These are fix styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index f236c19a8d..e6acf39b18 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -531,6 +531,10 @@ of each style or click on the style itself for a full description: "rigid/nve"_fix_rigid.html, "rigid/nvt"_fix_rigid.html, "rigid/small"_fix_rigid.html, +"rigid/small/nph"_fix_rigid.html, +"rigid/small/npt"_fix_rigid.html, +"rigid/small/nve"_fix_rigid.html, +"rigid/small/nvt"_fix_rigid.html, "setforce"_fix_setforce.html, "shake"_fix_shake.html, "spring"_fix_spring.html, diff --git a/doc/compute_voronoi_atom.html b/doc/compute_voronoi_atom.html index 2b086741ea..97c360769e 100644 --- a/doc/compute_voronoi_atom.html +++ b/doc/compute_voronoi_atom.html @@ -113,16 +113,16 @@ performed for the first invocation of the compute and then stored. For all following invocations of the compute the number of atoms in each Voronoi cell in the stored tessellation is counted. In this mode the compute returns a per-atom array with 2 columns. The first column -is the number of atoms currently in the Voronoi volume defined by this -atom at the time of the first invocation of the compute (note that the +is the number of atoms currently in the Voronoi volume defined by this +atom at the time of the first invocation of the compute (note that the atom may have moved significantly). The second column contains the -total number of atoms sharing the Voronoi cell of the stored -tessellation at the location of the current atom. Numbers in column one -can be any positive integer including zero, while column two values will -always be greater than zero. Column one data can be used to locate -vacancies (the coordinates are given by the atom coordinates at the -time step when the compute was first invoked), while column two data -can be used to identify interstitial atoms. +total number of atoms sharing the Voronoi cell of the stored +tessellation at the location of the current atom. Numbers in column +one can be any positive integer including zero, while column two +values will always be greater than zero. Column one data can be used +to locate vacancies (the coordinates are given by the atom coordinates +at the time step when the compute was first invoked), while column two +data can be used to identify interstitial atoms.
Syntax:
fix ID group-ID style bodystyle args keyword values ...
langevin values = Tstart Tstop Tperiod seed
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
@@ -70,7 +78,7 @@
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
infile filename
- filename = file with per-body values of mass, center-of-mass, moments of inertia
+ filename = file with per-body values of mass, center-of-mass, moments of inertia
mol value = template-ID
template-ID = ID of molecule template specified in a separate molecule command
@@ -87,7 +95,8 @@ fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
-fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
+fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
+fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0
Description:
@@ -292,17 +301,17 @@ iterations. The rigid/nve style uses the methods described in the paper by Miller, which are thought to provide better energy conservation than an iterative approach. -The rigid/nvt style performs constant NVT integration using a -Nose/Hoover thermostat with chains as described originally in -(Hoover) and (Martyna), which thermostats both -the translational and rotational degrees of freedom of the rigid -bodies. The rigid-body algorithm used by rigid/nvt is described in -the paper by Kamberaj. +
The rigid/nvt and rigid/nvt/small styles performs constant NVT +integration using a Nose/Hoover thermostat with chains as described +originally in (Hoover) and (Martyna), which +thermostats both the translational and rotational degrees of freedom +of the rigid bodies. The rigid-body algorithm used by rigid/nvt +is described in the paper by Kamberaj.
-The rigid/npt and rigid/nph styles perform constant NPT or NPH -integration using a Nose/Hoover barostat with chains. For the NPT -case, the same Nose/Hoover thermostat is also used as with -rigid/nvt. +
The rigid/npt and rigid/nph (and their /small counterparts) styles +perform constant NPT or NPH integration using a Nose/Hoover barostat +with chains. For the NPT case, the same Nose/Hoover thermostat is also +used as with rigid/nvt.
The barostat parameters are specified using one or more of the iso, aniso, x, y, z and couple keywords. These keywords give you @@ -312,8 +321,8 @@ they represent are varied together during a constant-pressure simulation. The effects of these keywords are similar to those defined in fix npt/nph
-NOTE: Currently the rigid/npt and rigid/nph styles do not support -triclinic (non-orthongonal) boxes. +
NOTE: Currently the rigid/npt and rigid/nph (and their /small +counterparts) styles do not support triclinic (non-orthongonal) boxes.
The target pressures for each of the 6 components of the stress tensor can be specified independently via the x, y, z keywords, which @@ -483,12 +492,10 @@ have to list attributes for every rigid body integrated by fix rigid. Only bodies which the file specifies will have their computed attributes overridden. The file can contain initial blank lines or comment lines starting with "#" which are ignored. The first -non-blank, non-comment line should list N, which is the number of -lines to follow. The N successive lines contain the following -information: +non-blank, non-comment line should list N = the number of lines to +follow. The N successive lines contain the following information:
-N
-ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
+ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
...
IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt
index ca23c5a74a..62bd5e2ee3 100644
--- a/doc/fix_rigid.txt
+++ b/doc/fix_rigid.txt
@@ -12,13 +12,17 @@ fix rigid/nvt command :h3
fix rigid/npt command :h3
fix rigid/nph command :h3
fix rigid/small command :h3
+fix rigid/nve/small command :h3
+fix rigid/nvt/small command :h3
+fix rigid/npt/small command :h3
+fix rigid/nph/small command :h3
[Syntax:]
fix ID group-ID style bodystyle args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
-style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {rigid/small} :l
+style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {rigid/small} or {rigid/nve/small} or {rigid/nvt/small} or {rigid/npt/small} or {rigid/nph/small} :l
bodystyle = {single} or {molecule} or {group} :l
{single} args = none
{molecule} args = none
@@ -27,7 +31,7 @@ bodystyle = {single} or {molecule} or {group} :l
groupID1, groupID2, ... = list of N group IDs :pre
zero or more keyword/value pairs may be appended :l
-keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} or {mol} :l
+keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
{langevin} values = Tstart Tstop Tperiod seed
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
@@ -57,7 +61,7 @@ keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {coup
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
{infile} filename
- filename = file with per-body values of mass, center-of-mass, moments of inertia
+ filename = file with per-body values of mass, center-of-mass, moments of inertia
{mol} value = template-ID
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command :pre
:ule
@@ -73,8 +77,9 @@ fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
-fix 1 water rigid/nph molecule iso 0.5 0.5 1.0 :pre
-
+fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
+fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
+
[Description:]
Treat one or more sets of atoms as independent rigid bodies. This
@@ -278,17 +283,17 @@ iterations. The {rigid/nve} style uses the methods described in the
paper by "Miller"_#Miller, which are thought to provide better energy
conservation than an iterative approach.
-The {rigid/nvt} style performs constant NVT integration using a
-Nose/Hoover thermostat with chains as described originally in
-"(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which thermostats both
-the translational and rotational degrees of freedom of the rigid
-bodies. The rigid-body algorithm used by {rigid/nvt} is described in
-the paper by "Kamberaj"_#Kamberaj.
+The {rigid/nvt} and {rigid/nvt/small} styles performs constant NVT
+integration using a Nose/Hoover thermostat with chains as described
+originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which
+thermostats both the translational and rotational degrees of freedom
+of the rigid bodies. The rigid-body algorithm used by {rigid/nvt}
+is described in the paper by "Kamberaj"_#Kamberaj.
-The {rigid/npt} and {rigid/nph} styles perform constant NPT or NPH
-integration using a Nose/Hoover barostat with chains. For the NPT
-case, the same Nose/Hoover thermostat is also used as with
-{rigid/nvt}.
+The {rigid/npt} and {rigid/nph} (and their /small counterparts) styles
+perform constant NPT or NPH integration using a Nose/Hoover barostat
+with chains. For the NPT case, the same Nose/Hoover thermostat is also
+used as with {rigid/nvt}.
The barostat parameters are specified using one or more of the {iso},
{aniso}, {x}, {y}, {z} and {couple} keywords. These keywords give you
@@ -298,8 +303,8 @@ they represent are varied together during a constant-pressure
simulation. The effects of these keywords are similar to those
defined in "fix npt/nph"_fix_nh.html
-NOTE: Currently the {rigid/npt} and {rigid/nph} styles do not support
-triclinic (non-orthongonal) boxes.
+NOTE: Currently the {rigid/npt} and {rigid/nph} (and their /small
+counterparts) styles do not support triclinic (non-orthongonal) boxes.
The target pressures for each of the 6 components of the stress tensor
can be specified independently via the {x}, {y}, {z} keywords, which
@@ -469,11 +474,9 @@ have to list attributes for every rigid body integrated by fix rigid.
Only bodies which the file specifies will have their computed
attributes overridden. The file can contain initial blank lines or
comment lines starting with "#" which are ignored. The first
-non-blank, non-comment line should list N, which is the number of
-lines to follow. The N successive lines contain the following
-information:
+non-blank, non-comment line should list N = the number of lines to
+follow. The N successive lines contain the following information:
-N
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
...