From bed966d556e0e7bad4a9e40618a355335b3087fc Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 16 Jan 2015 16:09:27 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12944 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_adapt.html | 12 +++++++++++- doc/fix_adapt.txt | 12 +++++++++++- doc/fix_adapt_fep.html | 12 +++++++++++- doc/fix_adapt_fep.txt | 12 +++++++++++- doc/fix_ave_spatial.html | 4 ++-- doc/fix_ave_spatial.txt | 4 ++-- doc/minimize.html | 22 +++++++++++++++++++++- doc/minimize.txt | 22 +++++++++++++++++++++- 8 files changed, 90 insertions(+), 10 deletions(-) diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html index 52a01fae6c..97142b263f 100644 --- a/doc/fix_adapt.html +++ b/doc/fix_adapt.html @@ -234,6 +234,12 @@ over the course of a 1000-step simulation: 
variable size equal ramp(1.0,0.1)
 fix 1 center adapt 10 atom diameter v_size
+

When the run style is respa, this fix changes +parameters only on the outer loop (largest) timesteps, which means +that the frequency parameter N has to be commensurate with the step +numbers for those outer steps. Otherwise invocation will be less +frequent than expected. +

Restart, fix_modify, output, run start/stop, minimize info: @@ -246,7 +252,11 @@ 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 +

Restrictions: +

+

When the run style is respa, this fix is only +invoked on outer loop time steps that are also commensurate with +the frequency parameter N.

Related commands:

diff --git a/doc/fix_adapt.txt b/doc/fix_adapt.txt index 11b34e79ee..03ebd4f894 100644 --- a/doc/fix_adapt.txt +++ b/doc/fix_adapt.txt @@ -220,6 +220,12 @@ over the course of a 1000-step simulation: variable size equal ramp(1.0,0.1) fix 1 center adapt 10 atom diameter v_size :pre +When the "run style"_run_style.html is {respa}, this fix changes +parameters only on the outer loop (largest) timesteps, which means +that the frequency parameter {N} has to be commensurate with the step +numbers for those outer steps. Otherwise invocation will be less +frequent than expected. + :line [Restart, fix_modify, output, run start/stop, minimize info:] @@ -232,7 +238,11 @@ commands"_Section_howto.html#howto_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 +[Restrictions:] + +When the "run style"_run_style.html is {respa}, this fix is only +invoked on outer loop time steps that are also commensurate with +the frequency parameter {N}. [Related commands:] diff --git a/doc/fix_adapt_fep.html b/doc/fix_adapt_fep.html index ffc2d9a8d1..ad958d2448 100644 --- a/doc/fix_adapt_fep.html +++ b/doc/fix_adapt_fep.html @@ -246,6 +246,12 @@ over the course of a 1000-step simulation: 
variable size equal ramp(1.0,0.1)
 fix 1 center adapt 10 atom diameter * v_size
+

When the run style is respa, this fix changes +parameters only on the outer loop (largest) timesteps, which means +that the frequency parameter N has to be commensurate with the step +numbers for those outer steps. Otherwise invocation will be less +frequent than expected. +

Restart, fix_modify, output, run start/stop, minimize info: @@ -258,7 +264,11 @@ 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 +

Restrictions: +

+

When the run style is respa, this fix is only +invoked on outer loop time steps that are also commensurate with +the frequency parameter N.

Related commands:

diff --git a/doc/fix_adapt_fep.txt b/doc/fix_adapt_fep.txt index db795ef853..1582ea1aca 100644 --- a/doc/fix_adapt_fep.txt +++ b/doc/fix_adapt_fep.txt @@ -232,6 +232,12 @@ over the course of a 1000-step simulation: variable size equal ramp(1.0,0.1) fix 1 center adapt 10 atom diameter * v_size :pre +When the "run style"_run_style.html is {respa}, this fix changes +parameters only on the outer loop (largest) timesteps, which means +that the frequency parameter {N} has to be commensurate with the step +numbers for those outer steps. Otherwise invocation will be less +frequent than expected. + :line [Restart, fix_modify, output, run start/stop, minimize info:] @@ -244,7 +250,11 @@ commands"_Section_howto.html#howto_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 +[Restrictions:] + +When the "run style"_run_style.html is {respa}, this fix is only +invoked on outer loop time steps that are also commensurate with +the frequency parameter {N}. [Related commands:] diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index 7fa779cb30..eef4ea7fa1 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -93,8 +93,8 @@ commands such as thermo_style custom, and can also be written to a file.

The group specified with the command means only atoms within the group -contribute to bin averages. If the region keyword is used, the -atom must be in both the group and the specified geometric +contribute to bin averages. If the region keyword is used, the atom +must be in both the specified group and the specified geometric region in order to contribute to bin averages.

Each listed value can be an atom attribute (position, velocity, force diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt index 34ece7e039..9737302122 100644 --- a/doc/fix_ave_spatial.txt +++ b/doc/fix_ave_spatial.txt @@ -78,8 +78,8 @@ commands"_Section_howto.html#howto_15 such as "thermo_style custom"_thermo_style.html, and can also be written to a file. The group specified with the command means only atoms within the group -contribute to bin averages. If the {region} keyword is used, the -atom must be in both the group and the specified geometric +contribute to bin averages. If the {region} keyword is used, the atom +must be in both the specified group and the specified geometric "region"_region.html in order to contribute to bin averages. Each listed value can be an atom attribute (position, velocity, force diff --git a/doc/minimize.html b/doc/minimize.html index 98ad208044..16f8be7b46 100644 --- a/doc/minimize.html +++ b/doc/minimize.html @@ -50,6 +50,11 @@ slowly drains all kinetic energy from the system. The fix +setforce to the other atoms. See a fuller +discussion of using fixes while minimizing below. +

The minimization styles cg, sd, and hftn involves an outer iteration loop which sets the search direction along which atom coordinates are changed. An inner iteration is then @@ -211,8 +216,23 @@ during the minimization.

Only a few other fixes (typically those that apply force constraints) are invoked during minimization. See the doc pages for individual -fix commands to see which ones are relevant. +fix commands to see which ones are relevant. Current +examples of fixes that can be used include:

+

IMPORTANT NOTE: Some fixes which are invoked during minimization have an associated potential energy. For that energy to be included in the total potential energy of the system (the quantity being minimized), diff --git a/doc/minimize.txt b/doc/minimize.txt index b47cd03daf..3fd2972ea5 100644 --- a/doc/minimize.txt +++ b/doc/minimize.txt @@ -47,6 +47,11 @@ slowly drains all kinetic energy from the system. The "pair_style soft"_pair_soft.html potential can be used to un-overlap atoms while running dynamics. +Note that you can minimize some atoms in the system while holding the +coordiates of other atoms fixed by applying "fix +setforce"_fix_setforce.html to the other atoms. See a fuller +discussion of using fixes while minimizing below. + The "minimization styles"_min_style.html {cg}, {sd}, and {hftn} involves an outer iteration loop which sets the search direction along which atom coordinates are changed. An inner iteration is then @@ -208,7 +213,22 @@ during the minimization. Only a few other fixes (typically those that apply force constraints) are invoked during minimization. See the doc pages for individual -"fix"_fix.html commands to see which ones are relevant. +"fix"_fix.html commands to see which ones are relevant. Current +examples of fixes that can be used include: + +"fix addforce"_fix_addforce.html +"fix addtorque"_fix_addtorque.html +"fix efield"_fix_efield.html +"fix enforce2d"_fix_enforce2d.html +"fix indent"_fix_indent.html +"fix lineforce"_fix_lineforce.html +"fix planeforce"_fix_planeforce.html +"fix setforce"_fix_setforce.html +"fix spring"_fix_spring.html +"fix spring/self"_fix_spring_self.html +"fix viscous"_fix_viscous.html +"fix wall"_fix_wall.html +"fix wall/region"_fix_wall_region.html :ul IMPORTANT NOTE: Some fixes which are invoked during minimization have an associated potential energy. For that energy to be included in the