LAMMPS-ICMS Documentation¶
Version info:¶
@@ -437,7 +437,7 @@ it gives quick access to documentation for all LAMMPS commands. @@ -338,7 +338,7 @@ occurs, the faster your simulation will run. @@ -367,7 +367,7 @@ storage by a single MPI process. @@ -428,7 +428,7 @@ supported. @@ -586,7 +586,7 @@ change in the future. @@ -303,7 +303,7 @@ MPI tasks to a (multi-core) socket, should solve this issue. @@ -205,7 +205,7 @@ of a run. On most machines for reasonable problem sizes, it will be a @@ -152,7 +152,7 @@ angle_coeff 1 300.0 107.0 50.0 3.0with an additional Urey_Bradley term based on the distance r between the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are coefficients defined for each angle type.
-See (MacKerell) for a description of the CHARMM force +
See (MacKerell) for a description of the CHARMM force field.
The following coefficients must be defined for each angle type via the angle_coeff command as in the example above, or in @@ -230,7 +230,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
@@ -151,7 +151,7 @@ angle_coeff * ba 3.6551 24.895 1.0119 1.5228where Ea is the angle term, Ebb is a bond-bond term, and Eba is a bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are the equilibrium bond lengths.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
Coefficients for the Ea, Ebb, and Eba formulas must be defined for each angle type via the angle_coeff command as in the example above, or in the data file or restart files read by the @@ -257,7 +257,7 @@ for more info on packages.
@@ -245,7 +245,7 @@ set, either in the input script or in a data file. @@ -215,7 +215,7 @@ MOLECULE package (which it is by default). See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/angle_cosine_delta.html b/doc/angle_cosine_delta.html index 1ffad090a7..ed7a2cbfd9 100644 --- a/doc/angle_cosine_delta.html +++ b/doc/angle_cosine_delta.html @@ -8,7 +8,7 @@ -
where C, B and n are coefficients defined for each angle type.
-See (Mayo) for a description of the DREIDING force field
+See (Mayo) for a description of the DREIDING force field
The following coefficients must be defined for each angle type via the
angle_coeff command as in the example above, or in
the data file or restart files read by the read_data
@@ -229,7 +229,7 @@ MOLECULE package (which it is by default). See the
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'9 Dec 2015',
+ VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
diff --git a/doc/angle_cosine_shift.html b/doc/angle_cosine_shift.html
index 58489df370..5e61e04759 100644
--- a/doc/angle_cosine_shift.html
+++ b/doc/angle_cosine_shift.html
@@ -8,7 +8,7 @@
-
| nparticle | -rigid body with N sub-particles | -
rounded/polygon | ++———————————–+—————————————————+ +| 2d convex polygon with N vertices | | ++———————————–+—————————————————+
The body style determines what attributes are stored for each body and thus how they can be used to compute pairwise body/body or bond/non-body (point particle) interactions. More details of each @@ -203,11 +196,23 @@ particles of different styles
These values are the current position of the sub-particle within the simulation domain, not a displacement from the center-of-mass (COM) of the body particle itself. These values are calculated using the -current COM and orientiation of the body particle.
+current COM and orientation of the body particle. ++
Specifics of body style rounded/polygon:
+The rounded/polygon body style represents body particles as a convex +polygon with a variable number N > 2 of vertices, which can only be +used for 2d models. One example use of this body style is for 2d +discrete element models, as described in Fraige. Similar to +body style nparticle, the atom_style body command for this body +style takes two additional arguments:
+atom_style body rounded/polygon Nmin Nmax
+Nmin = minimum # of vertices in any body in the system
+Nmax = maximum # of vertices in any body in the system
+The Nmin and Nmax arguments are used to bound the size of data +structures used internally by each particle.
+When the read_data command reads a data file for this +body style, the following information must be provided for each entry +in the Bodies section of the data file:
+atom-ID 1 M
+N
+ixx iyy izz ixy ixz iyz x1 y1 z1 ...
+...
+... xN yN zN i j j k ...
+N is the number of vertices in the body particle. M = 6 + 3*N + 2*N + +1. The integer line has a single value N. The floating point line(s) +list 6 moments of inertia followed by the coordinates of the N +vertices (x1 to zN) as 3N values on as many lines as required. Note +that this in not N lines, but 10 values per line; see the +read_data command for details. The next 2N elements +are the vertex indices corresponding to the ends of the N edges. The +vertex indices (i, j, k, ...) range from 0 to (N-1), consistent with +the order of the vertices listed. The last element is the radius of +the smallest circle encompassing the polygon, which is used to +facilitate the body/body contact detection.
+The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the +values consistent with the current orientation of the rigid body +around its center of mass. The values are with respect to the +simulation box XYZ axes, not with respect to the prinicpal axes of the +rigid body itself. LAMMPS performs the latter calculation internally. +The coordinates of each vertex are specified as its x,y,z displacement +from the center-of-mass of the body particle. The center-of-mass +position of the particle is specified by the x,y,z values in the +Atoms section of the data file.
+For example, the following information would specify a square +particles whose edge length is sqrt(2):
+3 1 27
+4
+1 1 4 0 0 0 -0.7071 -0.7071 0 -0.7071
+0.7071 0 0.7071 0.7071 0 0.7071 -0.7071 0 0 1
+1 2 2 3 3 0 1.0
+The pair_style body/rounded/polygon command +can be used with this body style to compute body/body interactions.
+For output purposes via the compute body/local and dump local +commands, this body style produces one datum for each of the N +sub-particles in a body particle. The datum has 3 values:
+1 = x position of vertex
+2 = y position of vertex
+3 = z position of vertex
+These values are the current position of the vertex within the +simulation domain, not a displacement from the center-of-mass (COM) of +the body particle itself. These values are calculated using the +current COM and orientation of the body particle.
++
(Fraige) F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, +Particuology, 6, 455 (2008).
@@ -303,7 +379,7 @@ current COM and orientiation of the body particle. @@ -147,7 +147,7 @@ bond_coeff 1 1.0 100.0 80.0 80.0The class2 bond style uses the potential
where r0 is the equilibrium bond distance.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
The following coefficients must be defined for each bond type via the bond_coeff command as in the example above, or in the data file or restart files read by the read_data @@ -222,7 +222,7 @@ for more info on packages.
@@ -242,7 +242,7 @@ either in the input script or in a data file. @@ -150,7 +150,7 @@ bond_coeff 1 30.0 1.5 1.0 1.0The fene bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential -(Kremer), used for bead-spring polymer models. The first +(Kremer), used for bead-spring polymer models. The first term is attractive, the 2nd Lennard-Jones term is repulsive. The first term extends to R0, the maximum extent of the bond. The 2nd term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
@@ -230,7 +230,7 @@ style. LAMMPS will issue a warning it that’s not the case. @@ -147,7 +147,7 @@ bond_coeff 1 30.0 1.5 1.0 1.0 0.5The fene/expand bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential -(Kremer), used for bead-spring polymer models. The first +(Kremer), used for bead-spring polymer models. The first term is attractive, the 2nd Lennard-Jones term is repulsive.
The fene/expand bond style is similar to fene except that an extra shift factor of delta (positive or negative) is added to r to @@ -231,7 +231,7 @@ style. LAMMPS will issue a warning it that’s not the case.
@@ -220,7 +220,7 @@ MOLECULE package (which it is by default). See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/bond_harmonic_shift.html b/doc/bond_harmonic_shift.html index 48b038770f..d3b91dd2c9 100644 --- a/doc/bond_harmonic_shift.html +++ b/doc/bond_harmonic_shift.html @@ -8,7 +8,7 @@ -The bin/sphere style defines a set of spherical shells around the -origin (xorig,*yorig*,*zorig*), using nsbin shells with radii -equally spaced between srmin and srmax, for effectively a 1d +
The bin/sphere style defines a set of spherical shell bins around +the origin (xorig,*yorig*,*zorig*), using nsbin bins with radii +equally spaced between srmin and srmax. This is effectively a 1d vector of bins. For example, if srmin = 1.0 and srmax = 10.0 and nsbin = 9, then the first bin spans 1.0 < r < 2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins is the same whether the @@ -298,29 +298,30 @@ simulation box is orthogonal or triclinic; i.e. the spherical shells are not tilted or scaled differently in different dimensions to transform them into ellipsoidal shells.
The bin/cylinder style defines bins for a cylinder oriented along -the axis dim with the axis position in the other two radial +the axis dim with the axis coordinates in the other two radial dimensions at (c1,*c2*). For dim = x, c1/c2 = y/z; for dim = y, -c1/c2 = x/z; for dim = z, c1/c2 = x/y. These can be thought of as a -2d array of bins, each of which is a pie-shaped wedge (radial -dimensions) of finite height (along the cylinder axis). The bin size +c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array +of bins. The first dimension is along the cylinder axis, the second +dimension is radially outward from the cylinder axis. The bin size and positions along the cylinder axis are specified by the origin and delta values, the same as for the bin/1d, bin/2d, and -bin/3d styles. There are ncbin concentric circles in the radial -direction from the cylinder axis with radii equally spaced between -crmin and crmax. For example, if crmin = 1.0 and crmax = 10.0 -and ncbin = 9, then the first bin spans 1.0 < r < 2.0, and the last -bin spans 9.0 < r 10.0. The geometry of the bins in the radial -dimensions is the same whether the simulation box is orthogonal or -triclinic; i.e. the circles are not tilted or scaled differently in -the two different dimensions to transform them into ellipses.
+bin/3d styles. There are ncbin concentric circle bins in the +radial direction from the cylinder axis with radii equally spaced +between crmin and crmax. For example, if crmin = 1.0 and +crmax = 10.0 and ncbin = 9, then the first bin spans 1.0 < r < +2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in +the radial dimensions is the same whether the simulation box is +orthogonal or triclinic; i.e. the concetric circles are not tilted or +scaled differently in the two different dimensions to transform them +into ellipses.The created bins (and hence the chunk IDs) are numbered consecutively -from 1 to the number of bins = Nchunk. For 2d and 3d bins, the +from 1 to the number of bins = Nchunk. For bin2d and bin3d, the numbering varies most rapidly in the first dimension (which could be x, y, or z), next rapidly in the 2nd dimension, and most slowly in the -3rd dimension. For spherical 1d bins, the innermost shell is chunk 1 -and the outermost shell is chunk Nchunk = nsbin. For cylindrical -2d bins, the numbering varies most rapidly in the dimension along the -cylinder axis and most slowly in the radial direction.
+3rd dimension. For bin/sphere, the bin with smallest radii is chunk +1 and the bni with largest radii is chunk Nchunk = ncbin. For +bin/cylinder, the numbering varies most rapidly in the dimension +along the cylinder axis and most slowly in the radial direction.Each time this compute is invoked, each atom is mapped to a bin based on its current position. Note that between reneighboring timesteps, atoms can move outside the current simulation box. If the box is @@ -718,7 +719,7 @@ the restarted simulation begins.
@@ -226,7 +226,7 @@ LAMMPS output options. @@ -238,7 +238,7 @@ above. @@ -210,7 +210,7 @@ distance units. @@ -234,7 +234,7 @@ distance units. @@ -203,7 +203,7 @@ above. @@ -242,7 +242,7 @@ explained above. @@ -206,7 +206,7 @@ LAMMPS was built with that package. See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/compute_dihedral_local.html b/doc/compute_dihedral_local.html index 4a3eb0c197..d330295936 100644 --- a/doc/compute_dihedral_local.html +++ b/doc/compute_dihedral_local.html @@ -8,7 +8,7 @@ -Description¶
Define a computation that calculates electron diffraction intensity as -described in (Coleman) on a mesh of reciprocal lattice nodes +described in (Coleman) on a mesh of reciprocal lattice nodes defined by the entire simulation domain (or manually) using simulated radiation of wavelength lambda.
The electron diffraction intensity I at each reciprocal lattice point @@ -330,7 +330,7 @@ Volume C: Mathematical and Chemical Tables, 554-95 (2004).
@@ -256,7 +256,7 @@ input quantities are in. @@ -201,7 +201,7 @@ LAMMPS was built with that package. See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/compute_smd_damage.html b/doc/compute_smd_damage.html index db64799071..de54818ea6 100644 --- a/doc/compute_smd_damage.html +++ b/doc/compute_smd_damage.html @@ -8,7 +8,7 @@ -Description¶
Define a computation that calculates x-ray diffraction intensity as described -in (Coleman) on a mesh of reciprocal lattice nodes defined +in (Coleman) on a mesh of reciprocal lattice nodes defined by the entire simulation domain (or manually) using a simulated radiation of wavelength lambda.
The x-ray diffraction intensity, I, at each reciprocal lattice point, k, @@ -356,7 +356,7 @@ Volume C: Mathematical and Chemical Tables, 249-429 (2004).
@@ -460,7 +460,7 @@ random, and units = lattice. @@ -258,7 +258,7 @@ molecule template files via the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/create_box.html b/doc/create_box.html index ef1a5ea372..b3b7528094 100644 --- a/doc/create_box.html +++ b/doc/create_box.html @@ -8,7 +8,7 @@ -Description¶
The charmm dihedral style uses the potential
-See (MacKerell) for a description of the CHARMM force +
See (MacKerell) for a description of the CHARMM force field. This dihedral style can also be used for the AMBER force field -(see comment on weighting factors below). See (Cornell) +(see comment on weighting factors below). See (Cornell) for a description of the AMBER force field.
The following coefficients must be defined for each dihedral type via the dihedral_coeff command as in the example above, or in @@ -252,7 +252,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
@@ -156,7 +156,7 @@ Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium bond lengths.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas must be defined for each dihedral type via the dihedral_coeff command as in the example above, @@ -315,7 +315,7 @@ section for more info on packages.
@@ -256,7 +256,7 @@ set, either in the input script or in a data file. @@ -229,7 +229,7 @@ section for more info on packages. @@ -222,7 +222,7 @@ section for more info on packages. @@ -230,7 +230,7 @@ MOLECULE package (which it is by default). See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/dihedral_helix.html b/doc/dihedral_helix.html index 76ca75fd21..0f3c7268fa 100644 --- a/doc/dihedral_helix.html +++ b/doc/dihedral_helix.html @@ -8,7 +8,7 @@ -
Full details of the lattice-Boltzmann algorithm used can be found in -Mackay et al..
+Mackay et al..The fluid is coupled to the MD particles described by group-ID through a velocity dependent force. The contribution to the fluid force on a given lattice mesh site j due to MD particle alpha is @@ -242,7 +242,7 @@ using the setArea keyword.
The user also has the option of specifying their own value for the force coupling constant, for all the MD particles associated with the fix, through the use of the setGamma keyword. This may be useful -when modelling porous particles. See Mackay et al. for a +when modelling porous particles. See Mackay et al. for a detailed description of the method by which the user can choose an appropriate gamma value.
@@ -256,7 +256,7 @@ This fix adds the hydrodynamic force to the total force acting on the
particles, after which any of the built-in LAMMPS integrators can be
used to integrate the particle motion. However, if the user specifies
their own value for the force coupling constant, as mentioned in
-Mackay et al., the built-in LAMMPS integrators may prove to
+Mackay et al., the built-in LAMMPS integrators may prove to
be unstable. Therefore, we have included our own integrators fix lb/rigid/pc/sphere, and fix lb/pc, to solve for the particle motion in these
cases. These integrators should not be used with the
lb/viscous fix, as they add hydrodynamic forces
@@ -341,7 +341,7 @@ N timesteps.
@@ -463,7 +463,7 @@ If walls are present, they are assumed to be stationary.
@@ -225,7 +225,7 @@ was built with that package. See the
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'9 Dec 2015',
+ VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
diff --git a/doc/fix_lb_pc.html b/doc/fix_lb_pc.html
index 312bceecc1..611665c640 100644
--- a/doc/fix_lb_pc.html
+++ b/doc/fix_lb_pc.html
@@ -8,7 +8,7 @@
- If the keyword trilinear is used, the trilinear stencil is used to interpolate the particle nodes onto the fluid mesh. By default, the immersed boundary method, Peskin stencil is used. Both of these -interpolation methods are described in Mackay et al..
+interpolation methods are described in Mackay et al..If the keyword D3Q19 is used, the 19 velocity (D3Q19) lattice is used by the lattice-Boltzmann algorithm. By default, the 15 velocity (D3Q15) lattice is used.
@@ -371,7 +371,7 @@ the fluid densities and velocities at each lattice site are printed to the screen every N timesteps.For further details, as well as descriptions and results of several -test runs, see Mackay et al.. Please include a citation to +test runs, see Mackay et al.. Please include a citation to this paper if the lb_fluid fix is used in work contributing to published research.
The equations of motion used are those of Shinoda et al in (Shinoda), which combine the hydrostatic equations of -Martyna, Tobias and Klein in (Martyna) with the strain +Martyna, Tobias and Klein in (Martyna) with the strain energy proposed by Parrinello and Rahman in -(Parrinello). The time integration schemes closely +(Parrinello). The time integration schemes closely follow the time-reversible measure-preserving Verlet and rRESPA -integrators derived by Tuckerman et al in (Tuckerman).
+integrators derived by Tuckerman et al in (Tuckerman).The thermostat parameters for fix styles nvt and npt is specified using the temp keyword. Other thermostat-related keywords are @@ -394,7 +394,7 @@ freedom. A value of 0 corresponds to no thermostatting of the barostat variables.
The mtk keyword controls whether or not the correction terms due to Martyna, Tuckerman, and Klein are included in the equations of motion -(Martyna). Specifying no reproduces the original +(Martyna). Specifying no reproduces the original Hoover barostat, whose volume probability distribution function differs from the true NPT and NPH ensembles by a factor of 1/V. Hence using yes is more correct, but in many cases the difference is @@ -403,7 +403,7 @@ negligible.
scheme at little extra cost. The initial and final updates of the thermostat variables are broken up into tloop substeps, each of length dt/tloop. This corresponds to using a first-order -Suzuki-Yoshida scheme (Tuckerman). The keyword ploop +Suzuki-Yoshida scheme (Tuckerman). The keyword ploop does the same thing for the barostat thermostat.The keyword nreset controls how often the reference dimensions used to define the strain energy are reset. If this keyword is not used, @@ -718,7 +718,7 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006).
@@ -295,7 +295,7 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006). @@ -281,7 +281,7 @@ shape attribute. @@ -279,7 +279,7 @@ be point particles. @@ -357,7 +357,7 @@ plus the additional ones mentioned above. @@ -304,7 +304,7 @@ shape attribute. @@ -300,7 +300,7 @@ be point particles. @@ -226,7 +226,7 @@ This fix is not invoked during var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html index 0a8d9a26ee..681cddd7b3 100644 --- a/doc/fix_nve_asphere.html +++ b/doc/fix_nve_asphere.html @@ -8,7 +8,7 @@ -- compute property/atom @@ -670,6 +670,10 @@ +
- compute temp/body + + +
- compute temp/chunk @@ -1122,6 +1126,10 @@ +
- fix nph/body + + +
- fix nph/sphere @@ -1134,6 +1142,10 @@ +
- fix npt/body + + +
- fix npt/sphere @@ -1157,12 +1169,12 @@
- fix nve/eff +
- fix nve/line @@ -1188,6 +1200,10 @@ +
- fix nvt/body + + +
- fix nvt/eff @@ -1660,6 +1676,10 @@ +
- pair_style body/rounded/polygon + + +
- pair_style bop @@ -1811,12 +1831,12 @@
- pair_style lj/smooth +
- pair_style lj96/cut @@ -2218,7 +2238,7 @@ @@ -424,7 +424,7 @@ those currently in the dynamic group. @@ -200,7 +200,7 @@ LAMMPS was built with that package. See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/if.html b/doc/if.html index bdf53f7254..fabdc71a2d 100644 --- a/doc/if.html +++ b/doc/if.html @@ -8,7 +8,7 @@ -
Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L would exist for an improper to be defined between the 4 atoms, but this is not required.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
Coefficients for the Ei and Eaa formulas must be defined for each improper type via the improper_coeff command as in the example above, or in the data file or restart files read by the @@ -259,7 +259,7 @@ section for more info on packages.
@@ -244,7 +244,7 @@ set, either in the input script or in a data file. @@ -231,7 +231,7 @@ section for more info on packages. @@ -228,7 +228,7 @@ MOLECULE package (which it is by default). See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/improper_distance.html b/doc/improper_distance.html index de6abe830d..018b404c1b 100644 --- a/doc/improper_distance.html +++ b/doc/improper_distance.html @@ -8,7 +8,7 @@ -If omega0 = 0 the potential term has a minimum for the planar structure. Otherwise it has two minima at +/- omega0, with a barrier in between.
-See (Mayo) for a description of the DREIDING force field.
+See (Mayo) for a description of the DREIDING force field.
The following coefficients must be defined for each improper type via
the improper_coeff command as in the example
above, or in the data file or restart files read by the
@@ -228,7 +228,7 @@ MOLECULE package (which it is by default). See the
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'9 Dec 2015',
+ VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
diff --git a/doc/include.html b/doc/include.html
index 60bdfb3754..6534c08532 100644
--- a/doc/include.html
+++ b/doc/include.html
@@ -8,7 +8,7 @@
-
Both the LJ and Coulombic terms require an inner and outer cutoff. @@ -357,7 +357,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
@@ -213,7 +213,7 @@ pair_coeff 1 1 100.0 3.5 9.0Rc is the cutoff.
The lj/class2/coul/cut and lj/class2/coul/long styles add a Coulombic term as described for the lj/cut pair styles.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples
above, or in the data file or restart files read by the
@@ -328,7 +328,7 @@ LAMMPS was built with that package. See the
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'9 Dec 2015',
+ VERSION:'15 Dec 2015',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html
index 2c537411e4..4769a6d8cb 100644
--- a/doc/pair_coeff.html
+++ b/doc/pair_coeff.html
@@ -8,7 +8,7 @@
-
Style hbond/dreiding/lj is the original DREIDING potential of -(Mayo). It uses a LJ 12/10 functional for the Donor-Acceptor +(Mayo). It uses a LJ 12/10 functional for the Donor-Acceptor interactions. To match the results in the original paper, use n = 4.
Style hbond/dreiding/morse is an improved version using a Morse potential for the Donor-Acceptor interactions. (Liu) showed @@ -377,7 +377,7 @@ thermo_style custom step temp epair v_E_hbond @@ -511,7 +511,7 @@ the same or else LAMMPS will generate an error.
@@ -255,7 +255,7 @@ kim-api package version 1.6.0 and higher. @@ -235,7 +235,7 @@ appropriate units if your simulation doesn’t use “metal” units @@ -268,7 +268,7 @@ line/line or line/particle interactions requires the use the @@ -281,7 +281,7 @@ LAMMPS is build with that package. See the Making @@ -515,7 +515,7 @@ Phys, 79, 926 (1983). @@ -251,7 +251,7 @@ details. @@ -264,7 +264,7 @@ support the inner, middle, outer keywords. @@ -255,7 +255,7 @@ to be specified in an input script that reads a restart file. @@ -357,7 +357,7 @@ the KSPACE package is installed by default. @@ -247,7 +247,7 @@ if LAMMPS was built with that package. See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'15 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/pair_lj_smooth.html b/doc/pair_lj_smooth.html index 7401dbeed7..5aafdb1c44 100644 --- a/doc/pair_lj_smooth.html +++ b/doc/pair_lj_smooth.html @@ -8,7 +8,7 @@ -