diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index 35b5419bc5..c168a5bd84 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/chunk command.

+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 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/chunk and compute ke/atom commands.

+with the fix ave/spatial 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/chunk and compute ke/atom commands. The fix tallies the +layers which can be monitored with the fix ave/spatial 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/chunk command, which determines +procedure can be monitored by the fix ave/spatial 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/chunk command. +monitored with the fix ave/spatial 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 3f41a6b156..7c6a5c2f0a 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 atom swapping and bond swapping
    • +
  • Monte Carlo via GCMC and tfMC and atom 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 f882ee234b..4522221d6c 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/atom, +doc/PDF/PDLammps_VES.pdf, atom_style peri, compute damage, pair_style peri/pmb, examples/peri

    @@ -1272,8 +1272,9 @@ 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 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 Section python 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 @@ -1426,7 +1427,7 @@ 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

    @@ -1474,8 +1475,8 @@ 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

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

    USER-TALLY Pairwise tallied computes Axel Kohlmeyer (Temple U) -compute XXX/tally +compute USER/tally
    -

    The pair_style body/rounded/polygon command -can be used with this body style to compute body/body interactions.

    +

    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:

    diff --git a/doc/html/compute_damage_atom.html b/doc/html/compute_damage_atom.html index 97a0eba0d0..bc378e49e8 100644 --- a/doc/html/compute_damage_atom.html +++ b/doc/html/compute_damage_atom.html @@ -170,8 +170,7 @@ LAMMPS was built with that package. See the diff --git a/doc/html/compute_dilatation_atom.html b/doc/html/compute_dilatation_atom.html index 798663b6a8..cf1947f3b2 100644 --- a/doc/html/compute_dilatation_atom.html +++ b/doc/html/compute_dilatation_atom.html @@ -172,8 +172,7 @@ 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 501319d8c8..0e46c9e7fe 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 54bffecbd2..11518b0c64 100644 --- a/doc/html/compute_plasticity_atom.html +++ b/doc/html/compute_plasticity_atom.html @@ -168,8 +168,7 @@ LAMMPS was built with that package. See the diff --git a/doc/html/fix_shardlow.html b/doc/html/fix_shardlow.html index 204f18df58..e54353f7eb 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 5be23f5d7b..77238ccae4 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 @@ -249,12 +249,14 @@ 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 ade80b4497..8ebde444af 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 1d279e5f3e..b0f9946dac 100644 --- a/doc/html/kspace_style.html +++ b/doc/html/kspace_style.html @@ -132,7 +132,7 @@ 
     none value = none
@@ -155,6 +155,8 @@
   accuracy = desired relative error in forces
 pppm/gpu value = accuracy
   accuracy = desired relative error in forces
+pppm/kk value = accuracy
+  accuracy = desired relative error in forces
 pppm/omp value = accuracy
   accuracy = desired relative error in forces
 pppm/cg/omp value = accuracy
@@ -195,7 +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:
    
 
@@ -385,6 +387,9 @@ If pppm/gpu is used with a GPU-enabled pair style, part of the PPPM
 calculation can be performed concurrently on the GPU while other
 calculations for non-bonded and bonded force calculation are performed
 on the CPU.
    
+
    The pppm/kk style also performs charge assignment and force
+interpolation calculations on the GPU while the FFTs themselves are
+calculated on the CPU in non-threaded mode.
    These accelerated styles are part of the GPU, USER-INTEL,
 KOKKOS, USER-OMP, and OPT packages respectively.  They are only
 enabled if LAMMPS was built with those packages.  See the Making LAMMPS section for more info.
    
@@ -406,10 +411,10 @@ the KSPACE package is installed by default.
    For MSM, a simulation must be 3d and one can use any combination of
 periodic, non-periodic, or shrink-wrapped boundaries (specified using
 the boundary command).
    
-
    For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions.
-The only exception is if the slab option is set with kspace_modify,
-in which case the xy dimensions must be periodic and the z dimension must be
-non-periodic.
    
+
    For Ewald and PPPM, a simulation must be 3d and periodic in all
+dimensions.  The only exception is if the slab option is set with
+kspace_modify, in which case the xy dimensions
+must be periodic and the z dimension must be non-periodic.
    
 
    Default
    
diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html
index eaf0a723c3..0f4bca68e6 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 a8b5437180..2325cfa256 100644
--- a/doc/html/pair_dipole.html
+++ b/doc/html/pair_dipole.html
@@ -268,15 +268,17 @@ 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 or the fix nvt/sphere update dipole command to rotate the
+
    Atoms with dipole moments should be integrated using the fix nve/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 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.
    
+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.
    
 
    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
@@ -346,8 +348,7 @@ currently supported.