From 7f430f9e62cf514eb0dce3e1483fec720909808f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 5 Jan 2015 22:28:23 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12869 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 28 ++++++++++++++-------------- doc/Section_commands.txt | 1 + doc/fix_bond_swap.html | 4 +++- doc/fix_bond_swap.txt | 4 +++- doc/neigh_modify.html | 17 +++++++++++------ doc/neigh_modify.txt | 17 +++++++++++------ 6 files changed, 43 insertions(+), 28 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 7b1d3ce650..20e547d4e2 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -399,20 +399,20 @@ This is indicated by additional letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

- - - - - - - - - - - - - - + + + + + + + + + + + + +
adaptaddforce (c)append/atomsaveforce (c)ave/atomave/correlateave/histoave/spatial
ave/timebalancebond/breakbond/createbond/swapbox/relaxdeformdeposit
dragdt/resetefieldenforce2d (c)evaporateexternalfreeze (c)gcmc
gldgravity (co)heatindentlangevin (k)lineforcemomentummove
msstnebnph (o)nphug (o)nph/asphere (o)nph/sphere (o)npt (co)npt/asphere (o)
npt/sphere (o)nve (cko)nve/aspherenve/asphere/noforcenve/bodynve/limitnve/linenve/noforce
nve/sphere (o)nve/trinvt (co)nvt/asphere (o)nvt/sllod (o)nvt/sphere (o)onewayorient/fcc
planeforcepoemspourpress/berendsenprintproperty/atomqeq/comb (o)qeq/dynamic
qeq/pointqeq/shieldedqeq/slaterreax/bondsrecenterrestrainrigid (o)rigid/nph (o)
rigid/npt (o)rigid/nve (o)rigid/nvt (o)rigid/small (o)rigid/small/nphrigid/small/nptrigid/small/nverigid/small/nvt
setforce (c)shake (c)springspring/rgspring/selfsrdstore/forcestore/state
temp/berendsen (c)temp/csvrtemp/rescale (c)thermal/conductivitytmdttmtune/kspacevector
viscosityviscous (c)wall/colloidwall/granwall/harmonicwall/lj1043wall/lj126wall/lj93
wall/pistonwall/reflectwall/regionwall/srd +
adaptaddforce (c)append/atomsatom/swapaveforce (c)ave/atomave/correlateave/histo
ave/spatialave/timebalancebond/breakbond/createbond/swapbox/relaxdeform
depositdragdt/resetefieldenforce2d (c)evaporateexternalfreeze (c)
gcmcgldgravity (co)heatindentlangevin (k)lineforcemomentum
movemsstnebnph (o)nphug (o)nph/asphere (o)nph/sphere (o)npt (co)
npt/asphere (o)npt/sphere (o)nve (cko)nve/aspherenve/asphere/noforcenve/bodynve/limitnve/line
nve/noforcenve/sphere (o)nve/trinvt (co)nvt/asphere (o)nvt/sllod (o)nvt/sphere (o)oneway
orient/fccplaneforcepoemspourpress/berendsenprintproperty/atomqeq/comb (o)
qeq/dynamicqeq/pointqeq/shieldedqeq/slaterreax/bondsrecenterrestrainrigid (o)
rigid/nph (o)rigid/npt (o)rigid/nve (o)rigid/nvt (o)rigid/small (o)rigid/small/nphrigid/small/nptrigid/small/nve
rigid/small/nvtsetforce (c)shake (c)springspring/rgspring/selfsrdstore/force
store/statetemp/berendsen (c)temp/csvrtemp/rescale (c)thermal/conductivitytmdttmtune/kspace
vectorviscosityviscous (c)wall/colloidwall/granwall/harmonicwall/lj1043wall/lj126
wall/lj93wall/pistonwall/reflectwall/regionwall/srd

These are additional fix styles in USER packages, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 08db07a1ec..09baad3151 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -468,6 +468,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "adapt"_fix_adapt.html, "addforce (c)"_fix_addforce.html, "append/atoms"_fix_append_atoms.html, +"atom/swap"_fix_atom_swap.html, "aveforce (c)"_fix_aveforce.html, "ave/atom"_fix_ave_atom.html, "ave/correlate"_fix_ave_correlate.html, diff --git a/doc/fix_bond_swap.html b/doc/fix_bond_swap.html index 2c38100e53..fbf2288613 100644 --- a/doc/fix_bond_swap.html +++ b/doc/fix_bond_swap.html @@ -183,7 +183,9 @@ hops away along the chain backbone. a bond swap are not considered. Thus a simulation that uses this fix cannot use a dihedral or improper potential.

-

Related commands: none +

Related commands: +

+

fix atom/swap

Default: none

diff --git a/doc/fix_bond_swap.txt b/doc/fix_bond_swap.txt index 2e418f9151..7523f1117f 100755 --- a/doc/fix_bond_swap.txt +++ b/doc/fix_bond_swap.txt @@ -180,7 +180,9 @@ Currently, energy changes in dihedral and improper interactions due to a bond swap are not considered. Thus a simulation that uses this fix cannot use a dihedral or improper potential. -[Related commands:] none +[Related commands:] + +"fix atom/swap"_fix_atom_swap.html [Default:] none diff --git a/doc/neigh_modify.html b/doc/neigh_modify.html index 93d77bcd90..f9445676ed 100644 --- a/doc/neigh_modify.html +++ b/doc/neigh_modify.html @@ -73,12 +73,17 @@ has passed). If the check setting is no, the list is built on the check setting is yes, then the list is only built on a particular step if some atom has moved more than half the skin distance (specified in the neighbor command) since the last -build. If the once setting is yes, then the neighbor list is only -built once at the beginning of each run, and never rebuilt. This -should only be done if you are certain atoms will not move far enough -that the list should be rebuilt. E.g. running a simulation of a cold -crystal. Note that it is not that expensive to check if neighbor -lists should be rebuilt. +build. +

+

If the once setting is yes, then the neighbor list is only built +once at the beginning of each run, and never rebuilt, except on steps +when a restart file is written, or steps when a fix forces a rebuild +to occur (e.g. fixes that create or delete atoms, such as fix +deposit or fix evaporate). +This setting should only be made if you are certain atoms will not +move far enough that the neighbor list should be rebuilt, e.g. running +a simulation of a cold crystal. Note that it is not that expensive to +check if neighbor lists should be rebuilt.

When the rRESPA integrator is used (see the run_style command), the every and delay parameters refer to the longest diff --git a/doc/neigh_modify.txt b/doc/neigh_modify.txt index 204f1ef3c0..2e862edcec 100644 --- a/doc/neigh_modify.txt +++ b/doc/neigh_modify.txt @@ -68,12 +68,17 @@ has passed). If the {check} setting is {no}, the list is built on the {check} setting is {yes}, then the list is only built on a particular step if some atom has moved more than half the skin distance (specified in the "neighbor"_neighbor.html command) since the last -build. If the {once} setting is yes, then the neighbor list is only -built once at the beginning of each run, and never rebuilt. This -should only be done if you are certain atoms will not move far enough -that the list should be rebuilt. E.g. running a simulation of a cold -crystal. Note that it is not that expensive to check if neighbor -lists should be rebuilt. +build. + +If the {once} setting is yes, then the neighbor list is only built +once at the beginning of each run, and never rebuilt, except on steps +when a restart file is written, or steps when a fix forces a rebuild +to occur (e.g. fixes that create or delete atoms, such as "fix +deposit"_fix_deposit.html or "fix evaporate"_fix_evaporate.html). +This setting should only be made if you are certain atoms will not +move far enough that the neighbor list should be rebuilt, e.g. running +a simulation of a cold crystal. Note that it is not that expensive to +check if neighbor lists should be rebuilt. When the rRESPA integrator is used (see the "run_style"_run_style.html command), the {every} and {delay} parameters refer to the longest