From 90a8dba7b1daeb0ad9c266e52ec5c5979e8dbf1d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 10 Oct 2007 22:28:11 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1001 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 12 ++++++------ doc/Section_commands.txt | 1 + doc/fix.html | 1 + doc/fix.txt | 1 + doc/fix_addforce.html | 10 +++++----- doc/fix_addforce.txt | 10 +++++----- doc/fix_ave_atom.html | 15 +++++++++++---- doc/fix_ave_atom.txt | 15 +++++++++++---- doc/fix_ave_spatial.html | 12 ++++++------ doc/fix_ave_spatial.txt | 12 ++++++------ doc/fix_ave_time.html | 12 ++++++------ doc/fix_ave_time.txt | 12 ++++++------ doc/fix_aveforce.html | 10 +++++----- doc/fix_aveforce.txt | 10 +++++----- doc/fix_com.html | 12 ++++++------ doc/fix_com.txt | 12 ++++++------ doc/fix_deform.html | 7 ++++--- doc/fix_deform.txt | 7 ++++--- doc/fix_deposit.html | 12 ++++++------ doc/fix_deposit.txt | 12 ++++++------ doc/fix_drag.html | 12 ++++++------ doc/fix_drag.txt | 12 ++++++------ doc/fix_efield.html | 12 ++++++------ doc/fix_efield.txt | 12 ++++++------ doc/fix_enforce2d.html | 10 +++++----- doc/fix_enforce2d.txt | 10 +++++----- doc/fix_freeze.html | 12 ++++++------ doc/fix_freeze.txt | 12 ++++++------ doc/fix_gran_diag.html | 12 ++++++------ doc/fix_gran_diag.txt | 12 ++++++------ doc/fix_gravity.html | 12 ++++++------ doc/fix_gravity.txt | 12 ++++++------ doc/fix_gyration.html | 12 ++++++------ doc/fix_gyration.txt | 12 ++++++------ doc/fix_heat.html | 12 ++++++------ doc/fix_heat.txt | 12 ++++++------ doc/fix_indent.html | 2 +- doc/fix_indent.txt | 2 +- doc/fix_langevin.html | 9 +++++---- doc/fix_langevin.txt | 9 +++++---- doc/fix_lineforce.html | 10 +++++----- doc/fix_lineforce.txt | 10 +++++----- doc/fix_momentum.html | 12 ++++++------ doc/fix_momentum.txt | 12 ++++++------ doc/fix_msd.html | 12 ++++++------ doc/fix_msd.txt | 12 ++++++------ doc/fix_nph.html | 2 +- doc/fix_nph.txt | 2 +- doc/fix_npt.html | 2 +- doc/fix_npt.txt | 2 +- doc/fix_npt_asphere.html | 2 +- doc/fix_npt_asphere.txt | 2 +- doc/fix_nve.html | 12 ++++++------ doc/fix_nve.txt | 12 ++++++------ doc/fix_nve_asphere.html | 12 ++++++------ doc/fix_nve_asphere.txt | 12 ++++++------ doc/fix_nve_dipole.html | 12 ++++++------ doc/fix_nve_dipole.txt | 12 ++++++------ doc/fix_nve_gran.html | 12 ++++++------ doc/fix_nve_gran.txt | 12 ++++++------ doc/fix_nve_limit.html | 12 ++++++------ doc/fix_nve_limit.txt | 12 ++++++------ doc/fix_nve_noforce.html | 12 ++++++------ doc/fix_nve_noforce.txt | 12 ++++++------ doc/fix_nvt.html | 2 +- doc/fix_nvt.txt | 2 +- doc/fix_nvt_asphere.html | 2 +- doc/fix_nvt_asphere.txt | 2 +- doc/fix_nvt_sllod.html | 2 +- doc/fix_nvt_sllod.txt | 2 +- doc/fix_orient_fcc.html | 2 +- doc/fix_orient_fcc.txt | 2 +- doc/fix_planeforce.html | 10 +++++----- doc/fix_planeforce.txt | 10 +++++----- doc/fix_poems.html | 12 ++++++------ doc/fix_poems.txt | 12 ++++++------ doc/fix_pour.html | 12 ++++++------ doc/fix_pour.txt | 12 ++++++------ doc/fix_print.html | 12 ++++++------ doc/fix_print.txt | 12 ++++++------ doc/fix_rdf.html | 12 ++++++------ doc/fix_rdf.txt | 12 ++++++------ doc/fix_recenter.html | 12 ++++++------ doc/fix_recenter.txt | 12 ++++++------ doc/fix_rigid.html | 12 ++++++------ doc/fix_rigid.txt | 12 ++++++------ doc/fix_setforce.html | 2 +- doc/fix_setforce.txt | 2 +- doc/fix_shake.html | 12 ++++++------ doc/fix_shake.txt | 12 ++++++------ doc/fix_spring.html | 12 ++++++------ doc/fix_spring.txt | 12 ++++++------ doc/fix_spring_rg.html | 12 ++++++------ doc/fix_spring_rg.txt | 12 ++++++------ doc/fix_spring_self.html | 12 ++++++------ doc/fix_spring_self.txt | 12 ++++++------ doc/fix_temp_rescale.html | 2 +- doc/fix_temp_rescale.txt | 2 +- doc/fix_tmd.html | 7 ++++--- doc/fix_tmd.txt | 7 ++++--- doc/fix_viscous.html | 12 ++++++------ doc/fix_viscous.txt | 12 ++++++------ doc/fix_wall_gran.html | 12 ++++++------ doc/fix_wall_gran.txt | 12 ++++++------ doc/fix_wall_lj126.html | 2 +- doc/fix_wall_lj126.txt | 2 +- doc/fix_wall_lj93.html | 2 +- doc/fix_wall_lj93.txt | 2 +- doc/fix_wall_reflect.html | 12 ++++++------ doc/fix_wall_reflect.txt | 12 ++++++------ doc/fix_wiggle.html | 12 ++++++------ doc/fix_wiggle.txt | 12 ++++++------ doc/thermo_style.html | 33 +++++++++++++++++++-------------- doc/thermo_style.txt | 33 +++++++++++++++++++-------------- doc/timestep.html | 4 ++-- doc/timestep.txt | 4 ++-- 116 files changed, 569 insertions(+), 536 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index fd0a843123..8a13aa2fc9 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -318,12 +318,12 @@ of each style or click on the style itself for a full description:

- - - - - - + + + + +
addforceaveforceave/atomave/spatialave/timecomdeformdeposit
dragefieldenforce2dfreezegran/diaggravitygyrationheat
indentlangevinlineforcemsdmomentumnphnptnpt/asphere
nvenve/aspherenve/dipolenve/grannve/limitnve/noforcenvtnvt/asphere
nvt/sllodorient/fccplaneforcepoemspourprintrdfrecenter
rigidsetforceshakespringspring/rgspring/selftemp/rescaletmd
viscouswall/granwall/lj126wall/lj93wall/reflectwiggle +
dragdt/resetefieldenforce2dfreezegran/diaggravitygyration
heatindentlangevinlineforcemsdmomentumnphnpt
npt/aspherenvenve/aspherenve/dipolenve/grannve/limitnve/noforcenvt
nvt/aspherenvt/sllodorient/fccplaneforcepoemspourprintrdf
recenterrigidsetforceshakespringspring/rgspring/selftemp/rescale
tmdviscouswall/granwall/lj126wall/lj93wall/reflectwiggle
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index ff38d5c6c5..566882f6ad 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -384,6 +384,7 @@ of each style or click on the style itself for a full description: "deform"_fix_deform.html, "deposit"_fix_deposit.html, "drag"_fix_drag.html, +"dt/reset"_fix_dt_reset.html, "efield"_fix_efield.html, "enforce2d"_fix_enforce2d.html, "freeze"_fix_freeze.html, diff --git a/doc/fix.html b/doc/fix.html index ba7101e40f..b515105663 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -90,6 +90,7 @@ for individual fixes for info on which ones can be restarted.
  • deform - change the simulation box size/shape
  • deposit - add new atoms above a surface
  • drag - drag atoms towards a defined coordinate +
  • dt/reset - reset the timestep based on velocity, forces
  • efield - impose electric field on system
  • enforce2d - zero out z-dimension velocity and force
  • freeze - freeze atoms in a granular simulation diff --git a/doc/fix.txt b/doc/fix.txt index 5281912381..2e5f033ced 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -87,6 +87,7 @@ Here is an alphabetic list of fix styles available in LAMMPS: "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface "drag"_fix_drag.html - drag atoms towards a defined coordinate +"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces "efield"_fix_efield.html - impose electric field on system "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force "freeze"_fix_freeze.html - freeze atoms in a granular simulation diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html index 6aeb7608e2..16c1dbe9f3 100644 --- a/doc/fix_addforce.html +++ b/doc/fix_addforce.html @@ -30,14 +30,14 @@ 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.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. No -parameter of this fix can be used with the start/stop keywords of -the run command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    The forces due to this fix are imposed during an energy minimization, invoked by the minimize command. diff --git a/doc/fix_addforce.txt b/doc/fix_addforce.txt index dde46e4e72..98562b3e13 100644 --- a/doc/fix_addforce.txt +++ b/doc/fix_addforce.txt @@ -27,14 +27,14 @@ 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. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/fix_ave_atom.html b/doc/fix_ave_atom.html index eb9ebd7682..d98e93211b 100644 --- a/doc/fix_ave_atom.html +++ b/doc/fix_ave_atom.html @@ -60,13 +60,20 @@ quantities per atom. This makes a difference in how the quantities are referenced in a dump custom command, e.g. c_ID versus c_ID[2].

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. No -parameter of this fix can be used with the start/stop keywords of +are relevant to this fix. No global scalar or vector quantities are +stored by this fix for access by various output +commands. +

    +

    This fix computes a scalar per-atom quantity or a vector of per-atom +quantities which can be accessed by the dump custom or +fix ave/spatial commands, as discussed in this +section. +

    +

    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/fix_ave_atom.txt b/doc/fix_ave_atom.txt index 1cab82da6a..7aa48ed190 100644 --- a/doc/fix_ave_atom.txt +++ b/doc/fix_ave_atom.txt @@ -57,13 +57,20 @@ quantities per atom. This makes a difference in how the quantities are referenced in a "dump custom"_dump.html command, e.g. c_ID versus c_ID\[2\]. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of +are relevant to this fix. No global scalar or vector quantities are +stored by this fix for access by various "output +commands"_Section_howto.html#4_15. + +This fix computes a scalar per-atom quantity or a vector of per-atom +quantities which can be accessed by the "dump custom"_dump.html or +"fix ave/spatial"_fix_ave_spatial.html commands, as discussed in "this +section"_Section_howto.html#4_15. + +No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index d481a6514f..0374af6fe7 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -193,15 +193,15 @@ only atoms in the fix group are included in the layer averaging. or creation of neighbor lists. If the compute is invoked too often by fix ave/spatial, it can slow down a simulation.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt index 7c55afb0a6..d47c22bfa4 100644 --- a/doc/fix_ave_spatial.txt +++ b/doc/fix_ave_spatial.txt @@ -179,15 +179,15 @@ Note that some computes perform costly calculations, involving use of or creation of neighbor lists. If the compute is invoked too often by fix ave/spatial, it can slow down a simulation. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html index 9142a7104d..66e7daf02a 100644 --- a/doc/fix_ave_time.html +++ b/doc/fix_ave_time.html @@ -86,15 +86,15 @@ simulation. However, if a constant pressure simulation is being run (fix npt or fix nph), LAMMPS is already calculating virial terms for the pressure every timestep.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt index 8b2f35d098..7a1ce199d6 100644 --- a/doc/fix_ave_time.txt +++ b/doc/fix_ave_time.txt @@ -83,15 +83,15 @@ simulation. However, if a constant pressure simulation is being run ("fix npt"_fix_npt.html or "fix nph"_fix_nph.html), LAMMPS is already calculating virial terms for the pressure every timestep. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html index 29f57680b8..4939ab4aaa 100644 --- a/doc/fix_aveforce.html +++ b/doc/fix_aveforce.html @@ -41,14 +41,14 @@ dimension are not changed. Note that this is not the same as specifying a 0.0 value, since that sets all forces to the same average value without adding in any additional force.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. No -parameter of this fix can be used with the start/stop keywords of -the run command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    The forces due to this fix are imposed during an energy minimization, invoked by the minimize command. diff --git a/doc/fix_aveforce.txt b/doc/fix_aveforce.txt index 4d6a3ae0bc..b6c00eade7 100644 --- a/doc/fix_aveforce.txt +++ b/doc/fix_aveforce.txt @@ -38,14 +38,14 @@ dimension are not changed. Note that this is not the same as specifying a 0.0 value, since that sets all forces to the same average value without adding in any additional force. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/fix_com.html b/doc/fix_com.html index e44fc277a8..0e99773160 100644 --- a/doc/fix_com.html +++ b/doc/fix_com.html @@ -30,15 +30,15 @@ including all effects due to atoms passing thru periodic boundaries. Write the results to the specified file.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_com.txt b/doc/fix_com.txt index 7d4305bcf1..d252382fe1 100644 --- a/doc/fix_com.txt +++ b/doc/fix_com.txt @@ -27,15 +27,15 @@ Compute the center-of-mass of the group of atoms every N steps, including all effects due to atoms passing thru periodic boundaries. Write the results to the specified file. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_deform.html b/doc/fix_deform.html index e5d428b66b..8c8f83aab2 100644 --- a/doc/fix_deform.html +++ b/doc/fix_deform.html @@ -362,12 +362,13 @@ been previously used to define the lattice spacing. Note that the units choice also affects the vel style parameters since it is defined in terms of distance/time.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various output +commands.

    This fix can perform deformation over multiple runs, using the start and stop keywords of the run command. See the diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt index 385c5950f0..63c988d89c 100644 --- a/doc/fix_deform.txt +++ b/doc/fix_deform.txt @@ -352,12 +352,13 @@ been previously used to define the lattice spacing. Note that the units choice also affects the {vel} style parameters since it is defined in terms of distance/time. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. This fix can perform deformation over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html index 768a2dfc8a..fcba024341 100644 --- a/doc/fix_deposit.html +++ b/doc/fix_deposit.html @@ -131,7 +131,7 @@ command must have been previously used to define the lattice spacing. Note that the units choice affects all the keyword values that have units of distance or velocity.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    No information about this fix is written to binary restart files. This means you must be careful when restarting a @@ -149,11 +149,11 @@ produce the same behavior if you adjust the fix deposit parameters appropriately.

    None of the fix_modify options are relevant to this -fix. No quantities calculated by this fix can be output by the -thermo_style custom command. 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. +fix. No global scalar or vector or per-atom quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_deposit.txt b/doc/fix_deposit.txt index 4867f9fe0a..ff220c1dcb 100644 --- a/doc/fix_deposit.txt +++ b/doc/fix_deposit.txt @@ -119,7 +119,7 @@ command must have been previously used to define the lattice spacing. Note that the units choice affects all the keyword values that have units of distance or velocity. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. This means you must be careful when restarting a @@ -137,11 +137,11 @@ produce the same behavior if you adjust the fix deposit parameters appropriately. None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No quantities calculated by this fix can be output by the -"thermo_style custom"_thermo_style.html command. No parameter of this -fix can be used with the {start/stop} keywords of the "run"_run.html -command. This fix is not invoked during "energy -minimization"_minimize.html. +fix. No global scalar or vector or per-atom quantities are stored by +this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_drag.html b/doc/fix_drag.html index aac8731c88..d1136a6244 100644 --- a/doc/fix_drag.html +++ b/doc/fix_drag.html @@ -39,15 +39,15 @@ application.

    This command can be used to steer one or more atoms to a new location in the simulation.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_drag.txt b/doc/fix_drag.txt index f360fb719a..57267d8c13 100644 --- a/doc/fix_drag.txt +++ b/doc/fix_drag.txt @@ -37,15 +37,15 @@ application. This command can be used to steer one or more atoms to a new location in the simulation. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_efield.html b/doc/fix_efield.html index 20f5204af5..e4bed32236 100644 --- a/doc/fix_efield.html +++ b/doc/fix_efield.html @@ -28,15 +28,15 @@

    Add a force F = qE to each charged atom in the group due to an external electric field being applied to the system.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_efield.txt b/doc/fix_efield.txt index 20aff825e2..3dfd69b5cc 100644 --- a/doc/fix_efield.txt +++ b/doc/fix_efield.txt @@ -25,15 +25,15 @@ fix kick external-field efield 1.0 0.0 0.0 :pre Add a force F = qE to each charged atom in the group due to an external electric field being applied to the system. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_enforce2d.html b/doc/fix_enforce2d.html index 5d2bd86362..59a3f6e445 100644 --- a/doc/fix_enforce2d.html +++ b/doc/fix_enforce2d.html @@ -28,14 +28,14 @@ This is useful when running a 2d simulation to insure that atoms do not move from their initial z coordinate.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. No -parameter of this fix can be used with the start/stop keywords of -the run command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    The forces due to this fix are imposed during an energy minimization, invoked by the minimize command. diff --git a/doc/fix_enforce2d.txt b/doc/fix_enforce2d.txt index 29db81fb74..5de8a73faf 100644 --- a/doc/fix_enforce2d.txt +++ b/doc/fix_enforce2d.txt @@ -25,14 +25,14 @@ Zero out the z-dimension velocity and force on each atom in the group. This is useful when running a 2d simulation to insure that atoms do not move from their initial z coordinate. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/fix_freeze.html b/doc/fix_freeze.html index 5ef6820fa3..580ca076b5 100644 --- a/doc/fix_freeze.html +++ b/doc/fix_freeze.html @@ -27,15 +27,15 @@

    Zero out the force and torque on a granular particle. This is useful for preventing certain particles from moving in a simulation.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_freeze.txt b/doc/fix_freeze.txt index 46f9625b57..b084ca982b 100644 --- a/doc/fix_freeze.txt +++ b/doc/fix_freeze.txt @@ -24,15 +24,15 @@ fix 2 bottom freeze :pre Zero out the force and torque on a granular particle. This is useful for preventing certain particles from moving in a simulation. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_gran_diag.html b/doc/fix_gran_diag.html index 8af8922912..83b3ed602e 100644 --- a/doc/fix_gran_diag.html +++ b/doc/fix_gran_diag.html @@ -36,15 +36,15 @@ system and extend upward with a thickness of layer for each bin. The quantities written to the file are averaged over all atoms in the bin.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_gran_diag.txt b/doc/fix_gran_diag.txt index a597f84c5f..cd4976ab5b 100644 --- a/doc/fix_gran_diag.txt +++ b/doc/fix_gran_diag.txt @@ -33,15 +33,15 @@ system and extend upward with a thickness of {layer} for each bin. The quantities written to the file are averaged over all atoms in the bin. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html index 5046c00c67..30f367ec32 100644 --- a/doc/fix_gravity.html +++ b/doc/fix_gravity.html @@ -85,15 +85,15 @@ and phi_grad are ignored.

    Style vector imposes an acceleration in the vector direction given by (x,y,z). For 2d systems, the z component is ignored.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_gravity.txt b/doc/fix_gravity.txt index 1dc30fec8b..cd2680ce8b 100644 --- a/doc/fix_gravity.txt +++ b/doc/fix_gravity.txt @@ -77,15 +77,15 @@ and {phi_grad} are ignored. Style {vector} imposes an acceleration in the vector direction given by (x,y,z). For 2d systems, the z component is ignored. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_gyration.html b/doc/fix_gyration.html index f2c498ddfd..dce19f1954 100644 --- a/doc/fix_gyration.html +++ b/doc/fix_gyration.html @@ -38,15 +38,15 @@ this formula

    where M is the total mass of the group and Rcm is the center-of-mass position of the group.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_gyration.txt b/doc/fix_gyration.txt index 911526a57e..fa7cdfa193 100644 --- a/doc/fix_gyration.txt +++ b/doc/fix_gyration.txt @@ -35,15 +35,15 @@ this formula where M is the total mass of the group and Rcm is the center-of-mass position of the group. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_heat.html b/doc/fix_heat.html index 93099a72c8..d035eddc87 100644 --- a/doc/fix_heat.html +++ b/doc/fix_heat.html @@ -59,15 +59,15 @@ not normally be used on atoms that have their temperature controlled by another fix - e.g. fix nvt or fix langevin fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_heat.txt b/doc/fix_heat.txt index c0839e9370..db14082b98 100644 --- a/doc/fix_heat.txt +++ b/doc/fix_heat.txt @@ -56,15 +56,15 @@ not normally be used on atoms that have their temperature controlled by another fix - e.g. "fix nvt"_fix_nvt.html or "fix langevin"_fix_langevin.html fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_indent.html b/doc/fix_indent.html index 56301f6364..5f3b4bf8db 100644 --- a/doc/fix_indent.html +++ b/doc/fix_indent.html @@ -94,7 +94,7 @@ choice affects not only the indenter's physical geometry, but also its velocity and force constant since they are defined in terms of distance as well.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    No information about this fix is written to binary restart files. diff --git a/doc/fix_indent.txt b/doc/fix_indent.txt index 232f0a6f42..cd67813a62 100644 --- a/doc/fix_indent.txt +++ b/doc/fix_indent.txt @@ -85,7 +85,7 @@ choice affects not only the indenter's physical geometry, but also its velocity and force constant since they are defined in terms of distance as well. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index 0397ad6ec0..c6e54a7734 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -117,7 +117,7 @@ should not normally be used on atoms that also have their temperature controlled by another fix - e.g. a nvt or temp/rescale fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    No information about this fix is written to binary restart files. Because the state of the random number generator @@ -126,9 +126,10 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior.

    -

    None of the fix_modify options -are relevant to this fix. No quantities calculated by this fix can be -output by the thermo_style custom command. +

    None of the fix_modify options are relevant to this +fix. No global scalar or vector or per-atom quantities are stored by +this fix for access by various output +commands.

    This fix can ramp its target temperature over multiple runs, using the start and stop keywords of the run command. See the diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt index f9d65e9b7e..d7f1bbde20 100644 --- a/doc/fix_langevin.txt +++ b/doc/fix_langevin.txt @@ -107,7 +107,7 @@ should not normally be used on atoms that also have their temperature controlled by another fix - e.g. a "nvt"_fix_nvt.html or "temp/rescale"_fix_temp_rescale.html fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. Because the state of the random number generator @@ -116,9 +116,10 @@ restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior. -None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global scalar or vector or per-atom quantities are stored by +this fix for access by various "output +commands"_Section_howto.html#4_15. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/fix_lineforce.html b/doc/fix_lineforce.html index 208351bd76..caac553f9d 100644 --- a/doc/fix_lineforce.html +++ b/doc/fix_lineforce.html @@ -33,14 +33,14 @@ line.

    If the initial velocity of the atom is 0.0 (or along the line), then it should continue to move along the line thereafter.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. No -parameter of this fix can be used with the start/stop keywords of -the run command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    The forces due to this fix are imposed during an energy minimization, invoked by the minimize command. diff --git a/doc/fix_lineforce.txt b/doc/fix_lineforce.txt index 151f0b70dd..ad958b3b47 100644 --- a/doc/fix_lineforce.txt +++ b/doc/fix_lineforce.txt @@ -30,14 +30,14 @@ line. If the initial velocity of the atom is 0.0 (or along the line), then it should continue to move along the line thereafter. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/fix_momentum.html b/doc/fix_momentum.html index 86da567691..8535876f7e 100644 --- a/doc/fix_momentum.html +++ b/doc/fix_momentum.html @@ -58,15 +58,15 @@ thermostatting).

    Note that the velocity command can be used to create initial velocities with zero aggregate linear and/or angular momentum.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_momentum.txt b/doc/fix_momentum.txt index 3ae5ff2091..06a1dabad6 100644 --- a/doc/fix_momentum.txt +++ b/doc/fix_momentum.txt @@ -50,15 +50,15 @@ thermostatting). Note that the "velocity"_velocity.html command can be used to create initial velocities with zero aggregate linear and/or angular momentum. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_msd.html b/doc/fix_msd.html index 7140c2caaf..a80e955bb2 100644 --- a/doc/fix_msd.html +++ b/doc/fix_msd.html @@ -42,7 +42,7 @@ MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a dump file containing coordinates of the atomss in the bodies.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the original coordinates of diffusing atoms to binary restart files, so that the mean-squared displacement @@ -52,11 +52,11 @@ a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

    None of the fix_modify options are relevant to this -fix. No quantities calculated by this fix can be output by the -thermo_style custom command. 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. +fix. No global scalar or vector or per-atom quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_msd.txt b/doc/fix_msd.txt index 3a4b07ca3e..9cbb5c7420 100644 --- a/doc/fix_msd.txt +++ b/doc/fix_msd.txt @@ -39,7 +39,7 @@ MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a "dump file"_dump.html containing coordinates of the atomss in the bodies. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the original coordinates of diffusing atoms to "binary restart files"_restart.html, so that the mean-squared displacement @@ -49,11 +49,11 @@ a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No quantities calculated by this fix can be output by the -"thermo_style custom"_thermo_style.html command. No parameter of this -fix can be used with the {start/stop} keywords of the "run"_run.html -command. This fix is not invoked during "energy -minimization"_minimize.html. +fix. No global scalar or vector or per-atom quantities are stored by +this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_nph.html b/doc/fix_nph.html index 0c4e9a6c33..4ec5813d58 100644 --- a/doc/fix_nph.html +++ b/doc/fix_nph.html @@ -146,7 +146,7 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_pressure will have no effect on this fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the state of the Nose/Hoover barostat to binary restart files. See the read_restart diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt index 3e9a170b25..a66ae68ea0 100644 --- a/doc/fix_nph.txt +++ b/doc/fix_nph.txt @@ -136,7 +136,7 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or {thermo_pressure} will have no effect on this fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover barostat to "binary restart files"_restart.html. See the "read_restart"_read_restart.html diff --git a/doc/fix_npt.html b/doc/fix_npt.html index c40ce4c25b..2f81a84fac 100644 --- a/doc/fix_npt.html +++ b/doc/fix_npt.html @@ -149,7 +149,7 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_pressure will have no effect on this fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the state of the Nose/Hoover thermostat and barostat to binary restart files. See the diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt index ba2471c4a5..92fbe3e84e 100644 --- a/doc/fix_npt.txt +++ b/doc/fix_npt.txt @@ -138,7 +138,7 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or {thermo_pressure} will have no effect on this fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat and barostat to "binary restart files"_restart.html. See the diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html index 6e11cd5018..0f51a8c1b1 100644 --- a/doc/fix_npt_asphere.html +++ b/doc/fix_npt_asphere.html @@ -150,7 +150,7 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the state of the Nose/Hoover thermostat and barostat to binary restart files. See the diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt index 011191b05c..d7920c24d7 100755 --- a/doc/fix_npt_asphere.txt +++ b/doc/fix_npt_asphere.txt @@ -139,7 +139,7 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or {thermo_press} will have no effect on this fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat and barostat to "binary restart files"_restart.html. See the diff --git a/doc/fix_nve.html b/doc/fix_nve.html index ab42591788..49336f0231 100644 --- a/doc/fix_nve.html +++ b/doc/fix_nve.html @@ -28,15 +28,15 @@ group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_nve.txt b/doc/fix_nve.txt index 2ff28977e4..fca542b675 100644 --- a/doc/fix_nve.txt +++ b/doc/fix_nve.txt @@ -25,15 +25,15 @@ Perform constant NVE updates of position and velocity for atoms in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html index 3f670bf0e5..4eb9af0237 100644 --- a/doc/fix_nve_asphere.html +++ b/doc/fix_nve_asphere.html @@ -29,15 +29,15 @@ angular velocity for aspherical or ellipsoidal particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_nve_asphere.txt b/doc/fix_nve_asphere.txt index b40be7224f..292e874f98 100755 --- a/doc/fix_nve_asphere.txt +++ b/doc/fix_nve_asphere.txt @@ -26,15 +26,15 @@ angular velocity for aspherical or ellipsoidal particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_nve_dipole.html b/doc/fix_nve_dipole.html index 4c90f1e613..5697f585e7 100644 --- a/doc/fix_nve_dipole.html +++ b/doc/fix_nve_dipole.html @@ -29,15 +29,15 @@ angular velocity for particles with point dipole moments in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_nve_dipole.txt b/doc/fix_nve_dipole.txt index ce54074c83..ddfc3c4743 100755 --- a/doc/fix_nve_dipole.txt +++ b/doc/fix_nve_dipole.txt @@ -26,15 +26,15 @@ angular velocity for particles with point dipole moments in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_nve_gran.html b/doc/fix_nve_gran.html index 1fae9ed3cc..21a5571651 100644 --- a/doc/fix_nve_gran.html +++ b/doc/fix_nve_gran.html @@ -30,15 +30,15 @@ rotational information as well as position and velocity, so this integrator updates translational and rotational degrees of freedom due to forces and torques.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_nve_gran.txt b/doc/fix_nve_gran.txt index 4423733b90..074e61db3f 100644 --- a/doc/fix_nve_gran.txt +++ b/doc/fix_nve_gran.txt @@ -27,15 +27,15 @@ rotational information as well as position and velocity, so this integrator updates translational and rotational degrees of freedom due to forces and torques. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_nve_limit.html b/doc/fix_nve_limit.html index 945bc8ac82..ed8463f199 100644 --- a/doc/fix_nve_limit.html +++ b/doc/fix_nve_limit.html @@ -50,15 +50,15 @@ exactly like the fix nve command. Since forces are unaltered, pressures computed by thermodynamic output will still be very large for overlapped configurations.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_nve_limit.txt b/doc/fix_nve_limit.txt index 2555580f4e..8bfd86b658 100644 --- a/doc/fix_nve_limit.txt +++ b/doc/fix_nve_limit.txt @@ -47,15 +47,15 @@ exactly like the "fix nve"_fix_nve.html command. Since forces are unaltered, pressures computed by thermodynamic output will still be very large for overlapped configurations. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_nve_noforce.html b/doc/fix_nve_noforce.html index bac32dc510..dcd51a2786 100644 --- a/doc/fix_nve_noforce.html +++ b/doc/fix_nve_noforce.html @@ -38,15 +38,15 @@ unchanged, and can thus be printed by the dump command queried with an equal-style variable that uses the fcm() group function to compute the total force on the group of atoms.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_nve_noforce.txt b/doc/fix_nve_noforce.txt index 12716b6be4..5442888b4b 100644 --- a/doc/fix_nve_noforce.txt +++ b/doc/fix_nve_noforce.txt @@ -35,15 +35,15 @@ unchanged, and can thus be printed by the "dump"_dump.html command or queried with an equal-style "variable"_variable.html that uses the fcm() group function to compute the total force on the group of atoms. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html index 64f1273ea6..e7a8b3e225 100644 --- a/doc/fix_nvt.html +++ b/doc/fix_nvt.html @@ -81,7 +81,7 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt index c43ff8a28f..d701aa56e7 100644 --- a/doc/fix_nvt.txt +++ b/doc/fix_nvt.txt @@ -72,7 +72,7 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat to "binary restart files"_restart.html. See the "read_restart"_read_restart.html diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html index 9b0f0efb63..8950fe0bd7 100644 --- a/doc/fix_nvt_asphere.html +++ b/doc/fix_nvt_asphere.html @@ -82,7 +82,7 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt index 8a1a8fc4c1..f75d9aef3a 100755 --- a/doc/fix_nvt_asphere.txt +++ b/doc/fix_nvt_asphere.txt @@ -73,7 +73,7 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat to "binary restart files"_restart.html. See the "read_restart"_read_restart.html diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html index 6a9918bf4d..3a139d54c3 100644 --- a/doc/fix_nvt_sllod.html +++ b/doc/fix_nvt_sllod.html @@ -108,7 +108,7 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart diff --git a/doc/fix_nvt_sllod.txt b/doc/fix_nvt_sllod.txt index 416970e5b0..5afa4b3236 100644 --- a/doc/fix_nvt_sllod.txt +++ b/doc/fix_nvt_sllod.txt @@ -99,7 +99,7 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the state of the Nose/Hoover thermostat to "binary restart files"_restart.html. See the "read_restart"_read_restart.html diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html index 1a8cc1cf40..52555dbdd1 100644 --- a/doc/fix_orient_fcc.html +++ b/doc/fix_orient_fcc.html @@ -116,7 +116,7 @@ symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are show below.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    No information about this fix is written to binary restart files. diff --git a/doc/fix_orient_fcc.txt b/doc/fix_orient_fcc.txt index 6385b1870e..30dcdb8b74 100644 --- a/doc/fix_orient_fcc.txt +++ b/doc/fix_orient_fcc.txt @@ -113,7 +113,7 @@ symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are show below. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. diff --git a/doc/fix_planeforce.html b/doc/fix_planeforce.html index 6560681e1a..5ce7487b76 100644 --- a/doc/fix_planeforce.html +++ b/doc/fix_planeforce.html @@ -32,14 +32,14 @@ by subtracting out components of force perpendicular to the plane.

    If the initial velocity of the atom is 0.0 (or in the plane), then it should continue to move in the plane thereafter.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. No -parameter of this fix can be used with the start/stop keywords of -the run command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    The forces due to this fix are imposed during an energy minimization, invoked by the minimize command. diff --git a/doc/fix_planeforce.txt b/doc/fix_planeforce.txt index 134d3c6d50..d425b830df 100644 --- a/doc/fix_planeforce.txt +++ b/doc/fix_planeforce.txt @@ -29,14 +29,14 @@ by subtracting out components of force perpendicular to the plane. If the initial velocity of the atom is 0.0 (or in the plane), then it should continue to move in the plane thereafter. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/fix_poems.html b/doc/fix_poems.html index b1e7c52173..bc0a79b9c9 100644 --- a/doc/fix_poems.html +++ b/doc/fix_poems.html @@ -110,15 +110,15 @@ body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_poems.txt b/doc/fix_poems.txt index 3b0634dc52..605daf5600 100644 --- a/doc/fix_poems.txt +++ b/doc/fix_poems.txt @@ -103,15 +103,15 @@ body contribution to the pressure virial is also accounted for. The latter is only correct if forces within the bodies have been turned off, and there is only a single fix poems defined. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_pour.html b/doc/fix_pour.html index d11f443c0b..d87287cf4f 100644 --- a/doc/fix_pour.html +++ b/doc/fix_pour.html @@ -101,7 +101,7 @@ completing all insertions, it prints a warning. or y direction (2d). This enables pouring particles from a successively higher height over time.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    No information about this fix is written to binary restart files. This means you must be careful when restarting a @@ -119,11 +119,11 @@ produce the same behavior if you adjust the fix pour parameters appropriately.

    None of the fix_modify options are relevant to this -fix. No quantities calculated by this fix can be output by the -thermo_style custom command. 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. +fix. No global scalar or vector or per-atom quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_pour.txt b/doc/fix_pour.txt index 37dd0f7590..7209a29fcd 100644 --- a/doc/fix_pour.txt +++ b/doc/fix_pour.txt @@ -90,7 +90,7 @@ The {rate} option moves the insertion volume in the z direction (3d) or y direction (2d). This enables pouring particles from a successively higher height over time. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. This means you must be careful when restarting a @@ -108,11 +108,11 @@ produce the same behavior if you adjust the fix pour parameters appropriately. None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No quantities calculated by this fix can be output by the -"thermo_style custom"_thermo_style.html command. No parameter of this -fix can be used with the {start/stop} keywords of the "run"_run.html -command. This fix is not invoked during "energy -minimization"_minimize.html. +fix. No global scalar or vector or per-atom quantities are stored by +this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_print.html b/doc/fix_print.html index faec35aa71..3b90ddc9ec 100644 --- a/doc/fix_print.html +++ b/doc/fix_print.html @@ -42,15 +42,15 @@ fix print line is output. Equal-style variables can calculate complex formulas involving atom and group properties, mathematical operations, other variables, etc.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_print.txt b/doc/fix_print.txt index d9f5f5e39b..712c86185e 100644 --- a/doc/fix_print.txt +++ b/doc/fix_print.txt @@ -39,15 +39,15 @@ fix print line is output. Equal-style variables can calculate complex formulas involving atom and group properties, mathematical operations, other variables, etc. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_rdf.html b/doc/fix_rdf.html index 71c25a4268..c5a1ab22ad 100644 --- a/doc/fix_rdf.html +++ b/doc/fix_rdf.html @@ -48,15 +48,15 @@ factor is set by the special_bonds command.

    The RDF statistics for each timestep are written to the specified file, as are the RDF values averaged over all timesteps.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_rdf.txt b/doc/fix_rdf.txt index e4b52a59ba..5475b38e36 100644 --- a/doc/fix_rdf.txt +++ b/doc/fix_rdf.txt @@ -45,15 +45,15 @@ factor is set by the "special_bonds"_special_bonds.html command. The RDF statistics for each timestep are written to the specified file, as are the RDF values averaged over all timesteps. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_recenter.html b/doc/fix_recenter.html index 0b569e760c..7433b3241d 100644 --- a/doc/fix_recenter.html +++ b/doc/fix_recenter.html @@ -95,15 +95,15 @@ the solvent would be cooled to compensate. A better solution for this simulation scenario is to use the fix spring command to tether the molecule in place.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_recenter.txt b/doc/fix_recenter.txt index 7af7917193..033ff17159 100644 --- a/doc/fix_recenter.txt +++ b/doc/fix_recenter.txt @@ -87,15 +87,15 @@ the solvent would be cooled to compensate. A better solution for this simulation scenario is to use the "fix spring"_fix_spring.html command to tether the molecule in place. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index 1ff3d7dbaa..9e9a25db4e 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -98,15 +98,15 @@ displacement for such atoms, and the image flag values written to a dump file will be different than they would be if the atoms were not in a rigid body.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index 32da5c38fe..f307bf8b95 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -91,15 +91,15 @@ displacement for such atoms, and the image flag values written to a "dump file"_dump.html will be different than they would be if the atoms were not in a rigid body. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html index 9b3f905102..4a81bd7d7f 100644 --- a/doc/fix_setforce.html +++ b/doc/fix_setforce.html @@ -35,7 +35,7 @@ force, assuming their initial velocity zero.

    Any of the fx,fy,fz values can be specified as NULL which means do not alter the force component in that dimension.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 diff --git a/doc/fix_setforce.txt b/doc/fix_setforce.txt index 29d12fe152..fcaad95d67 100644 --- a/doc/fix_setforce.txt +++ b/doc/fix_setforce.txt @@ -32,7 +32,7 @@ force, assuming their initial velocity zero. Any of the fx,fy,fz values can be specified as NULL which means do not alter the force component in that dimension. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options diff --git a/doc/fix_shake.html b/doc/fix_shake.html index c1e8870d41..87f875a803 100644 --- a/doc/fix_shake.html +++ b/doc/fix_shake.html @@ -85,15 +85,15 @@ in the bond are in the group specified with the SHAKE fix. for in temperature and pressure computations. Similarly, the SHAKE contribution to the pressure virial is also accounted for.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_shake.txt b/doc/fix_shake.txt index 3ce8e1f8b2..075f5891df 100644 --- a/doc/fix_shake.txt +++ b/doc/fix_shake.txt @@ -74,15 +74,15 @@ The degrees-of-freedom removed by SHAKE bonds and angles are accounted for in temperature and pressure computations. Similarly, the SHAKE contribution to the pressure virial is also accounted for. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_spring.html b/doc/fix_spring.html index 689ead3fca..e829989600 100644 --- a/doc/fix_spring.html +++ b/doc/fix_spring.html @@ -91,15 +91,15 @@ below the z = 0 center plane of the pore (umbrella sampling). The last example holds the ion a distance 5 away from the pore axis (assuming the center-of-mass of the pore in x,y is the pore axis).

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_spring.txt b/doc/fix_spring.txt index cfe2c6c00c..0d1fe30324 100644 --- a/doc/fix_spring.txt +++ b/doc/fix_spring.txt @@ -84,15 +84,15 @@ below the z = 0 center plane of the pore (umbrella sampling). The last example holds the ion a distance 5 away from the pore axis (assuming the center-of-mass of the pore in x,y is the pore axis). -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_spring_rg.html b/doc/fix_spring_rg.html index d42648e5e2..b5b9e8df4e 100644 --- a/doc/fix_spring_rg.html +++ b/doc/fix_spring_rg.html @@ -50,15 +50,15 @@ for the aggregate force on the group of atoms, not a per-atom force.

    If RG0 is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_spring_rg.txt b/doc/fix_spring_rg.txt index 5dafee6f98..1c5590cc2d 100644 --- a/doc/fix_spring_rg.txt +++ b/doc/fix_spring_rg.txt @@ -46,15 +46,15 @@ for the aggregate force on the group of atoms, not a per-atom force. If RG0 is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_spring_self.html b/doc/fix_spring_self.html index 9f0c1d4f4c..e1665f0d66 100644 --- a/doc/fix_spring_self.html +++ b/doc/fix_spring_self.html @@ -32,7 +32,7 @@ the magnitude of the force on each atom is -Kr, where r is the displacement of the atom from its current position to its initial position.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the original coordinates of tethered atoms to binary restart files, so that the spring effect will be the @@ -42,11 +42,11 @@ a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.

    None of the fix_modify options are relevant to this -fix. No quantities calculated by this fix can be output by the -thermo_style custom command. 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. +fix. No global scalar or vector or per-atom quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_spring_self.txt b/doc/fix_spring_self.txt index 466525d5ed..69084dd595 100644 --- a/doc/fix_spring_self.txt +++ b/doc/fix_spring_self.txt @@ -29,7 +29,7 @@ the magnitude of the force on each atom is -Kr, where r is the displacement of the atom from its current position to its initial position. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the original coordinates of tethered atoms to "binary restart files"_restart.html, so that the spring effect will be the @@ -39,11 +39,11 @@ a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No quantities calculated by this fix can be output by the -"thermo_style custom"_thermo_style.html command. No parameter of this -fix can be used with the {start/stop} keywords of the "run"_run.html -command. This fix is not invoked during "energy -minimization"_minimize.html. +fix. No global scalar or vector or per-atom quantities are stored by +this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html index bfc8b8d139..43268a0c4e 100644 --- a/doc/fix_temp_rescale.html +++ b/doc/fix_temp_rescale.html @@ -94,7 +94,7 @@ custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    No information about this fix is written to binary restart files. diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt index c0bdf97db7..63ce0b869e 100644 --- a/doc/fix_temp_rescale.txt +++ b/doc/fix_temp_rescale.txt @@ -90,7 +90,7 @@ custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} will have no effect on this fix. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. diff --git a/doc/fix_tmd.html b/doc/fix_tmd.html index c5ddf6755d..f2aa769e97 100644 --- a/doc/fix_tmd.html +++ b/doc/fix_tmd.html @@ -87,12 +87,13 @@ to prevent it being overwritten.

    For more information about TMD, see (Schlitter1) and (Schlitter2).

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various output +commands.

    This fix can ramp its rho parameter over multiple runs, using the start and stop keywords of the run command. See the diff --git a/doc/fix_tmd.txt b/doc/fix_tmd.txt index bd7096f506..3530b4f4e6 100644 --- a/doc/fix_tmd.txt +++ b/doc/fix_tmd.txt @@ -84,12 +84,13 @@ to prevent it being overwritten. For more information about TMD, see "(Schlitter1)"_#Schlitter1 and "(Schlitter2)"_#Schlitter2. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. This fix can ramp its rho parameter over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/fix_viscous.html b/doc/fix_viscous.html index 97b559dba4..24add7af27 100644 --- a/doc/fix_viscous.html +++ b/doc/fix_viscous.html @@ -75,15 +75,15 @@ langevin command adds both a viscous damping term and this random force to each atom; hence if using fix langevin you do not typically need to use fix viscous.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_viscous.txt b/doc/fix_viscous.txt index 9a9f8a517a..718b6269b6 100644 --- a/doc/fix_viscous.txt +++ b/doc/fix_viscous.txt @@ -65,15 +65,15 @@ langevin"_fix_langevin.html command adds both a viscous damping term and this random force to each atom; hence if using fix {langevin} you do not typically need to use fix {viscous}. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html index a57b6e4c2a..3c74a80c71 100644 --- a/doc/fix_wall_gran.html +++ b/doc/fix_wall_gran.html @@ -77,7 +77,7 @@ the amplitude, omega is 2 PI / period, and delta is elapsed time since the fix was specified. The velocity of the wall is also set to the derivative of this expression.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    This fix writes the shear friction state of atoms interacting with the wall to binary restart files, so that a simulation can @@ -88,11 +88,11 @@ restart file, so that the operation of the fix continues in an uninterrupted fashion.

    None of the fix_modify options are relevant to this -fix. No quantities calculated by this fix can be output by the -thermo_style custom command. 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. +fix. No global scalar or vector or per-atom quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_wall_gran.txt b/doc/fix_wall_gran.txt index 2f6c31ff14..12063bf23a 100644 --- a/doc/fix_wall_gran.txt +++ b/doc/fix_wall_gran.txt @@ -67,7 +67,7 @@ the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the elapsed time since the fix was specified. The velocity of the wall is also set to the derivative of this expression. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] This fix writes the shear friction state of atoms interacting with the wall to "binary restart files"_restart.html, so that a simulation can @@ -78,11 +78,11 @@ restart file, so that the operation of the fix continues in an uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this -fix. No quantities calculated by this fix can be output by the -"thermo_style custom"_thermo_style.html command. No parameter of this -fix can be used with the {start/stop} keywords of the "run"_run.html -command. This fix is not invoked during "energy -minimization"_minimize.html. +fix. No global scalar or vector or per-atom quantities are stored by +this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_wall_lj126.html b/doc/fix_wall_lj126.html index 3ddf4952c0..f18aadde6f 100644 --- a/doc/fix_wall_lj126.html +++ b/doc/fix_wall_lj126.html @@ -44,7 +44,7 @@ provided by the fix wall/lj93 command.

    The wall potential is shifted so that the energy of a wall-particle interaction is 0.0 at the cutoff distance.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    No information about this fix is written to binary restart files. diff --git a/doc/fix_wall_lj126.txt b/doc/fix_wall_lj126.txt index 2b51378601..19e08e6d01 100644 --- a/doc/fix_wall_lj126.txt +++ b/doc/fix_wall_lj126.txt @@ -41,7 +41,7 @@ provided by the "fix wall/lj93"_fix_wall_lj93.html command. The wall potential is shifted so that the energy of a wall-particle interaction is 0.0 at the cutoff distance. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. diff --git a/doc/fix_wall_lj93.html b/doc/fix_wall_lj93.html index d0f9f6d744..e4cdcc3611 100644 --- a/doc/fix_wall_lj93.html +++ b/doc/fix_wall_lj93.html @@ -45,7 +45,7 @@ wall/lj126 command.

    The wall potential is shifted so that the energy of a wall-particle interaction is 0.0 at the cutoff distance.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

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

    No information about this fix is written to binary restart files. diff --git a/doc/fix_wall_lj93.txt b/doc/fix_wall_lj93.txt index 3807aead23..e9417501a2 100644 --- a/doc/fix_wall_lj93.txt +++ b/doc/fix_wall_lj93.txt @@ -42,7 +42,7 @@ wall/lj126"_fix_wall_lj126.html command. The wall potential is shifted so that the energy of a wall-particle interaction is 0.0 at the cutoff distance. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. diff --git a/doc/fix_wall_reflect.html b/doc/fix_wall_reflect.html index f507974741..ea71ae7d49 100644 --- a/doc/fix_wall_reflect.html +++ b/doc/fix_wall_reflect.html @@ -43,15 +43,15 @@ in the input script, since the adjustments it makes to atom coordinates should come after the changes made by time integration. LAMMPS will warn you if your fixes are not ordered this way.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions:

    diff --git a/doc/fix_wall_reflect.txt b/doc/fix_wall_reflect.txt index 1d2d48cdeb..3b7b9441eb 100644 --- a/doc/fix_wall_reflect.txt +++ b/doc/fix_wall_reflect.txt @@ -40,15 +40,15 @@ in the input script, since the adjustments it makes to atom coordinates should come after the changes made by time integration. LAMMPS will warn you if your fixes are not ordered this way. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/fix_wiggle.html b/doc/fix_wiggle.html index 422b63a3cd..6399e686bd 100644 --- a/doc/fix_wiggle.html +++ b/doc/fix_wiggle.html @@ -40,15 +40,15 @@ the dim coordinate of each atom is set to elapsed time since the fix was specified. The velocity of the atom is set to the derivative of this expression.

    -

    Restart, fix_modify, thermo output, run start/stop, minimize info: +

    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 quantities calculated by this fix can be -output by the thermo_style custom command. 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. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored 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.

    Restrictions: none

    diff --git a/doc/fix_wiggle.txt b/doc/fix_wiggle.txt index a4f9dcdd5d..0c06e851f0 100644 --- a/doc/fix_wiggle.txt +++ b/doc/fix_wiggle.txt @@ -37,15 +37,15 @@ where {coord0} is the coordinate at the time the fix was specified, elapsed time since the fix was specified. The velocity of the atom is set to the derivative of this expression. -[Restart, fix_modify, thermo output, run start/stop, minimize info:] +[Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No quantities calculated by this fix can be -output by the "thermo_style custom"_thermo_style.html command. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy -minimization"_minimize.html. +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none diff --git a/doc/thermo_style.html b/doc/thermo_style.html index 5a03705167..03d5fe493e 100644 --- a/doc/thermo_style.html +++ b/doc/thermo_style.html @@ -207,12 +207,14 @@ been defined elsewhere in the input script. See the compute command for details. Note that only global scalar or vector quantites calculated by a compute can be output as thermodynamic data; per-atom quantities calcalated by a compute are -output by the dump custom command. Note that computes -typically calculate global quantities that are summed over all atoms -in the compute group. However the value printed by thermo_style -custom may be normalized by the total number of atoms in the -simulation depending on the thermo_modify norm -option being used. +output by the dump custom command. Note that some +computes calculate "intensive" global quantities like temperature; +others calculate "extensive" global quantities like kinetic energy +that are summed over all atoms in the compute group. Intensive +quantities are printed directly by thermo_style custom. Extensive +quantites may be normalized by the total number of atoms in the +simulation (NOT the number of atoms in the compute group) depending on +the thermo_modify norm option being used.

    If c_ID is used as a keyword, then the scalar quantity calculated by the compute is printed. If c_ID[N] is used, then the compute must @@ -224,20 +226,23 @@ are.

    The f_ID and f_ID[N] keywords allow global scalar or vector quantities calculated by a fix to be output. The ID in the keyword should be replaced by the actual ID of the fix that has been defined -elsewhere in the input script. Note that fixes typically calculate -global quantities that are summed over all atoms in the fix group. -However the value printed by thermo_style custom may be normalized by -the total number of atoms in the simulation depending on the -thermo_modify norm option being used. +elsewhere in the input script. Note that some fixes calculate +"intensive" global quantities like timestep size; others calculate +"extensive" global quantities like energy that are summed over all +atoms in the fix group. Intensive quantities are printed directly by +thermo_style custom. Extensive quantites may be normalized by the +total number of atoms in the simulation (NOT the number of atoms in +the compute group) depending on the thermo_modify +norm option being used.

    If f_ID is used as a keyword, then the scalar quantity calculated by the fix is printed. If f_ID[N] is used, then the fix must calculate a vector quantity and N must be an index from 1 to M where M is the length of the vector calculated by the fix. See the doc pages for individual fix styles for info on which fixes calculate these -global quantities and what they quantities are. For fixes that -compute a contribution to the potential energy of the system, the -scalar quantity f_ID is typically that quantity. +global quantities and what they are. For fixes that compute a +contribution to the potential energy of the system, the scalar +quantity f_ID is typically that quantity.

    The v_name keyword allow the current value of a variable to be output. The name in the keyword should be replaced by the actual namd diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt index 9216d24252..570b7d72c0 100644 --- a/doc/thermo_style.txt +++ b/doc/thermo_style.txt @@ -201,12 +201,14 @@ been defined elsewhere in the input script. See the "compute"_compute.html command for details. Note that only global scalar or vector quantites calculated by a compute can be output as thermodynamic data; per-atom quantities calcalated by a compute are -output by the "dump custom"_dump.html command. Note that computes -typically calculate global quantities that are summed over all atoms -in the compute group. However the value printed by thermo_style -custom may be normalized by the total number of atoms in the -simulation depending on the "thermo_modify norm"_thermo_modify.html -option being used. +output by the "dump custom"_dump.html command. Note that some +computes calculate "intensive" global quantities like temperature; +others calculate "extensive" global quantities like kinetic energy +that are summed over all atoms in the compute group. Intensive +quantities are printed directly by thermo_style custom. Extensive +quantites may be normalized by the total number of atoms in the +simulation (NOT the number of atoms in the compute group) depending on +the "thermo_modify norm"_thermo_modify.html option being used. If {c_ID} is used as a keyword, then the scalar quantity calculated by the compute is printed. If {c_ID\[N\]} is used, then the compute must @@ -218,20 +220,23 @@ are. The {f_ID} and {f_ID\[N\]} keywords allow global scalar or vector quantities calculated by a fix to be output. The ID in the keyword should be replaced by the actual ID of the fix that has been defined -elsewhere in the input script. Note that fixes typically calculate -global quantities that are summed over all atoms in the fix group. -However the value printed by thermo_style custom may be normalized by -the total number of atoms in the simulation depending on the -"thermo_modify norm"_thermo_modify.html option being used. +elsewhere in the input script. Note that some fixes calculate +"intensive" global quantities like timestep size; others calculate +"extensive" global quantities like energy that are summed over all +atoms in the fix group. Intensive quantities are printed directly by +thermo_style custom. Extensive quantites may be normalized by the +total number of atoms in the simulation (NOT the number of atoms in +the compute group) depending on the "thermo_modify +norm"_thermo_modify.html option being used. If {f_ID} is used as a keyword, then the scalar quantity calculated by the fix is printed. If {f_ID\[N\]} is used, then the fix must calculate a vector quantity and N must be an index from 1 to M where M is the length of the vector calculated by the fix. See the doc pages for individual fix styles for info on which fixes calculate these -global quantities and what they quantities are. For fixes that -compute a contribution to the potential energy of the system, the -scalar quantity f_ID is typically that quantity. +global quantities and what they are. For fixes that compute a +contribution to the potential energy of the system, the scalar +quantity f_ID is typically that quantity. The {v_name} keyword allow the current value of a variable to be output. The name in the keyword should be replaced by the actual namd diff --git a/doc/timestep.html b/doc/timestep.html index 0d267f4dfe..f28c99f798 100644 --- a/doc/timestep.html +++ b/doc/timestep.html @@ -29,8 +29,8 @@ See the units command for a discussion of time units. Note that using the units command also sets the timestep to its default value in the chosen units.

    -

    When the run style is respa, dt is the timestep for the outer loop -(largest) timestep. +

    When the run style is respa, dt is the timestep for +the outer loop (largest) timestep.

    Restrictions: none

    diff --git a/doc/timestep.txt b/doc/timestep.txt index b7bba0da5f..c028a9225d 100644 --- a/doc/timestep.txt +++ b/doc/timestep.txt @@ -26,8 +26,8 @@ See the "units"_units.html command for a discussion of time units. Note that using the units command also sets the timestep to its default value in the chosen units. -When the run style is {respa}, dt is the timestep for the outer loop -(largest) timestep. +When the "run style"_run_style.html is {respa}, dt is the timestep for +the outer loop (largest) timestep. [Restrictions:] none