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12
doc/Manual.txt
View File

@ -35,6 +35,10 @@ 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
@ -70,7 +74,10 @@ we can improve the LAMMPS documentation.
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 :ule,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
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
@ -116,6 +123,9 @@ we can improve the LAMMPS documentation.
: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

@ -459,6 +459,7 @@ 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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@ -21,7 +21,10 @@ 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 :all(b)
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)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -642,6 +645,145 @@ 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
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@ -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
potentials can be used in one simlulation
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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@ -43,7 +43,11 @@ 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:] none
[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.
[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, only coefficients for the Ea formula can be specified
in the input script. These are the 4 coefficients:
For this style, coefficients for the Ea formula can be specified in
the input script or data file. 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 must be specified in the
Coefficients for the Ebb and Eba formulas can only 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 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.
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.
[Related commands:]

6
doc/angle_cosine.txt
View File

@ -32,7 +32,11 @@ or "read_restart"_read_restart.html commands:
K (energy) :ul
[Restrictions:] none
[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.
[Related commands:]

6
doc/angle_cosine_squared.txt
View File

@ -37,7 +37,11 @@ theta0 (degrees) :ul
Theta0 is specified in degrees, but LAMMPS converts it to radians
internally.
[Restrictions:] none
[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.
[Related commands:]

4
doc/angle_harmonic.txt
View File

@ -39,6 +39,10 @@ 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

@ -49,7 +49,11 @@ 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:] none
[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.
[Related commands:]

27
doc/angle_style.txt
View File

@ -35,14 +35,22 @@ 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
@ -65,10 +73,11 @@ 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.
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.
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.
[Related commands:]

6
doc/bond_class2.txt
View File

@ -39,9 +39,9 @@ K4 (energy/distance^2) :ul
[Restrictions:]
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.
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.
[Related commands:]

6
doc/bond_fene.txt
View File

@ -39,7 +39,11 @@ R0 (distance)
epsilon (energy)
sigma (distance) :ul
[Restrictions:] none
[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.
[Related commands:]

6
doc/bond_fene_expand.txt
View File

@ -44,7 +44,11 @@ epsilon (energy)
sigma (distance)
delta (distance) :ul
[Restrictions:] none
[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.
[Related commands:]

6
doc/bond_harmonic.txt
View File

@ -34,7 +34,11 @@ or "read_restart"_read_restart.html commands:
K (energy/distance^2)
r0 (distance) :ul
[Restrictions:] none
[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.
[Related commands:]

6
doc/bond_hybrid.txt
View File

@ -42,7 +42,11 @@ 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:] none
[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.
[Related commands:]

6
doc/bond_morse.txt
View File

@ -35,7 +35,11 @@ D (energy)
alpha (inverse distance)
r0 (distance) :ul
[Restrictions:] none
[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.
[Related commands:]

6
doc/bond_nonlinear.txt
View File

@ -35,7 +35,11 @@ epsilon (energy)
r0 (distance)
lamda (distance) :ul
[Restrictions:] none
[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.
[Related commands:]

4
doc/bond_quartic.txt
View File

@ -72,6 +72,10 @@ 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 defined between pairs of atoms that
are within a cutoff distance and the set of active interactions
typically changes over time.
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.
Hybrid models where bonds are computed using different bond potentials
can be setup using the {hybrid} bond style.
@ -43,14 +43,22 @@ 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.
In the formulas listed for each bond style, {r} is the distance
between the 2 atoms in the bond.
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.
Note that when both a bond and pair style is defined, the
IMPORTANT NOTE: 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
@ -75,10 +83,11 @@ 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.
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.
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.
[Related commands:]

6
doc/dihedral_charmm.txt
View File

@ -62,7 +62,11 @@ 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:] none
[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.
[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, only coefficients for the Ed formula can be specified
in the input script. These are the 6 coefficients:
For this style, coefficients for the Ed formula can be specified in
either the input script or data file. 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 must be specified in the data
file.
Coefficients for all the other formulas can only 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 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.
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.
[Related commands:]

6
doc/dihedral_harmonic.txt
View File

@ -32,7 +32,11 @@ K (energy)
d (+1 or -1)
n (integer >= 0) :ul
[Restrictions:] none
[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.
[Related commands:]

6
doc/dihedral_helix.txt
View File

@ -40,7 +40,11 @@ A (energy)
B (energy)
C (energy) :ul
[Restrictions:] none
[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.
[Related commands:]

6
doc/dihedral_hybrid.txt
View File

@ -51,7 +51,11 @@ 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:] none
[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.
[Related commands:]

6
doc/dihedral_multi_harmonic.txt
View File

@ -34,7 +34,11 @@ A3 (energy)
A4 (energy)
A5 (energy) :ul
[Restrictions:] none
[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.
[Related commands:]

6
doc/dihedral_opls.txt
View File

@ -38,7 +38,11 @@ K2 (energy)
K3 (energy)
K4 (energy) :ul
[Restrictions:] none
[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.
[Related commands:]

33
doc/dihedral_style.txt
View File

@ -32,17 +32,27 @@ 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.
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.
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:
@ -81,10 +91,11 @@ 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.
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.
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.
[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_2 section for more info.
LAMMPS"_Section_start.html#2_3 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_2 section for more info. This is because
LAMMPS"_Section_start.html#2_3 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
View File

@ -35,8 +35,7 @@ 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. For example, see the "fix
setforce"_fix_setforce.html page for information on style {setforce}.
arguments and what it does, as listed below.
Fixes perform their operations at different stages of the timestep.
If 2 or more fixes both operate at the same stage of the timestep,
@ -45,10 +44,10 @@ 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" 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!
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!
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
@ -58,7 +57,18 @@ 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.
Here is an alphabetic list of fix styles defined in LAMMPS:
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:
"fix addforce"_fix_addforce.html - add a force to each atom
"fix aveforce"_fix_aveforce.html - add an averaged force to each atom
@ -124,12 +134,8 @@ Here is an alphabetic list of fix styles defined 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_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.
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.
[Related commands:]

13
doc/fix_addforce.html
View File

@ -30,8 +30,17 @@ the group. This command can be used to give an additional push to
atoms in a simulation, such as for a simulation of Poiseuille flow in
a channel.
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P><B>Restrictions:</B> none
</P>

13
doc/fix_addforce.txt
View File

@ -27,8 +27,17 @@ the group. This command can be used to give an additional push to
atoms in a simulation, such as for a simulation of Poiseuille flow in
a channel.
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
[Restrictions:] none

10
doc/fix_ave_spatial.html
View File

@ -143,6 +143,16 @@ the fix group and compute group do not match.
or creation of neighbor lists. If the compute is invoked too often by
fix ave/spatial, it can slow down a simulation.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

10
doc/fix_ave_spatial.txt
View File

@ -130,6 +130,16 @@ Note that some computes perform costly calculations, involving use of
or creation of neighbor lists. If the compute is invoked too often by
fix ave/spatial, it can slow down a simulation.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

10
doc/fix_ave_time.html
View File

@ -74,6 +74,16 @@ if a constant pressure simulation is being run (<A HREF = "fix_npt.html">fix npt
or <A HREF = "fix_nph.html">fix nph</A>), LAMMPS is already calculating virial terms
for the pressure every timestep.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

10
doc/fix_ave_time.txt
View File

@ -71,6 +71,16 @@ if a constant pressure simulation is being run ("fix npt"_fix_npt.html
or "fix nph"_fix_nph.html), LAMMPS is already calculating virial terms
for the pressure every timestep.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

13
doc/fix_aveforce.html
View File

@ -41,8 +41,17 @@ dimension are not changed. Note that this is not the same as
specifying a 0.0 value, since that sets all forces to the same average
value without adding in any additional force.
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P><B>Restrictions:</B> none
</P>

13
doc/fix_aveforce.txt
View File

@ -38,8 +38,17 @@ dimension are not changed. Note that this is not the same as
specifying a 0.0 value, since that sets all forces to the same average
value without adding in any additional force.
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
[Restrictions:] none

10
doc/fix_com.html
View File

@ -30,6 +30,16 @@
including all effects due to atoms passing thru periodic boundaries.
Write the results to the specified file.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none

10
doc/fix_com.txt
View File

@ -27,6 +27,16 @@ Compute the center-of-mass of the group of atoms every N steps,
including all effects due to atoms passing thru periodic boundaries.
Write the results to the specified file.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:] none

18
doc/fix_deform.html
View File

@ -111,8 +111,7 @@ triclinic, even if its initial tilt factors are 0.0.
end of the run are determined by the parameters of the fix deform
command. Every Nth timestep during the run, the simulation box is
expanded, contracted, or tilted to ramped values between the initial
and final values. The <A HREF = "run.html">run</A> command documents how to make
the ramping take place across multiple runs.
and final values.
</P>
<HR>
@ -352,8 +351,19 @@ been previously used to define the lattice spacing. Note that the
units choice also affects the <I>vel</I> style parameters since it is
defined in terms of distance/time.
</P>
<HR>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P>This fix can perform deformation over multiple runs, using the <I>start</I>
and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Any box dimension varied by this fix must be periodic.

41
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 (affine deformation)
x = remap coords of atoms in group into deforming box
v = remap velocities of all atoms when they cross periodic boundaries
none = no remapping of x or v
{units} value = {lattice} or {box}
@ -100,8 +100,7 @@ As described below, the desired simulation box size and shape at the
end of the run are determined by the parameters of the fix deform
command. Every Nth timestep during the run, the simulation box is
expanded, contracted, or tilted to ramped values between the initial
and final values. The "run"_run.html command documents how to make
the ramping take place across multiple runs.
and final values.
:line
@ -313,18 +312,13 @@ 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 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.
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.
IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are
performed using this fix, the option "remap v" should normally be
@ -346,13 +340,26 @@ been previously used to define the lattice spacing. Note that the
units choice also affects the {vel} style parameters since it is
defined in terms of distance/time.
:line
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command.
This fix can perform deformation over multiple runs, using the {start}
and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
Any box dimension varied by this fix must be periodic.
[Related commands:] none
[Related commands:]
"displace_box"_displace_box.html
[Default:]

24
doc/fix_deposit.html
View File

@ -131,6 +131,30 @@ command must have been previously used to define the lattice spacing.
Note that the units choice affects all the keyword values that have
units of distance or velocity.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. This means you must be careful when restarting a
deposition simulation, when the restart file was written in the middle
of the deposition operation. Specifically, you should use a new fix
deposit command in the input script for the restarted simulation that
continues the operation. You will need to adjust the arguments of the
original fix deposit command to do this.
</P>
<P>Also note that because the state of the random number generator is not
saved in restart files, you cannot do "exact" restarts with this fix,
where the simulation continues on the same as if no restart had taken
place. However, in a statistical sense, a restarted simulation should
produce the same behavior if you adjust the fix deposit parameters
appropriately.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix. No quantities calculated by this fix can be output by the
<A HREF = "thermo_style.html">thermo_style custom</A> command. No parameter of this
fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

24
doc/fix_deposit.txt
View File

@ -119,6 +119,30 @@ command must have been previously used to define the lattice spacing.
Note that the units choice affects all the keyword values that have
units of distance or velocity.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. This means you must be careful when restarting a
deposition simulation, when the restart file was written in the middle
of the deposition operation. Specifically, you should use a new fix
deposit command in the input script for the restarted simulation that
continues the operation. You will need to adjust the arguments of the
original fix deposit command to do this.
Also note that because the state of the random number generator is not
saved in restart files, you cannot do "exact" restarts with this fix,
where the simulation continues on the same as if no restart had taken
place. However, in a statistical sense, a restarted simulation should
produce the same behavior if you adjust the fix deposit parameters
appropriately.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No quantities calculated by this fix can be output by the
"thermo_style custom"_thermo_style.html command. No parameter of this
fix can be used with the {start/stop} keywords of the "run"_run.html
command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

10
doc/fix_drag.html
View File

@ -39,6 +39,16 @@ application.
<P>This command can be used to steer one or more atoms to a new location
in the simulation.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

10
doc/fix_drag.txt
View File

@ -37,6 +37,16 @@ application.
This command can be used to steer one or more atoms to a new location
in the simulation.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

10
doc/fix_efield.html
View File

@ -28,6 +28,16 @@
<P>Add a force F = qE to each charged atom in the group due to an
external electric field being applied to the system.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

10
doc/fix_efield.txt
View File

@ -25,6 +25,16 @@ fix kick external-field efield 1.0 0.0 0.0 :pre
Add a force F = qE to each charged atom in the group due to an
external electric field being applied to the system.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

13
doc/fix_enforce2d.html
View File

@ -28,8 +28,17 @@
This is useful when running a 2d simulation to insure that atoms do
not move from their initial z coordinate.
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P><B>Restrictions:</B> none
</P>

13
doc/fix_enforce2d.txt
View File

@ -25,8 +25,17 @@ Zero out the z-dimension velocity and force on each atom in the group.
This is useful when running a 2d simulation to insure that atoms do
not move from their initial z coordinate.
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
[Restrictions:] none

14
doc/fix_freeze.html
View File

@ -27,9 +27,21 @@
<P>Zero out the force and torque on a granular particle. This is useful
for preventing certain particles from moving in a simulation.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "granular" package.
<P>This fix is part of the "granular" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>There can only be a single freeze fix defined. This is because other
parts of the code (pair potentials, thermodynamics, etc) treat frozen

14
doc/fix_freeze.txt
View File

@ -24,9 +24,21 @@ fix 2 bottom freeze :pre
Zero out the force and torque on a granular particle. This is useful
for preventing certain particles from moving in a simulation.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
Can only be used if LAMMPS was built with the "granular" package.
This fix is 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.
There can only be a single freeze fix defined. This is because other
parts of the code (pair potentials, thermodynamics, etc) treat frozen

14
doc/fix_gran_diag.html
View File

@ -34,9 +34,21 @@ and file.str. The z bins begin at the bottom of the system and extend
upward with a thickness of <I>zlayer</I> for each bin. The quantities
written to the file are averaged over all atoms in the bin.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "granular" package.
<P>This fix is part of the "granular" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

14
doc/fix_gran_diag.txt
View File

@ -31,9 +31,21 @@ and file.str. The z bins begin at the bottom of the system and extend
upward with a thickness of {zlayer} for each bin. The quantities
written to the file are averaged over all atoms in the bin.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
Can only be used if LAMMPS was built with the "granular" package.
This fix is 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.
[Related commands:]

10
doc/fix_gravity.html
View File

@ -80,6 +80,16 @@ vector direction given by (x,y,z).
<P>The strength of the acceleration due to gravity is 1.0 in LJ units,
which are the only allowed units for granular systems.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Styles <I>chute</I>, <I>spherical</I>, and <I>gradient</I> can only be used with

10
doc/fix_gravity.txt
View File

@ -73,6 +73,16 @@ vector direction given by (x,y,z).
The strength of the acceleration due to gravity is 1.0 in LJ units,
which are the only allowed units for granular systems.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
Styles {chute}, {spherical}, and {gradient} can only be used with

10
doc/fix_gyration.html
View File

@ -38,6 +38,16 @@ this formula
<P>where M is the total mass of the group and Rcm is the center-of-mass
position of the group.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none

10
doc/fix_gyration.txt
View File

@ -35,6 +35,16 @@ this formula
where M is the total mass of the group and Rcm is the center-of-mass
position of the group.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:] none

10
doc/fix_heat.html
View File

@ -59,6 +59,16 @@ not normally be used on atoms that have their temperature controlled
by another fix - e.g. <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> fix.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

10
doc/fix_heat.txt
View File

@ -56,6 +56,16 @@ not normally be used on atoms that have their temperature controlled
by another fix - e.g. "fix nvt"_fix_nvt.html or "fix
langevin"_fix_langevin.html fix.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

52
doc/fix_indent.html
View File

@ -80,15 +80,9 @@ specified velocity.
<P>If the <I>rstart</I> keyword is specified, then the radius of the indenter
is a time-dependent quantity. R0 is the value assigned at the start
of the run; R is the value at the end. At intermediate times, the
radius is linearly interpolated between these two values. The
<A HREF = "run.html">run</A> command documents how to make the interpolation take
place across multiple runs. This option can be used, for example, to
grow/shrink a void within the simulation box. This option is not
relevant during an energy minimization; the indenter always has radius
R in that case. Note that if you do multiple runs, you may need to
re-specify the fix so that the indenter radius has the appropriate
value. If you do nothing, it will be reset to R0 at the beginning of
each run.
radius is linearly interpolated between these two values. This option
can be used, for example, to grow/shrink a void within the simulation
box.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
to define the indenter. A <I>box</I> value selects standard distance units
@ -100,18 +94,36 @@ choice affects not only the indenter's physical geometry, but also its
velocity and force constant since they are defined in terms of
distance as well.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The energy of each
particle interacting with the indenter is K/3 (r - R)^3. The
contribution can also be printed by itself via the keyword <I>f_fix-ID</I>
in the <A HREF = "thermo_style.html">thermo_style custom</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command. If you
want that energy to be included in the total potential energy of the
system (the quantity being minimized), you must enable the
<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy of interaction between atoms and the indenter to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. The energy of each particle interacting
with the indenter is K/3 (r - R)^3.
</P>
<P>The atom/indenter interaction energy can be printed as part of
thermodynamic output via the keyword f_ID, where ID is the fix-ID of
this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
details.
</P>
<P>This fix can adjust the indenter position and radius over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
command. See the <A HREF = "run.html">run</A> command for details of how to do
this.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command. The <I>rstart</I> keyword
does not change the indenter radius during an energy minimization; the
indenter always has a radius of its final value R in that case.
</P>
<P>IMPORTANT NOTE: If you want the atom/indenter interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
<I>energy</I> option for this fix.
</P>
<P><B>Restrictions:</B> none
</P>

52
doc/fix_indent.txt
View File

@ -71,15 +71,9 @@ specified velocity.
If the {rstart} keyword is specified, then the radius of the indenter
is a time-dependent quantity. R0 is the value assigned at the start
of the run; R is the value at the end. At intermediate times, the
radius is linearly interpolated between these two values. The
"run"_run.html command documents how to make the interpolation take
place across multiple runs. This option can be used, for example, to
grow/shrink a void within the simulation box. This option is not
relevant during an energy minimization; the indenter always has radius
R in that case. Note that if you do multiple runs, you may need to
re-specify the fix so that the indenter radius has the appropriate
value. If you do nothing, it will be reset to R0 at the beginning of
each run.
radius is linearly interpolated between these two values. This option
can be used, for example, to grow/shrink a void within the simulation
box.
The {units} keyword determines the meaning of the distance units used
to define the indenter. A {box} value selects standard distance units
@ -91,18 +85,36 @@ choice affects not only the indenter's physical geometry, but also its
velocity and force constant since they are defined in terms of
distance as well.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The energy of each
particle interacting with the indenter is K/3 (r - R)^3. The
contribution can also be printed by itself via the keyword {f_fix-ID}
in the "thermo_style custom"_thermo_style.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command. If you
want that energy to be included in the total potential energy of the
system (the quantity being minimized), you must enable the
"fix_modify"_fix_modify.html {energy} option for this fix.
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of interaction between atoms and the indenter to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html. The energy of each particle interacting
with the indenter is K/3 (r - R)^3.
The atom/indenter interaction energy can be printed as part of
thermodynamic output via the keyword f_ID, where ID is the fix-ID of
this fix. See the "thermo_style custom"_thermo_style.html command for
details.
This fix can adjust the indenter position and radius over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
command. See the "run"_run.html command for details of how to do
this.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command. The {rstart} keyword
does not change the indenter radius during an energy minimization; the
indenter always has a radius of its final value R in that case.
IMPORTANT NOTE: If you want the atom/indenter interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the "fix_modify"_fix_modify.html
{energy} option for this fix.
[Restrictions:] none

27
doc/fix_langevin.html
View File

@ -71,8 +71,7 @@ timestep size, and damp is the damping factor. Random numbers are
used to randomize the direction and magnitude of this force.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <A HREF = "run.html">run</A> command documents
how to make the ramping take place across multiple runs.
run from <I>Tstart</I> to <I>Tstop</I>.
</P>
<P>The <I>damp</I> parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0
@ -88,10 +87,7 @@ viscous</A> command for more details.
A Marsaglia random number generator is used. Each processor uses the
input seed to generate its own unique seed and its own stream of
random numbers. Thus the dynamics of the system will not be identical
on two runs on different numbers of processors. Also, the state of
the random number generator is not saved in a restart file. This
means you cannot do exact restarts when a fix <I>langevin</I> command is
used.
on two runs on different numbers of processors.
</P>
<P>The keyword <I>axes</I> can be used to specify which dimensions to add Ff
and Fr to. A flag of 0 means skip that dimension; a flag of 1 means
@ -121,6 +117,25 @@ should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. a <A HREF = "fix_nvt.html">nvt</A> or
<A HREF = "fix_temp_rescale.html">temp/rescale</A> fix.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

27
doc/fix_langevin.txt
View File

@ -61,8 +61,7 @@ timestep size, and damp is the damping factor. Random numbers are
used to randomize the direction and magnitude of this force.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The "run"_run.html command documents
how to make the ramping take place across multiple runs.
run from {Tstart} to {Tstop}.
The {damp} parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0
@ -78,10 +77,7 @@ The random # {seed} should be a non-zero integer with 1 to 8 digits.
A Marsaglia random number generator is used. Each processor uses the
input seed to generate its own unique seed and its own stream of
random numbers. Thus the dynamics of the system will not be identical
on two runs on different numbers of processors. Also, the state of
the random number generator is not saved in a restart file. This
means you cannot do exact restarts when a fix {langevin} command is
used.
on two runs on different numbers of processors.
The keyword {axes} can be used to specify which dimensions to add Ff
and Fr to. A flag of 0 means skip that dimension; a flag of 1 means
@ -111,6 +107,25 @@ should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. a "nvt"_fix_nvt.html or
"temp/rescale"_fix_temp_rescale.html fix.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. Because the state of the random number generator
is not saved in restart files, this means you cannot do "exact"
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.
None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

13
doc/fix_lineforce.html
View File

@ -33,8 +33,17 @@ line.
<P>If the initial velocity of the atom is 0.0 (or along the line), then
it should continue to move along the line thereafter.
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P><B>Restrictions:</B> none
</P>

13
doc/fix_lineforce.txt
View File

@ -30,8 +30,17 @@ line.
If the initial velocity of the atom is 0.0 (or along the line), then
it should continue to move along the line thereafter.
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
[Restrictions:] none

8
doc/fix_modify.html
View File

@ -58,10 +58,10 @@ default method for computing P.
<P>For fixes that calculate a contribution to the potential energy of the
system, the <I>energy</I> keyword will include that contribution in
thermodyanmic output of potential energy. See the
<A HREF = "thermo_style.html">thermo_style</A> 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.
<A HREF = "thermo_style.html">thermo_style</A> command for info on how potential
energy is output. The contribution by itself can be printed by using
the keyword f_ID in the thermo_style custom command, where ID is the
fix-ID of the appropriate fix.
</P>
<P><B>Restrictions:</B> none
</P>

29
doc/fix_modify.txt
View File

@ -27,33 +27,34 @@ fix_modify 1 energy yes :pre
[Description:]
Modify one or more parameters of a previously defined fix. Not all
fix styles support all parameters.
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.
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 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.
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.
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
defined their own compute by default, as described in their
define 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 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.
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 potential
energy is output. The contribution by itself can be printed by using
the keyword f_ID in the thermo_style custom command, where ID is the
fix-ID of the appropriate fix.
[Restrictions:] none

10
doc/fix_momentum.html
View File

@ -58,6 +58,16 @@ thermostatting).
<P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
initial velocities with zero aggregate linear and/or angular momentum.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

10
doc/fix_momentum.txt
View File

@ -50,6 +50,16 @@ thermostatting).
Note that the "velocity"_velocity.html command can be used to create
initial velocities with zero aggregate linear and/or angular momentum.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

16
doc/fix_msd.html
View File

@ -33,6 +33,22 @@ proportional to the diffusion coefficient of the diffusing atoms. The
"origin" of the displacement for each atom is its position at the time
the fix command was issued. Write the results to the specified file.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the original coordinates of diffusing atoms to <A HREF = "restart.html">binary
restart files</A>, so that the mean-squared displacement
will be accurate in a restarted simulation. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix. No quantities calculated by this fix can be output by the
<A HREF = "thermo_style.html">thermo_style custom</A> command. No parameter of this
fix can be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A>
command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B> none

16
doc/fix_msd.txt
View File

@ -30,6 +30,22 @@ proportional to the diffusion coefficient of the diffusing atoms. The
"origin" of the displacement for each atom is its position at the time
the fix command was issued. Write the results to the specified file.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
This fix writes the original coordinates of diffusing atoms to "binary
restart files"_restart.html, so that the mean-squared displacement
will be accurate 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, so that the
operation of the fix continues in an uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix. No quantities calculated by this fix can be output by the
"thermo_style custom"_thermo_style.html command. No parameter of this
fix can be used with the {start/stop} keywords of the "run"_run.html
command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:] none

47
doc/fix_nph.html
View File

@ -76,8 +76,7 @@ unchanged and controlling the pressure of a surrounding fluid.
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value. The <A HREF = "run.html">run</A> command documents how to make the
ramping take place across multiple runs.
the end value.
</P>
<P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the 3 dimensions
@ -142,19 +141,39 @@ this fix's temperature or pressure via the
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_pressure</I> will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
<I>thermo_pressure</I> will have no effect on this fix.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover barostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
</P>
<P>This fix can ramp its target pressure over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>

47
doc/fix_nph.txt
View File

@ -67,8 +67,7 @@ unchanged and controlling the pressure of a surrounding fluid.
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value. The "run"_run.html command documents how to make the
ramping take place across multiple runs.
the end value.
Style {xyz} means couple all 3 dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the 3 dimensions
@ -132,19 +131,39 @@ this fix's temperature or pressure via the
or pressure during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_pressure} will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
{thermo_pressure} will have no effect on this fix.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover barostat to "binary
restart files"_restart.html. 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, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
"thermo_style custom"_thermo_style.html command for details.
This fix can ramp its target pressure over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]

59
doc/fix_npt.html
View File

@ -57,12 +57,11 @@ temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <A HREF = "run.html">run</A> command documents
how to make the ramping take place across multiple runs. The <I>Tdamp</I>
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command).
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>The atoms in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
@ -81,8 +80,7 @@ unchanged and controlling the pressure of a surrounding fluid.
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value. The <A HREF = "run.html">run</A> command documents how to make the
ramping take place across multiple runs.
the end value.
</P>
<P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the 3 dimensions
@ -146,19 +144,40 @@ this fix's temperature or pressure via the
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_pressure</I> will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
<I>thermo_pressure</I> will have no effect on this fix.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat and barostat
to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
</P>
<P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
command. See the <A HREF = "run.html">run</A> command for details of how to do
this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>

59
doc/fix_npt.txt
View File

@ -46,12 +46,11 @@ temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The "run"_run.html command documents
how to make the ramping take place across multiple runs. The {Tdamp}
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the "units"_units.html command).
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
The atoms in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
@ -70,8 +69,7 @@ unchanged and controlling the pressure of a surrounding fluid.
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value. The "run"_run.html command documents how to make the
ramping take place across multiple runs.
the end value.
Style {xyz} means couple all 3 dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the 3 dimensions
@ -135,19 +133,40 @@ this fix's temperature or pressure via the
or pressure during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_pressure} will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all atoms. LAMMPS will warn you if you choose to
compute temperature on a subset of atoms.
{thermo_pressure} will have no effect on this fix.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat and barostat
to "binary restart files"_restart.html. 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, so that the
operation of the fix continues in an uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
"thermo_style custom"_thermo_style.html command for details.
This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
command. See the "run"_run.html command for details of how to do
this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]

65
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View File

@ -58,12 +58,11 @@ temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <A HREF = "run.html">run</A> command documents
how to make the ramping take place across multiple runs. The <I>Tdamp</I>
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command).
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
@ -82,8 +81,7 @@ unchanged and controlling the pressure of a surrounding fluid.
<P>The pressure can be controlled in one of several styles, as specified
by the <I>p-style</I> argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value. The <A HREF = "run.html">run</A> command documents how to make the
ramping take place across multiple runs.
the end value.
</P>
<P>Style <I>xyz</I> means couple all 3 dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the 3 dimensions
@ -115,7 +113,7 @@ is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods.
</P>
<P>For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary conditions (tilted box) are not
shape. Parinello-Rahman boundary conditions (tilted box) are not yet
implemented in LAMMPS.
</P>
<P>For all styles, the <I>Pdamp</I> parameter operates like the <I>Tdamp</I>
@ -147,23 +145,46 @@ fix's temperature or pressure via the
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all particles. LAMMPS will warn you if you choose
to compute temperature on a subset of particles.
<I>thermo_press</I> will have no effect on this fix.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat and barostat
to <A HREF = "restart.html">binary restart files</A>. See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by this fix. You can use them to assign a
<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
</P>
<P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
command. See the <A HREF = "run.html">run</A> command for details of how to do
this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package.
<P>This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be

65
doc/fix_npt_asphere.txt
View File

@ -47,12 +47,11 @@ temperature. This creates a system trajectory consistent with the
isothermal-isobaric ensemble.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The "run"_run.html command documents
how to make the ramping take place across multiple runs. The {Tdamp}
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the "units"_units.html command).
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
@ -71,8 +70,7 @@ unchanged and controlling the pressure of a surrounding fluid.
The pressure can be controlled in one of several styles, as specified
by the {p-style} argument. In each case, the desired pressure at each
timestep is a ramped value during the run from the starting value to
the end value. The "run"_run.html command documents how to make the
ramping take place across multiple runs.
the end value.
Style {xyz} means couple all 3 dimensions together when pressure is
computed (isotropic pressure), and dilate/contract the 3 dimensions
@ -104,7 +102,7 @@ is working. Typically a value between 0.2 to 2.0 is sufficient to
damp oscillations after a few periods.
For all pressure styles, the simulation box stays rectangular in
shape. Parinello-Rahman boundary conditions (tilted box) are not
shape. Parinello-Rahman boundary conditions (tilted box) are not yet
implemented in LAMMPS.
For all styles, the {Pdamp} parameter operates like the {Tdamp}
@ -136,23 +134,46 @@ fix's temperature or pressure via the
or pressure during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the
kinetic energy derived from T should be consistent with the virial
term computed using all particles. LAMMPS will warn you if you choose
to compute temperature on a subset of particles.
{thermo_press} will have no effect on this fix.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat and barostat
to "binary restart files"_restart.html. 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, so that the
operation of the fix continues in an uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by this fix. You can use them to assign a
"compute"_compute.html you have defined to this fix which will be used
in its thermostatting or barostatting procedure. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
"thermo_style custom"_thermo_style.html command for details.
This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html
command. See the "run"_run.html command for details of how to do
this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package.
This fix 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.
Any dimension being adjusted by this fix must be periodic. A
dimension whose target pressures are specified as NULL can be

10
doc/fix_nve.html
View File

@ -28,6 +28,16 @@
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

10
doc/fix_nve.txt
View File

@ -25,6 +25,16 @@ Perform constant NVE updates of position and velocity for atoms in the
group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

14
doc/fix_nve_asphere.html
View File

@ -29,9 +29,21 @@ angular velocity for aspherical or ellipsoidal particles in the group
each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package.
<P>This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

14
doc/fix_nve_asphere.txt
View File

@ -26,9 +26,21 @@ angular velocity for aspherical or ellipsoidal particles in the group
each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package.
This fix 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.
[Related commands:]

14
doc/fix_nve_dipole.html
View File

@ -29,9 +29,21 @@ angular velocity for particles with point dipole moments in the group
each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "dipole" package.
<P>This fix is part of the "dipole" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

14
doc/fix_nve_dipole.txt
View File

@ -26,9 +26,21 @@ angular velocity for particles with point dipole moments in the group
each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
Can only be used if LAMMPS was built with the "dipole" package.
This fix 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.
[Related commands:]

14
doc/fix_nve_gran.html
View File

@ -30,9 +30,21 @@ rotational information as well as position and velocity, so this
integrator updates translational and rotational degrees of freedom due
to forces and torques.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P>Can only be used if LAMMPS was built with the "granular" package.
<P>This fix is part of the "granular" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

14
doc/fix_nve_gran.txt
View File

@ -27,9 +27,21 @@ rotational information as well as position and velocity, so this
integrator updates translational and rotational degrees of freedom due
to forces and torques.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
Can only be used if LAMMPS was built with the "granular" package.
This fix is 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.
[Related commands:]

10
doc/fix_nve_noforce.html
View File

@ -38,6 +38,16 @@ unchanged, and can thus be printed by the <A HREF = "dump.html">dump</A> command
queried with an equal-style <A HREF = "variable.html">variable</A> that uses the
fcm() group function to compute the total force on the group of atoms.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>

10
doc/fix_nve_noforce.txt
View File

@ -35,6 +35,16 @@ unchanged, and can thus be printed by the "dump"_dump.html command or
queried with an equal-style "variable"_variable.html that uses the
fcm() group function to compute the total force on the group of atoms.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]

47
doc/fix_nvt.html
View File

@ -44,12 +44,11 @@ thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <A HREF = "run.html">run</A> command documents
how to make the ramping take place across multiple runs. The <I>Tdamp</I>
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command).
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>In some cases (e.g. for solids) the temperature of the system can
oscillate undesirably when a Nose/Hoover thermostat is applied. The
@ -80,15 +79,35 @@ This means you can change the attributes of this fix's temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
effect on this fix.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
defined to this fix which will be used in its thermostatting
procedure.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>

47
doc/fix_nvt.txt
View File

@ -35,12 +35,11 @@ thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The "run"_run.html command documents
how to make the ramping take place across multiple runs. The {Tdamp}
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the "units"_units.html command).
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
In some cases (e.g. for solids) the temperature of the system can
oscillate undesirably when a Nose/Hoover thermostat is applied. The
@ -71,15 +70,35 @@ This means you can change the attributes of this fix's temperature
during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the "fix_modify"_fix_modify.html command.
effect on this fix.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat to "binary
restart files"_restart.html. 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, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used in its thermostatting
procedure.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
"thermo_style custom"_thermo_style.html command for details.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]

51
doc/fix_nvt_asphere.html
View File

@ -45,12 +45,11 @@ V is volume; T is temperature. This creates a system trajectory
consistent with the canonical ensemble.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <A HREF = "run.html">run</A> command documents
how to make the ramping take place across multiple runs. The <I>Tdamp</I>
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command).
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>In some cases (e.g. for solids) the temperature of the system can
oscillate undesirably when a Nose/Hoover thermostat is applied. The
@ -81,19 +80,41 @@ This means you can change the attributes of this fix's temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
effect on this fix.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
defined to this fix which will be used in its thermostatting
procedure.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package.
<P>This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in

51
doc/fix_nvt_asphere.txt
View File

@ -36,12 +36,11 @@ V is volume; T is temperature. This creates a system trajectory
consistent with the canonical ensemble.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The "run"_run.html command documents
how to make the ramping take place across multiple runs. The {Tdamp}
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the "units"_units.html command).
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
In some cases (e.g. for solids) the temperature of the system can
oscillate undesirably when a Nose/Hoover thermostat is applied. The
@ -72,19 +71,41 @@ This means you can change the attributes of this fix's temperature
during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the "fix_modify"_fix_modify.html command.
effect on this fix.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat to "binary
restart files"_restart.html. 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, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used in its thermostatting
procedure.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
"thermo_style custom"_thermo_style.html command for details.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package.
This fix 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.
The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in

47
doc/fix_nvt_sllod.html
View File

@ -71,12 +71,11 @@ discussed in <A HREF = "#Tuckerman">(Tuckerman)</A> (eqs 4 and 5), which is what
implemented in LAMMPS in a velocity Verlet formulation.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <A HREF = "run.html">run</A> command documents
how to make the ramping take place across multiple runs. The <I>Tdamp</I>
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the <A HREF = "units.html">units</A> command).
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P>In some cases (e.g. for solids) the temperature of the system can
oscillate undesirably when a Nose/Hoover thermostat is applied. The
@ -107,15 +106,35 @@ This means you can change the attributes of this fix's temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
effect on this fix.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
defined to this fix which will be used in its thermostatting
procedure.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
</P>
<P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>

47
doc/fix_nvt_sllod.txt
View File

@ -62,12 +62,11 @@ discussed in "(Tuckerman)"_#Tuckerman (eqs 4 and 5), which is what is
implemented in LAMMPS in a velocity Verlet formulation.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}. The "run"_run.html command documents
how to make the ramping take place across multiple runs. The {Tdamp}
parameter is specified in time units and determines how rapidly the
temperature is relaxed. For example, a value of 100.0 means to relax
the temperature in a timespan of (roughly) 100 time units (tau or
fmsec or psec - see the "units"_units.html command).
run from {Tstart} to {Tstop}. The {Tdamp} parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
"units"_units.html command).
In some cases (e.g. for solids) the temperature of the system can
oscillate undesirably when a Nose/Hoover thermostat is applied. The
@ -98,15 +97,35 @@ This means you can change the attributes of this fix's temperature
during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix. Alternatively, you can directly assign a new
compute (for calculating temeperature) that you have defined to this
fix via the "fix_modify"_fix_modify.html command.
effect on this fix.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat to "binary
restart files"_restart.html. 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, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used in its thermostatting
procedure.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the
"thermo_style custom"_thermo_style.html command for details.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]

23
doc/fix_orient_fcc.html
View File

@ -116,11 +116,24 @@ symmetry, so the list must include one from each pair of
equal-and-opposite neighbors. A pair of orientation files for a
Sigma=5 tilt boundary are show below.
</P>
<P>This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the <A HREF = "fix_modify.html">fix_modify energy</A> option. The contribution can
also be printed by itself via the keyword <I>f_fix-ID</I> in the
<A HREF = "thermo_style.html">thermo_style custom</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the potential energy of atom interactions with the grain
boundary driving force to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>.
</P>
<P>The atom/grain-boundary interaction energy can be printed as part of
thermodynamic output via the keyword f_ID, where ID is the fix-ID of
this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for
details.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>

23
doc/fix_orient_fcc.txt
View File

@ -113,11 +113,24 @@ symmetry, so the list must include one from each pair of
equal-and-opposite neighbors. A pair of orientation files for a
Sigma=5 tilt boundary are show below.
This fix makes a contribution to the potential energy of the system
that can be included in thermodynamic output of potential energy using
the "fix_modify energy"_fix_modify.html option. The contribution can
also be printed by itself via the keyword {f_fix-ID} in the
"thermo_style custom"_thermo_style.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the potential energy of atom interactions with the grain
boundary driving force to the system's potential energy as part of
"thermodynamic output"_thermo_style.html.
The atom/grain-boundary interaction energy can be printed as part of
thermodynamic output via the keyword f_ID, where ID is the fix-ID of
this fix. See the "thermo_style custom"_thermo_style.html command for
details.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]

13
doc/fix_planeforce.html
View File

@ -32,8 +32,17 @@ by subtracting out components of force perpendicular to the plane.
<P>If the initial velocity of the atom is 0.0 (or in the plane), then it
should continue to move in the plane thereafter.
</P>
<P>The forces due to this fix are also imposed during an energy
minimization, invoked by the <A HREF = "minimize.html">minimize</A> command.
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P><B>Restrictions:</B> none
</P>

13
doc/fix_planeforce.txt
View File

@ -29,8 +29,17 @@ by subtracting out components of force perpendicular to the plane.
If the initial velocity of the atom is 0.0 (or in the plane), then it
should continue to move in the plane thereafter.
The forces due to this fix are also imposed during an energy
minimization, invoked by the "minimize"_minimize.html command.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
[Restrictions:] none

15
doc/fix_poems.html
View File

@ -110,9 +110,22 @@ body contribution to the pressure virial is also accounted for. The
latter is only correct if forces within the bodies have been turned
off, and there is only a single fix poems defined.
</P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No quantities calculated by this fix can be
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. No
parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "poems" package.
<P>This fix is part of the "poems" package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
built and linked with LAMMPS. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

15
doc/fix_poems.txt
View File

@ -103,9 +103,22 @@ body contribution to the pressure virial is also accounted for. The
latter is only correct if forces within the bodies have been turned
off, and there is only a single fix poems defined.
[Restart, fix_modify, thermo output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No quantities calculated by this fix can be
output by the "thermo_style custom"_thermo_style.html command. No
parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
Can only be used if LAMMPS was built with the "poems" package.
This fix is part of the "poems" package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
built and linked with LAMMPS. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]

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