From 5277242cfeed0e4f181121ae674ad421f97f6ea4 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 6 Sep 2016 22:56:36 +0000 Subject: [PATCH] GH changes to doc pages git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15552 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/Section_howto.html | 14 +-- doc/html/Section_intro.html | 2 +- doc/html/Section_modify.html | 122 +++++++++++++++++------- doc/html/Section_packages.html | 39 ++++---- doc/html/Section_start.html | 2 +- doc/html/accelerate_kokkos.html | 2 +- doc/html/compute_damage_atom.html | 3 +- doc/html/compute_dilatation_atom.html | 3 +- doc/html/compute_erotate_rigid.html | 2 +- doc/html/compute_plasticity_atom.html | 3 +- doc/html/compute_reduce.html | 2 +- doc/html/compute_temp_deform_eff.html | 7 +- doc/html/compute_temp_eff.html | 2 +- doc/html/dihedral_table.html | 2 +- doc/html/dump.html | 2 +- doc/html/dump_custom_vtk.html | 26 +++--- doc/html/fix_ave_chunk.html | 4 +- doc/html/fix_bond_create.html | 2 +- doc/html/fix_deform.html | 2 +- doc/html/fix_deposit.html | 2 +- doc/html/fix_ehex.html | 4 +- doc/html/fix_eos_table.html | 4 +- doc/html/fix_eos_table_rx.html | 2 +- doc/html/fix_lb_momentum.html | 2 +- doc/html/fix_lb_pc.html | 2 +- doc/html/fix_nh_eff.html | 2 +- doc/html/fix_phonon.html | 2 +- doc/html/fix_pour.html | 2 +- doc/html/fix_reax_bonds.html | 2 +- doc/html/fix_rx.html | 2 +- doc/html/fix_shardlow.html | 2 +- doc/html/fix_smd.html | 14 ++- doc/html/fix_wall_piston.html | 2 +- doc/html/kspace_style.html | 2 +- doc/html/molecule.html | 2 +- doc/html/neighbor.html | 2 +- doc/html/pair_brownian.html | 2 +- doc/html/pair_dipole.html | 17 ++-- doc/html/pair_dpd_fdt.html | 2 +- doc/html/pair_gayberne.html | 2 +- doc/html/pair_line_lj.html | 2 +- doc/html/pair_thole.html | 2 +- doc/html/pair_tri_lj.html | 2 +- doc/html/python.html | 2 +- doc/html/rerun.html | 2 +- doc/html/variable.html | 2 +- doc/src/Section_howto.txt | 14 +-- doc/src/Section_intro.txt | 2 +- doc/src/Section_modify.txt | 130 ++++++++++++++++++-------- doc/src/Section_packages.txt | 36 +++---- doc/src/Section_start.txt | 2 +- doc/src/accelerate_kokkos.txt | 2 +- doc/src/compute_damage_atom.txt | 4 +- doc/src/compute_dilatation_atom.txt | 4 +- doc/src/compute_erotate_rigid.txt | 2 +- doc/src/compute_plasticity_atom.txt | 4 +- doc/src/compute_rdf.txt | 2 +- doc/src/compute_reduce.txt | 2 +- doc/src/compute_temp_deform_eff.txt | 9 +- doc/src/compute_temp_eff.txt | 2 +- doc/src/dihedral_table.txt | 2 +- doc/src/dump.txt | 2 +- doc/src/dump_custom_vtk.txt | 26 +++--- doc/src/fix_ave_chunk.txt | 4 +- doc/src/fix_bond_create.txt | 2 +- doc/src/fix_deform.txt | 2 +- doc/src/fix_deposit.txt | 2 +- doc/src/fix_ehex.txt | 4 +- doc/src/fix_eos_table.txt | 4 +- doc/src/fix_eos_table_rx.txt | 2 +- doc/src/fix_lb_momentum.txt | 2 +- doc/src/fix_lb_pc.txt | 2 +- doc/src/fix_nh_eff.txt | 2 +- doc/src/fix_phonon.txt | 2 +- doc/src/fix_pour.txt | 2 +- doc/src/fix_reax_bonds.txt | 2 +- doc/src/fix_rx.txt | 2 +- doc/src/fix_shardlow.txt | 2 +- doc/src/fix_smd.txt | 10 +- doc/src/fix_wall_piston.txt | 2 +- doc/src/kspace_style.txt | 2 +- doc/src/molecule.txt | 2 +- doc/src/neighbor.txt | 2 +- doc/src/pair_brownian.txt | 2 +- doc/src/pair_dipole.txt | 18 ++-- doc/src/pair_dpd_fdt.txt | 2 +- doc/src/pair_gayberne.txt | 2 +- doc/src/pair_line_lj.txt | 2 +- doc/src/pair_thole.txt | 2 +- doc/src/pair_tri_lj.txt | 2 +- doc/src/python.txt | 2 +- doc/src/rerun.txt | 2 +- doc/src/variable.txt | 2 +- 93 files changed, 381 insertions(+), 280 deletions(-) diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index c168a5bd84..d29a4556f4 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 @@ -1773,9 +1773,9 @@ translation velocities but also rotational velocities for spherical and aspherical particles.

All of the barostatting fixes use the compute pressure compute to calculate a current pressure. By default, this compute is created with a simple compute temp (see the last argument of the compute pressure command), which is used to calculated -the kinetic componenet of the pressure. The barostatting fixes can +the kinetic component of the pressure. The barostatting fixes can also use temperature computes that remove bias for the purpose of -computing the kinetic componenet which contributes to the current +computing the kinetic component which contributes to the current pressure. See the doc pages for the individual fixes and for the fix_modify command for instructions on how to assign a temperature or pressure compute to a barostatting fix.

@@ -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_modify.html b/doc/html/Section_modify.html index 88ab26a836..1ddbd8f04a 100644 --- a/doc/html/Section_modify.html +++ b/doc/html/Section_modify.html @@ -1057,11 +1057,35 @@ then be accessed by variables) was discussed

    10.15. Submitting new features for inclusion in LAMMPS

    -

    We encourage users to submit new features to the developers that they add to -LAMMPS, especially if you think they will be of interest to other -users. The preferred way to do this is via GitHub. Once you have -prepared the content described below, see this tutorial for instructions on how to submit -your changes or new files.

    +

    We encourage users to submit new features or modifications for +LAMMPS to the core developers +so they can be added to the LAMMPS distribution. The preferred way to +manage and coordinate this is as of Fall 2016 via the LAMMPS project on +GitHub. An alternative is to contact +the LAMMPS developers or the indicated developer of a package or feature +directly and send in your contribution via e-mail.

    +

    For any larger modifications or programming project, you are encouraged +to contact the LAMMPS developers ahead of time, in order to discuss +implementation strategies and coding guidelines, that will make it +easier to integrate your contribution and result in less work for +everybody involved. You are also encouraged to search through the list +of open issues on GitHub and +submit a new issue for a planned feature, so you would not duplicate +the work of others (and possibly get scooped by them) or have your work +duplicated by others.

    +

    How quickly your contribution will be integrated +depends largely on how much effort it will cause to integrate and test +it, how much it requires changes to the core codebase, and of how much +interest it is to the larger LAMMPS community. Please see below for a +checklist of typical requirements. Once you have prepared everything, +see this tutorial for instructions on how to +submit your changes or new files through a GitHub pull request. If you +prefer to submit patches or full files, you should first make certain, +that your code works correctly with the latest patch-level version of +LAMMPS and contains all bugfixes from it. Then create a gzipped tar +file of all changed or added files or a corresponding patch file using +‘diff -u’ or ‘diff -c’ and compress it with gzip. Please only use +gzip compression, as this works well on all platforms.

    If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a standard package. Else we will add them as a user-contributed file or package. Examples of user packages are in @@ -1104,20 +1128,34 @@ changes in core LAMMPS files, you’ll need to -

    Here are the steps you need to follow to submit a single file or user -package for our consideration. Following these steps will save both -you and us time. See existing files in packages in the src dir for -examples.

    +

    Here is a checklist of steps you need to follow to submit a single file +or user package for our consideration. Following these steps will save +both you and us time. See existing files in packages in the src dir for +examples. If you are uncertain, please ask.

    Finally, as a general rule-of-thumb, the more clear and -self-explanatory you make your doc and README files, and the easier -you make it for people to get started, e.g. by providing example -scripts, the more likely it is that users will try out your new -feature.

    +self-explanatory you make your documentation and README files, and the +easier you make it for people to get started, e.g. by providing example +scripts, the more likely it is that users will try out your new feature.

    (Foo) Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).

    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
    • @@ -1914,7 +1913,7 @@ src/Make.py -h -voronoi” to see the details.

      USER-VTK VTK-style dumps Berger and Queteschiner (6) -compute custom/vtk +compute custom/vtk
      @@ -2004,7 +2003,7 @@ Dynamics. This package implements an atom, pair, and fix style which allows electrons to be treated as explicit particles in an MD calculation. See src/USER-AWPMD/README for more details.

      To build LAMMPS with this package ...

      -

      Supporting info: src/USER-AWPMD/README, fix awpmd/cut, examples/USER/awpmd

      +

      Supporting info: src/USER-AWPMD/README, fix awpmd/cut, examples/USER/awpmd

      Author: Ilya Valuev at the JIHT in Russia (valuev at physik.hu-berlin.de). Contact him directly if you have questions.

      @@ -2047,7 +2046,7 @@ have questions.

      calculating x-ray and electron diffraction intensities based on kinematic diffraction theory. See src/USER-DIFFRACTION/README for more details.

      -

      Supporting info: compute saed, compute xrd, fix saed.vtk, +

      Supporting info: compute saed, compute xrd, fix saed/vtk, examples/USER/diffraction

      Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at the University of Arkansas. Contact him directly if you have @@ -2065,11 +2064,13 @@ equations of motion are integrated efficiently through the Shardlow splitting algorithm. See src/USER-DPD/README for more details.

      Supporting info: /src/USER-DPD/README, compute dpd compute dpd/atom -fix eos/cv fix eos/table -fix shardlow -pair_dpd/conservative -pair_dpd/fdt -pair_dpd/fdt/energy, examples/USER/dpd

      +fix eos/cv fix eos/table

      +
      +
      +

      fix rx pair table/rx +pair dpd/fdt pair dpd/fdt/energy +pair exp6/rx pair multi/lucy +pair multi/lucy/rx, examples/USER/dpd

      Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil), Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com) and John Brennan (ARL) (john.k.brennan.civ at mail.mil). Contact them @@ -2144,7 +2145,7 @@ this package. Also see src/USER-INTEL/README for more details. See the KOKKOS, OPT, and USER-OMP packages, which also have CPU and Phi-enabled styles.

      Supporting info: examples/accelerate, src/USER-INTEL/TEST

      -

      Section_accelerate

      +

      Section_accelerate

      Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact him directly if you have questions.

      For the USER-INTEL package, you have 2 choices when building. You can @@ -2261,7 +2262,7 @@ to VMD, support for new file formats can be added to LAMMPS (or VMD or other programs that use them) without having to recompile the application itself.

      See this doc page to get started:

      -

      dump molfile

      +

      dump molfile

      The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions.

      @@ -2273,7 +2274,7 @@ application itself.

      other optimizations of various LAMMPS pair styles, dihedral styles, and fix styles.

      See this section of the manual to get started:

      -

      Section_accelerate

      +

      Section_accelerate

      The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions.

      For the USER-OMP package, your Makefile.machine needs additional diff --git a/doc/html/Section_start.html b/doc/html/Section_start.html index b31c4631b5..4d422cdc2a 100644 --- a/doc/html/Section_start.html +++ b/doc/html/Section_start.html @@ -1365,7 +1365,7 @@ supercomputer there may be dozens or 1000s of physical nodes.

      Note that the keywords do not use a leading minus sign. I.e. the keyword is “t”, not “-t”. Also note that each of the keywords has a default setting. Example of when to use these options and what -settings to use on different platforms is given in Section 5.8.

      +settings to use on different platforms is given in Section 5.8.

      • d or device
      • g or gpus
        • diff --git a/doc/html/accelerate_kokkos.html b/doc/html/accelerate_kokkos.html index d48007a2ca..e517e0e2c5 100644 --- a/doc/html/accelerate_kokkos.html +++ b/doc/html/accelerate_kokkos.html @@ -351,7 +351,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP provides alternative methods via environment variables for binding threads to hardware cores. More info on binding threads to cores is -given in this section.

        +given in this section.

        KOKKOS_ARCH=KNC enables compiler switches needed when compling for an Intel Phi processor.

        KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism diff --git a/doc/html/compute_damage_atom.html b/doc/html/compute_damage_atom.html index bc378e49e8..97a0eba0d0 100644 --- a/doc/html/compute_damage_atom.html +++ b/doc/html/compute_damage_atom.html @@ -170,7 +170,8 @@ 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 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.