Once you are familiar with LAMMPS, you may want to bookmark this +page at Section_commands.html#comm since +it gives quick access to documentation for all LAMMPS commands. +
PDF file of the entire manual, generated by htmldoc
@@ -106,6 +110,12 @@ we can improve the LAMMPS documentation. 4.10 Coupling LAMMPS to other codesThe example input scripts included in the LAMMPS distribution and highlighted in this section also show how to @@ -647,6 +650,145 @@ See the dump command for more information on XTC files +
By default, LAMMPS uses an orthogonal simulation box to encompass the +particles. The boundary 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 command is used with a region of style +prism, then a non-orthogonal domain is setup. See the +region command for details. If the +read_data 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 command for details. Finally, if the +read_restart 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 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 +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 +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. +
+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 command. The +fix nvt/sllod 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 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 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 can be used to +continuously strain a box by an arbitrary amount. As discussed in the +fix deform 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 should be set to "remap v", since that is what +fix nvt/sllod assumes to generate a velocity +profile consistent with the applied shear strain rate. +
+LAMMPS supports ellipsoidal particles via the atom_style +ellipsoid and shape commands. The +latter defines the 3 axes (diamaters) of a general ellipsoid. The +pair_style gayberne 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 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 command also contains +quaternions for each atom in the Atoms section if atom_style +ellipsoid is being used. The compute +temp/asphere 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 +nvt/asphere, or fix +npt/asphere 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. Alternatively, the pair_style +hybrid potential can be used, with the sphere-sphere +interactions computed by another pair potential, such as pair_style +lj/cut. +
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 for more info on packages.
Related commands:
diff --git a/doc/angle_charmm.txt b/doc/angle_charmm.txt index 5e6dffb793..e1356cb061 100644 --- a/doc/angle_charmm.txt +++ b/doc/angle_charmm.txt @@ -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:] diff --git a/doc/angle_class2.html b/doc/angle_class2.html index 369de1f385..229867ed0b 100644 --- a/doc/angle_class2.html +++ b/doc/angle_class2.html @@ -32,8 +32,8 @@ the equilibrium bond lengths.See (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 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 @@ -66,9 +66,9 @@ 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 for more info. +
This angle style can only be used if LAMMPS was built with the +"class2" package. See the Making LAMMPS +section for more info on packages.
Related commands:
diff --git a/doc/angle_class2.txt b/doc/angle_class2.txt index b49abf0a25..6d343f324c 100644 --- a/doc/angle_class2.txt +++ b/doc/angle_class2.txt @@ -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:] diff --git a/doc/angle_cosine.html b/doc/angle_cosine.html index b0cd186aeb..ebd6df2234 100644 --- a/doc/angle_cosine.html +++ b/doc/angle_cosine.html @@ -35,7 +35,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/angle_cosine.txt b/doc/angle_cosine.txt index ba161cd9ff..4c6cef912f 100644 --- a/doc/angle_cosine.txt +++ b/doc/angle_cosine.txt @@ -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:] diff --git a/doc/angle_cosine_squared.html b/doc/angle_cosine_squared.html index 53596a792c..333b6469cb 100644 --- a/doc/angle_cosine_squared.html +++ b/doc/angle_cosine_squared.html @@ -40,7 +40,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/angle_cosine_squared.txt b/doc/angle_cosine_squared.txt index 79e7d946bd..d39623ed31 100644 --- a/doc/angle_cosine_squared.txt +++ b/doc/angle_cosine_squared.txt @@ -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:] diff --git a/doc/angle_harmonic.html b/doc/angle_harmonic.html index 1f633cc0b5..d8691f63de 100644 --- a/doc/angle_harmonic.html +++ b/doc/angle_harmonic.html @@ -42,6 +42,10 @@ 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 for more info on packages. +
Related commands:
angle_coeff diff --git a/doc/angle_harmonic.txt b/doc/angle_harmonic.txt index 6ab256c57a..dc98882ee9 100644 --- a/doc/angle_harmonic.txt +++ b/doc/angle_harmonic.txt @@ -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 diff --git a/doc/angle_hybrid.html b/doc/angle_hybrid.html index 1c346bf86d..3822f8f622 100644 --- a/doc/angle_hybrid.html +++ b/doc/angle_hybrid.html @@ -52,7 +52,11 @@ angle type will then be ignored. 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 for more info on packages.
Related commands:
diff --git a/doc/angle_hybrid.txt b/doc/angle_hybrid.txt index 33df13030b..554fcf261b 100644 --- a/doc/angle_hybrid.txt +++ b/doc/angle_hybrid.txt @@ -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:] diff --git a/doc/angle_style.html b/doc/angle_style.html index 9975e92ba5..3b74fe9e98 100644 --- a/doc/angle_style.html +++ b/doc/angle_style.html @@ -37,14 +37,22 @@ 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 command.
+All angle potentials store their coefficient data in binary restart +files which means angle_style and angle_coeff +commands do not need to be re-specified in an input script that +restarts a simulation. See the read_restart +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 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 command often needs to be used to -turn off (or weight) the pairwise interactions that would otherwise -exist between the 3 bonded atoms. -
Here is an alphabetic list of angle styles defined in LAMMPS. Click on @@ -67,10 +75,11 @@ specified by the associated angle_coeff 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 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 for more info on packages. The +doc pages for individual bond potentials tell if it is part of a +package.
Related commands:
diff --git a/doc/angle_style.txt b/doc/angle_style.txt index 2d7ee8238b..897ba5ccab 100644 --- a/doc/angle_style.txt +++ b/doc/angle_style.txt @@ -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:] diff --git a/doc/bond_class2.html b/doc/bond_class2.html index 0e7309203c..0c27c29b4c 100644 --- a/doc/bond_class2.html +++ b/doc/bond_class2.html @@ -42,9 +42,9 @@ or read_restart commands: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 for more info. +
This bond style can only be used if LAMMPS was built with the "class2" +package. See the Making LAMMPS section for +more info on packages.
Related commands:
diff --git a/doc/bond_class2.txt b/doc/bond_class2.txt index 9f1befe12d..7fb7b83af9 100644 --- a/doc/bond_class2.txt +++ b/doc/bond_class2.txt @@ -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:] diff --git a/doc/bond_fene.html b/doc/bond_fene.html index bb7d5ec622..70eaad690f 100644 --- a/doc/bond_fene.html +++ b/doc/bond_fene.html @@ -42,7 +42,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/bond_fene.txt b/doc/bond_fene.txt index 0e938d3ff3..6b2b2d2a4a 100644 --- a/doc/bond_fene.txt +++ b/doc/bond_fene.txt @@ -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:] diff --git a/doc/bond_fene_expand.html b/doc/bond_fene_expand.html index 6df397aa4d..a122517286 100644 --- a/doc/bond_fene_expand.html +++ b/doc/bond_fene_expand.html @@ -47,7 +47,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/bond_fene_expand.txt b/doc/bond_fene_expand.txt index aa165a0271..e84623fba4 100644 --- a/doc/bond_fene_expand.txt +++ b/doc/bond_fene_expand.txt @@ -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:] diff --git a/doc/bond_harmonic.html b/doc/bond_harmonic.html index 7c11d0d1c8..37fd7f8cdb 100644 --- a/doc/bond_harmonic.html +++ b/doc/bond_harmonic.html @@ -37,7 +37,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/bond_harmonic.txt b/doc/bond_harmonic.txt index 3fea41d641..1ccbbd4f45 100644 --- a/doc/bond_harmonic.txt +++ b/doc/bond_harmonic.txt @@ -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:] diff --git a/doc/bond_hybrid.html b/doc/bond_hybrid.html index 4600020a47..3e1b7e4ad1 100644 --- a/doc/bond_hybrid.html +++ b/doc/bond_hybrid.html @@ -45,7 +45,11 @@ for K, R0, epsilon, sigma. 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 for more info on packages.
Related commands:
diff --git a/doc/bond_hybrid.txt b/doc/bond_hybrid.txt index 37cd829ddc..bf21d39bad 100644 --- a/doc/bond_hybrid.txt +++ b/doc/bond_hybrid.txt @@ -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:] diff --git a/doc/bond_morse.html b/doc/bond_morse.html index dd2f301103..0d69aedc5b 100644 --- a/doc/bond_morse.html +++ b/doc/bond_morse.html @@ -38,7 +38,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/bond_morse.txt b/doc/bond_morse.txt index 17ac841554..fd67478ef4 100644 --- a/doc/bond_morse.txt +++ b/doc/bond_morse.txt @@ -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:] diff --git a/doc/bond_nonlinear.html b/doc/bond_nonlinear.html index dc68e24130..6bbc5aedf8 100644 --- a/doc/bond_nonlinear.html +++ b/doc/bond_nonlinear.html @@ -38,7 +38,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/bond_nonlinear.txt b/doc/bond_nonlinear.txt index 7a3be2214c..480109ff48 100644 --- a/doc/bond_nonlinear.txt +++ b/doc/bond_nonlinear.txt @@ -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:] diff --git a/doc/bond_quartic.html b/doc/bond_quartic.html index 51ce7e1aca..b5c5fcc793 100644 --- a/doc/bond_quartic.html +++ b/doc/bond_quartic.html @@ -75,6 +75,10 @@ delete_bonds all bond 0 removeRestrictions:
+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 for more info on packages. +
The quartic style requires that special_bonds parameters be set to 1,1,1. Three- and four-body interactions (angle, dihedral, etc) cannot be used with quartic bonds. diff --git a/doc/bond_quartic.txt b/doc/bond_quartic.txt index 20baf5d152..fc7afa2b9e 100644 --- a/doc/bond_quartic.txt +++ b/doc/bond_quartic.txt @@ -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. diff --git a/doc/bond_style.html b/doc/bond_style.html index c36348a3fd..a7222c9acf 100644 --- a/doc/bond_style.html +++ b/doc/bond_style.html @@ -36,9 +36,9 @@ 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 or read_restart 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. @@ -46,14 +46,22 @@ 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 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 commands +do not need to be re-specified in an input script that restarts a +simulation. See the read_restart 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 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. +
Here is an alphabetic list of bond styles defined in LAMMPS. Click on @@ -78,10 +86,11 @@ specified by the associated bond_coeff 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 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 for more info on packages. The +doc pages for individual bond potentials tell if it is part of a +package.
Related commands:
diff --git a/doc/bond_style.txt b/doc/bond_style.txt index 962650dccf..cf2b7ec520 100644 --- a/doc/bond_style.txt +++ b/doc/bond_style.txt @@ -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:] diff --git a/doc/dihedral_charmm.html b/doc/dihedral_charmm.html index 5e3ad0f845..809afe4723 100644 --- a/doc/dihedral_charmm.html +++ b/doc/dihedral_charmm.html @@ -65,7 +65,11 @@ 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 for more info on packages.
Related commands:
diff --git a/doc/dihedral_charmm.txt b/doc/dihedral_charmm.txt index 62e6c24e4f..c9aefa7266 100644 --- a/doc/dihedral_charmm.txt +++ b/doc/dihedral_charmm.txt @@ -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:] diff --git a/doc/dihedral_class2.html b/doc/dihedral_class2.html index 64825020ce..f5a7bace10 100644 --- a/doc/dihedral_class2.html +++ b/doc/dihedral_class2.html @@ -35,8 +35,8 @@ bond lengths.See (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:
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: @@ -103,9 +103,9 @@ Coeffs" heading and each line lists 3 coefficients:
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 for more info. +
This dihedral style can only be used if LAMMPS was built with the +"class2" package. See the Making LAMMPS +section for more info on packages.
Related commands:
diff --git a/doc/dihedral_class2.txt b/doc/dihedral_class2.txt index a638f976ec..002896a3bd 100644 --- a/doc/dihedral_class2.txt +++ b/doc/dihedral_class2.txt @@ -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:] diff --git a/doc/dihedral_harmonic.html b/doc/dihedral_harmonic.html index a1e80cdcb5..b7313e9709 100644 --- a/doc/dihedral_harmonic.html +++ b/doc/dihedral_harmonic.html @@ -35,7 +35,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/dihedral_harmonic.txt b/doc/dihedral_harmonic.txt index ecae8a1113..6e9c5dee06 100644 --- a/doc/dihedral_harmonic.txt +++ b/doc/dihedral_harmonic.txt @@ -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:] diff --git a/doc/dihedral_helix.html b/doc/dihedral_helix.html index ace3fd3c2f..0a0e9c7668 100644 --- a/doc/dihedral_helix.html +++ b/doc/dihedral_helix.html @@ -43,7 +43,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/dihedral_helix.txt b/doc/dihedral_helix.txt index 7827c65c00..f68d66e6f8 100644 --- a/doc/dihedral_helix.txt +++ b/doc/dihedral_helix.txt @@ -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:] diff --git a/doc/dihedral_hybrid.html b/doc/dihedral_hybrid.html index 7c8325aea9..1401fb4f7e 100644 --- a/doc/dihedral_hybrid.html +++ b/doc/dihedral_hybrid.html @@ -54,7 +54,11 @@ dihedral type will then be ignored. 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 for more info on packages.
Related commands:
diff --git a/doc/dihedral_hybrid.txt b/doc/dihedral_hybrid.txt index 87e316a12d..d7eda64a3e 100644 --- a/doc/dihedral_hybrid.txt +++ b/doc/dihedral_hybrid.txt @@ -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:] diff --git a/doc/dihedral_multi_harmonic.html b/doc/dihedral_multi_harmonic.html index bbeb4c7ff0..03dcd350b8 100644 --- a/doc/dihedral_multi_harmonic.html +++ b/doc/dihedral_multi_harmonic.html @@ -37,7 +37,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/dihedral_multi_harmonic.txt b/doc/dihedral_multi_harmonic.txt index 53fffc0bfd..4c71dbc3ca 100644 --- a/doc/dihedral_multi_harmonic.txt +++ b/doc/dihedral_multi_harmonic.txt @@ -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:] diff --git a/doc/dihedral_opls.html b/doc/dihedral_opls.html index bf7ec1fbc9..6861fb6000 100644 --- a/doc/dihedral_opls.html +++ b/doc/dihedral_opls.html @@ -41,7 +41,11 @@ or read_restart commands: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 for more info on packages.
Related commands:
diff --git a/doc/dihedral_opls.txt b/doc/dihedral_opls.txt index 639e3a3f30..67c08e6543 100644 --- a/doc/dihedral_opls.txt +++ b/doc/dihedral_opls.txt @@ -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:] diff --git a/doc/dihedral_style.html b/doc/dihedral_style.html index 573fed9394..f22c6acc55 100644 --- a/doc/dihedral_style.html +++ b/doc/dihedral_style.html @@ -34,17 +34,27 @@ 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 command. +
The coefficients associated with a dihedral style can be specified in +a data or restart file or via the dihedral_coeff +command. +
+All dihedral potentials store their coefficient data in binary restart +files which means dihedral_style and +dihedral_coeff commands do not need to be +re-specified in an input script that restarts a simulation. See the +read_restart 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 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 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: @@ -83,10 +93,11 @@ specified by the associated dihedral_coeff c
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 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 for more info on packages. The +doc pages for individual dihedral potentials tell if it is part of a +package.
Related commands:
diff --git a/doc/dihedral_style.txt b/doc/dihedral_style.txt index ea01bc7205..e540c5540e 100644 --- a/doc/dihedral_style.txt +++ b/doc/dihedral_style.txt @@ -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:] diff --git a/doc/dump.html b/doc/dump.html index dd1f336ca3..2a24b7b333 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -300,11 +300,11 @@ option - see the Making LAMMPS section of documentation.The bond style is part of the "molecular" package. It is only -enabled if LAMMPS was built with that package. See the Making +enabled if LAMMPS was built with that package. See the Making LAMMPS 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 was built with that package. See the Making LAMMPS 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 diff --git a/doc/dump.txt b/doc/dump.txt index e7953c5f09..965d7453f5 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -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 diff --git a/doc/fix.html b/doc/fix.html index 86e63a692d..4e4bb699c0 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -38,8 +38,7 @@ defined in LAMMPS and new ones can be added - see fix -setforce 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, @@ -48,10 +47,10 @@ they are invoked in the order they were specified in the input script.
Fixes can be deleted with the unfix 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 command for a second run after using a +fix nvt command for the first run, will not cancel out +the NVT time integration invoked by the "fix nvt" command. Thus two +time integrators would be in place!
If you specify a new fix with the same ID and style as an existing fix, the old fix is deleted and the new one is created (presumably @@ -61,7 +60,18 @@ 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 command.
-Here is an alphabetic list of fix styles defined in LAMMPS: +
The fix modify 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 or +write_restart commands. This allows the fix to +continue on with its calculations in a restarted simulation. See the +read_restart 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:
Restrictions:
Some fix styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the Making -LAMMPS 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. +if LAMMPS was built with that package. See the Making +LAMMPS section for more info on packages. The +doc pages for individual fixes tell if it is part of a package.
Related commands:
diff --git a/doc/fix.txt b/doc/fix.txt index 8a6ffe5763..05ad174ece 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -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:] diff --git a/doc/fix_deform.html b/doc/fix_deform.html index d0e7be7a60..daf8ee6db7 100644 --- a/doc/fix_deform.html +++ b/doc/fix_deform.html @@ -60,7 +60,7 @@ 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
@@ -324,18 +324,13 @@ 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
@@ -363,7 +358,9 @@ defined in terms of distance/time.
Any box dimension varied by this fix must be periodic.
-Related commands: none
+
Related commands:
+
+
Default:
diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt
index ba195a261d..a7433832a8 100644
--- a/doc/fix_deform.txt
+++ b/doc/fix_deform.txt
@@ -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}
@@ -313,18 +313,13 @@ 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
@@ -352,7 +347,9 @@ defined in terms of distance/time.
Any box dimension varied by this fix must be periodic.
-[Related commands:] none
+[Related commands:]
+
+"displace_box"_displace_box.html
[Default:]
diff --git a/doc/fix_modify.html b/doc/fix_modify.html
index d3db35552f..8069485042 100644
--- a/doc/fix_modify.html
+++ b/doc/fix_modify.html
@@ -34,33 +34,34 @@ fix_modify 1 energy yes
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 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 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 command. The value of the -contribution can also be printed by itself using the thermo_style -custom 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 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.
Restrictions: none
diff --git a/doc/fix_modify.txt b/doc/fix_modify.txt index 19812f4cac..cd470bea43 100644 --- a/doc/fix_modify.txt +++ b/doc/fix_modify.txt @@ -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 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. [Restrictions:] none diff --git a/doc/improper_class2.html b/doc/improper_class2.html index c8b54dd8bb..57d4647543 100644 --- a/doc/improper_class2.html +++ b/doc/improper_class2.html @@ -39,8 +39,8 @@ equilibrium positions of those angles. the data file or restart files read by the read_data or read_restart commands: -For this style, only coefficients for the Ei formula can be specified -in the input script. These are the 2 coefficients: +
For this style, coefficients for the Ei formula can be specified in +eiher the input script or data file. These are the 2 coefficients:
X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2.
-Coefficients for the Eaa formula must be specified in the data file. -For the Eaa formula, the coefficients are listed under a +
Coefficients for the Eaa formula can only be specified in the data +file. For the Eaa formula, the coefficients are listed under a "AngleAngle Coeffs" heading and each line lists 6 coefficients:
Restrictions:
-This improper style is part of the "class2" package. It is only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. +
This improper style can only be used if LAMMPS was built with the +"class2" package. See the Making LAMMPS +section for more info on packages.
Related commands:
diff --git a/doc/improper_class2.txt b/doc/improper_class2.txt index f5390e56a2..5e27bb6aa2 100644 --- a/doc/improper_class2.txt +++ b/doc/improper_class2.txt @@ -36,8 +36,8 @@ The following coefficients must be defined for each improper type via the the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: -For this style, only coefficients for the Ei formula can be specified -in the input script. These are the 2 coefficients: +For this style, coefficients for the Ei formula can be specified in +eiher the input script or data file. These are the 2 coefficients: K (energy/radian^2) X0 (degrees) :ul @@ -45,8 +45,8 @@ X0 (degrees) :ul X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. -Coefficients for the Eaa formula must be specified in the data file. -For the Eaa formula, the coefficients are listed under a +Coefficients for the Eaa formula can only be specified in the data +file. For the Eaa formula, the coefficients are listed under a "AngleAngle Coeffs" heading and each line lists 6 coefficients: M1 (energy/distance) @@ -61,9 +61,9 @@ radians internally; hence the units of M are in energy/radian^2. [Restrictions:] -This improper style 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 improper style can only be used if LAMMPS was built with the +"class2" package. See the "Making LAMMPS"_Section_start.html#2_3 +section for more info on packages. [Related commands:] diff --git a/doc/improper_cvff.html b/doc/improper_cvff.html index 08f25a9744..5378186ceb 100644 --- a/doc/improper_cvff.html +++ b/doc/improper_cvff.html @@ -37,7 +37,11 @@ or read_restart commands:Restrictions: none +
Restrictions: +
+This improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the Making +LAMMPS section for more info on packages.
Related commands:
diff --git a/doc/improper_cvff.txt b/doc/improper_cvff.txt index d47660d79f..ddec5bcfe7 100644 --- a/doc/improper_cvff.txt +++ b/doc/improper_cvff.txt @@ -34,7 +34,11 @@ K (energy) d (+1 or -1) n (0,1,2,3,4,6) :ul -[Restrictions:] none +[Restrictions:] + +This improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. [Related commands:] diff --git a/doc/improper_harmonic.html b/doc/improper_harmonic.html index 52bb2c4033..4291f5c33c 100644 --- a/doc/improper_harmonic.html +++ b/doc/improper_harmonic.html @@ -40,7 +40,11 @@ or read_restart commands:X0 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 improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the Making +LAMMPS section for more info on packages.
Related commands:
diff --git a/doc/improper_harmonic.txt b/doc/improper_harmonic.txt index a5567428e1..9b66c35ec7 100644 --- a/doc/improper_harmonic.txt +++ b/doc/improper_harmonic.txt @@ -37,7 +37,11 @@ X0 (degrees) :ul X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. -[Restrictions:] none +[Restrictions:] + +This improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. [Related commands:] diff --git a/doc/improper_hybrid.html b/doc/improper_hybrid.html index dc97902130..d06294a481 100644 --- a/doc/improper_hybrid.html +++ b/doc/improper_hybrid.html @@ -53,7 +53,11 @@ type will then be ignored. improper_style hybrid and the corresponding improper_coeff commands, if you desire to turn off certain improper types. -Restrictions: none +
Restrictions: +
+This improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the Making +LAMMPS section for more info on packages.
Related commands:
diff --git a/doc/improper_hybrid.txt b/doc/improper_hybrid.txt index 3bed0c6c34..b6f2e92a93 100644 --- a/doc/improper_hybrid.txt +++ b/doc/improper_hybrid.txt @@ -50,7 +50,11 @@ An improper style of {none} can be specified as an argument to improper_style hybrid and the corresponding improper_coeff commands, if you desire to turn off certain improper types. -[Restrictions:] none +[Restrictions:] + +This improper style can only be used if LAMMPS was built with the +"molecular" package (which it is by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. [Related commands:] diff --git a/doc/improper_style.html b/doc/improper_style.html index 9f7d0c6c06..06e9538cbc 100644 --- a/doc/improper_style.html +++ b/doc/improper_style.html @@ -34,13 +34,23 @@ from a data or restart file.Hybrid models where impropers are computed using different improper potentials can be setup using the hybrid improper style.
-The coefficients associated with an improper style can be specified in a -data or restart file or via the improper_coeff command. +
The coefficients associated with an improper style can be specified in +a data or restart file or via the improper_coeff +command.
-Note that when both an improper and pair style is defined, the -special_bond command often needs to be used to -turn off (or weight) the pairwise interactions that would otherwise -exist between the 4 bonded atoms. +
All improper potentials store their coefficient data in binary restart +files which means improper_style and +improper_coeff commands do not need to be +re-specified in an input script that restarts a simulation. See the +read_restart command for details on how to do +this. The one exception is that improper_style hybrid only stores +the list of sub-styles in the restart file; improper coefficients need +to be re-specified. +
+IMPORTANT NOTE: When both an improper and pair style is defined, the +special_bonds command often needs to be used to +turn off (or weight) the pairwise interaction that would otherwise +exist between 4 bonded atoms.
Improper styles can only be set for atom_style choices that allow impropers to be defined.
-Improper styles are part of the "molecular" package or other packages -as noted in their documentation. They are only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. +
Most improper styles are part of the "molecular" package. They are +only enabled if LAMMPS was built with that package. See the Making +LAMMPS section for more info on packages. The +doc pages for individual improper potentials tell if it is part of a +package.
Related commands:
diff --git a/doc/improper_style.txt b/doc/improper_style.txt index 85fbc69183..420bbc0e75 100644 --- a/doc/improper_style.txt +++ b/doc/improper_style.txt @@ -31,13 +31,23 @@ from a data or restart file. Hybrid models where impropers are computed using different improper potentials can be setup using the {hybrid} improper style. -The coefficients associated with an improper style can be specified in a -data or restart file or via the "improper_coeff"_improper_coeff.html command. +The coefficients associated with an improper style can be specified in +a data or restart file or via the "improper_coeff"_improper_coeff.html +command. -Note that when both an improper and pair style is defined, the -"special_bond"_special_bond.html command often needs to be used to -turn off (or weight) the pairwise interactions that would otherwise -exist between the 4 bonded atoms. +All improper potentials store their coefficient data in binary restart +files which means improper_style and +"improper_coeff"_improper_coeff.html commands do not need to be +re-specified in an input script that restarts a simulation. See the +"read_restart"_read_restart.html command for details on how to do +this. The one exception is that improper_style {hybrid} only stores +the list of sub-styles in the restart file; improper coefficients need +to be re-specified. + +IMPORTANT NOTE: When both an improper and pair style is defined, the +"special_bonds"_special_bonds.html command often needs to be used to +turn off (or weight) the pairwise interaction that would otherwise +exist between 4 bonded atoms. :line @@ -59,10 +69,11 @@ specified by the associated "improper_coeff"_improper_coeff.html command: Improper styles can only be set for atom_style choices that allow impropers to be defined. -Improper styles are part of the "molecular" package or other packages -as noted in their documentation. They are only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +Most improper styles are part of the "molecular" package. They are +only enabled if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info on packages. The +doc pages for individual improper potentials tell if it is part of a +package. [Related commands:] diff --git a/doc/kspace_style.html b/doc/kspace_style.html index c21e49bdea..6a4d518812 100644 --- a/doc/kspace_style.html +++ b/doc/kspace_style.html @@ -77,7 +77,7 @@ or PPPM solver. The only exception is if the slab option is set with must be periodic and the z dimension must be non-periodic.Kspace styles are part of the "kspace" package. They are only enabled -if LAMMPS was built with that package. See the Making +if LAMMPS was built with that package. See the Making LAMMPS section for more info.
When using a long-range pairwise TIP4P potential, you must use kspace diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt index 3a8bd6d8cd..e7e5e24479 100644 --- a/doc/kspace_style.txt +++ b/doc/kspace_style.txt @@ -73,7 +73,7 @@ must be periodic and the z dimension must be non-periodic. Kspace styles are part of the "kspace" package. They are only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +LAMMPS"_Section_start.html#2_3 section for more info. When using a long-range pairwise TIP4P potential, you must use kspace style {pppm/tip4p} and vice versa. diff --git a/doc/pair_buck.html b/doc/pair_buck.html index f4421b7800..fa91f0c70c 100644 --- a/doc/pair_buck.html +++ b/doc/pair_buck.html @@ -86,20 +86,41 @@ Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command.
+Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+None of the Buckingham pair styles support mixing. Thus, coefficients +for all I,J pairs must be specified explicitly. +
+All of the Buckingham pair styles support the +pair_modify shift option for the energy of the +exp() and 1/r^6 portion of the pair interaction. +
+The buck/coul/long pair style does not support the +pair_modify table option since a tabulation +capability has not yet been added to this potential. +
+None of the Buckingham pair styles support the +pair_modify tail option for adding long-range tail +corrections to energy and pressure. +
+All of the Buckinham pair styles can calculate per-atom energy and +stress, as used by the compute epair/atom, +compute stress/atom, and dump +custom commands. +
+All of the Buckinham pair styles write their information to binary +restart files, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. +
Restrictions:
-The buck potentials do not support the -pair_modify mix option. Coefficients for all i,j -pairs must be specified explicitly. -
The buck/coul/long style is part of the "kspace" package. It is -only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -
-On some 64-bit machines, compiling with -O3 appears to break the -Coulombic tabling option used by the buck/coul/long style. See -the "Additional build tips" section of the Making LAMMPS documentation -pages for workarounds on this issue. +only enabled if LAMMPS was built with that package (which it is by +default). See the Making LAMMPS section for +more info.
Related commands:
diff --git a/doc/pair_buck.txt b/doc/pair_buck.txt index 9d23621c2a..e485597434 100644 --- a/doc/pair_buck.txt +++ b/doc/pair_buck.txt @@ -80,20 +80,41 @@ Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +None of the Buckingham pair styles support mixing. Thus, coefficients +for all I,J pairs must be specified explicitly. + +All of the Buckingham pair styles support the +"pair_modify"_pair_modify.html shift option for the energy of the +exp() and 1/r^6 portion of the pair interaction. + +The {buck/coul/long} pair style does not support the +"pair_modify"_pair_modify.html table option since a tabulation +capability has not yet been added to this potential. + +None of the Buckingham pair styles support the +"pair_modify"_pair_modify.html tail option for adding long-range tail +corrections to energy and pressure. + +All of the Buckinham pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the Buckinham pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + [Restrictions:] -The {buck} potentials do not support the -"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j -pairs must be specified explicitly. - The {buck/coul/long} style is part of the "kspace" package. It is -only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. - -On some 64-bit machines, compiling with -O3 appears to break the -Coulombic tabling option used by the {buck/coul/long} style. See -the "Additional build tips" section of the Making LAMMPS documentation -pages for workarounds on this issue. +only enabled if LAMMPS was built with that package (which it is by +default). See the "Making LAMMPS"_Section_start.html#2_3 section for +more info. [Related commands:] diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html index 2cf3321726..145f437b0b 100644 --- a/doc/pair_charmm.html +++ b/doc/pair_charmm.html @@ -95,7 +95,7 @@ faster (for the pairwise portion of the run time). types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart -commands: +commands, or by mixing as described below:If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule for epsilon and sigma for -all CHARMM potentials is to use the arithmetic formulas documented -by the pair_modify command. The pair_modify -mix setting is thus ignored for CHARMM potentials. +
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info:
+For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14, +and sigma_14 coefficients for all of the lj/charmm pair styles can be +mixed. They are always mixed with the value arithmetic. See the +"pair_modify" command for details. +
+None of the lj/charmm pair styles support the +pair_modify shift option, since the Lennard-Jones +portion of the pair interaction is smoothed to 0.0 at the cutoff. +
+The lj/charmm/coul/long and lj/charmm/coul/long/opt pair styles +support the pair_modify table option since they can +tabulate the short-range portion of the long-range Coulombic +interaction. +
+None of the lj/charmm pair styles support the +pair_modify tail option for adding long-range tail +corrections to energy and pressure, since the Lennard-Jones portion of +the pair interaction is smoothed to 0.0 at the cutoff. +
+All of the lj/charmm pair styles can calculate per-atom energy and +stress, as used by the compute epair/atom, +compute stress/atom, and dump +custom commands. +
+All of the lj/charmm pair styles write their information to binary +restart files, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. +
+Restrictions:
The lj/charmm/coul/charmm and lj/charmm/coul/charmm/implicit @@ -126,8 +155,8 @@ styles are part of the "molecule" package. The lj/charmm/coul/long style is part of the "kspace" package. The lj/charmm/coul/long/opt style is part of the "opt" package and also requires the "kspace" package. They are only enabled if LAMMPS was built with those -package(s). See the Making LAMMPS section -for more info. +package(s) (molecule and kspace are by default). See the Making +LAMMPS section for more info.
On some 64-bit machines, compiling with -O3 appears to break the Coulombic tabling option used by the lj/charmm/coul/long style. See diff --git a/doc/pair_charmm.txt b/doc/pair_charmm.txt index abc291acae..312ac09deb 100644 --- a/doc/pair_charmm.txt +++ b/doc/pair_charmm.txt @@ -88,7 +88,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -106,11 +106,40 @@ because this CHARMM force field does not allow varying cutoffs for individual atom pairs; all pairs use the global cutoff(s) specified in the pair_style command. -If the pair_coeff command is not used to define coefficients for a -particular I != J type pair, the mixing rule for epsilon and sigma for -all CHARMM potentials is to use the {arithmetic} formulas documented -by the "pair_modify"_pair_modify.html command. The "pair_modify -mix"_pair_modify.html setting is thus ignored for CHARMM potentials. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14, +and sigma_14 coefficients for all of the lj/charmm pair styles can be +mixed. They are always mixed with the value {arithmetic}. See the +"pair_modify" command for details. + +None of the lj/charmm pair styles support the +"pair_modify"_pair_modify.html shift option, since the Lennard-Jones +portion of the pair interaction is smoothed to 0.0 at the cutoff. + +The {lj/charmm/coul/long} and {lj/charmm/coul/long/opt} pair styles +support the "pair_modify"_pair_modify.html table option since they can +tabulate the short-range portion of the long-range Coulombic +interaction. + +None of the lj/charmm pair styles support the +"pair_modify"_pair_modify.html tail option for adding long-range tail +corrections to energy and pressure, since the Lennard-Jones portion of +the pair interaction is smoothed to 0.0 at the cutoff. + +All of the lj/charmm pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the lj/charmm pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + +:line [Restrictions:] @@ -119,8 +148,8 @@ styles are part of the "molecule" package. The {lj/charmm/coul/long} style is part of the "kspace" package. The {lj/charmm/coul/long/opt} style is part of the "opt" package and also requires the "kspace" package. They are only enabled if LAMMPS was built with those -package(s). See the "Making LAMMPS"_Section_start.html#2_3 section -for more info. +package(s) (molecule and kspace are by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. On some 64-bit machines, compiling with -O3 appears to break the Coulombic tabling option used by the {lj/charmm/coul/long} style. See diff --git a/doc/pair_class2.html b/doc/pair_class2.html index 3688e7cfb4..abc822c37d 100644 --- a/doc/pair_class2.html +++ b/doc/pair_class2.html @@ -66,7 +66,7 @@ styles. types via the pair_coeff command as in the examples above, or in the data file or restart files read by the read_data or read_restart -commands: +commands, or by mixing as described below:
: line +
If the pair_coeff command is not used to define coefficients for a particular I != J type pair, the mixing rule for epsilon and sigma for all class2 potentials is to use the sixthpower formulas documented @@ -94,17 +96,44 @@ mix setting is thus ignored for class2 potentials for epsilon and sigma. However it is still followed for mixing the cutoff distance.
+Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the lj/class2 pair styles can be mixed. +Epsilon and sigma are always mixed with the value sixthpower. The +cutoff distance is mixed by whatever option is set by the pair_modify +command (default = geometric). See the "pair_modify" command for +details. +
+All of the lj/class2 pair styles support the +pair_modify shift option for the energy of the +Lennard-Jones portion of the pair interaction. +
+The lj/class2/coul/long pair style does not support the +pair_modify table option since a tabulation +capability has not yet been added to this potential. +
+All of the lj/class2 pair styles support the +pair_modify tail option for adding a long-range +tail correction to the energy and pressure of the Lennard-Jones +portion of the pair interaction. +
+All of the lj/class2 pair styles can calculate per-atom energy and +stress, as used by the compute epair/atom, +compute stress/atom, and dump +custom commands. +
+All of the lj/class2 pair styles write their information to binary +restart files, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. +
Restrictions:
-These styles are part of the "class2" package. They are only enabled
-if LAMMPS was built with that package. See the Making
+ All of these pair styles are part of the "class2" package. They are
+only enabled if LAMMPS was built with that package. See the Making
LAMMPS section for more info.
On some 64-bit machines, compiling with -O3 appears to break the
-Coulombic tabling option used by the lj/class2/coul/long style. See
-the "Additional build tips" section of the Making LAMMPS documentation
-pages for workarounds on this issue.
- Related commands:
pair_coeff
diff --git a/doc/pair_class2.txt b/doc/pair_class2.txt
index 10deb96488..ed29ceaff3 100644
--- a/doc/pair_class2.txt
+++ b/doc/pair_class2.txt
@@ -60,7 +60,7 @@ The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
@@ -80,6 +80,8 @@ since a Coulombic cutoff cannot be specified for an individual I,J
type pair. All type pairs use the same global Coulombic cutoff
specified in the pair_style command.
+: line
+
If the pair_coeff command is not used to define coefficients for a
particular I != J type pair, the mixing rule for epsilon and sigma for
all class2 potentials is to use the {sixthpower} formulas documented
@@ -88,16 +90,43 @@ mix"_pair_modify.html setting is thus ignored for class2 potentials
for epsilon and sigma. However it is still followed for mixing the
cutoff distance.
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for all of the lj/class2 pair styles can be mixed.
+Epsilon and sigma are always mixed with the value {sixthpower}. The
+cutoff distance is mixed by whatever option is set by the pair_modify
+command (default = geometric). See the "pair_modify" command for
+details.
+
+All of the lj/class2 pair styles support the
+"pair_modify"_pair_modify.html shift option for the energy of the
+Lennard-Jones portion of the pair interaction.
+
+The {lj/class2/coul/long} pair style does not support the
+"pair_modify"_pair_modify.html table option since a tabulation
+capability has not yet been added to this potential.
+
+All of the lj/class2 pair styles support the
+"pair_modify"_pair_modify.html tail option for adding a long-range
+tail correction to the energy and pressure of the Lennard-Jones
+portion of the pair interaction.
+
+All of the lj/class2 pair styles can calculate per-atom energy and
+stress, as used by the "compute epair/atom"_compute_epair_atom.html,
+"compute stress/atom"_compute_stress_atom.html, and "dump
+custom"_dump.html commands.
+
+All of the lj/class2 pair styles write their information to "binary
+restart files"_restart.html, so pair_style and pair_coeff commands do
+not need to be specified in an input script that reads a restart file.
+
[Restrictions:]
-These styles are part of the "class2" package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
-
-On some 64-bit machines, compiling with -O3 appears to break the
-Coulombic tabling option used by the {lj/class2/coul/long} style. See
-the "Additional build tips" section of the Making LAMMPS documentation
-pages for workarounds on this issue.
+All of these pair styles are part of the "class2" package. They are
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html
index 88efbdb276..73a362aed7 100644
--- a/doc/pair_coeff.html
+++ b/doc/pair_coeff.html
@@ -40,7 +40,7 @@ can be used for each, as in the 1st example above. I <= J is
required. LAMMPS sets the coefficients for the symmetric J,I
interaction to the same values.
A wild-card asterik can be used in place of in conjunction with the
+ A wild-card asterik can be used in place of or in conjunction with the
I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the
number of atom types, then an asterik with no numeric values means all
@@ -73,8 +73,9 @@ as
For many potentials, if coefficients for type pairs with I != J are
not set explicity by a pair_coeff command, the values are inferred
from the I,I and J,J settings by mixing rules; see the
-pair_modify command for a discussion. Exceptions
-to the mixing rules are discussed with the individual pair styles.
+pair_modify command for a discussion. Details on
+this option as it pertains to individual potentials are described on
+the doc page for the potential.
@@ -83,21 +84,15 @@ the style to display the formula it computes, arguments specified in
the pair_style command, and coefficients specified by the associated
pair_coeff command:
If a pair_coeff command is not specified for I != J, then the -coefficients are mixed according the mixing rules defined by the -pair_modify command. The prefactor A is mixed like -the Lennard-Jones epsilon; sigma,d1,d2 are all mixed like the -Lennard-Jones sigma. +
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info:
+For atom type pairs I,J and I != J, the A, sigma, d1, and d2 +coefficients and cutoff distance for this pair style can be mixed. A +is an energy value mixed like a LJ epsilon. D1 and d2 are distance +values and are mixed like sigma. The default mix value is +geometric. See the "pair_modify" command for details. +
+This pair style supports the pair_modify shift +option for the energy of the pair interaction. +
+The pair_modify table option is not relevant +for this pair style. +
+This pair style does not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure. +
+This pair style can calculate per-atom energy and stress, as used by +the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes its information to binary restart +files, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. +
+Restrictions:
-The colloid style is part of the "colloid" package. It is only
-enabled if LAMMPS was built with that package. See the Making
+ This style is part of the "colloid" package. It is only enabled if
+LAMMPS was built with that package. See the Making
LAMMPS section for more info.
Related commands:
diff --git a/doc/pair_colloid.txt b/doc/pair_colloid.txt
index d7a263069a..72832c6646 100644
--- a/doc/pair_colloid.txt
+++ b/doc/pair_colloid.txt
@@ -59,7 +59,7 @@ The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
+commands, or by mixing as described below:
A (energy units)
sigma (distance units)
@@ -107,16 +107,42 @@ rule-of-thumb is to use a colloid-solvent cutoff that is half the big
diamter + 4 times the small diamter. I.e. 9 = 5 + 4 for the
colloid-solvent cutoff in this case.
-If a pair_coeff command is not specified for I != J, then the
-coefficients are mixed according the mixing rules defined by the
-"pair_modify"_pair_modify.html command. The prefactor A is mixed like
-the Lennard-Jones epsilon; sigma,d1,d2 are all mixed like the
-Lennard-Jones sigma.
+:line
+
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
+
+For atom type pairs I,J and I != J, the A, sigma, d1, and d2
+coefficients and cutoff distance for this pair style can be mixed. A
+is an energy value mixed like a LJ epsilon. D1 and d2 are distance
+values and are mixed like sigma. The default mix value is
+{geometric}. See the "pair_modify" command for details.
+
+This pair style supports the "pair_modify"_pair_modify.html shift
+option for the energy of the pair interaction.
+
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+:line
[Restrictions:]
-The {colloid} style is part of the "colloid" package. It is only
-enabled if LAMMPS was built with that package. See the "Making
+This style is part of the "colloid" package. It is only enabled if
+LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]
diff --git a/doc/pair_dipole.html b/doc/pair_dipole.html
index 046aebc7dc..f928ef9166 100644
--- a/doc/pair_dipole.html
+++ b/doc/pair_dipole.html
@@ -62,7 +62,7 @@ dipole
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distances for this pair style can be mixed. The default +mix value is geometric. See the "pair_modify" command for details. +
+For atom type pairs I,J and I != J, the A, sigma, d1, and d2 +coefficients and cutoff distance for this pair style can be mixed. A +is an energy value mixed like a LJ epsilon. D1 and d2 are distance +values and are mixed like sigma. The default mix value is +geometric. See the "pair_modify" command for details. +
+This pair style supports the pair_modify shift +option for the energy of the Lennard-Jones portion of the pair +interaction. +
+The pair_modify table option is not relevant +for this pair style. +
+This pair style does not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure. +
+This pair style can calculate per-atom energy and stress, as used by +the compute epair/atom, compute +stress/atom, and dump custom +commands. +
+This pair style writes its information to binary restart +files, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. +
Restrictions:
-Can only be used if LAMMPS was built with the "dipole" package. -
-The use of this potential requires additional fixes as described -above. +
This style is part of the "dipole" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info.
Related commands:
diff --git a/doc/pair_dipole.txt b/doc/pair_dipole.txt index 5d6662902c..cea8a63e82 100755 --- a/doc/pair_dipole.txt +++ b/doc/pair_dipole.txt @@ -59,7 +59,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -73,12 +73,46 @@ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this type pair. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distances for this pair style can be mixed. The default +mix value is {geometric}. See the "pair_modify" command for details. + +For atom type pairs I,J and I != J, the A, sigma, d1, and d2 +coefficients and cutoff distance for this pair style can be mixed. A +is an energy value mixed like a LJ epsilon. D1 and d2 are distance +values and are mixed like sigma. The default mix value is +{geometric}. See the "pair_modify" command for details. + +This pair style supports the "pair_modify"_pair_modify.html shift +option for the energy of the Lennard-Jones portion of the pair +interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style can calculate per-atom energy and stress, as used by +the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need +to be specified in an input script that reads a restart file. + [Restrictions:] -Can only be used if LAMMPS was built with the "dipole" package. - -The use of this potential requires additional fixes as described -above. +This style is part of the "dipole" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html index 5c28e85428..3ea6b95c93 100644 --- a/doc/pair_dpd.html +++ b/doc/pair_dpd.html @@ -56,16 +56,49 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma), where T is the temperature set by the pair_style command so it does not need to be specified. -Restrictions: none +
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info:
-This style is part of the "dpd" package. It is only enabled if LAMMPS
-was built with those package. See the Making
+ Thsi pair style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+ This pair style does not support the pair_modify
+shift option for the energy of the pair interaction.
+ The pair_modify table option is not relevant
+for this pair style.
+ This pair style does not support the pair_modify
+tail option for adding long-range tail corrections to energy and
+pressure.
+ This pair style can calculate per-atom energy and stress, as used by
+the compute epair/atom, compute
+stress/atom, and dump custom
+commands. However, only the first term with the A coefficienct
+(conservative force) is used for these computations. The drag force
+and random force terms are not.
+ This pair style writes its information to binary restart
+files, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file. Note
+that the user-specifice random number seed is stored in the restart
+file, so when a simulation is restarted, each processor will
+re-initialize its random number generator the same way it did
+intially. This means the random forces will be random, but will not
+be the same as they would have been if the original simulation had
+continued past the restart time.
+ Restrictions:
+ This style is part of the "dpd" package. It is only enabled if
+LAMMPS was built with that package. See the Making
LAMMPS section for more info.
The dpd potential does not support the
-pair_modify mix option. Coefficients for all i,j
-pairs must be specified explicitly.
- The default frequency for rebuilding neighbor lists is every 10 steps
(see the neigh_modify command). This may be too
infrequent for DPD simulations since particles move rapidly and can
diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt
index cfd8c5f565..95dc12146a 100644
--- a/doc/pair_dpd.txt
+++ b/doc/pair_dpd.txt
@@ -53,15 +53,48 @@ cutoff is used. Note that sigma is set equal to sqrt(2 T gamma),
where T is the temperature set by the "pair_style"_pair_style.html
command so it does not need to be specified.
-[Restrictions:] none
+:line
-This style is part of the "dpd" package. It is only enabled if LAMMPS
-was built with those package. See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+[Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info]:
-The {dpd} potential does not support the
-"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
-pairs must be specified explicitly.
+Thsi pair style does not support mixing. Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift option for the energy of the pair interaction.
+
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can calculate per-atom energy and stress, as used by
+the "compute epair/atom"_compute_epair_atom.html, "compute
+stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html
+commands. However, only the first term with the A coefficienct
+(conservative force) is used for these computations. The drag force
+and random force terms are not.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file. Note
+that the user-specifice random number seed is stored in the restart
+file, so when a simulation is restarted, each processor will
+re-initialize its random number generator the same way it did
+intially. This means the random forces will be random, but will not
+be the same as they would have been if the original simulation had
+continued past the restart time.
+
+:line
+
+[Restrictions:]
+
+This style is part of the "dpd" package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#2_3 section for more info.
The default frequency for rebuilding neighbor lists is every 10 steps
(see the "neigh_modify"_neigh_modify.html command). This may be too
diff --git a/doc/pair_eam.html b/doc/pair_eam.html
index 8c2e5e4a39..5b07c4cc6f 100644
--- a/doc/pair_eam.html
+++ b/doc/pair_eam.html
@@ -322,11 +322,46 @@ are listed.
Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info:
+ For atom type pairs I,J and I != J, mixing is performed by LAMMPS as
+described above with the individual styles. You never need to specify
+a pair_coeff command with I != J arguments for the eam styles.
+ This pair style does not support the pair_modify
+shift option for the energy of the pair interaction.
+ The pair_modify shift option is not relevant
+for this pair style.
+ The pair_modify table option is not relevant
+for this pair style.
+ The pair_modify tail option is not relevant
+for this pair style.
+ All of the eam pair styles can calculate per-atom energy and stress,
+as used by the compute epair/atom, compute
+stress/atom, and dump custom
+commands. These quantities include the contribution from the
+embedding term in the EAM formulas.
+ None of the eam pair styles write their information to binary restart
+files, since the info is tabulated in potential files.
+Thus, you need to re-specify the pair style and coefficient commands
+in an input script that reads a restart file.
+ Restrictions:
The opt styles are part of the "opt" package. They are only enabled
-if LAMMPS was built with that package. See the Making
-LAMMPS section for more info.
+ All of these styles except those ending in opt are part of the
+"manybody" package. They are only enabled if LAMMPS was built with
+that package (which it is by default). The styles ending in opt are
+part of the "opt" package and also require the "manybody" package.
+They are only enabled if LAMMPS was built with those packages. See
+the Making LAMMPS section for more info.
Related commands:
The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
The epsilon and sigma parameters are mixed for I != J atom pairings
-the same as Lennard-Jones parameters; see the pair_modify
-mix documentation for details.
- The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.
@@ -119,17 +115,49 @@ than the full Gay-Berne formula. Thus you should insure epsilon a,b,c
are set to 1.0 for spherical particle types and use epsilon and sigma
to specify its interaction with other spherical particles.
Mixing, shift, table, tail correction, per-atom energy/stress, and
+restart info:
+ For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for this pair style can be mixed. The default mix
+value is geometric. See the "pair_modify" command for details.
+ This pair styles supports the pair_modify shift
+option for the energy of the Lennard-Jones portion of the pair
+interaction, but only for sphere-sphere interactions. There is no
+shifting performed for ellipsoidal interactions due to the anisotropic
+dependence of the interaction.
+ The pair_modify table option is not relevant
+for this pair style.
+ This pair style does not support the pair_modify
+tail option for adding long-range tail corrections to energy and
+pressure.
+ This pair style does not calculate per-atom energy and stress, as used
+by the compute epair/atom, compute
+stress/atom, and dump custom
+commands.
+ This pair style writes its information to binary restart
+files, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+ Restrictions:
Can only be used if LAMMPS was built with the "asphere" package.
+ This style is part of the "asphere" package. It is only enabled if
+LAMMPS was built with that package. See the Making
+LAMMPS section for more info.
The "shift yes" option in pair_modify only applies
-to sphere-sphere interactions for this potential; there is no shifting
-performed for ellipsoidal interactions due to the anisotropic
-dependence of the interaction. The Gay-Berne potential does not
-become isotropic as r increases (Everaers). The
-distance-of-closest-approach approximation used by LAMMPS becomes less
-accurate when high-aspect ratio ellipsoids are used.
+ The Gay-Berne potential does not become isotropic as r increases
+(Everaers). The distance-of-closest-approach
+approximation used by LAMMPS becomes less accurate when high-aspect
+ratio ellipsoids are used.
Related commands:
Restrictions: none
All of these styles are part of the "granular" package. It is only
-enabled if LAMMPS was built with that package. See the Making
+enabled if LAMMPS was built with that package. See the Making
LAMMPS section for more info.
You must use atom style granular with these pair
diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt
index 15d2ca24ea..8e42ad5637 100644
--- a/doc/pair_gran.txt
+++ b/doc/pair_gran.txt
@@ -67,7 +67,7 @@ See the citation for more discussion of the granular potentials.
All of these styles are part of the "granular" package. It is only
enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+LAMMPS"_Section_start.html#2_3 section for more info.
You must use "atom style"_atom_style.html {granular} with these pair
styles.
diff --git a/doc/pair_lj.html b/doc/pair_lj.html
index bc5479fcd9..33f227d3c5 100644
--- a/doc/pair_lj.html
+++ b/doc/pair_lj.html
@@ -139,7 +139,7 @@ how to use the TIP4P pair style.
types via the pair_coeff command as in the examples
above, or in the data file or restart files read by the
read_data or read_restart
-commands:
+commands, or by mixing as described below:
+
+
+
+
+
+
+
Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info: +
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the lj/cut pair styles can be mixed. +The default mix value is geometric. See the "pair_modify" command +for details. +
+All of the lj/cut pair styles support the +pair_modify shift option for the energy of the +Lennard-Jones portion of the pair interaction. +
+The lj/cut/coul/long and lj/cut/coul/long/tip4p pair styles +support the pair_modify table option since they can +tabulate the short-range portion of the long-range Coulombic +interaction. +
+All of the lj/cut pair styles support the +pair_modify tail option for adding a long-range +tail correction to the energy and pressure of the Lennard-Jones +portion of the pair interaction. +
+All of the lj/cut pair styles can calculate per-atom energy and +stress, as used by the compute epair/atom, +compute stress/atom, and dump +custom commands. +
+All of the lj/cut pair styles write their information to binary +restart files, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. +
+Restrictions:
-The lj/cut/coul/long style is part of the "kspace" package. It is -only enabled if LAMMPS was built with that package. The lj/cut/opt -style is part of the "opt" package. It is only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. +
The lj/cut/coul/long and lj/cut/coul/long/tip4p styles are part of +the "kspace" package. They are only enabled if LAMMPS was built with +that package (which it is by default). The lj/cut/opt style is part +of the "opt" package. It is only enabled if LAMMPS was built with +that package. See the Making LAMMPS section +for more info.
On some 64-bit machines, compiling with -O3 appears to break the Coulombic tabling option used by the lj/cut/coul/long style. See diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt index 5730d0a91c..154045a722 100644 --- a/doc/pair_lj.txt +++ b/doc/pair_lj.txt @@ -131,7 +131,7 @@ The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands: +commands, or by mixing as described below: epsilon (energy units) sigma (distance units) @@ -155,13 +155,49 @@ can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, and +restart info]: + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the lj/cut pair styles can be mixed. +The default mix value is {geometric}. See the "pair_modify" command +for details. + +All of the lj/cut pair styles support the +"pair_modify"_pair_modify.html shift option for the energy of the +Lennard-Jones portion of the pair interaction. + +The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} pair styles +support the "pair_modify"_pair_modify.html table option since they can +tabulate the short-range portion of the long-range Coulombic +interaction. + +All of the lj/cut pair styles support the +"pair_modify"_pair_modify.html tail option for adding a long-range +tail correction to the energy and pressure of the Lennard-Jones +portion of the pair interaction. + +All of the lj/cut pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the lj/cut pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + +:line + [Restrictions:] -The {lj/cut/coul/long} style is part of the "kspace" package. It is -only enabled if LAMMPS was built with that package. The {lj/cut/opt} -style is part of the "opt" package. It is only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. +The {lj/cut/coul/long} and {lj/cut/coul/long/tip4p} styles are part of +the "kspace" package. They are only enabled if LAMMPS was built with +that package (which it is by default). The {lj/cut/opt} style is part +of the "opt" package. It is only enabled if LAMMPS was built with +that package. See the "Making LAMMPS"_Section_start.html#2_3 section +for more info. On some 64-bit machines, compiling with -O3 appears to break the Coulombic tabling option used by the {lj/cut/coul/long} style. See diff --git a/doc/pair_modify.html b/doc/pair_modify.html index c14d6d4376..6d887880fa 100644 --- a/doc/pair_modify.html +++ b/doc/pair_modify.html @@ -19,8 +19,8 @@
shift value = yes or no
- mix value = geometric or arithmetic or sixthpower
+ mix value = geometric or arithmetic or sixthpower
+ shift value = yes or no
table value = N
2^N = # of values in table
tabinner value = cutoff
@@ -40,51 +40,56 @@ pair_modify table 12
Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
-The shift keyword determines whether the Lennard-Jones potential is
-shifted at its cutoff to 0.0. If so, this adds an energy term to each
-pairwise interaction which will be printed in the thermodynamic
-output, but does not affect atom dynamics (forces). Pair styles that
-are already 0.0 at their cutoff such as lj/charmm/coul/charmm are
-not affected by this setting.
+
The mix keyword affects pair coefficients for interactions between
+atoms of type I and J, when I != J and the coefficients are not
+explicity set in the input script. Note that coefficients for I = J
+must be set explicitly, either in the input script via the
+"pair_coeff" command or in the "Pair Coeffs" section of the data
+file. For some pair styles is is not necessary to
+specify coefficients when I != J, since a "mixing" rule will create
+them from the I,I and J,J settings. The pair_modify mix value
+determines what formulas are used to compute the mixed coefficients.
+In each case, the cutoff distance is mixed the same way as sigma.
-The mix keyword affects how Lennard-Jones coefficients for epsilon,
-sigma, and the cutoff are generated for interactions between atoms of
-type I and J, when I != J. Coefficients for I = J are set explicitly
-in the data file or input script. The pair_coeff
-command can be used in the input script to specify epilon/sigma for a
-specific I != J pairing, which overrides the setting of the mix
-keyword.
+
Note that not all pair styles support mixing. Also, some mix options
+are not available for certain pair styles. See the doc page for
+individual pair styles for those restrictions. Note also that the
+pair_coeff command also can be to directly set
+coefficients for a specific I != J pairing, in which case no mixing is
+performed.
-These are the formulas used by the 3 mix options. In each case, the
-LJ cutoff is mixed the same way as sigma. Note that some of these
-options are not available for certain pair styles. See the doc page
-for individual pair styles for those restrictions.
-
-geometric
+
mix geometric
epsilon_ij = sqrt(epsilon_i * epsilon_j)
sigma_ij = sqrt(sigma_i * sigma_j)
-arithmetic
+
mix arithmetic
epsilon_ij = sqrt(epsilon_i * epsilon_j)
sigma_ij = (sigma_i + sigma_j) / 2
-sixthpower
+
mix sixthpower
epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
(sigma_i^6 + sigma_j^6)
sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
+The shift keyword determines whether a Lennard-Jones potential is
+shifted at its cutoff to 0.0. If so, this adds an energy term to each
+pairwise interaction which will be included in the thermodynamic
+output, but does not affect pair forces or atom trajectories. See the
+doc page for individual pair styles to see which ones support this
+option.
+
The table keyword applies to pair styles with a long-range Coulombic
-term (lj/cut/coul/long and lj/charmm/coul/long). If N is non-zero, a
-table of length 2^N is pre-computed for forces and energies, which can
-shrink their computational cost by up to a factor of 2. The table is
-indexed via a bit-mapping technique (Wolff) and a linear
-interpolation is performed between adjacent table values. In our
-experiments with different table styles (lookup, linear, spline), this
-method typically gave the best performance in terms of speed and
-accuracy.
+term; see the doc page for individual styles to see which potentials
+support this option. If N is non-zero, a table of length 2^N is
+pre-computed for forces and energies, which can shrink their
+computational cost by up to a factor of 2. The table is indexed via a
+bit-mapping technique (Wolff) and a linear interpolation is
+performed between adjacent table values. In our experiments with
+different table styles (lookup, linear, spline), this method typically
+gave the best performance in terms of speed and accuracy.
The choice of table length is a tradeoff in accuracy versus speed. A
larger N yields more accurate force computations, but requires more
@@ -106,19 +111,16 @@ nearly all pairwise interactions are computed via table lookup for
simulations with "real" units, but some close pairs may be computed
directly (non-table) for simulations with "lj" units.
-When the tail keyword is set to yes, long-range VanderWaals tail
-"corrections" are added to the energy and pressure. These are
-included in the calculation and printing of thermodynamic quantities
-(see the thermo_style command). Their effect will
-also be included in constant NPT or NPH simulations where the pressure
-influences the simulation box dimensions (see the fix
-npt and fix nph commands).
-
-The tail keyword is only supported by pair_style
-pairwise potentials which include Lennard-Jones interactions which are
-cutoff at a non-zero energy. This does not include the LJ CHARMM
-potentials or lj/smooth since they go to zero at the cutoff. The
-formulas used for the long-range corrections come from equation 5 of
+
When the tail keyword is set to yes, certain pair styles will add
+a long-range VanderWaals tail "correction" to the energy and pressure.
+See the doc page for individual styles to see which support this
+option. These corrections are included in the calculation and
+printing of thermodynamic quantities (see the
+thermo_style command). Their effect will also be
+included in constant NPT or NPH simulations where the pressure
+influences the simulation box dimensions (e.g. the fix
+npt and fix nph commands). The formulas
+used for the long-range corrections come from equation 5 of
(Sun).
Several assumptions are inherent in using tail corrections, including
@@ -144,13 +146,8 @@ those interactions.
Restrictions: none
-Not all pair styles support mixing. See the doc page for individual -pair styles for details. -
You cannot use shift yes with tail yes, since those are -conflicting options. -
-You cannot use tail yes with 2d simulations. +conflicting options. You cannot use tail yes with 2d simulations.
Related commands:
@@ -159,9 +156,11 @@ conflicting options.Default:
-The option defaults are shift = no, mix = arithmetic (for lj/charmm -pair styles), mix = geometric (for other pair styles), table = 12, -and tabinner = sqrt(2.0), tail = no. +
The option defaults are mix = geometric, shift = no, table = 12, +tabinner = sqrt(2.0), tail = no. +
+Note that some pair styles perform mixing, but only a certain style of +mixing. See the doc pages for individual pair styles for details.
Hybrid models where specified pairs of atom types interact via @@ -62,9 +59,18 @@ different pair potentials can be setup using the hybrid pair style. each pair of atom types, and are specified by the pair_coeff command or read from a file by the read_data or read_restart -commands. Mixing, shifting, and tail corrections for the potentials -is discussed is the documentation for the -pair_modify command. +commands. +
+The pair_modify command sets options for mixing of +type I-J interaction coefficients and adding energy offsets or tail +corrections to Lennard-Jones potentials. Details on these options as +they pertain to individual potentials are described on the doc page +for the potential. Likewise, info on whether the potential +information is stored in a restart file or +whether the potential supports calculation of per-atom energy and +stress by the compute epair/atom and +compute stress/atom commands is given on +the potential doc page.
In the formulas listed for each pair style, E is the energy of a pairwise interaction between two atoms separated by a distance r. @@ -95,18 +101,15 @@ the pair_style command, and coefficients specified by the associated
Some pair styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the Making -LAMMPS section for more info. +if LAMMPS was built with that package. See the Making +LAMMPS section for more info on packages. The +doc pages for individual pair potentials tell if it is part of a +package.
Related commands:
diff --git a/doc/pair_style.txt b/doc/pair_style.txt index d546574415..9a6384a8a1 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -14,17 +14,14 @@ pair_style style args :pre style = one of the following :ulb,l -{none}, {hybrid}, {buck}, {buck/coul/cut}, {buck/coul/long}, -{colloid}, {dipole/cut}, {dpd}, {eam}, {eam/opt}, {eam/alloy}, -{eam/alloy/opt}, {eam/fs}, {eam/fs/opt}, {gayberne}, -{gran/hertzian}, {gran/history}, {gran/no_history}, -{lj/charmm/coul/charmm}, {lj/charmm/coul/charmm/opt}, -{lj/charmm/coul/charmm/implicit}, {lj/charmm/coul/long}, -{lj/class2}, {lj/class2/coul/cut}, {lj/class2/coul/long}, -{lj/cut}, {lj/cut/opt}, {lj/cut/coul/cut}, -{lj/cut/coul/debye}, {lj/cut/coul/long}, {lj/cut/coul/long/tip4p}, -{lj/expand}, {lj/smooth}, {meam}, {morse}, {morse/opt}, {soft}, {sw}, {table}, -{tersoff}, {yukawa} :ul +{none}, {hybrid}, {airebo}, {buck}, {buck/coul/cut}, {buck/coul/long}, +{dpd}, {eam}, {eam/alloy} or {eam/fs}, {gran/hertzian}, +{gran/history}, {gran/no_history}, {lj/charmm/coul/charmm}, +{lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long}, +{lj/class2}, {lj/class2/coul/cut} or {lj/class2/coul/long}, {lj/cut}, +{lj/cut/coul/cut} or {lj/cut/coul/debye}, {lj/cut/coul/long}, +{lj/cut/coul/long/tip4p}, {lj/expand}, {lj/smooth}, {meam}, {morse}, +{soft}, {sw}, {table}, {tersoff}, {yukawa} :ul args = arguments used by a particular style :l,ule @@ -49,7 +46,7 @@ In LAMMPS, pairwise force fields encompass a variety of interactions, some of which include many-body effects, e.g. EAM, Stillinger-Weber, Tersoff, REBO potentials. They are still classified as "pairwise" potentials because the set of interacting atoms changes with time -(unlike a bonded system) and thus a neighbor list is used to find +(unlike molecular bonds) and thus a neighbor list is used to find nearby interacting atoms. Hybrid models where specified pairs of atom types interact via @@ -59,9 +56,18 @@ The coefficients associated with a pair style are typically set for each pair of atom types, and are specified by the "pair_coeff"_pair_coeff.html command or read from a file by the "read_data"_read_data.html or "read_restart"_read_restart.html -commands. Mixing, shifting, and tail corrections for the potentials -is discussed is the documentation for the -"pair_modify"_pair_modify.html command. +commands. + +The "pair_modify"_pair_modify.html command sets options for mixing of +type I-J interaction coefficients and adding energy offsets or tail +corrections to Lennard-Jones potentials. Details on these options as +they pertain to individual potentials are described on the doc page +for the potential. Likewise, info on whether the potential +information is stored in a "restart file"_write_restart.html or +whether the potential supports calculation of per-atom energy and +stress by the "compute epair/atom"_compute_epair_atom.html and +"compute stress/atom"_compute_stress_atom.html commands is given on +the potential doc page. In the formulas listed for each pair style, {E} is the energy of a pairwise interaction between two atoms separated by a distance {r}. @@ -92,18 +98,15 @@ the pair_style command, and coefficients specified by the associated "pair_style none"_pair_none.html - turn off pairwise interactions "pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul +"pair_style airebo"_pair_airebo.html - AI-REBO potential "pair_style buck"_pair_buck.html - Buckingham potential "pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb "pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb "pair_style colloid"_pair_colloid.html - integrated colloidal potential -"pair_style dipole/cut"_pair_dpd.html - point dipole potential "pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD) "pair_style eam"_pair_eam.html - embedded atom method (EAM) -"pair_style eam/opt"_pair_eam.html - optimized embedded atom method (EAM) "pair_style eam/alloy"_pair_eam.html - alloy EAM -"pair_style eam/alloy/opt"_pair_eam.html - optimized alloy EAM "pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM -"pair_style eam/fs/opt"_pair_eam.html - optimized Finnis-Sinclair EAM "pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential "pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions "pair_style gran/history"_pair_gran.html - granular potential with history effects @@ -111,12 +114,10 @@ the pair_style command, and coefficients specified by the associated "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb -"pair_style lj/charmm/coul/long/opt"_pair_charmm.html - optimized CHARMM with long-range Coulomb "pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb "pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb "pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb "pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb -"pair_style lj/cut/opt"_pair_lj.html - optimized cutoff Lennard-Jones potential with no Coulomb "pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb "pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye damping added to Coulomb "pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb @@ -125,7 +126,6 @@ the pair_style command, and coefficients specified by the associated "pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style morse"_pair_morse.html - Morse potential -"pair_style morse/opt"_pair_morse.html - optimized Morse potential "pair_style soft"_pair_soft.html - Soft (cosine) potential "pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential "pair_style table"_pair_table.html - tabulated pair potential @@ -142,7 +142,9 @@ This command must be used before any coefficients are set by the Some pair styles are part of specific packages. They are only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +LAMMPS"_Section_start.html#2_3 section for more info on packages. The +doc pages for individual pair potentials tell if it is part of a +package. [Related commands:] diff --git a/doc/read_restart.html b/doc/read_restart.html index ae9d5b4299..73976f1027 100644 --- a/doc/read_restart.html +++ b/doc/read_restart.html @@ -27,8 +27,9 @@ read_restart poly.*.%Description:
-Read in a previously saved problem from a restart file. This allows -continuation of a previous run. +
Read in a previously saved simulation from a restart file. This +allows continuation of a previous run. Information about what is +stored in a restart file is given below.
Restart files are saved in binary format to enable exact restarts, meaning that the trajectories of a restarted run will precisely match @@ -39,11 +40,11 @@ include running on a different number of processors or changing certain settings such as those set by the newton or processors commands. LAMMPS will issue a WARNING in these cases. Certain fixes will also not restart exactly, though they -should provide statistically similar results. These include the shake -and langevin styles. If a restarted run is immediately different than -the run which produced the restart file, it could be a LAMMPS bug, so -consider reporting it if you think the -behavior is wrong. +should provide statistically similar results. These include fix +shake and fix langevin. If a +restarted run is immediately different than the run which produced the +restart file, it could be a LAMMPS bug, so consider reporting +it if you think the behavior is wrong.
Because restart files are binary, they may not be portable to other machines. They can be converted to ASCII data files using the @@ -77,36 +78,39 @@ current LAMMPS simulation.
A restart file stores the units and atom style, simulation box -attibutes (including whether it is an orthogonal box or a -non-orthogonal parallelepiped with triclinic symmetry), individual -atoms and their attributes including molecular topology, force field -styles and coefficients, special_bonds settings, -and atom group definitions. This means that commands for these -quantities do not need to be specified in your input script that reads -the restart file. The exceptions to this are listed below in the -Restrictions section. +
A restart file stores the following information about a simulation: +units and atom style, simulation box size and shape and boundary +settings, group definitions, atom type settings such as mass and +particle shape, individual atoms and their group assignments and +molecular topology attributes, force field styles and coefficients, +and special_bonds settings. This means that +commands for these quantities do not need to be re-specified in the +input script that reads the restart file, though you can redefine +settings after the restart file is read.
-Information about the kspace_style settings are -not stored in the restart file. Hence if you wish to invoke an Ewald -or PPPM solver, this command must be re-issued after the restart file -is read. +
One exception is that some pair styles do not store their info in +restart files. The doc pages for individual pair styles note if this +is the case. This is also true of bond_style hybrid (and angle_style, +dihedral_style, improper_style hybrid).
-The restart file also stores values for any fixes that require state -information to enable restarting where they left off. These include -the nvt and npt styles that have a global state, as well as the -msd and wall/gran styles that store information about each atom. +
Information about kspace_style settings are not +stored in the restart file. Hence if you wish to use an Ewald or PPPM +solver, these commands must be re-issued after the restart file is +read.
-Fix commands are not stored in the restart file which means -they must be specified in the input script that reads the restart -file. To re-enable a fix whose state was stored in the restart file, -the fix command in the new input script must use the same fix-ID and -group-ID as the input script that wrote the restart file. LAMMPS will -print a message indicating that the fix is being re-enabled. -
-Note that no other information is stored in the restart file. This -means that your new input script should specify settings for -quantities like timestep size, thermodynamic and dump output, etc. +
The list of fixes used for a simulation is not stored in +the restart file. This means the new input script should specify all +fixes it will use. Note that some fixes store an internal "state" +which is written to the restart file. This allows the fix to continue +on with its calculations in a restarted simulation. To re-enable such +a fix, the fix command in the new input script must use the same +fix-ID and group-ID as was used in the input script that wrote the +restart file. If a match is found, LAMMPS prints a message indicating +that the fix is being re-enabled. If no match is found before the +first run or minimization is performed by the new script, the "state" +information for the saved fix is discarded. See the doc pages for +individual fixes for info on which ones can be restarted in this +manner.
Bond interactions (angle, etc) that have been turned off by the fix shake or delete_bonds command will @@ -118,15 +122,13 @@ file is read. to the restart file as broken bonds with a type of 0. Thus these bonds will still be broken when the restart file is read.
-Restrictions: +
IMPORTANT NOTE: No other information is stored in the restart file. +This means that an input script that reads a restart file should +specify settings for quantities like timestep size, +thermodynamic and dump output, +geometric regions, etc.
-The pair_style eam, table, and hybrid styles -do not store coefficient data for individual atom type pairs in the -restart file. Nor does the bond_style hybrid style -(angle, dihedral hybrid, etc). Thus for these styles you must use new -pair_coeff and bond_coeff (angle, -dihedral, etc) commands to read the appropriate tabulated files or -reset the coefficients after the restart file is read. +
Restrictions: none
Related commands:
diff --git a/doc/read_restart.txt b/doc/read_restart.txt index 48a94a6950..04a4e8d795 100644 --- a/doc/read_restart.txt +++ b/doc/read_restart.txt @@ -24,8 +24,9 @@ read_restart poly.*.% :pre [Description:] -Read in a previously saved problem from a restart file. This allows -continuation of a previous run. +Read in a previously saved simulation from a restart file. This +allows continuation of a previous run. Information about what is +stored in a restart file is given below. Restart files are saved in binary format to enable exact restarts, meaning that the trajectories of a restarted run will precisely match @@ -36,11 +37,11 @@ include running on a different number of processors or changing certain settings such as those set by the "newton"_newton.html or "processors"_processors.html commands. LAMMPS will issue a WARNING in these cases. Certain fixes will also not restart exactly, though they -should provide statistically similar results. These include the shake -and langevin styles. If a restarted run is immediately different than -the run which produced the restart file, it could be a LAMMPS bug, so -consider "reporting it"_Section_errors.html#9_2 if you think the -behavior is wrong. +should provide statistically similar results. These include "fix +shake"_fix_shake.html and "fix langevin"_fix_langevin.html. If a +restarted run is immediately different than the run which produced the +restart file, it could be a LAMMPS bug, so consider "reporting +it"_Section_errors.html#9_2 if you think the behavior is wrong. Because restart files are binary, they may not be portable to other machines. They can be converted to ASCII data files using the @@ -74,36 +75,39 @@ current LAMMPS simulation. :line -A restart file stores the units and atom style, simulation box -attibutes (including whether it is an orthogonal box or a -non-orthogonal parallelepiped with triclinic symmetry), individual -atoms and their attributes including molecular topology, force field -styles and coefficients, "special_bonds"_special_bonds.html settings, -and atom group definitions. This means that commands for these -quantities do not need to be specified in your input script that reads -the restart file. The exceptions to this are listed below in the -Restrictions section. +A restart file stores the following information about a simulation: +units and atom style, simulation box size and shape and boundary +settings, group definitions, atom type settings such as mass and +particle shape, individual atoms and their group assignments and +molecular topology attributes, force field styles and coefficients, +and "special_bonds"_special_bonds.html settings. This means that +commands for these quantities do not need to be re-specified in the +input script that reads the restart file, though you can redefine +settings after the restart file is read. -Information about the "kspace_style"_kspace_style.html settings are -not stored in the restart file. Hence if you wish to invoke an Ewald -or PPPM solver, this command must be re-issued after the restart file -is read. +One exception is that some pair styles do not store their info in +restart files. The doc pages for individual pair styles note if this +is the case. This is also true of bond_style hybrid (and angle_style, +dihedral_style, improper_style hybrid). -The restart file also stores values for any fixes that require state -information to enable restarting where they left off. These include -the {nvt} and {npt} styles that have a global state, as well as the -{msd} and {wall/gran} styles that store information about each atom. +Information about "kspace_style"_kspace_style.html settings are not +stored in the restart file. Hence if you wish to use an Ewald or PPPM +solver, these commands must be re-issued after the restart file is +read. -"Fix"_fix.html commands are not stored in the restart file which means -they must be specified in the input script that reads the restart -file. To re-enable a fix whose state was stored in the restart file, -the fix command in the new input script must use the same fix-ID and -group-ID as the input script that wrote the restart file. LAMMPS will -print a message indicating that the fix is being re-enabled. - -Note that no other information is stored in the restart file. This -means that your new input script should specify settings for -quantities like timestep size, thermodynamic and dump output, etc. +The list of "fixes"_fix.html used for a simulation is not stored in +the restart file. This means the new input script should specify all +fixes it will use. Note that some fixes store an internal "state" +which is written to the restart file. This allows the fix to continue +on with its calculations in a restarted simulation. To re-enable such +a fix, the fix command in the new input script must use the same +fix-ID and group-ID as was used in the input script that wrote the +restart file. If a match is found, LAMMPS prints a message indicating +that the fix is being re-enabled. If no match is found before the +first run or minimization is performed by the new script, the "state" +information for the saved fix is discarded. See the doc pages for +individual fixes for info on which ones can be restarted in this +manner. Bond interactions (angle, etc) that have been turned off by the "fix shake"_fix_shake.html or "delete_bonds"_delete_bonds.html command will @@ -115,15 +119,13 @@ Bonds that are broken (e.g. by a bond-breaking potential) are written to the restart file as broken bonds with a type of 0. Thus these bonds will still be broken when the restart file is read. -[Restrictions:] +IMPORTANT NOTE: No other information is stored in the restart file. +This means that an input script that reads a restart file should +specify settings for quantities like "timestep size"_timestep.html, +"thermodynamic"_thermo_style.html and "dump"_dump.html output, +"geometric regions"_region.html, etc. -The "pair_style"_pair_style.html {eam}, {table}, and {hybrid} styles -do not store coefficient data for individual atom type pairs in the -restart file. Nor does the "bond_style hybrid"_bond_style.html style -(angle, dihedral hybrid, etc). Thus for these styles you must use new -"pair_coeff"_pair_coeff.html and "bond_coeff"_bond_coeff.html (angle, -dihedral, etc) commands to read the appropriate tabulated files or -reset the coefficients after the restart file is read. +[Restrictions:] none [Related commands:] diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html index 3107dda6c1..d31b85b196 100644 --- a/doc/thermo_modify.html +++ b/doc/thermo_modify.html @@ -47,11 +47,11 @@ thermo_modify line multi format float %g by LAMMPS.IMPORTANT NOTE: These options apply to the currently defined thermo -style (thermo_style one by default). When you specify a -thermo_style command, all thermodynamic settings -are restored to their default values. Thus a thermo_style command -will wipe out any options previously specified by the -thermo_modify command. +style. When you specify a thermo_style command, +all thermodynamic settings are restored to their default values, +including those previously set by a thermo_modify command. Thus if +your input script specifies a thermo_style command, you should use the +thermo_modify command after it.
The lost keyword determines whether LAMMPS checks for lost atoms each time it computes thermodynamics and what it does if atoms are diff --git a/doc/thermo_modify.txt b/doc/thermo_modify.txt index 67e60be88e..432b3a4137 100644 --- a/doc/thermo_modify.txt +++ b/doc/thermo_modify.txt @@ -41,11 +41,11 @@ Set options for how thermodynamic information is computed and printed by LAMMPS. IMPORTANT NOTE: These options apply to the currently defined thermo -style (thermo_style {one} by default). When you specify a -"thermo_style"_thermo_style.html command, all thermodynamic settings -are restored to their default values. Thus a thermo_style command -will wipe out any options previously specified by the -"thermo_modify"_thermo_modify.html command. +style. When you specify a "thermo_style"_thermo_style.html command, +all thermodynamic settings are restored to their default values, +including those previously set by a thermo_modify command. Thus if +your input script specifies a thermo_style command, you should use the +thermo_modify command after it. The {lost} keyword determines whether LAMMPS checks for lost atoms each time it computes thermodynamics and what it does if atoms are diff --git a/doc/thermo_style.html b/doc/thermo_style.html index b18cfe9909..4d0c794878 100644 --- a/doc/thermo_style.html +++ b/doc/thermo_style.html @@ -108,11 +108,11 @@ be used to set the one- or multi-line format of the print-out, the normalization of energy quantities (total or per-atom), and the numeric precision of each printed value.
-IMPORTANT NOTE: When you specify a thermo_style -command, all thermodynamic settings are restored to their default -values. Thus a thermo_style command will wipe out any options -previously specified by the thermo_modify -command. +
IMPORTANT NOTE: When you specify a "thermo_style command, all +thermodynamic settings are restored to their default values, including +those previously set by a :thermo_modify command. +Thus if your input script specifies a thermo_style command, you should +use the thermo_modify command after it.
If c_ID is used as a keyword, then the scalar quantity calculated by the compute is printed. If c_ID[N] is used, then N in the range from 1-M will print the Nth component of the M-length vector -calculated by the compute. +calculated by the compute. See the doc pages for individual compute +styles for info on what these quantities are.
The f_ID and f_ID[N] keywords allow scalar or vector quantities calculated by a fix to be output. The ID in the keyword should be replaced by the actual ID of the fix that has been defined elsewhere -in the input script. See the fix command for details. +in the input script.
If f_ID is used as a keyword, then the scalar quantity calculated by the fix is printed. If f_ID[N] is used, then N in the range from 1-M will print the Nth component of the M-length vector calculated by -the fix. +the fix. See the doc pages for individual fix styles for info on what +these quantities are. For fixes that compute a contribution to the +potential energy of the system, the scalar quantity f_ID is typically +that quantity.
The v_name keyword allow the current value of a variable to be output. The name in the keyword should be replaced by the actual namd @@ -234,7 +239,8 @@ periodically during a simulation.
See this section for information on how to add new compute and fix styles as well as variable options to LAMMPS that -calculate quantities that could then be output with these keywords. +calculate quantities that could then be output with these keywords as +part of thermodyanmic information.