diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index c168a5bd84..35b5419bc5 100644 --- a/doc/html/Section_howto.html +++ b/doc/html/Section_howto.html @@ -1086,7 +1086,7 @@ 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.

+the fix ave/chunk 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 computational efficiency to be 1/2 of the parallel box @@ -2011,13 +2011,13 @@ on each of two regions to add/subtract specified amounts of energy to both regions. In both cases, the resulting temperatures of the two regions can be monitored with the “compute temp/region” command and the temperature profile of the intermediate region can be monitored -with the fix ave/spatial and compute ke/atom commands.

+with the fix ave/chunk and compute ke/atom commands.

The third method is to perform a reverse non-equilibrium MD simulation using the fix thermal/conductivity command which implements the rNEMD algorithm of Muller-Plathe. Kinetic energy is swapped between atoms in two different layers of the simulation box. This induces a temperature gradient between the two -layers which can be monitored with the fix ave/spatial and compute ke/atom commands. The fix tallies the +layers which can be monitored with the fix ave/chunk and compute ke/atom commands. The fix tallies the cumulative energy transfer that it performs. See the fix thermal/conductivity command for details.

The fourth method is based on the Green-Kubo (GK) formula which @@ -2060,7 +2060,7 @@ used to shear the fluid in between them, again with some kind of thermostat that modifies only the thermal (non-shearing) components of velocity to prevent the fluid from heating up.

In both cases, the velocity profile setup in the fluid by this -procedure can be monitored by the fix ave/spatial command, which determines +procedure can be monitored by the fix ave/chunk command, which determines grad(Vstream) in the equation above. E.g. the derivative in the y-direction of the Vx component of fluid motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of the pressure or stress @@ -2073,7 +2073,7 @@ using the fix ave/spatial command. +monitored with the fix ave/chunk command. The fix tallies the cummulative momentum transfer that it performs. See the fix viscosity command for details.

The fourth method is based on the Green-Kubo (GK) formula which diff --git a/doc/html/Section_intro.html b/doc/html/Section_intro.html index 7c6a5c2f0a..3f41a6b156 100644 --- a/doc/html/Section_intro.html +++ b/doc/html/Section_intro.html @@ -391,7 +391,7 @@ molecular dynamics options:

  • coupled rigid body integration via the POEMS library
  • QM/MM coupling
  • path-integral molecular dynamics (PIMD) and this as well
    • -
  • Monte Carlo via GCMC and tfMC and atom swapping
    • +
  • Monte Carlo via GCMC and tfMC atom swapping and bond swapping
  • Direct Simulation Monte Carlo for low-density fluids
  • Peridynamics mesoscale modeling
  • Lattice Boltzmann fluid
    • diff --git a/doc/html/Section_packages.html b/doc/html/Section_packages.html index 4522221d6c..f882ee234b 100644 --- a/doc/html/Section_packages.html +++ b/doc/html/Section_packages.html @@ -1224,7 +1224,7 @@ styles which implement different materials models.

    Supporting info: doc/PDF/PDLammps_overview.pdf, doc/PDF/PDLammps_EPS.pdf, -doc/PDF/PDLammps_VES.pdf, atom_style peri, compute damage, +doc/PDF/PDLammps_VES.pdf, atom_style peri, compute damage/atom, pair_style peri/pmb, examples/peri

    @@ -1272,9 +1272,8 @@ one step. Type “python src/Make.py -h -poems” to see the details.

    4.1.22. PYTHON package

    Contents: A python command which allow you to execute Python code from a LAMMPS input script. The code can be in a separate -file or embedded in the input script itself. See Section python 11.2 for an overview of using Python from -LAMMPS and Section python for other ways to use -LAMMPS and Python together.

    +file or embedded in the input script itself. See Section python 11.2 for an overview of using Python from +LAMMPS and for other ways to use LAMMPS and Python together.

    Building with the PYTHON package assumes you have a Python shared library available on your system, which needs to be a Python 2 version, 2.6 or later. Python 3 is not supported. The build uses the @@ -1427,7 +1426,7 @@ few large bodies or many small bodies.

    Supporting info: compute erotate/rigid, -fix shake, fix rattle, fix rigid/*, examples/ASPHERE, examples/rigid

    +fix shake, fix rattle, fix rigid/*, examples/ASPHERE, examples/rigid

    @@ -1475,8 +1474,8 @@ properties of the potential are also included.

    Make.py -p ^snap -a machine
    -

    Supporting info: pair snap, compute sna/atom, compute snad/atom, -compute snav/atom, examples/snap

    +

    Supporting info: pair snap, compute sna/atom, compute snad/atom, +compute snav/atom, examples/snap

    @@ -1900,7 +1899,7 @@ src/Make.py -h -voronoi” to see the details.

    USER-TALLY Pairwise tallied computes Axel Kohlmeyer (Temple U) -compute +compute XXX/tally USER/tally
    diff --git a/doc/html/compute_dilatation_atom.html b/doc/html/compute_dilatation_atom.html index cf1947f3b2..798663b6a8 100644 --- a/doc/html/compute_dilatation_atom.html +++ b/doc/html/compute_dilatation_atom.html @@ -172,7 +172,8 @@ LAMMPS was built with that package. See the diff --git a/doc/html/compute_erotate_rigid.html b/doc/html/compute_erotate_rigid.html index 0e46c9e7fe..501319d8c8 100644 --- a/doc/html/compute_erotate_rigid.html +++ b/doc/html/compute_erotate_rigid.html @@ -172,7 +172,7 @@ LAMMPS was built with that package. See the diff --git a/doc/html/compute_plasticity_atom.html b/doc/html/compute_plasticity_atom.html index 11518b0c64..54bffecbd2 100644 --- a/doc/html/compute_plasticity_atom.html +++ b/doc/html/compute_plasticity_atom.html @@ -168,7 +168,8 @@ LAMMPS was built with that package. See the diff --git a/doc/html/fix_shardlow.html b/doc/html/fix_shardlow.html index e54353f7eb..204f18df58 100644 --- a/doc/html/fix_shardlow.html +++ b/doc/html/fix_shardlow.html @@ -148,7 +148,7 @@ integrate the DPD equations of motion. The SSA splits the integration into a stochastic and deterministic integration step. The fix shardlow performs the stochastic integration step and must be used -in conjunction with a deterministic integrator (e.g. fix nve or fix nph). The stochastic +in conjunction with a deterministic integrator (e.g. fix nve or fix nph). The stochastic integration of the dissipative and random forces is performed prior to the deterministic integration of the conservative force. Further details regarding the method are provided in (Lisal) and diff --git a/doc/html/fix_smd.html b/doc/html/fix_smd.html index 77238ccae4..5be23f5d7b 100644 --- a/doc/html/fix_smd.html +++ b/doc/html/fix_smd.html @@ -168,10 +168,10 @@

    Description

    This fix implements several options of steered MD (SMD) as reviewed in -(Izrailev), which allows to induce conformational changes +(Izrailev), which allows to induce conformational changes in systems and to compute the potential of mean force (PMF) along the -assumed reaction coordinate (Park) based on Jarzynski’s -equality (Jarzynski). This fix borrows a lot from fix spring and fix setforce.

    +assumed reaction coordinate (Park) based on Jarzynski’s +equality (Jarzynski). This fix borrows a lot from fix spring and fix setforce.

    You can apply a moving spring force to a group of atoms (tether style) or between two groups of atoms (couple style). The spring can then be used in either constant velocity (cvel) mode or in @@ -249,14 +249,12 @@ LAMMPS was built with that package. See the fix spring/rg

    Default: none

    -

    (Izrailev) Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, +

    (Izrailev) Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, Wriggers, Schulten. Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.

    -

    (Park) -Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)

    -

    (Jarzynski) -Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)

    +

    (Park) Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)

    +

    (Jarzynski) Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)

    diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html index 8ebde444af..ade80b4497 100644 --- a/doc/html/fix_wall_piston.html +++ b/doc/html/fix_wall_piston.html @@ -205,7 +205,7 @@ define the lattice spacings.

    Restart, fix_modify, output, run start/stop, minimize info

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output commands. No parameter of this fix can +by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

    diff --git a/doc/html/kspace_style.html b/doc/html/kspace_style.html index b0f9946dac..53a0c22ce2 100644 --- a/doc/html/kspace_style.html +++ b/doc/html/kspace_style.html @@ -197,7 +197,7 @@ style, the cutoff for Coulombic or 1/r^N interactions is effectively infinite. If the Coulombic case, this means each charge in the system interacts with charges in an infinite array of periodic images of the simulation domain.

    -

    Note that using a long-range solver requires use of a matching pair style to perform consistent short-range pairwise +

    Note that using a long-range solver requires use of a matching pair style to perform consistent short-range pairwise calculations. This means that the name of the pair style contains a matching keyword to the name of the KSpace style, as in this table:

    diff --git a/doc/html/molecule.html b/doc/html/molecule.html index 85087417db..094f231291 100644 --- a/doc/html/molecule.html +++ b/doc/html/molecule.html @@ -297,7 +297,7 @@ manner.

    Whether a section is required depends on how the molecule template is used by other LAMMPS commands. For example, to add a molecule via the fix deposit command, the Coords -and Types sections are required. To add a rigid body via the fix pour command, the Bonds (Angles, etc) sections are not +and Types sections are required. To add a rigid body via the fix pour command, the Bonds (Angles, etc) sections are not required, since the molecule will be treated as a rigid body. Some sections are optional. For example, the fix pour command can be used to add “molecules” which are clusters of diff --git a/doc/html/neighbor.html b/doc/html/neighbor.html index d1c2630e8b..65a47dfcc1 100644 --- a/doc/html/neighbor.html +++ b/doc/html/neighbor.html @@ -192,7 +192,7 @@ are printed to the screen and log file. See

    Related commands

    neigh_modify, units, -comm_modify

    +comm_modify

    Default

    diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html index 0f4bca68e6..eaf0a723c3 100644 --- a/doc/html/pair_brownian.html +++ b/doc/html/pair_brownian.html @@ -227,7 +227,7 @@ to be specified in an input script that reads a restart file.

    Restrictions

    These styles are part of the COLLOID package. 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.

    Only spherical monodisperse particles are allowed for pair_style brownian.

    Only spherical particles are allowed for pair_style brownian/poly.

    diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html index 2325cfa256..a8b5437180 100644 --- a/doc/html/pair_dipole.html +++ b/doc/html/pair_dipole.html @@ -268,17 +268,15 @@ dipole interactions. The long-range portion is calculated by using ewald_disp of the kspace_style command. If flag_coul is set to off, Coulombic and dipole interactions are not computed at all.

    -

    Atoms with dipole moments should be integrated using the fix nve/sphere update dipole command to rotate the +

    Atoms with dipole moments should be integrated using the fix nve/sphere update dipole or the fix nvt/sphere update dipole command to rotate the dipole moments. The omega option on the fix langevin command can be used to thermostat the rotational motion. The compute temp/sphere command can be used to monitor the temperature, since it includes -rotational degrees of freedom. The atom_style dipole command should be used since it defines the -point dipoles and their rotational state. The magnitude of the dipole -moment for each type of particle can be defined by the -dipole command or in the “Dipoles” section of the data -file read in by the read_data command. Their initial -orientation can be defined by the set dipole command or in -the “Atoms” section of the data file.

    +rotational degrees of freedom. The atom_style hybrid dipole sphere command should be used since +it defines the point dipoles and their rotational state. +The magnitude and orientation of the dipole moment for each particle +can be defined by the set command or in the “Atoms” section +of the data file read in by the read_data command.

    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 @@ -348,7 +346,8 @@ currently supported.