From c5ea28b3723537b6d411b080ac4a49c1131f6ea0 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 7 May 2010 15:11:21 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4107 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 10 +++++++--- doc/Manual.txt | 4 +++- doc/Section_howto.html | 8 ++++---- doc/Section_howto.txt | 10 +++++----- doc/Section_intro.html | 4 ++-- doc/Section_intro.txt | 4 ++-- doc/Section_tools.html | 8 ++++---- doc/Section_tools.txt | 4 ++-- doc/compute_displace_atom.html | 2 +- doc/compute_displace_atom.txt | 2 +- doc/compute_erotate_asphere.html | 2 +- doc/compute_erotate_asphere.txt | 2 +- doc/compute_erotate_sphere.html | 2 +- doc/compute_erotate_sphere.txt | 2 +- doc/compute_heat_flux.html | 2 +- doc/compute_heat_flux.txt | 2 +- doc/compute_modify.html | 2 +- doc/compute_modify.txt | 2 +- doc/compute_temp_com.html | 2 +- doc/compute_temp_com.txt | 2 +- doc/compute_temp_deform.html | 2 +- doc/compute_temp_deform.txt | 2 +- doc/compute_temp_partial.html | 2 +- doc/compute_temp_partial.txt | 2 +- doc/compute_temp_profile.html | 2 +- doc/compute_temp_profile.txt | 2 +- doc/compute_temp_ramp.html | 2 +- doc/compute_temp_ramp.txt | 2 +- doc/compute_temp_region.html | 2 +- doc/compute_temp_region.txt | 2 +- doc/dump.html | 2 +- doc/dump.txt | 2 +- doc/fix_addforce.html | 12 ++++++------ doc/fix_addforce.txt | 12 ++++++------ doc/fix_atc.html | 4 ++-- doc/fix_atc.txt | 4 ++-- doc/fix_aveforce.html | 6 +++--- doc/fix_aveforce.txt | 6 +++--- doc/fix_deform.html | 2 +- doc/fix_deform.txt | 2 +- doc/fix_heat.html | 4 ++-- doc/fix_heat.txt | 4 ++-- doc/fix_indent.html | 6 +++--- doc/fix_indent.txt | 6 +++--- doc/fix_nh.html | 2 +- doc/fix_nh.txt | 2 +- doc/fix_press_berendsen.html | 8 ++++---- doc/fix_press_berendsen.txt | 8 ++++---- doc/fix_rigid.html | 6 +++--- doc/fix_rigid.txt | 8 ++++---- doc/fix_setforce.html | 12 ++++++------ doc/fix_setforce.txt | 12 ++++++------ doc/fix_store_coord.html | 2 +- doc/fix_store_coord.txt | 4 ++-- doc/fix_store_force.html | 2 +- doc/fix_store_force.txt | 2 +- doc/fix_ttm.html | 2 +- doc/fix_ttm.txt | 2 +- doc/fix_wall_reflect.html | 4 ++-- doc/fix_wall_reflect.txt | 4 ++-- doc/group.html | 2 +- doc/group.txt | 2 +- doc/kspace_style.html | 7 ++++--- doc/kspace_style.txt | 7 ++++--- doc/lattice.html | 2 +- doc/lattice.txt | 2 +- doc/min_style.html | 2 +- doc/min_style.txt | 2 +- doc/minimize.html | 15 ++++++++------- doc/minimize.txt | 15 ++++++++------- doc/pair_dipole.html | 3 +-- doc/pair_dipole.txt | 3 +-- doc/pair_hybrid.html | 22 +++++++++++----------- doc/pair_hybrid.txt | 22 +++++++++++----------- doc/prd.html | 2 +- doc/prd.txt | 2 +- doc/reset_timestep.html | 2 +- doc/reset_timestep.txt | 2 +- doc/set.html | 15 ++++++++------- doc/set.txt | 15 ++++++++------- doc/thermo_style.html | 2 +- doc/thermo_style.txt | 2 +- doc/variable.html | 4 ++-- doc/variable.txt | 6 +++--- 84 files changed, 208 insertions(+), 198 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index 221e6ee325..c5efc81d93 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -33,7 +33,7 @@ National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

-

The primary developers of LAMMPS are Steve Plimpton, Paul +

The primary developers of LAMMPS are Steve Plimpton, Paul Crozier, and Aidan Thompson who can be contacted at sjplimp,pscrozi,athomps at sandia.gov. The LAMMPS WWW Site at http://lammps.sandia.gov has more information about the code and its @@ -100,7 +100,7 @@ listed above.
2.8 Running on GPUs
- 2.9 Tips for users of previous versions + 2.9 Tips for users of previous versions

  • Commands @@ -148,7 +148,7 @@ listed above.
    4.16 Thermostatting, barostatting, and compute temperature
    - 4.17 Walls + 4.17 Walls
  • Example problems @@ -247,6 +247,10 @@ listed above. + + + + diff --git a/doc/Manual.txt b/doc/Manual.txt index 9a1a05def6..73b7da2fa3 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -36,7 +36,7 @@ sjplimp,pscrozi,athomps at sandia.gov. The "LAMMPS WWW Site"_lws at http://lammps.sandia.gov has more information about the code and its uses. -:link(sjp,http://www.cs.sandia.gov/~sjplimp) +:link(sjp,http://www.sandia.gov/~sjplimp) :line @@ -134,6 +134,7 @@ listed above. :link(2_6,Section_start.html#2_6) :link(2_7,Section_start.html#2_7) :link(2_8,Section_start.html#2_8) +:link(2_9,Section_start.html#2_9) :link(3_1,Section_commands.html#3_1) :link(3_2,Section_commands.html#3_2) @@ -157,6 +158,7 @@ listed above. :link(4_14,Section_howto.html#4_14) :link(4_15,Section_howto.html#4_15) :link(4_16,Section_howto.html#4_16) +:link(4_17,Section_howto.html#4_17) :link(9_1,Section_errors.html#9_1) :link(9_2,Section_errors.html#9_2) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index ef1d0367ef..f5e26496cb 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -639,12 +639,12 @@ files. The second is the lmp2arc tool wh converts LAMMPS dump files into Accelrys' Insight MD program files. The third is the lmp2cfg tool which converts LAMMPS dump files into CFG files which can be read into the -AtomEye visualizer. +AtomEye visualizer.

    A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of user-specified atom information, and convert them to various formats -or pipe them into visualization software directly. See the Pizza.py +or pipe them into visualization software directly. See the Pizza.py WWW site for details. Specifically, Pizza.py can convert LAMMPS dump files into PDB, XYZ, Ensight, and VTK formats. Pizza.py can pipe LAMMPS dump files directly into the Raster3d and @@ -861,7 +861,7 @@ that generate torque:

  • pair_style gran/no_history
  • pair_style dipole/cut
  • pair_style gayberne -
  • pair_style resquared +
  • pair_style resquared
  • pair_style lubricate

    The granular pair styles are used with atom_style @@ -1254,7 +1254,7 @@ pressure command calculates pressure.

    All but the first 3 calculate velocity biases (i.e. advection velocities) that are removed when computing the thermal temperature. -Fix temp/sphere and fix +Compute temp/sphere and compute temp/asphere compute kinetic energy for extended particles that includes rotational degrees of freedom. They both allow, as an extra argument, which is another temperature compute diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index ba5e855d24..e4ec66aae0 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -662,10 +662,10 @@ LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS file format which can also be read by "VMD"_vmd for visualization. See the "dump"_dump.html command for more information on XTC files. -:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) :link(vmd,http://www.ks.uiuc.edu/Research/vmd) :link(ensight,http://www.ensight.com) -:link(atomeye,http://164.107.79.177/Archive/Graphics/A) +:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) :line @@ -854,7 +854,7 @@ that generate torque: "pair_style gran/no_history"_pair_gran.html "pair_style dipole/cut"_pair_dipole.html "pair_style gayberne"_pair_gayberne.html -"pair_style resquared"_pair_resuared.html +"pair_style resquared"_pair_resquared.html "pair_style lubricate"_pair_lubricate.html :ul The "granular pair styles"_pair_gran.html are used with "atom_style @@ -1243,8 +1243,8 @@ pressure"_compute_pressure.html command calculates pressure. All but the first 3 calculate velocity biases (i.e. advection velocities) that are removed when computing the thermal temperature. -"Fix temp/sphere"_fix_temp_sphere.html and "fix -temp/asphere"_fix_temp_asphere.html compute kinetic energy for +"Compute temp/sphere"_compute_temp_sphere.html and "compute +temp/asphere"_compute_temp_asphere.html compute kinetic energy for extended particles that includes rotational degrees of freedom. They both allow, as an extra argument, which is another temperature compute that subtracts a velocity bias. This allows the translational diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 210759bef0..8165316b0e 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -237,7 +237,7 @@ molecular dynamics options:

  • parallel tempering
  • parallel replica dynamics
  • Direct Simulation Monte Carlo for low-density fluids -
  • Peridynamics mesoscale modeling +
  • Peridynamics mesoscale modeling
  • targeted and steered molecular dynamics
  • two-temperature electron model @@ -485,7 +485,7 @@ add it to the Publications page of the LAMM for a picture or movie for the Pictures or Movies pages.

    The core group of LAMMPS developers is at Sandia National Labs. They -include Steve Plimpton, Paul Crozier, and Aidan Thompson and can +include Steve Plimpton, Paul Crozier, and Aidan Thompson and can be contacted via email: sjplimp, pscrozi, athomps at sandia.gov.

    Here are various folks who have made significant contributions to diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index af7ebae66b..77d27e4bee 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -233,7 +233,7 @@ coupled rigid body integration via the "POEMS"_fix_poems.html library "parallel tempering"_temper.html "parallel replica dynamics"_prd.html "Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids -"Peridynamics mesoscale modeling"_pair_peri.html +"Peridynamics mesoscale modeling"_pair_peri_pmb.html "targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics "two-temperature electron model"_fix_ttm.html :ul @@ -478,7 +478,7 @@ Here are various folks who have made significant contributions to features in LAMMPS. The most recent contributions are at the top of the list. -:link(sjp,http://www.cs.sandia.gov/~sjplimp) +:link(sjp,http://www.sandia.gov/~sjplimp) pair yukawa/colloid : Randy Schunk (Sandia) fix wall/colloid : Jeremy Lechman (Sandia) diff --git a/doc/Section_tools.html b/doc/Section_tools.html index f4fb38d1b7..71104c2256 100644 --- a/doc/Section_tools.html +++ b/doc/Section_tools.html @@ -20,9 +20,9 @@ additional tools are provided with the LAMMPS distribution and are described in this section.

    Our group has also written and released a separate toolkit called -Pizza.py which provides tools for doing setup, analysis, +Pizza.py which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is -written in Python and is available for download from the +written in Python and is available for download from the Pizza.py WWW site.

    @@ -172,7 +172,7 @@ Greathouse at Sandia (jagreat at sandia.gov).

    The lmp2cfg sub-directory contains a tool for converting LAMMPS output files into a series of *.cfg files which can be read into the -AtomEye visualizer. See +AtomEye visualizer. See the README file for more information.

    This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). @@ -281,7 +281,7 @@ that perform common LAMMPS post-processing tasks, like

  • sort the snapshots in a dump file by atom ID
  • convert dump files into XYZ, CFG, or PDB format for viz by other packages -

    These are simple scripts built on Pizza.py modules. See the +

    These are simple scripts built on Pizza.py modules. See the README for more info on Pizza.py and how to use these scripts.

    diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index f3cfb5d77f..4cccfa734a 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -22,7 +22,7 @@ plotting, and visualization for LAMMPS simulations. Pizza.py is written in "Python"_python and is available for download from "the Pizza.py WWW site"_pizza. -:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) :link(python,http://www.python.org) Note that many users write their own setup or analysis tools or use @@ -168,7 +168,7 @@ lmp2cfg tool :h4,link(cfg) The lmp2cfg sub-directory contains a tool for converting LAMMPS output files into a series of *.cfg files which can be read into the -"AtomEye"_http://164.107.79.177/Archive/Graphics/A visualizer. See +"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer. See the README file for more information. This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index 76e34cbfc3..95fe27320f 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -40,7 +40,7 @@ command had been issued: 

    fix compute-ID_store_coord group-ID store/coord
    -

    See the fix store/coord command for details. +

    See the fix store/coord command for details. Note that the ID of the new fix is the compute-ID + underscore + "store_coord", and the group for the new fix is the same as the compute group. diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt index a351e57dc5..efbcf584dd 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -37,7 +37,7 @@ command had been issued: fix compute-ID_store_coord group-ID store/coord :pre -See the "fix store/coord"_fix_coord_original.html command for details. +See the "fix store/coord"_fix_store_coord.html command for details. Note that the ID of the new fix is the compute-ID + underscore + "store_coord", and the group for the new fix is the same as the compute group. diff --git a/doc/compute_erotate_asphere.html b/doc/compute_erotate_asphere.html index 07c915cedc..05cd1c7b03 100644 --- a/doc/compute_erotate_asphere.html +++ b/doc/compute_erotate_asphere.html @@ -63,7 +63,7 @@ particles, but they can be aspherical or spherical.

    Related commands: none

    -

    compute erotate/sphere +

    compute erotate/sphere

    Default: none

    diff --git a/doc/compute_erotate_asphere.txt b/doc/compute_erotate_asphere.txt index 6cd67a7027..92f03596de 100644 --- a/doc/compute_erotate_asphere.txt +++ b/doc/compute_erotate_asphere.txt @@ -60,6 +60,6 @@ particles, but they can be aspherical or spherical. [Related commands:] none -"compute erotate/sphere"_compute_rotate_sphere.html +"compute erotate/sphere"_compute_erotate_sphere.html [Default:] none diff --git a/doc/compute_erotate_sphere.html b/doc/compute_erotate_sphere.html index 911e76e113..58c65d3838 100644 --- a/doc/compute_erotate_sphere.html +++ b/doc/compute_erotate_sphere.html @@ -56,7 +56,7 @@ contribute to the rotational energy.

    Related commands:

    -

    compute erotate/asphere +

    compute erotate/asphere

    Default: none

    diff --git a/doc/compute_erotate_sphere.txt b/doc/compute_erotate_sphere.txt index ca58e9309d..f7bf941e26 100644 --- a/doc/compute_erotate_sphere.txt +++ b/doc/compute_erotate_sphere.txt @@ -53,6 +53,6 @@ contribute to the rotational energy. [Related commands:] -"compute erotate/asphere"_compute_rotate_asphere.html +"compute erotate/asphere"_compute_erotate_asphere.html [Default:] none diff --git a/doc/compute_heat_flux.html b/doc/compute_heat_flux.html index 5875e7cbee..b16764b554 100644 --- a/doc/compute_heat_flux.html +++ b/doc/compute_heat_flux.html @@ -34,7 +34,7 @@ or to calculate a thermal conductivity using the Green-Kubo formalism.

    See the fix thermal/conductivity command for details on how to compute thermal conductivity in an -alternate way, via the Muller-Plathe method. See the fix +alternate way, via the Muller-Plathe method. See the fix heat command for a way to control the heat added or subtracted to a group of atoms.

    diff --git a/doc/compute_heat_flux.txt b/doc/compute_heat_flux.txt index 9b1f9f3070..e5a213aabf 100644 --- a/doc/compute_heat_flux.txt +++ b/doc/compute_heat_flux.txt @@ -32,7 +32,7 @@ or to calculate a thermal conductivity using the Green-Kubo formalism. See the "fix thermal/conductivity"_fix_thermal_conductivity.html command for details on how to compute thermal conductivity in an alternate way, via the Muller-Plathe method. See the "fix -heat"_fix_heat command for a way to control the heat added or +heat"_fix_heat.html command for a way to control the heat added or subtracted to a group of atoms. The compute takes three arguments which are IDs of other diff --git a/doc/compute_modify.html b/doc/compute_modify.html index 793a767786..7106c3d22a 100644 --- a/doc/compute_modify.html +++ b/doc/compute_modify.html @@ -47,7 +47,7 @@ this option. The default is 2 or 3 for 2d or 3d systems which is a correction factor for an ensemble of velocities with zero total linear momentum. You can use a negative number for the extra parameter if you need to add -degrees-of-freedom. See the compute +degrees-of-freedom. See the compute temp/asphere command for an example.

    The dynamic keyword determines whether the number of atoms N in the diff --git a/doc/compute_modify.txt b/doc/compute_modify.txt index d903b0f15c..7606dc7828 100644 --- a/doc/compute_modify.txt +++ b/doc/compute_modify.txt @@ -41,7 +41,7 @@ systems"_dimension.html which is a correction factor for an ensemble of velocities with zero total linear momentum. You can use a negative number for the {extra} parameter if you need to add degrees-of-freedom. See the "compute -temp/asphere"_compute_temp_aspher.html command for an example. +temp/asphere"_compute_temp_asphere.html command for an example. The {dynamic} keyword determines whether the number of atoms N in the compute group is re-computed each time a temperature is computed. diff --git a/doc/compute_temp_com.html b/doc/compute_temp_com.html index 1472f34732..d55c85a074 100644 --- a/doc/compute_temp_com.html +++ b/doc/compute_temp_com.html @@ -57,7 +57,7 @@ that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include fix nvt, fix -temp/rescale, fix +temp/rescale, fix temp/berendsen, and fix langevin.

    diff --git a/doc/compute_temp_com.txt b/doc/compute_temp_com.txt index fe1e2bd027..80cc4ea737 100644 --- a/doc/compute_temp_com.txt +++ b/doc/compute_temp_com.txt @@ -55,7 +55,7 @@ each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen, and "fix +temp/berendsen"_fix_temp_berendsen.html, and "fix langevin"_fix_langevin.html. This compute subtracts out degrees-of-freedom due to fixes that diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html index 75c81403b4..31ba8d6776 100644 --- a/doc/compute_temp_deform.html +++ b/doc/compute_temp_deform.html @@ -81,7 +81,7 @@ command that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include fix nvt, fix -temp/rescale, fix +temp/rescale, fix temp/berendsen, and fix langevin.

    diff --git a/doc/compute_temp_deform.txt b/doc/compute_temp_deform.txt index 389e8e171a..26703f1d02 100644 --- a/doc/compute_temp_deform.txt +++ b/doc/compute_temp_deform.txt @@ -79,7 +79,7 @@ from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen, and "fix +temp/berendsen"_fix_temp_berendsen.html, and "fix langevin"_fix_langevin.html. This compute subtracts out degrees-of-freedom due to fixes that diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html index f7df8c55ce..9ea238c850 100644 --- a/doc/compute_temp_partial.html +++ b/doc/compute_temp_partial.html @@ -57,7 +57,7 @@ that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include fix nvt, fix -temp/rescale, fix +temp/rescale, fix temp/berendsen, and fix langevin.

    diff --git a/doc/compute_temp_partial.txt b/doc/compute_temp_partial.txt index 82908d3520..7b999f69c3 100644 --- a/doc/compute_temp_partial.txt +++ b/doc/compute_temp_partial.txt @@ -55,7 +55,7 @@ each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen, and "fix +temp/berendsen"_fix_temp_berendsen.html, and "fix langevin"_fix_langevin.html. This compute subtracts out degrees-of-freedom due to fixes that diff --git a/doc/compute_temp_profile.html b/doc/compute_temp_profile.html index 73e5107897..242674a005 100644 --- a/doc/compute_temp_profile.html +++ b/doc/compute_temp_profile.html @@ -95,7 +95,7 @@ command that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include fix nvt, fix -temp/rescale, fix +temp/rescale, fix temp/berendsen, and fix langevin.

    diff --git a/doc/compute_temp_profile.txt b/doc/compute_temp_profile.txt index 4d13acbd26..bf2d921287 100644 --- a/doc/compute_temp_profile.txt +++ b/doc/compute_temp_profile.txt @@ -88,7 +88,7 @@ from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen, and "fix +temp/berendsen"_fix_temp_berendsen.html, and "fix langevin"_fix_langevin.html. This compute subtracts out degrees-of-freedom due to fixes that diff --git a/doc/compute_temp_ramp.html b/doc/compute_temp_ramp.html index c504d7f1d6..fa8b6b0ecf 100644 --- a/doc/compute_temp_ramp.html +++ b/doc/compute_temp_ramp.html @@ -76,7 +76,7 @@ command that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include fix nvt, fix -temp/rescale, fix +temp/rescale, fix temp/berendsen, and fix langevin.

    diff --git a/doc/compute_temp_ramp.txt b/doc/compute_temp_ramp.txt index f7e5d92adf..4f1ccc5963 100644 --- a/doc/compute_temp_ramp.txt +++ b/doc/compute_temp_ramp.txt @@ -73,7 +73,7 @@ from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen, and "fix +temp/berendsen"_fix_temp_berendsen.html, and "fix langevin"_fix_langevin.html. This compute subtracts out degrees-of-freedom due to fixes that diff --git a/doc/compute_temp_region.html b/doc/compute_temp_region.html index 291746fa7c..abed8dfb0f 100644 --- a/doc/compute_temp_region.html +++ b/doc/compute_temp_region.html @@ -66,7 +66,7 @@ compute is used with a fix command that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include -fix nvt, fix temp/rescale, fix +fix nvt, fix temp/rescale, fix temp/berendsen, and fix langevin. This means any of the thermostatting fixes can operate on a geometric region of atoms, as defined by this diff --git a/doc/compute_temp_region.txt b/doc/compute_temp_region.txt index c3e6092e46..823ecd1b0e 100644 --- a/doc/compute_temp_region.txt +++ b/doc/compute_temp_region.txt @@ -64,7 +64,7 @@ this bias will be subtracted from each atom, thermostatting of the remaining thermal velocity will be performed, and the bias will be added back in. Thermostatting fixes that work in this way include "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix -temp/berendsen"_fix_temp_berendsen, and "fix +temp/berendsen"_fix_temp_berendsen.html, and "fix langevin"_fix_langevin.html. This means any of the thermostatting fixes can operate on a geometric region of atoms, as defined by this compute. diff --git a/doc/dump.html b/doc/dump.html index 2dac4ae213..ed14199987 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -123,7 +123,7 @@ individual values and the file itself.

    The atom, local, and custom styles create files in a simple text format that is self-explanatory when viewing a dump file. Many of the LAMMPS post-processing tools, including -Pizza.py, work with +Pizza.py, work with this format.

    For post-processing purposes the atom and custom text files are diff --git a/doc/dump.txt b/doc/dump.txt index 6751d510a1..263510ac29 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -113,7 +113,7 @@ individual values and the file itself. The {atom}, {local}, and {custom} styles create files in a simple text format that is self-explanatory when viewing a dump file. Many of the LAMMPS "post-processing tools"_Section_tools.html, including -"Pizza.py"_http://www.cs.sandia.gov/~sjplimp/pizza.html, work with +"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this format. For post-processing purposes the {atom} and {custom} text files are diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html index 2cdc82377a..c2a33dfff6 100644 --- a/doc/fix_addforce.html +++ b/doc/fix_addforce.html @@ -47,12 +47,12 @@ the group. This command can be used to give an additional push to atoms in a simulation, such as for a simulation of Poiseuille flow in a channel.

    -

    Any of the 3 quantities defining the force components can be -specified as an equal-style or atom-style variable, namely -fx, fy, fz. If the value is a variable, it should be specified -as v_ID, where ID is the variable ID. In this case, the variable will -be evaluated each timestep, and its value used to determine the -force component. +

    Any of the 3 quantities defining the force components can be specified +as an equal-style or atom-style variable, namely fx, +fy, fz. If the value is a variable, it should be specified as +v_ID, where ID is the variable ID. In this case, the variable will be +evaluated each timestep, and its value used to determine the force +component.

    Equal-style variables can specify formulas with various mathematical functions, and include thermo_style command diff --git a/doc/fix_addforce.txt b/doc/fix_addforce.txt index 0ee9a42f0c..31d132eef6 100644 --- a/doc/fix_addforce.txt +++ b/doc/fix_addforce.txt @@ -37,12 +37,12 @@ the group. This command can be used to give an additional push to atoms in a simulation, such as for a simulation of Poiseuille flow in a channel. -Any of the 3 quantities defining the force components can be -specified as an equal-style or atom-style "variable"_variable, namely -{fx}, {fy}, {fz}. If the value is a variable, it should be specified -as v_ID, where ID is the variable ID. In this case, the variable will -be evaluated each timestep, and its value used to determine the -force component. +Any of the 3 quantities defining the force components can be specified +as an equal-style or atom-style "variable"_variable.html, namely {fx}, +{fy}, {fz}. If the value is a variable, it should be specified as +v_ID, where ID is the variable ID. In this case, the variable will be +evaluated each timestep, and its value used to determine the force +component. Equal-style variables can specify formulas with various mathematical functions, and include "thermo_style"_thermo_style.html command diff --git a/doc/fix_atc.html b/doc/fix_atc.html index 85efdbdd70..83c3207406 100644 --- a/doc/fix_atc.html +++ b/doc/fix_atc.html @@ -205,7 +205,7 @@ conditions.

    miscellaneous fix_modify commands:

    -