From 8f4c6e3720518b9d90d686edf895de9bd07c784b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 13 Jan 2009 14:38:26 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2452 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_rigid.html | 117 ++++++++++++++++++++++++++++++++++++--------- doc/fix_rigid.txt | 116 +++++++++++++++++++++++++++++++++++--------- doc/units.html | 7 ++- doc/units.txt | 7 ++- 4 files changed, 199 insertions(+), 48 deletions(-) diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index e51b61000f..2c489dfe35 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -13,25 +13,41 @@

Syntax:

-
fix ID group-ID rigid keyword values 
+
fix ID group-ID rigid bodystyle args keyword values ... 
 

 
 
Examples:
 

 
fix 1 clump rigid single
+fix 1 clump rigid single force 1 off off on
 fix 1 polychains rigid molecule
-fix 2 fluid rigid group clump1 clump2 clump3 
+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 torque * off off off 
 

 
Description:
 

@@ -46,20 +62,44 @@ for simulating a system of colloidal particles.
 a constant-energy time integration, so you should not update the same
 atoms via other fixes (e.g. nve, nvt, npt).
 

-
Each body must have two or more atoms.  Which atoms are in which
-bodies can be defined via several options.
+
Each body must have two or more atoms.  An atom can belong to at most
+one rigid body.  Which atoms are in which bodies can be defined via
+several options.
 

-
For option single the entire group of atoms is treated as one rigid
-body.
+
For bodystyle single the entire fix group of atoms is treated as one
+rigid body.
 

-
For option molecule, each set of atoms in the group with a different
-molecule ID is treated as a rigid body.
+
For bodystyle molecule, each set of atoms in the fix group with a
+different molecule ID is treated as a rigid body.
 

-
For option group, each of the listed groups is treated as a separate
-rigid body.  Note that only atoms that are also in the fix group are
+
For bodystyle group, each of the listed groups is treated as a
+separate rigid body.  Only atoms that are also in the fix group are
 included in each rigid body.
 

-
For computational efficiency, you should also turn off pairwise and
+
By default, each rigid body is acted on by other atoms which induce a
+force and torque on its center of mass, causing it to translate and
+rotate.  Components of the center-of-mass force and torque can be
+turned off by the force and torque keywords.  This may be useful
+if you wish a body to rotate but not translate, or vice versa.  Note
+that if you expect a rigid body not to move or rotate by using these
+keywords, you must insure its initial center-of-mass translational or
+angular velocity is 0.0.
+

+
An xflag, yflag, or zflag set to off means turn off the component of
+force of torque in that dimension.  A setting of on means turn on
+the component, which is the default.  Which rigid body(s) the settings
+apply to is determined by the first argument of the force and
+torque keywords.  It can be an integer M from 1 to Nbody, where
+Nbody is the number of rigid bodies defined.  A wild-card asterisk can
+be used in place of, or in conjunction with, the M argument to set the
+flags for multiple rigid bodies.  This takes the form "*" or "*n" or
+"n*" or "m*n".  If N = the number of rigid bodies, then an asterisk
+with no numeric values means all bodies from 1 to N.  A leading
+asterisk means all bodies from 1 to n (inclusive).  A trailing
+asterisk means all bodies from n to N (inclusive).  A middle asterisk
+means all types from m to n (inclusive).
+

+
For computational efficiency, you may wish to turn off pairwise and
 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.
@@ -83,7 +123,13 @@ degree-of-freedom must be subtracted manually using the
 compute_modify command.  E.g. for a simulation
 of 10 such rigid bodies, use "compute_modify thermo_temp extra 13",
 after the thermo_style command, where 3 is the default setting and an
-additional 10 degrees-of-freedom are subtracted.
+additional 10 degrees-of-freedom are subtracted.  You may also wish to
+manually subtract additional degrees-of-freedom if you use the force
+and torque keywords to eliminate certain motions of the rigid body.
+Alternatively, you can define the temperature compute
+to exclude atoms in rigid bodies, which may be a better strategy,
+i.e. measure the temperature of the free atoms around the rigid body
+or bodies.
 

 
IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
 modified when the center-of-mass of the rigid body moves across a
@@ -103,11 +149,32 @@ the system size.
 

 
No information about this fix is written to binary restart
 files.  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.  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.
+

+
This fix computes a global vector of quantities which can be accessed
+by various output commands.  For each rigid
+body, 12 values are stored: the xyz coords of the center of mass
+(COM), the xyz components of the COM velocity, the xyz components of
+the force acting on the COM, and the xyz components of the torque
+acting on the COM.  The force and torque values in the vector are not
+affected by the force and torque keywords in the fix rigid
+command; they reflect values before any changes are made by those
+keywords.
+

+
The total length of the vector is 12*Nbody where Nbody is the number
+of rigid bodies defined by the fix.  Thus the 15th value in the vector
+would be the z-coord of the COM of the 2nd rigid body.  LAMMPS chooses
+the ordering of the rigid bodies internally.  The ordering of the
+rigid bodies is as follows.  For the single keyword there is just
+one rigid body.  For the molecule keyword, the bodies are ordered by
+ascending molecule ID.  For the group keyword, the list of group IDs
+determines the ordering of bodies.  The vector values calculated by
+this fix 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.
 

 
Restrictions:
 

@@ -124,13 +191,17 @@ rigid body.
 stationary.  A better way to do this is to not include those atoms in
 your time integration fix.  E.g. use "fix 1 mobile nve" instead of
 "fix 1 all nve", where "mobile" is the group of atoms that you want to
-move.
+move.  Alternatively, you can also set the force on those atoms to 0.0
+via the fix setforce command.
 

 
Related commands:
 

 
delete_bonds, neigh_modify
 exclude
 

-
Default: none
+
Default:
+

+
The option defaults are force * 1 1 1 and torque * 1 1 1, meaning
+all rigid bodies are acted on by center-of-mass force and torque.
 

 
diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt
index 63b030dfc0..c06f2b9550 100644
--- a/doc/fix_rigid.txt
+++ b/doc/fix_rigid.txt
@@ -10,21 +10,35 @@ fix rigid :h3
 
 [Syntax:]
 
-fix ID group-ID rigid keyword values :pre
+fix ID group-ID rigid 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
-keyword = {single} or {molecule} or {group} :l
-  {single} values = none
-  {molecule} values = none
-  {group} values = list of group IDs :pre
+bodystyle = {single} or {molecule} or {group} :l
+  {single} args = none
+  {molecule} args = none
+  {group} args = N groupID1 groupID2 ...
+    N = # of groups
+    groupID1, groupID2, ... = list of N group IDs :pre
+
+zero or more keyword/value pairs may be appended :l
+keyword = {force} or {torque} :l
+  {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
+    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 :pre
 :ule
 
 [Examples:]
 
 fix 1 clump rigid single
+fix 1 clump rigid single force 1 off off on
 fix 1 polychains rigid molecule
-fix 2 fluid rigid group clump1 clump2 clump3 :pre
+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 torque * off off off :pre
 
 [Description:]
 
@@ -39,20 +53,44 @@ 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).
 
-Each body must have two or more atoms.  Which atoms are in which
-bodies can be defined via several options.
+Each body must have two or more atoms.  An atom can belong to at most
+one rigid body.  Which atoms are in which bodies can be defined via
+several options.
 
-For option {single} the entire group of atoms is treated as one rigid
-body.
+For bodystyle {single} the entire fix group of atoms is treated as one
+rigid body.
 
-For option {molecule}, each set of atoms in the group with a different
-molecule ID is treated as a rigid body.
+For bodystyle {molecule}, each set of atoms in the fix group with a
+different molecule ID is treated as a rigid body.
 
-For option {group}, each of the listed groups is treated as a separate
-rigid body.  Note that only atoms that are also in the fix group are
+For bodystyle {group}, each of the listed groups is treated as a
+separate rigid body.  Only atoms that are also in the fix group are
 included in each rigid body.
 
-For computational efficiency, you should also turn off pairwise and
+By default, each rigid body is acted on by other atoms which induce a
+force and torque on its center of mass, causing it to translate and
+rotate.  Components of the center-of-mass force and torque can be
+turned off by the {force} and {torque} keywords.  This may be useful
+if you wish a body to rotate but not translate, or vice versa.  Note
+that if you expect a rigid body not to move or rotate by using these
+keywords, you must insure its initial center-of-mass translational or
+angular velocity is 0.0.
+
+An xflag, yflag, or zflag set to {off} means turn off the component of
+force of torque in that dimension.  A setting of {on} means turn on
+the component, which is the default.  Which rigid body(s) the settings
+apply to is determined by the first argument of the {force} and
+{torque} keywords.  It can be an integer M from 1 to Nbody, where
+Nbody is the number of rigid bodies defined.  A wild-card asterisk can
+be used in place of, or in conjunction with, the M argument to set the
+flags for multiple rigid bodies.  This takes the form "*" or "*n" or
+"n*" or "m*n".  If N = the number of rigid bodies, then an asterisk
+with no numeric values means all bodies from 1 to N.  A leading
+asterisk means all bodies from 1 to n (inclusive).  A trailing
+asterisk means all bodies from n to N (inclusive).  A middle asterisk
+means all types from m to n (inclusive).
+
+For computational efficiency, you may wish to turn off pairwise and
 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.
@@ -76,7 +114,13 @@ degree-of-freedom must be subtracted manually using the
 "compute_modify"_compute_modify.html command.  E.g. for a simulation
 of 10 such rigid bodies, use "compute_modify thermo_temp extra 13",
 after the thermo_style command, where 3 is the default setting and an
-additional 10 degrees-of-freedom are subtracted.
+additional 10 degrees-of-freedom are subtracted.  You may also wish to
+manually subtract additional degrees-of-freedom if you use the {force}
+and {torque} keywords to eliminate certain motions of the rigid body.
+Alternatively, you can define the temperature "compute"_compute.html
+to exclude atoms in rigid bodies, which may be a better strategy,
+i.e. measure the temperature of the free atoms around the rigid body
+or bodies.
 
 IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
 modified when the center-of-mass of the rigid body moves across a
@@ -96,11 +140,32 @@ the system size.
 
 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 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.
+are relevant to this fix.
+
+This fix computes a global vector of quantities which can be accessed
+by various "output commands"_Section_howto.html#4_15.  For each rigid
+body, 12 values are stored: the xyz coords of the center of mass
+(COM), the xyz components of the COM velocity, the xyz components of
+the force acting on the COM, and the xyz components of the torque
+acting on the COM.  The force and torque values in the vector are not
+affected by the {force} and {torque} keywords in the fix rigid
+command; they reflect values before any changes are made by those
+keywords.
+
+The total length of the vector is 12*Nbody where Nbody is the number
+of rigid bodies defined by the fix.  Thus the 15th value in the vector
+would be the z-coord of the COM of the 2nd rigid body.  LAMMPS chooses
+the ordering of the rigid bodies internally.  The ordering of the
+rigid bodies is as follows.  For the {single} keyword there is just
+one rigid body.  For the {molecule} keyword, the bodies are ordered by
+ascending molecule ID.  For the {group} keyword, the list of group IDs
+determines the ordering of bodies.  The vector values calculated by
+this fix 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.
 
 [Restrictions:]
 
@@ -117,11 +182,16 @@ You should not use this fix if you just want to hold group of atoms
 stationary.  A better way to do this is to not include those atoms in
 your time integration fix.  E.g. use "fix 1 mobile nve" instead of
 "fix 1 all nve", where "mobile" is the group of atoms that you want to
-move.
+move.  Alternatively, you can also set the force on those atoms to 0.0
+via the "fix setforce"_fix_setforce.html command.
 
 [Related commands:]
 
 "delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html
 exclude
 
-[Default:] none
+[Default:]
+
+The option defaults are force * 1 1 1 and torque * 1 1 1, meaning
+all rigid bodies are acted on by center-of-mass force and torque.
+
diff --git a/doc/units.html b/doc/units.html
index 27daf61bf0..2d9c086aa6 100644
--- a/doc/units.html
+++ b/doc/units.html
@@ -49,6 +49,7 @@ results from a unitless LJ simulation into physical quantities.
 
  • energy = epsilon, where E* = E / epsilon
 
  • velocity = sigma/tau, where v* = v tau / sigma
 
  • force = epsilon/sigma, where f* = f sigma / epsilon
+
  • torque = epsilon, where t* = t / epsilon
 
  • temperature = reduced LJ temperature, where T* = T Kb / epsilon
 
  • pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon
 
  • viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau
@@ -64,6 +65,7 @@ results from a unitless LJ simulation into physical quantities.
 
  • energy = Kcal/mole 
 
  • velocity = Angstroms/femtosecond 
 
  • force = Kcal/mole-Angstrom
+
  • torque = Kcal/mole
 
  • temperature = degrees K
 
  • pressure = atmospheres
 
  • viscosity = Poise
@@ -79,6 +81,7 @@ results from a unitless LJ simulation into physical quantities.
 
  • energy = eV
 
  • velocity = Angstroms/picosecond 
 
  • force = eV/Angstrom
+
  • torque = eV
 
  • temperature = degrees K
 
  • pressure = bars
 
  • viscosity = Poise
@@ -94,6 +97,7 @@ results from a unitless LJ simulation into physical quantities.
 
  • energy = Joules
 
  • velocity = meters/second
 
  • force = Newtons
+
  • torque = Newton-meters
 
  • temperature = degrees K
 
  • pressure = Pascals
 
  • viscosity = Pascal*second
@@ -107,8 +111,9 @@ results from a unitless LJ simulation into physical quantities.
 
  • distance = centimeters
 
  • time = seconds
 
  • energy = ergs
-
  • velocity = cm/second
+
  • velocity = centimeters/second
 
  • force = dynes
+
  • torque = dyne-centimeters
 
  • temperature = degrees K
 
  • pressure = dyne/cm^2 or barye = 1.0e-6 bars
 
  • viscosity = Poise
diff --git a/doc/units.txt b/doc/units.txt
index 6560180604..0aebddeba8 100644
--- a/doc/units.txt
+++ b/doc/units.txt
@@ -46,6 +46,7 @@ time = tau, where tau = t* = t (epsilon / m / sigma^2)^1/2
 energy = epsilon, where E* = E / epsilon
 velocity = sigma/tau, where v* = v tau / sigma
 force = epsilon/sigma, where f* = f sigma / epsilon
+torque = epsilon, where t* = t / epsilon
 temperature = reduced LJ temperature, where T* = T Kb / epsilon
 pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon
 viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau
@@ -61,6 +62,7 @@ time = femtoseconds
 energy = Kcal/mole 
 velocity = Angstroms/femtosecond 
 force = Kcal/mole-Angstrom
+torque = Kcal/mole
 temperature = degrees K
 pressure = atmospheres
 viscosity = Poise
@@ -76,6 +78,7 @@ time = picoseconds
 energy = eV
 velocity = Angstroms/picosecond 
 force = eV/Angstrom
+torque = eV
 temperature = degrees K
 pressure = bars
 viscosity = Poise
@@ -91,6 +94,7 @@ time = seconds
 energy = Joules
 velocity = meters/second
 force = Newtons
+torque = Newton-meters
 temperature = degrees K
 pressure = Pascals
 viscosity = Pascal*second
@@ -104,8 +108,9 @@ mass = grams
 distance = centimeters
 time = seconds
 energy = ergs
-velocity = cm/second
+velocity = centimeters/second
 force = dynes
+torque = dyne-centimeters
 temperature = degrees K
 pressure = dyne/cm^2 or barye = 1.0e-6 bars
 viscosity = Poise