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12
doc/Manual.txt
View File

@ -35,10 +35,6 @@ 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"_Section_commands.html#comm at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://www.easysw.com/htmldoc
@ -74,10 +70,7 @@ it gives quick access to documentation for all LAMMPS commands.
4.8 "TIP4P water model"_4_8 :b
4.9 "SPC water model"_4_9 :b
4.10 "Coupling LAMMPS to other codes"_4_10 :b
4.11 "Visualizing LAMMPS snapshots"_4_11 :b
4.12 "Non-orthogonal simulation boxes"_4_12 :b
4.13 "NEMD simulations"_4_13 :b
4.14 "Aspherical particles"_4_14 :ule,b
4.11 "Visualizing LAMMPS snapshots"_4_11 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
@ -123,9 +116,6 @@ it gives quick access to documentation for all LAMMPS commands.
:link(4_9,Section_howto.html#4_9)
:link(4_10,Section_howto.html#4_10)
:link(4_11,Section_howto.html#4_11)
:link(4_12,Section_howto.html#4_12)
:link(4_13,Section_howto.html#4_13)
:link(4_14,Section_howto.html#4_14)
:link(9_1,Section_errors.html#9_1)
:link(9_2,Section_errors.html#9_2)

1
doc/Section_commands.txt
View File

@ -459,7 +459,6 @@ full description:
"none"_pair_none.html,
"hybrid"_pair_hybrid.html,
"airebo"_pair_airebo.html,
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
"buck/coul/long"_pair_buck.html,

144
doc/Section_howto.txt
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@ -21,10 +21,7 @@ certain kinds of LAMMPS simulations.
4.8 "TIP4P water model"_#4_8
4.9 "SPC water model"_#4_9
4.10 "Coupling LAMMPS to other codes"_#4_10
4.11 "Visualizing LAMMPS snapshots"_#4_11
4.12 "Non-orthogonal simulation boxes"_#4_12
4.13 "NEMD simulations"_#4_13
4.14 "Aspherical particles"_#4_14 :all(b)
4.11 "Visualizing LAMMPS snapshots"_#4_11 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -645,145 +642,6 @@ See the "dump"_dump.html command for more information on XTC files.
:line
4.12 Non-orthogonal simulation boxes :link(4_12),h4
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The "boundary"_boundary.html command sets the boundary
conditions of the box (periodic, non-periodic, etc). If the box size
is xprd by yprd by zprd then the 3 mutually orthogonal edge vectors of
an orthogonal simulation box are a = (xprd,0,0), b = (0,yprd,0), and c
= (0,0,zprd).
LAMMPS also allows non-orthogonal simulation boxes (triclinic
symmetry) to be defined with 3 additional "tilt" parameters which
change the edge vectors of the simulation box to be a = (xprd,0,0), b
= (xy,yprd,0), and c = (xz,yz,zprd). The xy, xz, and yz parameters
can be positive or negative. The simulation box must be periodic in
both dimensions associated with a tilt factor. For example, if xz !=
0.0, then the x and z dimensions must be periodic.
To avoid extremely tilted boxes (which would be computationally
inefficient), no tilt factor can skew the box more than half the
distance of the parallel box length, which is the 1st dimension in the
tilt factor (x for xz). For example, if xlo = 2 and xhi = 12, then
the x box length is 10 and the xy tilt factor must be between -5 and
5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and
+(yhi-ylo)/2. Note that this is not a limitation, since if the
maximum tilt factor is 5 (as in this example), then configurations
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
You tell LAMMPS to use a non-orthogonal box when the simulation box is
defined. This happens in one of 3 ways. If the
"create_box"_create_box.html command is used with a region of style
{prism}, then a non-orthogonal domain is setup. See the
"region"_region.html command for details. If the
"read_data"_read_data.html command is used to define the simulation
box, and the header of the data file contains a line with the "xy xz
yz" keyword, then a non-orthogonal domain is setup. See the
"read_data"_read_data.html command for details. Finally, if the
"read_restart"_read_restart.html command reads a restart file which
was written from a simulation using a triclinic box, then a
non-orthogonal box will be enabled for the restarted simulation.
Note that you can define a non-orthogonal box with all 3 tilt factors
= 0.0, so that it is initially orthogonal. This is necessary if the
box will ever become non-orthogonal.
One use of non-orthogonal boxes is to model solid-state crystals with
triclinic symmetry. The "lattice"_lattice.html command can be used
with non-orthogonal basis vectors to define a lattice that will tile a
non-orthogonal simulation box via the "create_atoms"_create_atoms.html
command. Note that while the box edge vectors a,b,c cannot be
arbitrary vectors (e.g. a must be aligned with the x axis), it is
possible to rotate any crystal's basis vectors so that they meet these
restrictions.
A second use of non-orthogonal boxes is to shear a bulk solid to study
the response of the material. The "fix deform"_fix_deform.html
command can be used for this purpose. It allows dynamic control of
the xy, xz, and yz tilt factors as a simulation runs.
Another use of non-orthogonal boxes is to perform non-equilibrium MD
(NEMD) simulations, as discussed in the next section.
:line
4.13 NEMD simulations :link(4_13),h4
Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceeding Howto section).
A shear strain can be applied to the simualation box at a desired
strain rate by using the "fix deform"_fix_deform.html command. The
"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses "compute
temp/deform"_compute_temp_deform.html to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/spatial"_fix_ave_spatial.html command.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computation efficiency to be 1/2 of the paralell box
length. However, "fix deform"_fix_deform.html can be used to
continuously strain a box by an arbitrary amount. As discussed in the
"fix deform"_fix_deform.html command, when the tilt reaches a limit,
the box is re-shaped to the opposite limit which is an equivalent
tiling of the periodic plane. The strain rate can then continue to
change as before. In a long NEMD simulation these box re-shaping may
occur any number of times.
In a NEMD simulation, the "remap" option of "fix
deform"_fix_deform.html should be set to "remap v", since that is what
"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
profile consistent with the applied shear strain rate.
:line
4.14 Aspherical particles :link(4_14),h4
LAMMPS supports ellipsoidal particles via the "atom_style
ellipsoid"_atom_style.html and "shape"_shape.html commands. The
latter defines the 3 axes (diamaters) of a general ellipsoid. The
"pair_style gayberne"_pair_gayberne.html command can be used to define
a Gay-Berne (GB) potential for how such particles interact with each
other and with spherical particles. The GB potential is like a
Lennard-Jones (LJ) potential generalized for ellipsoids interacting in
an orientiation-dependent manner.
The orientation of ellipsoidal particles is stored as a quaternion.
See the "set"_set.html command for a brief explanation of quaternions
and how the orientation of such particles can be initialized. The
data file read by the "read_data"_read_data.html command also contains
quaternions for each atom in the Atoms section if "atom_style
ellipsoid"_atom_style.html is being used. The "compute
temp/asphere"_compute_temp_asphere.html command can be used to
calculate the temperature of a group of ellipsoidal particles, taking
account of rotational degrees of freedom. The motion of the particles
can be integrated via the "fix nve/asphere"_fix_nve_asphere.html, "fix
nvt/asphere"_fix_nvt_asphere.html, or "fix
npt/asphere"_fix_npt_asphere.html commands. All of these commands are
part of the ASPHERE package in LAMMPS.
Computationally, the cost for two ellipsoidal particles to interact is
30x or more expensive than for 2 LJ particles. Thus if you are
modeling a system with many spherical particles (e.g. as the solvent),
then you should insure sphere-sphere interactions are computed with
the a cheaper potential than GB. This can be done by setting the
particle's 3 shape parameters to all be equal (a sphere).
Additionally, the corresponding GB potential coefficients can be set
so the GB potential will treat the pair of particles as LJ spheres.
Details are given in the doc page for the "pair_style
gayberne"_pair_gayberne.html. Alternatively, the "pair_style
hybrid"_pair_hybrid.html potential can be used, with the sphere-sphere
interactions computed by another pair potential, such as "pair_style
lj/cut"_pair_lj.html.
:line
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).

2
doc/Section_intro.txt
View File

@ -129,7 +129,7 @@ commands)
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, class 2 (COMPASS)
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used in one simlulation
potentials can be used
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
long-range Coulombics: Ewald, PPPM (similar to particle-mesh Ewald)

6
doc/angle_charmm.txt
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@ -43,11 +43,7 @@ r_ub (distance) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

12
doc/angle_class2.txt
View File

@ -29,8 +29,8 @@ the equilibrium bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
For this style, coefficients for the Ea formula can be specified in
the input script or data file. These are the 4 coefficients:
For this style, only coefficients for the Ea formula can be specified
in the input script. These are the 4 coefficients:
theta0 (degrees)
K2 (energy/radian^2)
@ -40,7 +40,7 @@ K4 (energy/radian^2) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
Coefficients for the Ebb and Eba formulas can only be specified in the
Coefficients for the Ebb and Eba formulas must be specified in the
data file.
For the Ebb formula, the coefficients are listed under a "BondBond
@ -63,9 +63,9 @@ same value from the Ea formula.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"class2" package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info on packages.
This angle style is part of the "class2" package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

6
doc/angle_cosine.txt
View File

@ -32,11 +32,7 @@ or "read_restart"_read_restart.html commands:
K (energy) :ul
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/angle_cosine_squared.txt
View File

@ -37,11 +37,7 @@ theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

4
doc/angle_harmonic.txt
View File

@ -39,10 +39,6 @@ internally; hence the units of K are in energy/radian^2.
[Restrictions:] none
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Related commands:]
"angle_coeff"_angle_coeff.html

6
doc/angle_hybrid.txt
View File

@ -49,11 +49,7 @@ An angle style of {none} can be specified as an argument to
angle_style hybrid and the corresponding angle_coeff commands, if you
desire to turn off certain angle types.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

27
doc/angle_style.txt
View File

@ -35,22 +35,14 @@ potentials can be setup using the {hybrid} angle style.
The coefficients associated with a angle style can be specified in a
data or restart file or via the "angle_coeff"_angle_coeff.html command.
All angle potentials store their coefficient data in binary restart
files which means angle_style and "angle_coeff"_angle_coeff.html
commands do not need to be re-specified in an input script that
restarts a simulation. See the "read_restart"_read_restart.html
command for details on how to do this. The one exception is that
angle_style {hybrid} only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified.
IMPORTANT NOTE: When both an angle and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 3 bonded atoms.
In the formulas listed for each angle style, {theta} is the angle
between the 3 atoms in the angle.
Note that when both an angle and pair style is defined, the
"special_bond"_special_bond.html command often needs to be used to
turn off (or weight) the pairwise interactions that would otherwise
exist between the 3 bonded atoms.
:line
Here is an alphabetic list of angle styles defined in LAMMPS. Click on
@ -73,11 +65,10 @@ specified by the associated "angle_coeff"_angle_coeff.html command:
Angle styles can only be set for atom_styles that allow angles to be
defined.
Most angle styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages. The
doc pages for individual bond potentials tell if it is part of a
package.
Angle styles are part of the "molecular" package or other packages as
noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

6
doc/bond_class2.txt
View File

@ -39,9 +39,9 @@ K4 (energy/distance^2) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the "class2"
package. See the "Making LAMMPS"_Section_start.html#2_3 section for
more info on packages.
This bond style is part of the "class2" package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

6
doc/bond_fene.txt
View File

@ -39,11 +39,7 @@ R0 (distance)
epsilon (energy)
sigma (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/bond_fene_expand.txt
View File

@ -44,11 +44,7 @@ epsilon (energy)
sigma (distance)
delta (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/bond_harmonic.txt
View File

@ -34,11 +34,7 @@ or "read_restart"_read_restart.html commands:
K (energy/distance^2)
r0 (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/bond_hybrid.txt
View File

@ -42,11 +42,7 @@ A bond style of {none} can be specified as an argument to bond_style
hybrid and the corresponding bond_coeff commands, if you desire to
turn off certain bond types.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/bond_morse.txt
View File

@ -35,11 +35,7 @@ D (energy)
alpha (inverse distance)
r0 (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/bond_nonlinear.txt
View File

@ -35,11 +35,7 @@ epsilon (energy)
r0 (distance)
lamda (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

4
doc/bond_quartic.txt
View File

@ -72,10 +72,6 @@ delete_bonds all bond 0 remove :pre
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with {quartic} bonds.

29
doc/bond_style.txt
View File

@ -33,9 +33,9 @@ remain in force for the duration of the simulation (unless the bond
breaks which is possible in some bond potentials). The list of bonded
atoms is read in by a "read_data"_read_data.html or
"read_restart"_read_restart.html command from a data or restart file.
By contrast, pair potentials are typically defined between all pairs
of atoms within a cutoff distance and the set of active interactions
changes over time.
By contrast, pair potentials are defined between pairs of atoms that
are within a cutoff distance and the set of active interactions
typically changes over time.
Hybrid models where bonds are computed using different bond potentials
can be setup using the {hybrid} bond style.
@ -43,22 +43,14 @@ can be setup using the {hybrid} bond style.
The coefficients associated with a bond style can be specified in a
data or restart file or via the "bond_coeff"_bond_coeff.html command.
All bond potentials store their coefficient data in binary restart
files which means bond_style and "bond_coeff"_bond_coeff.html commands
do not need to be re-specified in an input script that restarts a
simulation. See the "read_restart"_read_restart.html command for
details on how to do this. The one exception is that bond_style
{hybrid} only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.
In the formulas listed for each bond style, {r} is the distance
between the 2 atoms in the bond.
IMPORTANT NOTE: When both a bond and pair style is defined, the
Note that when both a bond and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 2 bonded atoms.
In the formulas listed for each bond style, {r} is the distance
between the 2 atoms in the bond.
:line
Here is an alphabetic list of bond styles defined in LAMMPS. Click on
@ -83,11 +75,10 @@ specified by the associated "bond_coeff"_bond_coeff.html command:
Bond styles can only be set for atom styles that allow bonds to be
defined.
Most bond styles are part of the "molecular" package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages. The
doc pages for individual bond potentials tell if it is part of a
package.
Bond styles are part of the "molecular" package or other packages as
noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

6
doc/dihedral_charmm.txt
View File

@ -62,11 +62,7 @@ weighting factors (4th coeff above) should be set to 0.0. In this
case, you can use any pair style you wish, since the dihedral does not
need any 1-4 information.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

14
doc/dihedral_class2.txt
View File

@ -32,8 +32,8 @@ bond lengths.
See "(Sun)"_#Sun for a description of the COMPASS class2 force field.
For this style, coefficients for the Ed formula can be specified in
either the input script or data file. These are the 6 coefficients:
For this style, only coefficients for the Ed formula can be specified
in the input script. These are the 6 coefficients:
K1 (energy)
phi1 (degrees)
@ -42,8 +42,8 @@ phi2 (degrees)
K3 (energy)
phi3 (degrees) :ul
Coefficients for all the other formulas can only be specified in the
data file.
Coefficients for all the other formulas must be specified in the data
file.
For the Embt formula, the coefficients are listed under a
"MiddleBondTorsion Coeffs" heading and each line lists 4 coefficients:
@ -100,9 +100,9 @@ r3 (distance) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
"class2" package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info on packages.
This dihedral style is part of the "class2" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

6
doc/dihedral_harmonic.txt
View File

@ -32,11 +32,7 @@ K (energy)
d (+1 or -1)
n (integer >= 0) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/dihedral_helix.txt
View File

@ -40,11 +40,7 @@ A (energy)
B (energy)
C (energy) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/dihedral_hybrid.txt
View File

@ -51,11 +51,7 @@ A dihedral style of {none} can be specified as an argument to
dihedral_style hybrid and the corresponding dihedral_coeff commands,
if you desire to turn off certain dihedral types.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/dihedral_multi_harmonic.txt
View File

@ -34,11 +34,7 @@ A3 (energy)
A4 (energy)
A5 (energy) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/dihedral_opls.txt
View File

@ -38,11 +38,7 @@ K2 (energy)
K3 (energy)
K4 (energy) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

33
doc/dihedral_style.txt
View File

@ -32,27 +32,17 @@ from a data or restart file.
Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the {hybrid} dihedral style.
The coefficients associated with a dihedral style can be specified in
a data or restart file or via the "dihedral_coeff"_dihedral_coeff.html
command.
All dihedral potentials store their coefficient data in binary restart
files which means dihedral_style and
"dihedral_coeff"_dihedral_coeff.html commands do not need to be
re-specified in an input script that restarts a simulation. See the
"read_restart"_read_restart.html command for details on how to do
this. The one exception is that dihedral_style {hybrid} only stores
the list of sub-styles in the restart file; dihedral coefficients need
to be re-specified.
IMPORTANT NOTE: When both a dihedral and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.
The coefficients associated with a dihedral style can be specified in a
data or restart file or via the "dihedral_coeff"_dihedral_coeff.html command.
In the formulas listed for each dihedral style, {phi} is the torsional
angle defined by the quadruplet of atoms.
Note that when both a dihedral and pair style is defined, the
"special_bond"_special_bond.html command often needs to be used to
turn off (or weight) the pairwise interactions that would otherwise
exist between the 4 bonded atoms.
Here are some important points to take note of when defining the
LAMMPS dihedral coefficients in the formulas that follow so that they
are compatible with other force fields:
@ -91,11 +81,10 @@ specified by the associated "dihedral_coeff"_dihedral_coeff.html command:
Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
Most dihedral styles are part of the "molecular" package. They are
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages. The
doc pages for individual dihedral potentials tell if it is part of a
package.
Dihedral styles are part of the "molecular" package or other packages
as noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

4
doc/dump.txt
View File

@ -291,11 +291,11 @@ documentation.
The {bond} style is part of the "molecular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#2_2 section for more info.
The {xtc} style is part of the "xtc" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. This is because
LAMMPS"_Section_start.html#2_2 section for more info. This is because
some machines may not support the lo-level XDR data format that XTC
files are written with, which will result in a compile-time error when
a lo-level include file is not found. Putting this style in a package

32
doc/fix.txt
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@ -35,7 +35,8 @@ defined in LAMMPS and new ones can be added - see "this
section"_Section_modify.html for a discussion.
Each fix style has its own documentation page which describes its
arguments and what it does, as listed below.
arguments and what it does. For example, see the "fix
setforce"_fix_setforce.html page for information on style {setforce}.
Fixes perform their operations at different stages of the timestep.
If 2 or more fixes both operate at the same stage of the timestep,
@ -44,10 +45,10 @@ they are invoked in the order they were specified in the input script.
Fixes can be deleted with the "unfix"_unfix.html command. Note that
this is the only way to turn off a fix; simply specifying a new fix
with a similar style will not turn off the first one. For example,
using a "fix nve"_fix_nve.html command for a second run after using a
"fix nvt"_fix_nvt.html command for the first run, will not cancel out
the NVT time integration invoked by the "fix nvt" command. Thus two
time integrators would be in place!
using a "fix nve" command for a second run after using a "fix nvt"
command for the first run, will not cancel out the NVT time
integration invoked by the "fix nvt" command. Thus two time
integrators would be in place!
If you specify a new fix with the same ID and style as an existing
fix, the old fix is deleted and the new one is created (presumably
@ -57,18 +58,7 @@ same order relative to the existing fixes as the old one originally
was. Note that this operation also wipes out any additional changes
made to the old fix via the "fix_modify"_fix_modify.html command.
The "fix modify"_fix_modify.html command allows settings for some
fixes to be reset. See the doc page for individual fixes for details.
Some fixes store an internal "state" which is written to binary
restart files via the "restart"_restart.html or
"write_restart"_write_restart.html commands. This allows the fix to
continue on with its calculations in a restarted simulation. See the
"read_restart"_read_restart.html command for info on how to re-specify
a fix in an input script that reads a restart file. See the doc pages
for individual fixes for info on which ones can be restarted.
Here is an alphabetic list of fix styles available in LAMMPS:
Here is an alphabetic list of fix styles defined in LAMMPS:
"fix addforce"_fix_addforce.html - add a force to each atom
"fix aveforce"_fix_aveforce.html - add an averaged force to each atom
@ -134,8 +124,12 @@ Here is an alphabetic list of fix styles available in LAMMPS:
Some fix styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages. The
doc pages for individual fixes tell if it is part of a package.
LAMMPS"_Section_start.html#2_2 section for more info.
The {freeze}, {gran/diag}, {gravity}, {nve/gran}, {pour}, and
{wall/gran} styles are part of the "granular" package.
The {poems} style is part of the "poems" package.
[Related commands:]

25
doc/fix_deform.txt
View File

@ -50,7 +50,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
zero or more keyword/value pairs may be appended to the args :l
keyword = {remap} or {units} :l
{remap} value = {x} or {v} or {none}
x = remap coords of atoms in group into deforming box
x = remap coords of atoms in group into deforming box (affine deformation)
v = remap velocities of all atoms when they cross periodic boundaries
none = no remapping of x or v
{units} value = {lattice} or {box}
@ -313,13 +313,18 @@ remapped into the new box in the appropriate manner.
Each time the box size or shape is changed, the {remap} keyword
determines whether atom positions are re-mapped to the new box. If
{remap} is set to {x} (the default), atoms in the fix group are
re-mapped; otherwise they are not. If {remap} is set to {v}, then any
atom in the fix group that crosses a periodic boundary will have a
delta added to its velocity equal to the difference in velocities
between the lo and hi boundaries. Note that this velocity difference
can include tilt components, e.g. a delta in the x velocity when an
atom crosses the y periodic boundary. If {remap} is set to {none},
then neither of these remappings take place.
re-mapped; otherwise they are not. If all atoms are remapped, this is
effectively an "affine" deformation.
If {remap} is set to {v}, then any atom in the fix group that crosses
a periodic boundary will have a delta added to its velocity equal to
the difference in velocities between the lo and hi boundaries. Note
that this velocity difference can include tilt components, e.g. a
delta in the x velocity when an atom crosses the y periodic boundary.
If {remap} is set to {none}, then neither of these remappings take
place. Note that unlike remap x which changes atom coords
continuously as the box deforms, this remapping of v is done ONLY when
an atom crosses a periodic boundary.
IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are
performed using this fix, the option "remap v" should normally be
@ -347,9 +352,7 @@ defined in terms of distance/time.
Any box dimension varied by this fix must be periodic.
[Related commands:]
"displace_box"_displace_box.html
[Related commands:] none
[Default:]

29
doc/fix_modify.txt
View File

@ -27,34 +27,33 @@ fix_modify 1 energy yes :pre
[Description:]
Modify one or more parameters of a previously defined fix. Only
specific fix styles support specific parameters. See the doc pages
for individual fix commands for info on which ones support which
fix_modify parameters.
Modify one or more parameters of a previously defined fix. Not all
fix styles support all parameters.
The {temp} keyword is used to determine how a fix computes
temperature. The specified compute ID must have been previously
defined by the user via the "compute"_compute.html command and it must
be a style of compute that calculates a temperature. All fixes that
compute temperatures define their own compute by default, as described
in their documentation. Thus this option allows the user to override
the default method for computing T.
compute temperatures defined their own compute by default, as
described in their documentation. Thus this option allows the user to
override the default method for computing T.
The {press} keyword is used to determine how a fix computes pressure.
The specified compute ID must have been previously defined by the user
via the "compute"_compute.html command and it must be a style of
compute that calculates a pressure. All fixes that compute pressures
define their own compute by default, as described in their
defined their own compute by default, as described in their
documentation. Thus this option allows the user to override the
default method for computing P.
For fixes that calculate a contribution to the potential energy of the
system, the {energy} keyword will include that contribution in
thermodyanmic output of potential energy. See the
"thermo_style"_thermo_style.html command for info on how to output
potential energy is printed. The contribution itself can also be
printed by using the keyword f_ID in the thermo_style custom command,
where ID is the fix-ID of the appropriate fix.
For fixes that calculates a contribution to the potential energy of
the system, the {energy} keyword will include that contribution in
thermodyanmic output of the potential energy, as invoked by the
"thermo_style"_thermo_style.html command. The value of the
contribution can also be printed by itself using the "thermo_style
custom"_thermo_style.html keywords. The documentation for individual
fix commands specifies whether they make a contribution to the
potential energy.
[Restrictions:] none

14
doc/improper_class2.txt
View File

@ -36,8 +36,8 @@ The following coefficients must be defined for each improper type via the
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
For this style, coefficients for the Ei formula can be specified in
eiher the input script or data file. These are the 2 coefficients:
For this style, only coefficients for the Ei formula can be specified
in the input script. These are the 2 coefficients:
K (energy/radian^2)
X0 (degrees) :ul
@ -45,8 +45,8 @@ X0 (degrees) :ul
X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
Coefficients for the Eaa formula can only be specified in the data
file. For the Eaa formula, the coefficients are listed under a
Coefficients for the Eaa formula must be specified in the data file.
For the Eaa formula, the coefficients are listed under a
"AngleAngle Coeffs" heading and each line lists 6 coefficients:
M1 (energy/distance)
@ -61,9 +61,9 @@ radians internally; hence the units of M are in energy/radian^2.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
"class2" package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info on packages.
This improper style is part of the "class2" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

6
doc/improper_cvff.txt
View File

@ -34,11 +34,7 @@ K (energy)
d (+1 or -1)
n (0,1,2,3,4,6) :ul
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/improper_harmonic.txt
View File

@ -37,11 +37,7 @@ X0 (degrees) :ul
X0 is specified in degrees, but LAMMPS converts it to radians
internally; hence the units of K are in energy/radian^2.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

6
doc/improper_hybrid.txt
View File

@ -50,11 +50,7 @@ An improper style of {none} can be specified as an argument to
improper_style hybrid and the corresponding improper_coeff commands,
if you desire to turn off certain improper types.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
"molecular" package (which it is by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages.
[Restrictions:] none
[Related commands:]

31
doc/improper_style.txt
View File

@ -31,23 +31,13 @@ from a data or restart file.
Hybrid models where impropers are computed using different improper
potentials can be setup using the {hybrid} improper style.
The coefficients associated with an improper style can be specified in
a data or restart file or via the "improper_coeff"_improper_coeff.html
command.
The coefficients associated with an improper style can be specified in a
data or restart file or via the "improper_coeff"_improper_coeff.html command.
All improper potentials store their coefficient data in binary restart
files which means improper_style and
"improper_coeff"_improper_coeff.html commands do not need to be
re-specified in an input script that restarts a simulation. See the
"read_restart"_read_restart.html command for details on how to do
this. The one exception is that improper_style {hybrid} only stores
the list of sub-styles in the restart file; improper coefficients need
to be re-specified.
IMPORTANT NOTE: When both an improper and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 4 bonded atoms.
Note that when both an improper and pair style is defined, the
"special_bond"_special_bond.html command often needs to be used to
turn off (or weight) the pairwise interactions that would otherwise
exist between the 4 bonded atoms.
:line
@ -69,11 +59,10 @@ specified by the associated "improper_coeff"_improper_coeff.html command:
Improper styles can only be set for atom_style choices that allow
impropers to be defined.
Most improper styles are part of the "molecular" package. They are
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages. The
doc pages for individual improper potentials tell if it is part of a
package.
Improper styles are part of the "molecular" package or other packages
as noted in their documentation. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

2
doc/kspace_style.txt
View File

@ -73,7 +73,7 @@ must be periodic and the z dimension must be non-periodic.
Kspace styles are part of the "kspace" package. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#2_2 section for more info.
When using a long-range pairwise TIP4P potential, you must use kspace
style {pppm/tip4p} and vice versa.

43
doc/pair_buck.txt
View File

@ -80,41 +80,20 @@ Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
None of the Buckingham pair styles support mixing. Thus, coefficients
for all I,J pairs must be specified explicitly.
All of the Buckingham pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
exp() and 1/r^6 portion of the pair interaction.
The {buck/coul/long} pair style does not support the
"pair_modify"_pair_modify.html table option since a tabulation
capability has not yet been added to this potential.
None of the Buckingham pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail
corrections to energy and pressure.
All of the Buckinham pair styles can calculate per-atom energy and
stress, as used by the "compute epair/atom"_compute_epair_atom.html,
"compute stress/atom"_compute_stress_atom.html, and "dump
custom"_dump.html commands.
All of the Buckinham pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
[Restrictions:]
The {buck} potentials do not support the
"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
pairs must be specified explicitly.
The {buck/coul/long} style is part of the "kspace" package. It is
only enabled if LAMMPS was built with that package (which it is by
default). See the "Making LAMMPS"_Section_start.html#2_3 section for
more info.
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
On some 64-bit machines, compiling with -O3 appears to break the
Coulombic tabling option used by the {buck/coul/long} style. See
the "Additional build tips" section of the Making LAMMPS documentation
pages for workarounds on this issue.
[Related commands:]

45
doc/pair_charmm.txt
View File

@ -88,7 +88,7 @@ The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
commands:
epsilon (energy units)
sigma (distance units)
@ -106,40 +106,11 @@ because this CHARMM force field does not allow varying cutoffs for
individual atom pairs; all pairs use the global cutoff(s) specified in
the pair_style command.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
and sigma_14 coefficients for all of the lj/charmm pair styles can be
mixed. They are always mixed with the value {arithmetic}. See the
"pair_modify" command for details.
None of the lj/charmm pair styles support the
"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
portion of the pair interaction is smoothed to 0.0 at the cutoff.
The {lj/charmm/coul/long} and {lj/charmm/coul/long/opt} pair styles
support the "pair_modify"_pair_modify.html table option since they can
tabulate the short-range portion of the long-range Coulombic
interaction.
None of the lj/charmm pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail
corrections to energy and pressure, since the Lennard-Jones portion of
the pair interaction is smoothed to 0.0 at the cutoff.
All of the lj/charmm pair styles can calculate per-atom energy and
stress, as used by the "compute epair/atom"_compute_epair_atom.html,
"compute stress/atom"_compute_stress_atom.html, and "dump
custom"_dump.html commands.
All of the lj/charmm pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
:line
If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all CHARMM potentials is to use the {arithmetic} formulas documented
by the "pair_modify"_pair_modify.html command. The "pair_modify
mix"_pair_modify.html setting is thus ignored for CHARMM potentials.
[Restrictions:]
@ -148,8 +119,8 @@ styles are part of the "molecule" package. The {lj/charmm/coul/long}
style is part of the "kspace" package. The {lj/charmm/coul/long/opt}
style is part of the "opt" package and also requires the "kspace"
package. They are only enabled if LAMMPS was built with those
package(s) (molecule and kspace are by default). See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
package(s). See the "Making LAMMPS"_Section_start.html#2_3 section
for more info.
On some 64-bit machines, compiling with -O3 appears to break the
Coulombic tabling option used by the {lj/charmm/coul/long} style. See

47
doc/pair_class2.txt
View File

@ -60,7 +60,7 @@ The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
commands:
epsilon (energy units)
sigma (distance units)
@ -80,8 +80,6 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
: line
If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all class2 potentials is to use the {sixthpower} formulas documented
@ -90,43 +88,16 @@ mix"_pair_modify.html setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/class2 pair styles can be mixed.
Epsilon and sigma are always mixed with the value {sixthpower}. The
cutoff distance is mixed by whatever option is set by the pair_modify
command (default = geometric). See the "pair_modify" command for
details.
All of the lj/class2 pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The {lj/class2/coul/long} pair style does not support the
"pair_modify"_pair_modify.html table option since a tabulation
capability has not yet been added to this potential.
All of the lj/class2 pair styles support the
"pair_modify"_pair_modify.html tail option for adding a long-range
tail correction to the energy and pressure of the Lennard-Jones
portion of the pair interaction.
All of the lj/class2 pair styles can calculate per-atom energy and
stress, as used by the "compute epair/atom"_compute_epair_atom.html,
"compute stress/atom"_compute_stress_atom.html, and "dump
custom"_dump.html commands.
All of the lj/class2 pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
[Restrictions:]
All of these pair styles are part of the "class2" package. They are
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
These styles are part of the "class2" package. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
On some 64-bit machines, compiling with -O3 appears to break the
Coulombic tabling option used by the {lj/class2/coul/long} style. See
the "Additional build tips" section of the Making LAMMPS documentation
pages for workarounds on this issue.
[Related commands:]

17
doc/pair_coeff.txt
View File

@ -37,7 +37,7 @@ can be used for each, as in the 1st example above. I <= J is
required. LAMMPS sets the coefficients for the symmetric J,I
interaction to the same values.
A wild-card asterik can be used in place of or in conjunction with the
A wild-card asterik can be used in place of in conjunction with the
I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
number of atom types, then an asterik with no numeric values means all
@ -70,9 +70,8 @@ as
For many potentials, if coefficients for type pairs with I != J are
not set explicity by a pair_coeff command, the values are inferred
from the I,I and J,J settings by mixing rules; see the
"pair_modify"_pair_modify.html command for a discussion. Details on
this option as it pertains to individual potentials are described on
the doc page for the potential.
"pair_modify"_pair_modify.html command for a discussion. Exceptions
to the mixing rules are discussed with the individual pair styles.
:line
@ -81,15 +80,20 @@ the style to display the formula it computes, arguments specified in
the pair_style command, and coefficients specified by the associated
"pair_coeff"_pair_coeff.html command:
"pair_style airebo"_pair_airebo.html - AI-REBO potential
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
"pair_style colloid"_pair_colloid.html - integrated colloidal potential
"pair_style dipole/cut"_pair_dpd.html - point dipole potential
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/opt"_pair_eam.html - optimized embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM
"pair_style eam/alloy/opt"_pair_eam.html - optimized alloy EAM
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style eam/fs/opt"_pair_eam.html - optimized Finnis-Sinclair EAM
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_gran.html - granular potential with history effects
@ -97,10 +101,12 @@ the pair_style command, and coefficients specified by the associated
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized CHARMM with long-range Coulomb
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/opt"_pair_lj.html - optimized cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
@ -109,6 +115,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
"pair_style morse"_pair_morse.html - Morse potential
"pair_style morse/opt"_pair_morse.html - optimized Morse potential
"pair_style soft"_pair_soft.html - Soft (cosine) potential
"pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential
"pair_style table"_pair_table.html - tabulated pair potential

42
doc/pair_colloid.txt
View File

@ -59,7 +59,7 @@ The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
commands:
A (energy units)
sigma (distance units)
@ -107,42 +107,16 @@ rule-of-thumb is to use a colloid-solvent cutoff that is half the big
diamter + 4 times the small diamter. I.e. 9 = 5 + 4 for the
colloid-solvent cutoff in this case.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
{geometric}. See the "pair_modify" command for details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style can calculate per-atom energy and stress, as used by
the "compute epair/atom"_compute_epair_atom.html, "compute
stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
commands.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
:line
If a pair_coeff command is not specified for I != J, then the
coefficients are mixed according the mixing rules defined by the
"pair_modify"_pair_modify.html command. The prefactor A is mixed like
the Lennard-Jones epsilon; sigma,d1,d2 are all mixed like the
Lennard-Jones sigma.
[Restrictions:]
This style is part of the "colloid" package. It is only enabled if
LAMMPS was built with that package. See the "Making
The {colloid} style is part of the "colloid" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]

44
doc/pair_dipole.txt
View File

@ -59,7 +59,7 @@ The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
commands:
epsilon (energy units)
sigma (distance units)
@ -73,46 +73,12 @@ and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distances for this pair style can be mixed. The default
mix value is {geometric}. See the "pair_modify" command for details.
For atom type pairs I,J and I != J, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
{geometric}. See the "pair_modify" command for details.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the Lennard-Jones portion of the pair
interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style can calculate per-atom energy and stress, as used by
the "compute epair/atom"_compute_epair_atom.html, "compute
stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
commands.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
[Restrictions:]
This style is part of the "dipole" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
Can only be used if LAMMPS was built with the "dipole" package.
The use of this potential requires additional fixes as described
above.
[Related commands:]

47
doc/pair_dpd.txt
View File

@ -53,48 +53,15 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
where T is the temperature set by the "pair_style"_pair_style.html
command so it does not need to be specified.
:line
[Restrictions:] none
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
This style is part of the "dpd" package. It is only enabled if LAMMPS
was built with those package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
Thsi pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style can calculate per-atom energy and stress, as used by
the "compute epair/atom"_compute_epair_atom.html, "compute
stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
commands. However, only the first term with the A coefficienct
(conservative force) is used for these computations. The drag force
and random force terms are not.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file. Note
that the user-specifice random number seed is stored in the restart
file, so when a simulation is restarted, each processor will
re-initialize its random number generator the same way it did
intially. This means the random forces will be random, but will not
be the same as they would have been if the original simulation had
continued past the restart time.
:line
[Restrictions:]
This style is part of the "dpd" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
The {dpd} potential does not support the
"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
pairs must be specified explicitly.
The default frequency for rebuilding neighbor lists is every 10 steps
(see the "neigh_modify"_neigh_modify.html command). This may be too

41
doc/pair_eam.txt
View File

@ -314,46 +314,11 @@ are listed.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
For atom type pairs I,J and I != J, mixing is performed by LAMMPS as
described above with the individual styles. You never need to specify
a pair_coeff command with I != J arguments for the eam styles.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html shift option is not relevant
for this pair style.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
The "pair_modify"_pair_modify.html tail option is not relevant
for this pair style.
All of the eam pair styles can calculate per-atom energy and stress,
as used by the "compute epair/atom"_compute_epair_atom.html, "compute
stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
commands. These quantities include the contribution from the
embedding term in the EAM formulas.
None of the eam pair styles write their information to "binary restart
files"_restart.html, since the info is tabulated in potential files.
Thus, you need to re-specify the pair style and coefficient commands
in an input script that reads a restart file.
:line
[Restrictions:]
All of these styles except those ending in {opt} are part of the
"manybody" package. They are only enabled if LAMMPS was built with
that package (which it is by default). The styles ending in {opt} are
part of the "opt" package and also require the "manybody" package.
They are only enabled if LAMMPS was built with those packages. See
the "Making LAMMPS"_Section_start.html#2_3 section for more info.
The {opt} styles are part of the "opt" package. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]

52
doc/pair_gayberne.txt
View File

@ -79,6 +79,10 @@ cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
The epsilon and sigma parameters are mixed for I != J atom pairings
the same as Lennard-Jones parameters; see the "pair_modify
mix"_pair_modify.html documentation for details.
The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.
@ -112,49 +116,17 @@ than the full Gay-Berne formula. Thus you should insure epsilon a,b,c
are set to 1.0 for spherical particle types and use epsilon and sigma
to specify its interaction with other spherical particles.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
value is {geometric}. See the "pair_modify" command for details.
This pair styles supports the "pair_modify"_pair_modify.html shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style does not calculate per-atom energy and stress, as used
by the "compute epair/atom"_compute_epair_atom.html, "compute
stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
commands.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
:line
[Restrictions:]
This style is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
Can only be used if LAMMPS was built with the "asphere" package.
The Gay-Berne potential does not become isotropic as r increases
"(Everaers)"_#Everaers. The distance-of-closest-approach
approximation used by LAMMPS becomes less accurate when high-aspect
ratio ellipsoids are used.
The "shift yes" option in "pair_modify"_pair_modify.html only applies
to sphere-sphere interactions for this potential; there is no shifting
performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction. The Gay-Berne potential does not
become isotropic as r increases "(Everaers)"_#Everaers. The
distance-of-closest-approach approximation used by LAMMPS becomes less
accurate when high-aspect ratio ellipsoids are used.
[Related commands:]

2
doc/pair_gran.txt
View File

@ -67,7 +67,7 @@ See the citation for more discussion of the granular potentials.
All of these styles are part of the "granular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
LAMMPS"_Section_start.html#2_2 section for more info.
You must use "atom style"_atom_style.html {granular} with these pair
styles.

48
doc/pair_lj.txt
View File

@ -131,7 +131,7 @@ The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
commands:
epsilon (energy units)
sigma (distance units)
@ -155,49 +155,13 @@ can be specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
:line
[Mixing, shift, table, tail correction, per-atom energy/stress, and
restart info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
All of the lj/cut pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} pair styles
support the "pair_modify"_pair_modify.html table option since they can
tabulate the short-range portion of the long-range Coulombic
interaction.
All of the lj/cut pair styles support the
"pair_modify"_pair_modify.html tail option for adding a long-range
tail correction to the energy and pressure of the Lennard-Jones
portion of the pair interaction.
All of the lj/cut pair styles can calculate per-atom energy and
stress, as used by the "compute epair/atom"_compute_epair_atom.html,
"compute stress/atom"_compute_stress_atom.html, and "dump
custom"_dump.html commands.
All of the lj/cut pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
:line
[Restrictions:]
The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of
the "kspace" package. They are only enabled if LAMMPS was built with
that package (which it is by default). The {lj/cut/opt} style is part
of the "opt" package. It is only enabled if LAMMPS was built with
that package. See the "Making LAMMPS"_Section_start.html#2_3 section
for more info.
The {lj/cut/coul/long} style is part of the "kspace" package. It is
only enabled if LAMMPS was built with that package. The {lj/cut/opt}
style is part of the "opt" package. It is only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
On some 64-bit machines, compiling with -O3 appears to break the
Coulombic tabling option used by the {lj/cut/coul/long} style. See

103
doc/pair_modify.txt
View File

@ -14,8 +14,8 @@ pair_modify keyword value ... :pre
one or more keyword/value pairs may be listed :ulb,l
keyword = {shift} or {mix} or {table} or {tabinner} or {tail} :l
{mix} value = {geometric} or {arithmetic} or {sixthpower}
{shift} value = {yes} or {no}
{mix} value = {geometric} or {arithmetic} or {sixthpower}
{table} value = N
2^N = # of values in table
{tabinner} value = cutoff
@ -34,56 +34,51 @@ pair_modify table 12 :pre
Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
The {mix} keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
explicity set in the input script. Note that coefficients for I = J
must be set explicitly, either in the input script via the
"pair_coeff" command or in the "Pair Coeffs" section of the "data
file"_read_data.html. For some pair styles is is not necessary to
specify coefficients when I != J, since a "mixing" rule will create
them from the I,I and J,J settings. The pair_modify {mix} value
determines what formulas are used to compute the mixed coefficients.
In each case, the cutoff distance is mixed the same way as sigma.
The {shift} keyword determines whether the Lennard-Jones potential is
shifted at its cutoff to 0.0. If so, this adds an energy term to each
pairwise interaction which will be printed in the thermodynamic
output, but does not affect atom dynamics (forces). Pair styles that
are already 0.0 at their cutoff such as {lj/charmm/coul/charmm} are
not affected by this setting.
Note that not all pair styles support mixing. Also, some mix options
are not available for certain pair styles. See the doc page for
individual pair styles for those restrictions. Note also that the
"pair_coeff"_pair_coeff.html command also can be to directly set
coefficients for a specific I != J pairing, in which case no mixing is
performed.
The {mix} keyword affects how Lennard-Jones coefficients for epsilon,
sigma, and the cutoff are generated for interactions between atoms of
type I and J, when I != J. Coefficients for I = J are set explicitly
in the data file or input script. The "pair_coeff"_pair_coeff.html
command can be used in the input script to specify epilon/sigma for a
specific I != J pairing, which overrides the setting of the {mix}
keyword.
mix {geometric}
These are the formulas used by the 3 {mix} options. In each case, the
LJ cutoff is mixed the same way as sigma. Note that some of these
options are not available for certain pair styles. See the doc page
for individual pair styles for those restrictions.
{geometric}
epsilon_ij = sqrt(epsilon_i * epsilon_j)
sigma_ij = sqrt(sigma_i * sigma_j) :pre
mix {arithmetic}
{arithmetic}
epsilon_ij = sqrt(epsilon_i * epsilon_j)
sigma_ij = (sigma_i + sigma_j) / 2 :pre
mix {sixthpower}
{sixthpower}
epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
The {shift} keyword determines whether a Lennard-Jones potential is
shifted at its cutoff to 0.0. If so, this adds an energy term to each
pairwise interaction which will be included in the thermodynamic
output, but does not affect pair forces or atom trajectories. See the
doc page for individual pair styles to see which ones support this
option.
The {table} keyword applies to pair styles with a long-range Coulombic
term; see the doc page for individual styles to see which potentials
support this option. If N is non-zero, a table of length 2^N is
pre-computed for forces and energies, which can shrink their
computational cost by up to a factor of 2. The table is indexed via a
bit-mapping technique "(Wolff)"_#Wolff and a linear interpolation is
performed between adjacent table values. In our experiments with
different table styles (lookup, linear, spline), this method typically
gave the best performance in terms of speed and accuracy.
term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a
table of length 2^N is pre-computed for forces and energies, which can
shrink their computational cost by up to a factor of 2. The table is
indexed via a bit-mapping technique "(Wolff)"_#Wolff and a linear
interpolation is performed between adjacent table values. In our
experiments with different table styles (lookup, linear, spline), this
method typically gave the best performance in terms of speed and
accuracy.
The choice of table length is a tradeoff in accuracy versus speed. A
larger N yields more accurate force computations, but requires more
@ -105,16 +100,19 @@ nearly all pairwise interactions are computed via table lookup for
simulations with "real" units, but some close pairs may be computed
directly (non-table) for simulations with "lj" units.
When the {tail} keyword is set to {yes}, certain pair styles will add
a long-range VanderWaals tail "correction" to the energy and pressure.
See the doc page for individual styles to see which support this
option. These corrections are included in the calculation and
printing of thermodynamic quantities (see the
"thermo_style"_thermo_style.html command). Their effect will also be
included in constant NPT or NPH simulations where the pressure
influences the simulation box dimensions (e.g. the "fix
npt"_fix_npt.html and "fix nph"_fix_nph.html commands). The formulas
used for the long-range corrections come from equation 5 of
When the {tail} keyword is set to {yes}, long-range VanderWaals tail
"corrections" are added to the energy and pressure. These are
included in the calculation and printing of thermodynamic quantities
(see the "thermo_style"_thermo_style.html command). Their effect will
also be included in constant NPT or NPH simulations where the pressure
influences the simulation box dimensions (see the "fix
npt"_fix_npt.html and "fix nph"_fix_nph.html commands).
The {tail} keyword is only supported by "pair_style"_pair_style.html
pairwise potentials which include Lennard-Jones interactions which are
cutoff at a non-zero energy. This does not include the LJ CHARMM
potentials or {lj/smooth} since they go to zero at the cutoff. The
formulas used for the long-range corrections come from equation 5 of
"(Sun)"_#Sun.
Several assumptions are inherent in using tail corrections, including
@ -140,8 +138,13 @@ those interactions. :l,ule
[Restrictions:] none
Not all pair styles support mixing. See the doc page for individual
pair styles for details.
You cannot use {shift} yes with {tail} yes, since those are
conflicting options. You cannot use {tail} yes with 2d simulations.
conflicting options.
You cannot use {tail} yes with 2d simulations.
[Related commands:]
@ -150,11 +153,9 @@ conflicting options. You cannot use {tail} yes with 2d simulations.
[Default:]
The option defaults are mix = geometric, shift = no, table = 12,
tabinner = sqrt(2.0), tail = no.
Note that some pair styles perform mixing, but only a certain style of
mixing. See the doc pages for individual pair styles for details.
The option defaults are shift = no, mix = arithmetic (for lj/charmm
pair styles), mix = geometric (for other pair styles), table = 12,
and tabinner = sqrt(2.0), tail = no.
:line

48
doc/pair_style.txt
View File

@ -14,14 +14,17 @@ pair_style style args :pre
style = one of the following :ulb,l
{none}, {hybrid}, {airebo}, {buck}, {buck/coul/cut}, {buck/coul/long},
{dpd}, {eam}, {eam/alloy} or {eam/fs}, {gran/hertzian},
{gran/history}, {gran/no_history}, {lj/charmm/coul/charmm},
{lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long},
{lj/class2}, {lj/class2/coul/cut} or {lj/class2/coul/long}, {lj/cut},
{lj/cut/coul/cut} or {lj/cut/coul/debye}, {lj/cut/coul/long},
{lj/cut/coul/long/tip4p}, {lj/expand}, {lj/smooth}, {meam}, {morse},
{soft}, {sw}, {table}, {tersoff}, {yukawa} :ul
{none}, {hybrid}, {buck}, {buck/coul/cut}, {buck/coul/long},
{colloid}, {dipole/cut}, {dpd}, {eam}, {eam/opt}, {eam/alloy},
{eam/alloy/opt}, {eam/fs}, {eam/fs/opt}, {gayberne},
{gran/hertzian}, {gran/history}, {gran/no_history},
{lj/charmm/coul/charmm}, {lj/charmm/coul/charmm/opt},
{lj/charmm/coul/charmm/implicit}, {lj/charmm/coul/long},
{lj/class2}, {lj/class2/coul/cut}, {lj/class2/coul/long},
{lj/cut}, {lj/cut/opt}, {lj/cut/coul/cut},
{lj/cut/coul/debye}, {lj/cut/coul/long}, {lj/cut/coul/long/tip4p},
{lj/expand}, {lj/smooth}, {meam}, {morse}, {morse/opt}, {soft}, {sw}, {table},
{tersoff}, {yukawa} :ul
args = arguments used by a particular style :l,ule
@ -46,7 +49,7 @@ In LAMMPS, pairwise force fields encompass a variety of interactions,
some of which include many-body effects, e.g. EAM, Stillinger-Weber,
Tersoff, REBO potentials. They are still classified as "pairwise"
potentials because the set of interacting atoms changes with time
(unlike molecular bonds) and thus a neighbor list is used to find
(unlike a bonded system) and thus a neighbor list is used to find
nearby interacting atoms.
Hybrid models where specified pairs of atom types interact via
@ -56,18 +59,9 @@ The coefficients associated with a pair style are typically set for
each pair of atom types, and are specified by the
"pair_coeff"_pair_coeff.html command or read from a file by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
The "pair_modify"_pair_modify.html command sets options for mixing of
type I-J interaction coefficients and adding energy offsets or tail
corrections to Lennard-Jones potentials. Details on these options as
they pertain to individual potentials are described on the doc page
for the potential. Likewise, info on whether the potential
information is stored in a "restart file"_write_restart.html or
whether the potential supports calculation of per-atom energy and
stress by the "compute epair/atom"_compute_epair_atom.html and
"compute stress/atom"_compute_stress_atom.html commands is given on
the potential doc page.
commands. Mixing, shifting, and tail corrections for the potentials
is discussed is the documentation for the
"pair_modify"_pair_modify.html command.
In the formulas listed for each pair style, {E} is the energy of a
pairwise interaction between two atoms separated by a distance {r}.
@ -98,15 +92,18 @@ the pair_style command, and coefficients specified by the associated
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul
"pair_style airebo"_pair_airebo.html - AI-REBO potential
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
"pair_style colloid"_pair_colloid.html - integrated colloidal potential
"pair_style dipole/cut"_pair_dpd.html - point dipole potential
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/opt"_pair_eam.html - optimized embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM
"pair_style eam/alloy/opt"_pair_eam.html - optimized alloy EAM
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style eam/fs/opt"_pair_eam.html - optimized Finnis-Sinclair EAM
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions
"pair_style gran/history"_pair_gran.html - granular potential with history effects
@ -114,10 +111,12 @@ the pair_style command, and coefficients specified by the associated
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized CHARMM with long-range Coulomb
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/opt"_pair_lj.html - optimized cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
@ -126,6 +125,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
"pair_style morse"_pair_morse.html - Morse potential
"pair_style morse/opt"_pair_morse.html - optimized Morse potential
"pair_style soft"_pair_soft.html - Soft (cosine) potential
"pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential
"pair_style table"_pair_table.html - tabulated pair potential
@ -142,9 +142,7 @@ This command must be used before any coefficients are set by the
Some pair styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info on packages. The
doc pages for individual pair potentials tell if it is part of a
package.
LAMMPS"_Section_start.html#2_2 section for more info.
[Related commands:]

86
doc/read_restart.txt
View File

@ -24,9 +24,8 @@ read_restart poly.*.% :pre
[Description:]
Read in a previously saved simulation from a restart file. This
allows continuation of a previous run. Information about what is
stored in a restart file is given below.
Read in a previously saved problem from a restart file. This allows
continuation of a previous run.
Restart files are saved in binary format to enable exact restarts,
meaning that the trajectories of a restarted run will precisely match
@ -37,11 +36,11 @@ include running on a different number of processors or changing
certain settings such as those set by the "newton"_newton.html or
"processors"_processors.html commands. LAMMPS will issue a WARNING in
these cases. Certain fixes will also not restart exactly, though they
should provide statistically similar results. These include "fix
shake"_fix_shake.html and "fix langevin"_fix_langevin.html. If a
restarted run is immediately different than the run which produced the
restart file, it could be a LAMMPS bug, so consider "reporting
it"_Section_errors.html#9_2 if you think the behavior is wrong.
should provide statistically similar results. These include the shake
and langevin styles. If a restarted run is immediately different than
the run which produced the restart file, it could be a LAMMPS bug, so
consider "reporting it"_Section_errors.html#9_2 if you think the
behavior is wrong.
Because restart files are binary, they may not be portable to other
machines. They can be converted to ASCII data files using the
@ -75,39 +74,36 @@ current LAMMPS simulation.
:line
A restart file stores the following information about a simulation:
units and atom style, simulation box size and shape and boundary
settings, group definitions, atom type settings such as mass and
particle shape, individual atoms and their group assignments and
molecular topology attributes, force field styles and coefficients,
and "special_bonds"_special_bonds.html settings. This means that
commands for these quantities do not need to be re-specified in the
input script that reads the restart file, though you can redefine
settings after the restart file is read.
A restart file stores the units and atom style, simulation box
attibutes (including whether it is an orthogonal box or a
non-orthogonal parallelepiped with triclinic symmetry), individual
atoms and their attributes including molecular topology, force field
styles and coefficients, "special_bonds"_special_bonds.html settings,
and atom group definitions. This means that commands for these
quantities do not need to be specified in your input script that reads
the restart file. The exceptions to this are listed below in the
Restrictions section.
One exception is that some pair styles do not store their info in
restart files. The doc pages for individual pair styles note if this
is the case. This is also true of bond_style hybrid (and angle_style,
dihedral_style, improper_style hybrid).
Information about the "kspace_style"_kspace_style.html settings are
not stored in the restart file. Hence if you wish to invoke an Ewald
or PPPM solver, this command must be re-issued after the restart file
is read.
Information about "kspace_style"_kspace_style.html settings are not
stored in the restart file. Hence if you wish to use an Ewald or PPPM
solver, these commands must be re-issued after the restart file is
read.
The restart file also stores values for any fixes that require state
information to enable restarting where they left off. These include
the {nvt} and {npt} styles that have a global state, as well as the
{msd} and {wall/gran} styles that store information about each atom.
The list of "fixes"_fix.html used for a simulation is not stored in
the restart file. This means the new input script should specify all
fixes it will use. Note that some fixes store an internal "state"
which is written to the restart file. This allows the fix to continue
on with its calculations in a restarted simulation. To re-enable such
a fix, the fix command in the new input script must use the same
fix-ID and group-ID as was used in the input script that wrote the
restart file. If a match is found, LAMMPS prints a message indicating
that the fix is being re-enabled. If no match is found before the
first run or minimization is performed by the new script, the "state"
information for the saved fix is discarded. See the doc pages for
individual fixes for info on which ones can be restarted in this
manner.
"Fix"_fix.html commands are not stored in the restart file which means
they must be specified in the input script that reads the restart
file. To re-enable a fix whose state was stored in the restart file,
the fix command in the new input script must use the same fix-ID and
group-ID as the input script that wrote the restart file. LAMMPS will
print a message indicating that the fix is being re-enabled.
Note that no other information is stored in the restart file. This
means that your new input script should specify settings for
quantities like timestep size, thermodynamic and dump output, etc.
Bond interactions (angle, etc) that have been turned off by the "fix
shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command will
@ -119,13 +115,15 @@ Bonds that are broken (e.g. by a bond-breaking potential) are written
to the restart file as broken bonds with a type of 0. Thus these
bonds will still be broken when the restart file is read.
IMPORTANT NOTE: No other information is stored in the restart file.
This means that an input script that reads a restart file should
specify settings for quantities like "timestep size"_timestep.html,
"thermodynamic"_thermo_style.html and "dump"_dump.html output,
"geometric regions"_region.html, etc.
[Restrictions:]
[Restrictions:] none
The "pair_style"_pair_style.html {eam}, {table}, and {hybrid} styles
do not store coefficient data for individual atom type pairs in the
restart file. Nor does the "bond_style hybrid"_bond_style.html style
(angle, dihedral hybrid, etc). Thus for these styles you must use new
"pair_coeff"_pair_coeff.html and "bond_coeff"_bond_coeff.html (angle,
dihedral, etc) commands to read the appropriate tabulated files or
reset the coefficients after the restart file is read.
[Related commands:]

10
doc/thermo_modify.txt
View File

@ -41,11 +41,11 @@ Set options for how thermodynamic information is computed and printed
by LAMMPS.
IMPORTANT NOTE: These options apply to the currently defined thermo
style. When you specify a "thermo_style"_thermo_style.html command,
all thermodynamic settings are restored to their default values,
including those previously set by a thermo_modify command. Thus if
your input script specifies a thermo_style command, you should use the
thermo_modify command after it.
style (thermo_style {one} by default). When you specify a
"thermo_style"_thermo_style.html command, all thermodynamic settings
are restored to their default values. Thus a thermo_style command
will wipe out any options previously specified by the
"thermo_modify"_thermo_modify.html command.
The {lost} keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are

30
doc/thermo_style.txt
View File

@ -102,11 +102,11 @@ be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
IMPORTANT NOTE: When you specify a "thermo_style" command, all
thermodynamic settings are restored to their default values, including
those previously set by a :thermo_modify"_thermo_modify.html command.
Thus if your input script specifies a thermo_style command, you should
use the thermo_modify command after it.
IMPORTANT NOTE: When you specify a "thermo_style"_thermo_style.html
command, all thermodynamic settings are restored to their default
values. Thus a thermo_style command will wipe out any options
previously specified by the "thermo_modify"_thermo_modify.html
command.
:line
@ -198,29 +198,24 @@ The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector quantities
calculated by a compute to be output. The ID in the keyword should be
replaced by the actual ID of the compute that has been defined
elsewhere in the input script. See the "compute"_compute.html command
for details. Note that only global scalar or vector quantites
calculated by a compute can be output as thermodynamic data; per-atom
quantities calcalated by a compute are output by the "dump
custom"_dump.html command.
for details. Note that per-atom quantities calcalated by a compute
cannot be output as part of thermodynamics. Rather, these quantities
are output by the "dump custom"_dump.html command.
If {c_ID} is used as a keyword, then the scalar quantity calculated by
the compute is printed. If {c_ID\[N\]} is used, then N in the range
from 1-M will print the Nth component of the M-length vector
calculated by the compute. See the doc pages for individual compute
styles for info on what these quantities are.
calculated by the compute.
The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector quantities
calculated by a fix to be output. The ID in the keyword should be
replaced by the actual ID of the fix that has been defined elsewhere
in the input script.
in the input script. See the "fix"_fix.html command for details.
If {f_ID} is used as a keyword, then the scalar quantity calculated by
the fix is printed. If {f_ID\[N\]} is used, then N in the range from
1-M will print the Nth component of the M-length vector calculated by
the fix. See the doc pages for individual fix styles for info on what
these quantities are. For fixes that compute a contribution to the
potential energy of the system, the scalar quantity f_ID is typically
that quantity.
the fix.
The {v_name} keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd
@ -233,8 +228,7 @@ periodically during a simulation.
See "this section"_Section_modify.html for information on how to add
new compute and fix styles as well as variable options to LAMMPS that
calculate quantities that could then be output with these keywords as
part of thermodyanmic information.
calculate quantities that could then be output with these keywords.
:line