git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11838 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -402,10 +402,10 @@ of each style or click on the style itself for a full description:
 <TR ALIGN="center"><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_oneway.html">oneway</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/small/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/nvt</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_csvr.html">temp/csvr</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A> 
+<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A> 
 </TD></TR></TABLE></DIV>
 
 <P>These are fix styles contributed by users, which can be used if

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,

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 
+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 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 
+total number of atoms sharing the Voronoi cell of the stored
-tessellation at the location of the current atom. Numbers in column one
+tessellation at the location of the current atom. Numbers in column
-can be any positive integer including zero, while column two values will 
+one can be any positive integer including zero, while column two
-always be greater than zero. Column one data can be used to locate 
+values will always be greater than zero. Column one data can be used
-vacancies (the coordinates are given by the atom coordinates at the 
+to locate vacancies (the coordinates are given by the atom coordinates
-time step when the compute was first invoked), while column two data
+at the time step when the compute was first invoked), while column two
-can be used to identify interstitial atoms.
+data can be used to identify interstitial atoms.
 </P>
 <HR>
 

doc/fix_rigid.html

@@ -21,13 +21,21 @@
 </H3>
 <H3>fix rigid/small command 
 </H3>
+<H3>fix rigid/nve/small command 
+</H3>
+<H3>fix rigid/nvt/small command 
+</H3>
+<H3>fix rigid/npt/small command 
+</H3>
+<H3>fix rigid/nph/small command 
+</H3>
 <P><B>Syntax:</B>
 </P>
 <PRE>fix ID group-ID style bodystyle args keyword values ... 
 </PRE>
 <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command 
 
-<LI>style = <I>rigid</I> or <I>rigid/nve</I> or <I>rigid/nvt</I> or <I>rigid/npt</I> or <I>rigid/nph</I> or <I>rigid/small</I> 
+<LI>style = <I>rigid</I> or <I>rigid/nve</I> or <I>rigid/nvt</I> or <I>rigid/npt</I> or <I>rigid/nph</I> or <I>rigid/small</I> or <I>rigid/nve/small</I> or <I>rigid/nvt/small</I> or <I>rigid/npt/small</I> or <I>rigid/nph/small</I> 
 
 <LI>bodystyle = <I>single</I> or <I>molecule</I> or <I>group</I> 
 
@@ -39,7 +47,7 @@
 </PRE>
 <LI>zero or more keyword/value pairs may be appended 
 
-<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tparam</I> or <I>pchain</I> or <I>dilate</I> or <I>force</I> or <I>torque</I> or <I>infile</I> or <I>mol</I> 
+<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tparam</I> or <I>pchain</I> or <I>dilate</I> or <I>force</I> or <I>torque</I> or <I>infile</I> 
 
 <PRE>  <I>langevin</I> 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
   <I>infile</I> 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 
   <I>mol</I> value = template-ID
     template-ID = ID of molecule template specified in a separate <A HREF = "molecule.html">molecule</A> command 
 </PRE>
@@ -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 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -292,17 +301,17 @@ iterations.  The <I>rigid/nve</I> style uses the methods described in the
 paper by <A HREF = "#Miller">Miller</A>, which are thought to provide better energy
 conservation than an iterative approach.
 </P>
-<P>The <I>rigid/nvt</I> style performs constant NVT integration using a
+<P>The <I>rigid/nvt</I> and <I>rigid/nvt/small</I> styles performs constant NVT 
-Nose/Hoover thermostat with chains as described originally in
+integration using a Nose/Hoover thermostat with chains as described 
-<A HREF = "#Hoover">(Hoover)</A> and <A HREF = "#Martyna">(Martyna)</A>, which thermostats both
+originally in <A HREF = "#Hoover">(Hoover)</A> and <A HREF = "#Martyna">(Martyna)</A>, which 
-the translational and rotational degrees of freedom of the rigid
+thermostats both the translational and rotational degrees of freedom 
-bodies.  The rigid-body algorithm used by <I>rigid/nvt</I> is described in
+of the rigid bodies.  The rigid-body algorithm used by <I>rigid/nvt</I> 
-the paper by <A HREF = "#Kamberaj">Kamberaj</A>.
+is described in the paper by <A HREF = "#Kamberaj">Kamberaj</A>.
 </P>
-<P>The <I>rigid/npt</I> and <I>rigid/nph</I> styles perform constant NPT or NPH
+<P>The <I>rigid/npt</I> and <I>rigid/nph</I> (and their /small counterparts) styles 
-integration using a Nose/Hoover barostat with chains.  For the NPT
+perform constant NPT or NPH integration using a Nose/Hoover barostat 
-case, the same Nose/Hoover thermostat is also used as with
+with chains.  For the NPT case, the same Nose/Hoover thermostat is also 
-<I>rigid/nvt</I>.
+used as with <I>rigid/nvt</I>.
 </P>
 <P>The barostat parameters are specified using one or more of the <I>iso</I>,
 <I>aniso</I>, <I>x</I>, <I>y</I>, <I>z</I> and <I>couple</I> 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 <A HREF = "fix_nh.html">fix npt/nph</A>
 </P>
-<P>NOTE: Currently the <I>rigid/npt</I> and <I>rigid/nph</I> styles do not support
+<P>NOTE: Currently the <I>rigid/npt</I> and <I>rigid/nph</I> (and their /small 
-triclinic (non-orthongonal) boxes.
+counterparts) styles do not support triclinic (non-orthongonal) boxes.
 </P>
 <P>The target pressures for each of the 6 components of the stress tensor
 can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I> 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
+non-blank, non-comment line should list N = the number of lines to
-lines to follow.  The N successive lines contain the following
+follow.  The N successive lines contain the following information:
-information:
 </P>
-<PRE>N
+<PRE>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 

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
+The {rigid/nvt} and {rigid/nvt/small} styles performs constant NVT 
-Nose/Hoover thermostat with chains as described originally in
+integration using a Nose/Hoover thermostat with chains as described 
-"(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which thermostats both
+originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which 
-the translational and rotational degrees of freedom of the rigid
+thermostats both the translational and rotational degrees of freedom 
-bodies.  The rigid-body algorithm used by {rigid/nvt} is described in
+of the rigid bodies.  The rigid-body algorithm used by {rigid/nvt} 
-the paper by "Kamberaj"_#Kamberaj.
+is described in the paper by "Kamberaj"_#Kamberaj.
 
-The {rigid/npt} and {rigid/nph} styles perform constant NPT or NPH
+The {rigid/npt} and {rigid/nph} (and their /small counterparts) styles 
-integration using a Nose/Hoover barostat with chains.  For the NPT
+perform constant NPT or NPH integration using a Nose/Hoover barostat 
-case, the same Nose/Hoover thermostat is also used as with
+with chains.  For the NPT case, the same Nose/Hoover thermostat is also 
-{rigid/nvt}.
+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
+NOTE: Currently the {rigid/npt} and {rigid/nph} (and their /small 
-triclinic (non-orthongonal) boxes.
+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
+non-blank, non-comment line should list N = the number of lines to
-lines to follow.  The N successive lines contain the following
+follow.  The N successive lines contain the following information:
-information:
 
-N
 ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ...