x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)c_ID = scalar or vector calculated by a compute with ID +x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) + c_ID = scalar or vector calculated by a compute with ID c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID f_ID = scalar or vector calculated by a fix with ID f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID diff --git a/doc/fix_ave_histo.txt b/doc/fix_ave_histo.txt index 9d580f0ec1..9fe881f46c 100644 --- a/doc/fix_ave_histo.txt +++ b/doc/fix_ave_histo.txt @@ -21,7 +21,8 @@ lo,hi = lo/hi bounds within which to histogram Nbin = # of histogram bins one or more input values can be listed :l value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)c_ID = scalar or vector calculated by a compute with ID + x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) + c_ID = scalar or vector calculated by a compute with ID c_ID\[I\] = Ith component of vector or Ith column of array calculated by a compute with ID f_ID = scalar or vector calculated by a fix with ID f_ID\[I\] = Ith component of vector or Ith column of array calculated by a fix with ID diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index cd8b86f9bf..9d944fb4a9 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -9,15 +9,21 @@
-fix rigid +
fix rigid command +
+fix rigid/nve command +
+fix rigid/nvt command +
+fix rigid/npt command
Syntax:
-fix ID group-ID rigid bodystyle args keyword values ... +fix ID group-ID style bodystyle args keyword values ...
force values = M xflag yflag zflag
+ temp values = Tstart Tstop Tperiod
+ Tstart,Tstop = desired temperature at start/stop of run (temperature units)
+ Tdamp = temperature damping parameter (time units)
+ press values = Pstart Pstop Pperiod
+ Pstart,Pstop = desired temperature at start/stop of run (pressure units)
+ Pdamp = pressure damping parameter (time units)
+ tparam values = Tchain Titer Torder
+ Tchain = length of Nose/Hoover thermostat chain
+ Titer = number of thermostat iterations performed
+ Torder = 3 or 5 = Yoshida-Suzuki integration parameters
+ pparam values = Pchain
+ Pchain = length of Nose/Hoover barostat chain
+ force values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass force is active
torque values = M xflag yflag zflag
@@ -44,9 +62,9 @@
fix 1 clump rigid single
fix 1 clump rigid single force 1 off off on
-fix 1 polychains rigid molecule
+fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
-fix 2 fluid rigid group 3 clump1 clump2 clump3
+fix 2 fluid rigid group 3 clump1 clump2 clump3 temp 300.0 320.0 100.0 press 0.0 0.0 1000.0
fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
Description:
@@ -71,26 +89,35 @@ command can also be used to rigidify small molecules of 2, 3, or 4
atoms, e.g. water molecules. That fix treats the constituent atoms as
point masses.
-The constituent particles within a rigid body can be point particles
-(the default in LAMMPS) or finite-size particles, such as spheroids
-and ellipsoids. See the shape command and atom_style
-granular for more details on these kinds of
-particles. Finite-size particles contribute differently to the moment
-of inertia of a rigid body than do point particles. Finite-size
-particles can also experience torque (e.g. due to frictional granular
-interactions) and have an orientation. These
-contributions are accounted for by the fix.
+
These fixes also update the positions and velocities of the atoms in
+each rigid body via time integration. The rigid and rigid/nve
+styles do this via constant NVE integration. The only difference is
+that the rigid style uses an integration technique based on
+Richardson 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.
-Forces between particles within a body do not contribute to the
-external force or torque on the body. Thus for computational
-efficiency, you may wish to turn off pairwise and bond interactions
-between particles within each rigid body. The neigh_modify
-exclude and delete_bonds
-commands are used to do this. For finite-size particles this also
-means the particles can be highly overlapped when creating the rigid
-body.
+
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.
-IMPORTANT NOTE: This fix is overkill if you simply want to hold a
+
The rigid/npt style performs constant NPT integration using a
+Nose/Hoover thermostat and barostat with chains, as described
+originally in (Hoover) and (Martyna). As with
+rigid/nvt, the thermostat affects both the translational and
+rotational degrees of freedom of the rigid bodies. The barostat
+adjusts the simulation box size isotropically. The rigid-body
+algorithm used by rigid/nvt is described in the paper by
+Kamberaj.
+
+IMPORTANT NOTE: You should not update the atoms in rigid bodies via
+other time-integration fixes (e.g. nve, nvt, npt), or you will be
+integrating their motion more than once each timestep.
+
+IMPORTANT NOTE: These fixes are overkill if you simply want to hold a
collection of atoms stationary or have them move with a constant
velocity. A simpler way to hold atoms stationary is to not include
those atoms in your time integration fix. E.g. use "fix 1 mobile nve"
@@ -101,9 +128,26 @@ command), setting the force on them to 0.0 (via the fix nve command).
-IMPORTANT NOTE: This fix updates the positions and velocities of the
-rigid atoms with a constant-energy time integration, so you should not
-update the same atoms via other fixes (e.g. nve, nvt, npt).
+
+
+The constituent particles within a rigid body can be point particles
+(the default in LAMMPS) or finite-size particles, such as spheroids
+and ellipsoids. See the shape command and atom_style
+granular for more details on these kinds of
+particles. Finite-size particles contribute differently to the moment
+of inertia of a rigid body than do point particles. Finite-size
+particles can also experience torque (e.g. due to frictional granular
+interactions) and have an orientation. These
+contributions are accounted for by these fixes.
+
+Forces between particles within a body do not contribute to the
+external force or torque on the body. Thus for computational
+efficiency, you may wish to turn off pairwise and bond interactions
+between particles within each rigid body. The neigh_modify
+exclude and delete_bonds
+commands are used to do this. For finite-size particles this also
+means the particles can be highly overlapped when creating the rigid
+body.
@@ -155,24 +199,82 @@ bond interactions within each rigid body, as they no longer contribute
to the motion. The neigh_modify exclude and
delete_bonds commands are used to do this.
-For computational efficiency, you should define one fix rigid which
-includes all the desired rigid bodies. LAMMPS will allow multiple
-rigid fixes to be defined, but it is more expensive.
+
For computational efficiency, you should typically define one fix
+rigid which includes all the desired rigid bodies. LAMMPS will allow
+multiple rigid fixes to be defined, but it is more expensive.
-This fix uses constant-energy NVE-style integration, so you may need
-to impose additional constraints to control the temperature of an
-ensemble of rigid bodies. You can use fix
-langevin for this purpose to treat the system as
+
+
+As stated above, the rigid and rigid/nve styles
+perform constant NVE time integration. Thus the
+temp, press, tparam, and pparam keywords cannot
+be used with these styles.
+
+The rigid/nvt style performs constant NVT time integration, using a
+temperature it computes for the rigid bodies which includes their
+translational and rotational motion. The temp keyword must be used
+with this style. The desired temperature at each timestep is a ramped
+value during the run from Tstart to Tstop. The Tdamp parameter
+is specified in time units and determines how rapidly the temperature
+is relaxed. For example, a value of 100.0 means to relax the
+temperature in a timespan of (roughly) 100 time units (tau or fmsec or
+psec - see the units command).
+
+Nose/Hoover chains are used in conjunction with this thermostat. The
+tparam keyword can optionally be used to change the chain settings
+used. Tchain is the number of thermostats in the Nose Hoover chain.
+This value, along with Tdamp can be varied to dampen undesirable
+oscillations in temperature that can occur in a simulation. As a rule
+of thumb, increasing the chain length should lead to smaller
+oscillations. The rigid/nvt style does not allow the use of the
+press and pparam keywords.
+
+The rigid/npt style performs constant NPT time integration, using a
+temperature it computes for the rigid bodies which includes their
+translational and rotational motion, and a pressure which includes the
+conribution of the rigid bodies to the virial of the system. The
+temp and press keywords must be used with this style. The desired
+temperature at each timestep is a ramped value during the run from
+Tstart to Tstop. The Tdamp parameter is specified in time units
+and determines how rapidly the temperature is relaxed. For example, a
+value of 100.0 means to relax the temperature in a timespan of
+(roughly) 100 time units (tau or fmsec or psec - see the
+units command). Similarly, the desired pressure at each
+timestep is a ramped value during the run from Pstart to Pstop.
+The Pdamp parameter is specified in time units and determines how
+rapidly the presssure is relaxed. For example, a value of 1000.0
+means to relax the temperature in a timespan of (roughly) 1000 time
+units. The pressure of the system is controlled by varying the box
+volume via isotropic rescaling. This means the simulation box retains
+its aspect ratio, and the center-of-mass of each rigid body is
+rescaled to new coordinates.
+
+Nose/Hoover chains are used in conjunction with this
+thermostat/barostat combination. The pparam keyword can optionally
+be used to change the chain settings used. Pchain is the number of
+thermostats in the Nose Hoover chain. This value, along with Tdamp
+and Pdamp can be varied to dampen undesirable oscillations in
+pressure that can occur in a simulation. As a rule of thumb,
+increasing the chain length should lead to smaller oscillations. The
+rigid/npt style does not allow the use of the tparam keyword.
+
+There are alternate ways to thermostat a system of rigid bodies. You
+can use fix langevin to treat the system as
effectively immersed in an implicit solvent, e.g. a Brownian dynamics
-model. Or you can thermostat only the non-rigid atoms that surround
-one or more rigid bodies (i.e. explicit solvent) by appropriate choice
-of groups in the compute and fix commands for temperature and
-thermostatting.
+model. For hybrid systems with both rigid bodies and solvent
+particles, you can thermostat only the solvent particles that surround
+one or more rigid bodies by appropriate choice of groups in the
+compute and fix commands for temperature and thermostatting. The
+solvent interactions with the rigid bodies should then effectively
+thermostat the rigid body temperature as well.
-If you calculate a temperature for particles in the rigid bodies, the
-degrees-of-freedom removed by each rigid body are accounted for in the
-temperature (and pressure) computation, but only if the temperature
-group includes all the particles in a particular rigid body.
+
+
+If you use a temperature compute with a group that
+includes particles in rigid bodies, the degrees-of-freedom removed by
+each rigid body are accounted for in the temperature (and pressure)
+computation, but only if the temperature group includes all the
+particles in a particular rigid body.
A 3d rigid body has 6 degrees of freedom (3 translational, 3
rotational), except for a collection of point particles lying on a
@@ -181,7 +283,7 @@ degrees of freedom (2 translational, 1 rotational).
IMPORTANT NOTE: You may wish to explicitly subtract additional
degrees-of-freedom if you use the force and torque keywords to
-eliminate certain motions of one or more rigid bodies, as LAMMPS does
+eliminate certain motions of one or more rigid bodies. LAMMPS does
not do this automatically.
The rigid body contribution to the pressure of the system (virial) is
@@ -201,13 +303,22 @@ between a pair of rigid bodies and the bond straddles a periodic
boundary, you cannot use the replicate command to increase
the system size.
+
+
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 information about the rigid and rigid/nve fixes are written to
+binary restart files. For style rigid/nvt and
+rigid/npt, the state of the Nose/Hoover thermostat/barostat is
+written to binary restart files. See the
+read_restart command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
-This fix computes a global array of values which can be accessed by
+
None of the fix_modify options are relevant to these
+fixes.
+
+These fixes compute a global array of values which can be accessed by
various output commands. The number of rows
in the array is equal to the number of rigid bodies. The number of
columns is 12. Thus for each rigid body, 12 values are stored: the
@@ -224,18 +335,19 @@ For the single keyword there is just one rigid body. For the
For the group keyword, the list of group IDs determines the ordering
of bodies.
-The array values calculated by this fix are "intensive", meaning they
-are independent of the number of atoms in the simulation.
+
The array values calculated by these fixes are "intensive", meaning
+they are independent of the number of atoms in the simulation.
-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.
+
No parameter of these fixes can be used with the start/stop keywords
+of the run command. These fixse are not invoked during
+energy minimization.
Restrictions:
-This fix performs an MPI_Allreduce each timestep that is proportional
-in length to the number of rigid bodies. Hence it will not scale well
-in parallel if large numbers of rigid bodies are simulated.
+
These fixes performs an MPI_Allreduce each timestep that is
+proportional in length to the number of rigid bodies. Hence they will
+not scale well in parallel if large numbers of rigid bodies are
+simulated.
If the atoms in a single rigid body initially straddle a periodic
boundary, the input data file must define the image flags for each
@@ -249,11 +361,30 @@ exclude
Default:
-The option defaults are force * on on on and torque * on on on meaning
-all rigid bodies are acted on by center-of-mass force and torque.
+
The option defaults are force * on on on and torque * on on on,
+meaning all rigid bodies are acted on by center-of-mass force and
+torque. Also Tchain = 10, Titer = 1, Torder = 3, and Pchain = 10.
+
+
+(Hoover) Hoover, Phys Rev A, 31, 1695 (1985).
+
+
+
+(Kamberaj) Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
+
+
+
+(Martyna) Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
+Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
+
+
+
+(Miller) Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
+J Chem Phys, 116, 8649 (2002).
+
(Zhang) Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt
index 7d25107a44..90a4836d27 100644
--- a/doc/fix_rigid.txt
+++ b/doc/fix_rigid.txt
@@ -6,14 +6,17 @@
:line
-fix rigid :h3
+fix rigid command :h3
+fix rigid/nve command :h3
+fix rigid/nvt command :h3
+fix rigid/npt command :h3
[Syntax:]
-fix ID group-ID rigid bodystyle args keyword values ... :pre
+fix ID group-ID style bodystyle args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
-rigid = style name of this fix command :l
+style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} :l
bodystyle = {single} or {molecule} or {group} :l
{single} args = none
{molecule} args = none
@@ -22,7 +25,19 @@ 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 = {force} or {torque} :l
+keyword = {temp} or {press} or {tparam} or {pparam} or {force} or {torque} :l
+ {temp} values = Tstart Tstop Tperiod
+ Tstart,Tstop = desired temperature at start/stop of run (temperature units)
+ Tdamp = temperature damping parameter (time units)
+ {press} values = Pstart Pstop Pperiod
+ Pstart,Pstop = desired temperature at start/stop of run (pressure units)
+ Pdamp = pressure damping parameter (time units)
+ {tparam} values = Tchain Titer Torder
+ Tchain = length of Nose/Hoover thermostat chain
+ Titer = number of thermostat iterations performed
+ Torder = 3 or 5 = Yoshida-Suzuki integration parameters
+ {pparam} values = Pchain
+ Pchain = length of Nose/Hoover barostat chain
{force} values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass force is active
@@ -35,9 +50,9 @@ keyword = {force} or {torque} :l
fix 1 clump rigid single
fix 1 clump rigid single force 1 off off on
-fix 1 polychains rigid molecule
+fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
-fix 2 fluid rigid group 3 clump1 clump2 clump3
+fix 2 fluid rigid group 3 clump1 clump2 clump3 temp 300.0 320.0 100.0 press 0.0 0.0 1000.0
fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off :pre
[Description:]
@@ -62,26 +77,35 @@ command can also be used to rigidify small molecules of 2, 3, or 4
atoms, e.g. water molecules. That fix treats the constituent atoms as
point masses.
-The constituent particles within a rigid body can be point particles
-(the default in LAMMPS) or finite-size particles, such as spheroids
-and ellipsoids. See the "shape"_shape.html command and "atom_style
-granular"_atom_style.html for more details on these kinds of
-particles. Finite-size particles contribute differently to the moment
-of inertia of a rigid body than do point particles. Finite-size
-particles can also experience torque (e.g. due to "frictional granular
-interactions"_pair_gran.html) and have an orientation. These
-contributions are accounted for by the fix.
+These fixes also update the positions and velocities of the atoms in
+each rigid body via time integration. The {rigid} and {rigid/nve}
+styles do this via constant NVE integration. The only difference is
+that the {rigid} style uses an integration technique based on
+Richardson 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.
-Forces between particles within a body do not contribute to the
-external force or torque on the body. Thus for computational
-efficiency, you may wish to turn off pairwise and bond interactions
-between particles within each rigid body. The "neigh_modify
-exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
-commands are used to do this. For finite-size particles this also
-means the particles can be highly overlapped when creating the rigid
-body.
+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.
-IMPORTANT NOTE: This fix is overkill if you simply want to hold a
+The {rigid/npt} style performs constant NPT integration using a
+Nose/Hoover thermostat and barostat with chains, as described
+originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna. As with
+{rigid/nvt}, the thermostat affects both the translational and
+rotational degrees of freedom of the rigid bodies. The barostat
+adjusts the simulation box size isotropically. The rigid-body
+algorithm used by {rigid/nvt} is described in the paper by
+"Kamberaj"_#Kamberaj.
+
+IMPORTANT NOTE: You should not update the atoms in rigid bodies via
+other time-integration fixes (e.g. nve, nvt, npt), or you will be
+integrating their motion more than once each timestep.
+
+IMPORTANT NOTE: These fixes are overkill if you simply want to hold a
collection of atoms stationary or have them move with a constant
velocity. A simpler way to hold atoms stationary is to not include
those atoms in your time integration fix. E.g. use "fix 1 mobile nve"
@@ -92,9 +116,26 @@ command), setting the force on them to 0.0 (via the "fix
setforce"_fix_setforce.html command), and integrating them as usual
(e.g. via the "fix nve"_fix_nve.html command).
-IMPORTANT NOTE: This fix updates the positions and velocities of the
-rigid atoms with a constant-energy time integration, so you should not
-update the same atoms via other fixes (e.g. nve, nvt, npt).
+:line
+
+The constituent particles within a rigid body can be point particles
+(the default in LAMMPS) or finite-size particles, such as spheroids
+and ellipsoids. See the "shape"_shape.html command and "atom_style
+granular"_atom_style.html for more details on these kinds of
+particles. Finite-size particles contribute differently to the moment
+of inertia of a rigid body than do point particles. Finite-size
+particles can also experience torque (e.g. due to "frictional granular
+interactions"_pair_gran.html) and have an orientation. These
+contributions are accounted for by these fixes.
+
+Forces between particles within a body do not contribute to the
+external force or torque on the body. Thus for computational
+efficiency, you may wish to turn off pairwise and bond interactions
+between particles within each rigid body. The "neigh_modify
+exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
+commands are used to do this. For finite-size particles this also
+means the particles can be highly overlapped when creating the rigid
+body.
:line
@@ -146,24 +187,82 @@ bond interactions within each rigid body, as they no longer contribute
to the motion. The "neigh_modify exclude"_neigh_modify.html and
"delete_bonds"_delete_bonds.html commands are used to do this.
-For computational efficiency, you should define one fix rigid which
-includes all the desired rigid bodies. LAMMPS will allow multiple
-rigid fixes to be defined, but it is more expensive.
+For computational efficiency, you should typically define one fix
+rigid which includes all the desired rigid bodies. LAMMPS will allow
+multiple rigid fixes to be defined, but it is more expensive.
-This fix uses constant-energy NVE-style integration, so you may need
-to impose additional constraints to control the temperature of an
-ensemble of rigid bodies. You can use "fix
-langevin"_fix_langevin.html for this purpose to treat the system as
+:line
+
+As stated above, the {rigid} and {rigid/nve} styles
+perform constant NVE time integration. Thus the
+{temp}, {press}, {tparam}, and {pparam} keywords cannot
+be used with these styles.
+
+The {rigid/nvt} style performs constant NVT time integration, using a
+temperature it computes for the rigid bodies which includes their
+translational and rotational motion. The {temp} keyword must be used
+with this style. The desired temperature at each timestep is a ramped
+value during the run from {Tstart} to {Tstop}. The {Tdamp} parameter
+is specified in time units and determines how rapidly the temperature
+is relaxed. For example, a value of 100.0 means to relax the
+temperature in a timespan of (roughly) 100 time units (tau or fmsec or
+psec - see the "units"_units.html command).
+
+Nose/Hoover chains are used in conjunction with this thermostat. The
+{tparam} keyword can optionally be used to change the chain settings
+used. {Tchain} is the number of thermostats in the Nose Hoover chain.
+This value, along with {Tdamp} can be varied to dampen undesirable
+oscillations in temperature that can occur in a simulation. As a rule
+of thumb, increasing the chain length should lead to smaller
+oscillations. The {rigid/nvt} style does not allow the use of the
+{press} and {pparam} keywords.
+
+The {rigid/npt} style performs constant NPT time integration, using a
+temperature it computes for the rigid bodies which includes their
+translational and rotational motion, and a pressure which includes the
+conribution of the rigid bodies to the virial of the system. The
+{temp} and {press} keywords must be used with this style. The desired
+temperature at each timestep is a ramped value during the run from
+{Tstart} to {Tstop}. The {Tdamp} parameter is specified in time units
+and determines how rapidly the temperature is relaxed. For example, a
+value of 100.0 means to relax the temperature in a timespan of
+(roughly) 100 time units (tau or fmsec or psec - see the
+"units"_units.html command). Similarly, the desired pressure at each
+timestep is a ramped value during the run from {Pstart} to {Pstop}.
+The {Pdamp} parameter is specified in time units and determines how
+rapidly the presssure is relaxed. For example, a value of 1000.0
+means to relax the temperature in a timespan of (roughly) 1000 time
+units. The pressure of the system is controlled by varying the box
+volume via isotropic rescaling. This means the simulation box retains
+its aspect ratio, and the center-of-mass of each rigid body is
+rescaled to new coordinates.
+
+Nose/Hoover chains are used in conjunction with this
+thermostat/barostat combination. The {pparam} keyword can optionally
+be used to change the chain settings used. {Pchain} is the number of
+thermostats in the Nose Hoover chain. This value, along with {Tdamp}
+and {Pdamp} can be varied to dampen undesirable oscillations in
+pressure that can occur in a simulation. As a rule of thumb,
+increasing the chain length should lead to smaller oscillations. The
+{rigid/npt} style does not allow the use of the {tparam} keyword.
+
+There are alternate ways to thermostat a system of rigid bodies. You
+can use "fix langevin"_fix_langevin.html to treat the system as
effectively immersed in an implicit solvent, e.g. a Brownian dynamics
-model. Or you can thermostat only the non-rigid atoms that surround
-one or more rigid bodies (i.e. explicit solvent) by appropriate choice
-of groups in the compute and fix commands for temperature and
-thermostatting.
+model. For hybrid systems with both rigid bodies and solvent
+particles, you can thermostat only the solvent particles that surround
+one or more rigid bodies by appropriate choice of groups in the
+compute and fix commands for temperature and thermostatting. The
+solvent interactions with the rigid bodies should then effectively
+thermostat the rigid body temperature as well.
-If you calculate a temperature for particles in the rigid bodies, the
-degrees-of-freedom removed by each rigid body are accounted for in the
-temperature (and pressure) computation, but only if the temperature
-group includes all the particles in a particular rigid body.
+:line
+
+If you use a "temperature compute"_compute.html with a group that
+includes particles in rigid bodies, the degrees-of-freedom removed by
+each rigid body are accounted for in the temperature (and pressure)
+computation, but only if the temperature group includes all the
+particles in a particular rigid body.
A 3d rigid body has 6 degrees of freedom (3 translational, 3
rotational), except for a collection of point particles lying on a
@@ -172,7 +271,7 @@ degrees of freedom (2 translational, 1 rotational).
IMPORTANT NOTE: You may wish to explicitly subtract additional
degrees-of-freedom if you use the {force} and {torque} keywords to
-eliminate certain motions of one or more rigid bodies, as LAMMPS does
+eliminate certain motions of one or more rigid bodies. LAMMPS does
not do this automatically.
The rigid body contribution to the pressure of the system (virial) is
@@ -192,13 +291,22 @@ between a pair of rigid bodies and the bond straddles a periodic
boundary, you cannot use the "replicate"_replicate command to increase
the system size.
+:line
+
[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 information about the {rigid} and {rigid/nve} fixes are written to
+"binary restart files"_restart.html. For style {rigid/nvt} and
+{rigid/npt}, the state of the Nose/Hoover thermostat/barostat is
+written to "binary restart files"_restart.html. See the
+"read_restart"_read_restart.html command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
-This fix computes a global array of values which can be accessed by
+None of the "fix_modify"_fix_modify.html options are relevant to these
+fixes.
+
+These fixes compute a global array of values which can be accessed by
various "output commands"_Section_howto.html#4_15. The number of rows
in the array is equal to the number of rigid bodies. The number of
columns is 12. Thus for each rigid body, 12 values are stored: the
@@ -215,18 +323,19 @@ For the {single} keyword there is just one rigid body. For the
For the {group} keyword, the list of group IDs determines the ordering
of bodies.
-The array values calculated by this fix are "intensive", meaning they
-are independent of the number of atoms in the simulation.
+The array values calculated by these fixes are "intensive", meaning
+they are independent of the number of atoms in the simulation.
-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.
+No parameter of these fixes can be used with the {start/stop} keywords
+of the "run"_run.html command. These fixse are not invoked during
+"energy minimization"_minimize.html.
[Restrictions:]
-This fix performs an MPI_Allreduce each timestep that is proportional
-in length to the number of rigid bodies. Hence it will not scale well
-in parallel if large numbers of rigid bodies are simulated.
+These fixes performs an MPI_Allreduce each timestep that is
+proportional in length to the number of rigid bodies. Hence they will
+not scale well in parallel if large numbers of rigid bodies are
+simulated.
If the atoms in a single rigid body initially straddle a periodic
boundary, the input data file must define the image flags for each
@@ -240,10 +349,25 @@ exclude
[Default:]
-The option defaults are force * on on on and torque * on on on meaning
-all rigid bodies are acted on by center-of-mass force and torque.
+The option defaults are force * on on on and torque * on on on,
+meaning all rigid bodies are acted on by center-of-mass force and
+torque. Also Tchain = 10, Titer = 1, Torder = 3, and Pchain = 10.
:line
+:link(Hoover)
+[(Hoover)] Hoover, Phys Rev A, 31, 1695 (1985).
+
+:link(Kamberaj)
+[(Kamberaj)] Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
+
+:link(Martyna)
+[(Martyna)] Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
+Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
+
+:link(Miller)
+[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
+J Chem Phys, 116, 8649 (2002).
+
:link(Zhang)
[(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).