id, mol, proc, procp1, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
angmomx, angmomy, angmomz, tqx, tqy, tqz,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
id = atom ID
mol = molecule ID

12
doc/src/dump_custom_vtk.txt
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@ -20,14 +20,14 @@ file = name of file to write dump info to :l
args = list of arguments for a particular style :l
{custom/vtk} args = list of atom attributes
possible attributes = id, mol, proc, procp1, type, element, mass,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
x, y, z, xs, ys, zs, xu, yu, zu,
xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
angmomx, angmomy, angmomz, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
id = atom ID
mol = molecule ID

20
doc/src/dump_modify.txt
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@ -215,17 +215,17 @@ to the dump file. The {every} keyword cannot be used with the dump
For example, the following commands will
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
variable s equal logfreq(10,3,10)
dump 1 all atom 100 tmp.dump
dump_modify 1 every v_s first yes :pre
variable s equal logfreq(10,3,10)
dump 1 all atom 100 tmp.dump
dump_modify 1 every v_s first yes :pre
The following commands would write snapshots at the timesteps listed
in file tmp.times:
variable f file tmp.times
variable s equal next(f)
dump 1 all atom 100 tmp.dump
dump_modify 1 every v_s :pre
variable s equal next(f)
dump 1 all atom 100 tmp.dump
dump_modify 1 every v_s :pre
NOTE: When using a file-style variable with the {every} keyword, the
file of timesteps must list a first timestep that is beyond the
@ -686,10 +686,10 @@ this is used.
variable colors string &
"red green blue yellow white &
purple pink orange lime gray"
variable mol atom mol%10
dump 1 all image 250 image.*.jpg v_mol type &
zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
variable mol atom mol%10
dump 1 all image 250 image.*.jpg v_mol type &
zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
In this case, 10 colors are defined, and molecule IDs are
mapped to one of the colors, even if there are 1000s of molecules.

2
doc/src/fix_ave_correlate.txt
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@ -58,7 +58,7 @@ keyword = {type} or {ave} or {start} or {prefactor} or {file} or {overwrite} or
fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
type upper ave running title1 "My correlation data" :pre
type upper ave running title1 "My correlation data" :pre
fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\]
[Description:]

2
doc/src/fix_ave_correlate_long.txt
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@ -55,7 +55,7 @@ keyword = {type} or {start} or {file} or {overwrite} or {title1} or {title2} or
fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
fix 1 all ave/correlate/long 1 10000 &
c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
type upper title1 "My correlation data" nlen 15 ncount 3 :pre
type upper title1 "My correlation data" nlen 15 ncount 3 :pre
[Description:]

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doc/src/fix_bond_break.txt Executable file → Normal file
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doc/src/fix_deform.txt
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@ -28,7 +28,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
factor = multiplicative factor for change in box length at end of run
{vel} value = V
V = change box length at this velocity (distance/time units),
effectively an engineering strain rate
effectively an engineering strain rate
{erate} value = R
R = engineering strain rate (1/time units)
{trate} value = R
@ -36,10 +36,10 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
{volume} value = none = adjust this dim to preserve volume of system
{wiggle} values = A Tp
A = amplitude of oscillation (distance units)
Tp = period of oscillation (time units)
Tp = period of oscillation (time units)
{variable} values = v_name1 v_name2
v_name1 = variable with name1 for box length change as function of time
v_name2 = variable with name2 for change rate as function of time
v_name2 = variable with name2 for change rate as function of time
{xy}, {xz}, {yz} args = style value
style = {final} or {delta} or {vel} or {erate} or {trate} or {wiggle}
{final} value = tilt
@ -48,17 +48,17 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
dtilt = change in tilt factor at end of run (distance units)
{vel} value = V
V = change tilt factor at this velocity (distance/time units),
effectively an engineering shear strain rate
effectively an engineering shear strain rate
{erate} value = R
R = engineering shear strain rate (1/time units)
{trate} value = R
R = true shear strain rate (1/time units)
{wiggle} values = A Tp
A = amplitude of oscillation (distance units)
Tp = period of oscillation (time units)
Tp = period of oscillation (time units)
{variable} values = v_name1 v_name2
v_name1 = variable with name1 for tilt change as function of time
v_name2 = variable with name2 for change rate as function of time :pre
v_name2 = variable with name2 for change rate as function of time :pre
zero or more keyword/value pairs may be appended :l
keyword = {remap} or {flip} or {units} :l

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doc/src/fix_msst.txt
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@ -120,7 +120,7 @@ The global vector contains four values in this order:
To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested:
fix msst all msst z
fix msst all msst z
fix_modify msst energy yes
variable dhug equal f_msst\[1\]
variable dray equal f_msst\[2\]

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doc/src/fix_nvt_asphere.txt Executable file → Normal file
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0
doc/src/fix_nvt_body.txt Executable file → Normal file
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0
doc/src/fix_nvt_sphere.txt Executable file → Normal file
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16
doc/src/fix_qbmsst.txt
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@ -167,14 +167,14 @@ headers, the following LAMMPS commands are suggested. Here the
the thermo keyword {etotal} to print the quantity <i>etot</i>. See
also the "thermo_style"_thermo_style.html command.
fix fix_id all msst z
fix_modify fix_id energy yes
variable dhug equal f_fix_id\[1\]
variable dray equal f_fix_id\[2\]
variable lgr_vel equal f_fix_id\[3\]
variable lgr_pos equal f_fix_id\[4\]
variable T_qm equal f_fix_id\[5\]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre
fix fix_id all msst z
fix_modify fix_id energy yes
variable dhug equal f_fix_id\[1\]
variable dray equal f_fix_id\[2\]
variable lgr_vel equal f_fix_id\[3\]
variable lgr_pos equal f_fix_id\[4\]
variable T_qm equal f_fix_id\[5\]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre
The global scalar under the entry f_fix_id is the quantity of thermo
energy as an extra part of <i>etot</i>. This global scalar and the

2
doc/src/fix_rx.txt
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@ -75,7 +75,7 @@ but no more than max_steps will be taken. If max_steps is reached, an error warn
is printed and the simulation is stopped.
After each ODE step, the solution error {e} is tested and weighted using the absTol
and relTol values. The error vector is weighted as {e} / (relTol * | {u} | + absTol)
and relTol values. The error vector is weighted as {e} / (relTol * |{u}| + absTol)
where {u} is the solution vector. If the norm of the error is <= 1, the solution is
accepted, {h} is increased by a proportional amount, and the next ODE step is begun.
Otherwise, {h} is shrunk and the ODE step is repeated.

2
doc/src/fix_shake.txt
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@ -172,7 +172,7 @@ more instructions on how to use the accelerated styles effectively.
The velocity constraints lead to a linear system of equations which
can be solved analytically. The implementation of the algorithm in
LAMMPS closely follows ("Andersen (1983)"_#Andersen).
NOTE: The fix rattle command modifies forces and velocities and thus
should be defined after all other integration fixes in your input
script. If you define other fixes that modify velocities or forces

4
doc/src/fix_store_state.txt
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@ -17,8 +17,8 @@ store/state = style name of this fix command :l
N = store atom attributes every N steps, N = 0 for initial store only :l
input = one or more atom attributes :l
possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,

0
doc/src/fix_ti_spring.txt Executable file → Normal file
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2
doc/src/group.txt
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@ -253,7 +253,7 @@ group mobile dynamic all region ss
fix 1 mobile nve
run $\{nsteps\}
group mobile static
run $\{nsteps\} :pre
run $\{nsteps\} :pre
NOTE: All fixes and computes take a group ID as an argument, but they
do not all allow for use of a dynamic group. If you get an error

18
doc/src/if.txt
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@ -109,19 +109,19 @@ Here is an example of a double loop which uses the if and
"jump"_jump.html commands to break out of the inner loop when a
condition is met, then continues iterating thru the outer loop.
label loopa
label loopa
variable a loop 5
label loopb
label loopb
variable b loop 5
print "A,B = $a,$b"
print "A,B = $a,$b"
run 10000
if "$b > 2" then "jump SELF break"
next b
jump in.script loopb
label break
if "$b > 2" then "jump SELF break"
next b
jump in.script loopb
label break
variable b delete
next a
jump SELF loopa :pre
next a
jump SELF loopa :pre
:line

18
doc/src/jump.txt
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@ -103,19 +103,19 @@ Here is an example of a double loop which uses the if and
"jump"_jump.html commands to break out of the inner loop when a
condition is met, then continues iterating thru the outer loop.
label loopa
label loopa
variable a loop 5
label loopb
label loopb
variable b loop 5
print "A,B = $a,$b"
print "A,B = $a,$b"
run 10000
if "$b > 2" then "jump SELF break"
next b
jump in.script loopb
label break
if "$b > 2" then "jump SELF break"
next b
jump in.script loopb
label break
variable b delete
next a
jump SELF loopa :pre
next a
jump SELF loopa :pre
[Restrictions:]

0
doc/src/min_style.txt Executable file → Normal file
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18
doc/src/next.txt
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@ -116,19 +116,19 @@ Here is an example of a double loop which uses the "if"_if.html and
"jump"_jump.html commands to break out of the inner loop when a
condition is met, then continues iterating thru the outer loop.
label loopa
label loopa
variable a loop 5
label loopb
label loopb
variable b loop 5
print "A,B = $a,$b"
print "A,B = $a,$b"
run 10000
if $b > 2 then "jump in.script break"
next b
jump in.script loopb
label break
if $b > 2 then "jump in.script break"
next b
jump in.script loopb
label break
variable b delete :pre
next a
jump in.script loopa :pre
next a
jump in.script loopa :pre
[Restrictions:]

0
doc/src/pair_dipole.txt Executable file → Normal file
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0
doc/src/pair_gayberne.txt Executable file → Normal file
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2
doc/src/pair_hybrid.txt
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@ -170,7 +170,7 @@ so that there is effectively no interaction (e.g. epsilon = 0.0 in a
LJ potential). Or, for {hybrid} and {hybrid/overlay} simulations, you
can use this form of the pair_coeff command in your input script:
pair_coeff 2 3 none :pre
pair_coeff 2 3 none :pre
or this form in the "Pair Coeffs" section of the data file:

6
doc/src/pair_meam.txt
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@ -188,9 +188,9 @@ lattce(I,J) = lattice structure of I-J reference structure:
bcc = body centered cubic
dim = dimer
b1 = rock salt (NaCl structure)
hcp = hexagonal close-packed
c11 = MoSi2 structure
l12 = Cu3Au structure (lower case L, followed by 12)
hcp = hexagonal close-packed
c11 = MoSi2 structure
l12 = Cu3Au structure (lower case L, followed by 12)
b2 = CsCl structure (interpenetrating simple cubic)
nn2(I,J) = turn on second-nearest neighbor MEAM formulation for
I-J pair (see for example "(Lee)"_#Lee).

14
doc/src/pair_reax_c.txt
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@ -41,7 +41,9 @@ supplemental information of the following paper: "(Chenoweth et al.,
2008)"_#Chenoweth_2008. The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010. For more
technical details about the pair reax/c implementation of ReaxFF, see
the "(Aktulga)"_#Aktulga paper.
the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially
implemented as a stand-alone C code and is now integrated into LAMMPS
as a package.
The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is
derived from the {reax/c} style. The Kokkos version can run on GPUs and
@ -163,11 +165,11 @@ To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
compute reax all pair reax/c
variable eb equal c_reax\[1\]
variable ea equal c_reax\[2\]
variable eb equal c_reax\[1\]
variable ea equal c_reax\[2\]
\[...\]
variable eqeq equal c_reax\[14\]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
variable eqeq equal c_reax\[14\]
thermo_style custom step temp epair v_eb v_ea \[...\] v_eqeq :pre
Only a single pair_coeff command is used with the {reax/c} style which
specifies a ReaxFF potential file with parameters for all needed
@ -237,7 +239,7 @@ nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
regarding the bonded interactions. (default value = 5.0)
hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
bond interactions.(default value = 7.5. Value of 0.0 turns off
bond interactions.(default value = 7.5. A value of 0.0 turns off
hydrogen bonds)
bond_graph_cutoff: is the threshold used in determining what is a

0
doc/src/pair_resquared.txt Executable file → Normal file
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4
doc/src/pair_smtbq.txt Executable file → Normal file
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@ -158,7 +158,7 @@ Divided line :ul
3) Potential parameters:
Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2. If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
Potential parameter: <pre><br/> If type of potential is 'second_moment' : {A (eV)}, {p}, {&#958<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (&#197), {r<sub>c2</sub>} (&#197) and {r<sub>0</sub>} (&#197) <br/> If type of potential is 'buck' : {C} (eV) and {&#961} (&#197) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {&#961} (&#197) <br/> {D} (eV), {B} (&#197<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (&#197) and {r<sub>2</sub><sup>OO</sup>} (&#197) </pre>
Potential parameter: <pre><br/> If type of potential is 'second_moment' : {A (eV)}, {p}, {&#958<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (&#197), {r<sub>c2</sub>} (&#197) and {r<sub>0</sub>} (&#197) <br/> If type of potential is 'buck' : {C} (eV) and {&#961} (&#197) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {&#961} (&#197) <br/> {D} (eV), {B} (&#197<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (&#197) and {r<sub>2</sub><sup>OO</sup>} (&#197) </pre>
Divided line :ul
4) Tables parameters:
@ -185,7 +185,7 @@ Divided line :ul
8) Mode for the electronegativity equalization (Qeq) :
Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
Keyword mode: <pre> <br/> QEqAll (one QEq group) | no parameters <br/> QEqAllParallel (several QEq groups) | no parameters <br/> Surface | zlim (QEq only for z>zlim) </pre>
Parameter if necessary
Divided line :ul

18
doc/src/pair_snap.txt
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@ -96,15 +96,15 @@ tantalum potential provided in the LAMMPS potentials directory
combines the {snap} and {zbl} pair styles. It is invoked
by the following commands:
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
pair_style hybrid/overlay &
zbl $\{zblcutinner\} $\{zblcutouter\} snap
pair_coeff * * zbl 0.0
pair_coeff 1 1 zbl $\{zblz\}
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
../potentials/Ta06A.snapparam Ta :pre
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
pair_style hybrid/overlay &
zbl $\{zblcutinner\} $\{zblcutouter\} snap
pair_coeff * * zbl 0.0
pair_coeff 1 1 zbl $\{zblz\}
pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
../potentials/Ta06A.snapparam Ta :pre
It is convenient to keep these commands in a separate file that can
be inserted in any LAMMPS input script using the "include"_include.html

5
doc/src/replicate.txt
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@ -74,11 +74,14 @@ larger version of your molecule as a pre-processing step and input a
new data file to LAMMPS.
If the current simulation was read in from a restart file (before a
run is performed), there can have been no fix information stored in
run is performed), there must not be any fix information stored in
the file for individual atoms. Similarly, no fixes can be defined at
the time the replicate command is used that require vectors of atom
information to be stored. This is because the replicate command does
not know how to replicate that information for new atoms it creates.
To work around this restriction, restart files may be converted into
data files and fixes may be undefined via the "unfix"_unfix.html
command before and redefined after the replicate command.
[Related commands:] none

4
doc/src/restart.txt
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@ -113,8 +113,8 @@ For example, the following commands will write restart files
every step from 1100 to 1200, and could be useful for debugging
a simulation where something goes wrong at step 1163:
variable s equal stride(1100,1200,1)
restart v_s tmp.restart :pre
variable s equal stride(1100,1200,1)
restart v_s tmp.restart :pre
:line

8
doc/src/run.txt
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@ -66,11 +66,11 @@ keywords.
For example, consider this fix followed by 10 run commands:
fix 1 all nvt 200.0 300.0 1.0
run 1000 start 0 stop 10000
run 1000 start 0 stop 10000
fix 1 all nvt 200.0 300.0 1.0
run 1000 start 0 stop 10000
run 1000 start 0 stop 10000
...
run 1000 start 0 stop 10000 :pre
run 1000 start 0 stop 10000 :pre
The NVT fix ramps the target temperature from 200.0 to 300.0 during a
run. If the run commands did not have the start/stop keywords (just

16
doc/src/run_style.txt
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@ -20,7 +20,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
n1, n2, ... = loop factor between rRESPA levels (N-1 values)
zero or more keyword/value pairings may be appended to the loop factors
keyword = {bond} or {angle} or {dihedral} or {improper} or
{pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
{pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
{bond} value = M
M = which level (1-N) to compute bond forces in
{angle} value = M
@ -33,14 +33,14 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
M = which level (1-N) to compute pair forces in
{inner} values = M cut1 cut2
M = which level (1-N) to compute pair inner forces in
cut1 = inner cutoff between pair inner and
pair middle or outer (distance units)
cut2 = outer cutoff between pair inner and
pair middle or outer (distance units)
cut1 = inner cutoff between pair inner and
pair middle or outer (distance units)
cut2 = outer cutoff between pair inner and
pair middle or outer (distance units)
{middle} values = M cut1 cut2
M = which level (1-N) to compute pair middle forces in
cut1 = inner cutoff between pair middle and pair outer (distance units)
cut2 = outer cutoff between pair middle and pair outer (distance units)
cut1 = inner cutoff between pair middle and pair outer (distance units)
cut2 = outer cutoff between pair middle and pair outer (distance units)
{outer} value = M
M = which level (1-N) to compute pair outer forces in
{hybrid} values = M1 M2 ... (as many values as there are hybrid sub-styles
@ -230,7 +230,7 @@ rRESPA:
fix 2 all shake 0.000001 500 0 m 1.0 a 1
timestep 4.0
run_style respa 2 2 inner 1 4.0 5.0 outer 2 :pre
run_style respa 2 2 inner 1 4.0 5.0 outer 2 :pre
With these settings, users can expect good energy conservation and
roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a

12
doc/src/set.txt
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@ -17,13 +17,13 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l
one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{charge} or {dipole} or {dipole/random} or {quat} or \
{quat/random} or {diameter} or {shape} or \
{length} or {tri} or {theta} or {theta/random} or \
{quat/random} or {diameter} or {shape} or \
{length} or {tri} or {theta} or {theta/random} or \
{angmom} or {omega} or \
{mass} or {density} or {volume} or {image} or \
{bond} or {angle} or {dihedral} or {improper} or \
{meso/e} or {meso/cv} or {meso/rho} or \
{smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
{mass} or {density} or {volume} or {image} or \
{bond} or {angle} or {dihedral} or {improper} or \
{meso/e} or {meso/cv} or {meso/rho} or \
{smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
{i_name} or {d_name} :l
{type} value = atom type
value can be an atom-style variable (see below)

4
doc/src/thermo.txt
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@ -45,8 +45,8 @@ options for "equal-style variables"_variable.html.
For example, the following commands will output thermodynamic info at
timesteps 0,10,20,30,100,200,300,1000,2000,etc:
variable s equal logfreq(10,3,10)
thermo v_s :pre
variable s equal logfreq(10,3,10)
thermo v_s :pre
[Restrictions:] none

10
doc/src/thermo_style.txt
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@ -23,12 +23,12 @@ args = list of arguments for a particular style :l
evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
emol, elong, etail,
vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
xy, xz, yz, xlat, ylat, zlat,
xy, xz, yz, xlat, ylat, zlat,
bonds, angles, dihedrals, impropers,
pxx, pyy, pzz, pxy, pxz, pyz,
fmax, fnorm, nbuild, ndanger,
cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
c_ID, c_ID\[I\], c_ID\[I\]\[J\],
pxx, pyy, pzz, pxy, pxz, pyz,
fmax, fnorm, nbuild, ndanger,
cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
c_ID, c_ID\[I\], c_ID\[I\]\[J\],
f_ID, f_ID\[I\], f_ID\[I\]\[J\],
v_name, v_name\[I\]
step = timestep

30
doc/src/variable.txt
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@ -52,18 +52,18 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
stride(x,y,z), stride2(x,y,z,a,b,c),
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
stride(x,y,z), stride2(x,y,z,a,b,c),
vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
group functions = count(group), mass(group), charge(group),
xcm(group,dim), vcm(group,dim), fcm(group,dim),
bound(group,dir), gyration(group), ke(group),
angmom(group,dim), torque(group,dim),
xcm(group,dim), vcm(group,dim), fcm(group,dim),
bound(group,dir), gyration(group), ke(group),
angmom(group,dim), torque(group,dim),
inertia(group,dimdim), omega(group,dim)
region functions = count(group,region), mass(group,region), charge(group,region),
xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region)
xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
atom value = id\[i\], mass\[i\], type\[i\], mol\[i\], x\[i\], y\[i\], z\[i\], vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\], q\[i\]
@ -219,13 +219,13 @@ script or when the input script is looped over. This can be useful
when breaking out of a loop via the "if"_if.html and "jump"_jump.html
commands before the variable would become exhausted. For example,
label loop
label loop
variable a loop 5
print "A = $a"
if "$a > 2" then "jump in.script break"
next a
jump in.script loop
label break
print "A = $a"
if "$a > 2" then "jump in.script break"
next a
jump in.script loop
label break
variable a delete :pre
:line