git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13352 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_deposit.html

@@ -162,8 +162,8 @@ shake</A> command which also appears in your input script.
 <P>Each timestep a particle is inserted, the coordinates for its atoms
 are chosen as follows.  For insertion of individual atoms, the
 "position" referred to in the following description is the coordinate
-of the atom.  For insertion of molecule, the "position<A HREF = "molecule.html"> is the
+of the atom.  For insertion of molecule, the "position" is the
-geometric center of the molecule; see the (molecule</A> doc
+geometric center of the molecule; see the <A HREF = "molecule.html">molecule</A> doc
 page for details.  A random rotation of the molecule around its center
 point is performed, which determines the coordinates all the
 individual atoms.
@@ -183,14 +183,22 @@ particles is less than the <I>delta</I> setting.
 <P>Once a trial x,y,z position has been selected, the insertion is only
 performed if no current atom in the simulation is within a distance R
 of any atom in the new particle, including the effect of periodic
-boundary conditions if applicable.  Note that the default value for R
+boundary conditions if applicable.  R is defined by the <I>near</I>
-is 0.0, which will allow atoms to strongly overlap if you are
+keyword.  Note that the default value for R is 0.0, which will allow
-inserting where other atoms are present.  This distance test is
+atoms to strongly overlap if you are inserting where other atoms are
-performed independently for each atom in an inserted molecule, based
+present.  This distance test is performed independently for each atom
-on the randomly rotated configuration of the molecule.  If this test
+in an inserted molecule, based on the randomly rotated configuration
-fails, a new random position within the insertion volume is chosen and
+of the molecule.  If this test fails, a new random position within the
-another trial is made.  Up to Q attempts are made.  If the particle is
+insertion volume is chosen and another trial is made.  Up to Q
-not successfully inserted, LAMMPS prints a warning message.
+attempts are made.  If the particle is not successfully inserted,
+LAMMPS prints a warning message.
+</P>
+<P>IMPORTANT NOTE: If you are inserting finite size particles or a
+molecule or rigid body consisting of finite-size particles, then you
+should typically set R larger than the distance at which any inserted
+particle may overlap with either a previouly inserted particle or an
+existing particle.  LAMMPS will issue a warning if R is smaller than
+this value, based on the radii of existing and inserted particles.
 </P>
 <P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
 or y direction (2d).  This enables particles to be inserted from a

doc/fix_deposit.txt

@@ -151,7 +151,7 @@ Each timestep a particle is inserted, the coordinates for its atoms
 are chosen as follows.  For insertion of individual atoms, the
 "position" referred to in the following description is the coordinate
 of the atom.  For insertion of molecule, the "position" is the
-geometric center of the molecule; see the (molecule"_molecule.html doc
+geometric center of the molecule; see the "molecule"_molecule.html doc
 page for details.  A random rotation of the molecule around its center
 point is performed, which determines the coordinates all the
 individual atoms.
@@ -171,14 +171,22 @@ particles is less than the {delta} setting.
 Once a trial x,y,z position has been selected, the insertion is only
 performed if no current atom in the simulation is within a distance R
 of any atom in the new particle, including the effect of periodic
-boundary conditions if applicable.  Note that the default value for R
+boundary conditions if applicable.  R is defined by the {near}
-is 0.0, which will allow atoms to strongly overlap if you are
+keyword.  Note that the default value for R is 0.0, which will allow
-inserting where other atoms are present.  This distance test is
+atoms to strongly overlap if you are inserting where other atoms are
-performed independently for each atom in an inserted molecule, based
+present.  This distance test is performed independently for each atom
-on the randomly rotated configuration of the molecule.  If this test
+in an inserted molecule, based on the randomly rotated configuration
-fails, a new random position within the insertion volume is chosen and
+of the molecule.  If this test fails, a new random position within the
-another trial is made.  Up to Q attempts are made.  If the particle is
+insertion volume is chosen and another trial is made.  Up to Q
-not successfully inserted, LAMMPS prints a warning message.
+attempts are made.  If the particle is not successfully inserted,
+LAMMPS prints a warning message.
+
+IMPORTANT NOTE: If you are inserting finite size particles or a
+molecule or rigid body consisting of finite-size particles, then you
+should typically set R larger than the distance at which any inserted
+particle may overlap with either a previouly inserted particle or an
+existing particle.  LAMMPS will issue a warning if R is smaller than
+this value, based on the radii of existing and inserted particles.
 
 The {rate} option moves the insertion volume in the z direction (3d)
 or y direction (2d).  This enables particles to be inserted from a

doc/fix_rigid.html

@@ -129,7 +129,7 @@ ensemble, as described below.
 rigid/small.  The NVE/NVT/NPT/NHT versions belong to one of the two
 variants, as their style names indicate.  
 </P>
-<P>IMPORTANT NOTE: Not all of the bodystyle options and keyword/value
+<P>IMPORTANT NOTE: Not all of the <I>bodystyle</I> options and keyword/value
 options are available for both the <I>rigid</I> and <I>rigid/small</I> variants.
 See details below.
 </P>
@@ -183,6 +183,8 @@ command), setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html
 setforce</A> command), and integrating them as usual
 (e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).
 </P>
+<P>NOTE: edit this
+</P>
 <P>IMPORTANT NOTE: The aggregate properties of each rigid body are
 calculated at the start of each simulation run.  These include its
 center of mass, moments of inertia, and net velocity and angular
@@ -201,9 +203,9 @@ via several options.
 </P>
 <P>IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
 <I>molecule</I>, you can define a system that has no rigid bodies
-initially.  This is useful when you are adding rigid bodies on-the-fly
+initially.  This is useful when you are using the <I>mol</I> keyword in
-via commands such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix
+conjunction with another fix that is adding rigid bodies on-the-fly,
-pour</A>.
+such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix pour</A>.
 </P>
 <P>For bodystyle <I>single</I> the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for fix rigid and its
@@ -471,17 +473,25 @@ associated with the fix rigid commands.
 </P>
 <HR>
 
-<P>The <I>mol</I> keyword can only be used with fix rigid/small.  It should be
+<P>The <I>mol</I> keyword can only be used with fix rigid/small.  It must be
 used when other commands, such as <A HREF = "fix_deposit.html">fix deposit</A> or
 <A HREF = "fix_pour.html">fix pour</A>, add rigid bodies on-the-fly during a
 simulation.  You specify a <I>template-ID</I> previously defined using the
 <A HREF = "molecule.html">molecule</A> command, which reads a file that defines the
-molecule.  You must use the same <I>template-ID</I> that the command adding
+molecule.  You must use the same <I>template-ID</I> that the other fix
-rigid bodies uses.  The coordinates, atom types, atom diameters,
+which is adding rigid bodies uses.  The coordinates, atom types, atom
-center-of-mass, and moments of inertia can be specified in the
+diameters, center-of-mass, and moments of inertia can be specified in
-molecule file.  See the <A HREF = "molecule.html">molecule</A> command for details.
+the molecule file.  See the <A HREF = "molecule.html">molecule</A> command for
-The only settings required to be in this file are the coordinates and
+details.  The only settings required to be in this file are the
-types of atoms in the molecule.
+coordinates and types of atoms in the molecule, in which case the
+molecule command calculates the other quantities itself.
+</P>
+<P>Note that these other fixes create new rigid bodies, in addition to
+those defined initially by this fix via the <I>bodystyle</I> setting.
+</P>
+<P>Also note that when using the <I>mol</I> keyword, extra restart information
+about all rigid bodies is written out whenever a restart file is
+written out.  See the IMPORTANT NOTE in the next section for details.
 </P>
 <HR>
 
@@ -505,6 +515,8 @@ comment lines starting with "#" which are ignored.  The first
 non-blank, non-comment line should list N = the number of lines to
 follow.  The N successive lines contain the following information:
 </P>
+<P>NOTE: edit this
+</P>
 <PRE>ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ...
@@ -528,26 +540,16 @@ the simulation box XYZ axes, not with respect to the prinicpal axes of
 the rigid body itself.  LAMMPS performs the latter calculation
 internally.
 </P>
-<P>IMPORTANT NOTE: If you use the <I>infile</I> keyword and write restart
+<P>IMPORTANT NOTE: If you use the <I>infile</I> or <I>mol</I> keywords and write
-files during a simulation, then each time a restart file is written,
+restart files during a simulation, then each time a restart file is
-the fix also write an auxiliary restart file with the name
+written, the fix also write an auxiliary restart file with the name
 rfile.rigid, where "rfile" is the name of the restart file,
 e.g. tmp.restart.10000 and tmp.restart.10000.rigid.  This auxiliary
-file is in the same format described above and contains info on the
+file is in the same format described above.  Thus it can be used in a
-current center-of-mass and 6 moments of inertia.  Thus it can be used
+new input script that restarts the run and re-specifies a rigid fix
-in a new input script that restarts the run and re-specifies a rigid
+using an <I>infile</I> keyword and the appropriate filename.  Note that the
-fix using an <I>infile</I> keyword and the appropriate filename.  Note that
+auxiliary file will contain one line for every rigid body, even if the
-the auxiliary file will contain one line for every rigid body, even if
+original file only listed a subset of the rigid bodies.
-the original file only listed a subset of the rigid bodies.
-</P>
-<P>IMPORTANT NOTE: If you are using fix rigid/small and defining a system
-that has no rigid bodies initially, because they will be added
-on-the-fly by commands such as <A HREF = "fix_deposit.html">fix deposit</A> or <A HREF = "fix_pour.html">fix
-pour</A>, you may still wish to use the <I>infile</I> keyword.
-This is so that restart files written during the simulation will
-output an auxiliary restart file as described above with information
-on the new rigid bodies.  In this case the initial <I>infile</I> file
-should use N = 0.
 </P>
 <HR>
 
@@ -656,9 +658,12 @@ more instructions on how to use the accelerated styles effectively.
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>
 <P>No information about the <I>rigid</I> and <I>rigid/small</I> and <I>rigid/nve</I>
-fixes are written to <A HREF = "restart.html">binary restart files</A>.  For style
+fixes are written to <A HREF = "restart.html">binary restart files</A>.  The
-<I>rigid/nvt</I> the state of the Nose/Hoover thermostat is written to
+exception is if the <I>infile</I> or <I>mol</I> keyword is used, in which case
-<A HREF = "restart.html">binary restart files</A>.  See the
+an auxiliary file is written out with rigid body information each time
+a restart file is written, as explained above for the <I>infile</I>
+keyword.  For style <I>rigid/nvt</I> the state of the Nose/Hoover
+thermostat is written to <A HREF = "restart.html">binary restart files</A>.  See the
 <A HREF = "read_restart.html">read_restart</A> 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.

doc/fix_rigid.txt

@@ -111,7 +111,7 @@ There are two main variants of this fix, fix rigid and fix
 rigid/small.  The NVE/NVT/NPT/NHT versions belong to one of the two
 variants, as their style names indicate.  
 
-IMPORTANT NOTE: Not all of the bodystyle options and keyword/value
+IMPORTANT NOTE: Not all of the {bodystyle} options and keyword/value
 options are available for both the {rigid} and {rigid/small} variants.
 See details below.
 
@@ -165,6 +165,10 @@ 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).
 
+
+NOTE: edit this
+
+
 IMPORTANT NOTE: The aggregate properties of each rigid body are
 calculated at the start of each simulation run.  These include its
 center of mass, moments of inertia, and net velocity and angular
@@ -183,9 +187,9 @@ via several options.
 
 IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
 {molecule}, you can define a system that has no rigid bodies
-initially.  This is useful when you are adding rigid bodies on-the-fly
+initially.  This is useful when you are using the {mol} keyword in
-via commands such as "fix deposit"_fix_deposit.html or "fix
+conjunction with another fix that is adding rigid bodies on-the-fly,
-pour"_fix_pour.html.
+such as "fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html.
 
 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for fix rigid and its
@@ -453,17 +457,25 @@ associated with the fix rigid commands.
 
 :line
 
-The {mol} keyword can only be used with fix rigid/small.  It should be
+The {mol} keyword can only be used with fix rigid/small.  It must be
 used when other commands, such as "fix deposit"_fix_deposit.html or
 "fix pour"_fix_pour.html, add rigid bodies on-the-fly during a
 simulation.  You specify a {template-ID} previously defined using the
 "molecule"_molecule.html command, which reads a file that defines the
-molecule.  You must use the same {template-ID} that the command adding
+molecule.  You must use the same {template-ID} that the other fix
-rigid bodies uses.  The coordinates, atom types, atom diameters,
+which is adding rigid bodies uses.  The coordinates, atom types, atom
-center-of-mass, and moments of inertia can be specified in the
+diameters, center-of-mass, and moments of inertia can be specified in
-molecule file.  See the "molecule"_molecule.html command for details.
+the molecule file.  See the "molecule"_molecule.html command for
-The only settings required to be in this file are the coordinates and
+details.  The only settings required to be in this file are the
-types of atoms in the molecule.
+coordinates and types of atoms in the molecule, in which case the
+molecule command calculates the other quantities itself.
+
+Note that these other fixes create new rigid bodies, in addition to
+those defined initially by this fix via the {bodystyle} setting.
+
+Also note that when using the {mol} keyword, extra restart information
+about all rigid bodies is written out whenever a restart file is
+written out.  See the IMPORTANT NOTE in the next section for details.
 
 :line
 
@@ -487,6 +499,8 @@ comment lines starting with "#" which are ignored.  The first
 non-blank, non-comment line should list N = the number of lines to
 follow.  The N successive lines contain the following information:
 
+NOTE: edit this
+
 ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ...
@@ -510,26 +524,16 @@ the simulation box XYZ axes, not with respect to the prinicpal axes of
 the rigid body itself.  LAMMPS performs the latter calculation
 internally.
 
-IMPORTANT NOTE: If you use the {infile} keyword and write restart
+IMPORTANT NOTE: If you use the {infile} or {mol} keywords and write
-files during a simulation, then each time a restart file is written,
+restart files during a simulation, then each time a restart file is
-the fix also write an auxiliary restart file with the name
+written, the fix also write an auxiliary restart file with the name
 rfile.rigid, where "rfile" is the name of the restart file,
 e.g. tmp.restart.10000 and tmp.restart.10000.rigid.  This auxiliary
-file is in the same format described above and contains info on the
+file is in the same format described above.  Thus it can be used in a
-current center-of-mass and 6 moments of inertia.  Thus it can be used
+new input script that restarts the run and re-specifies a rigid fix
-in a new input script that restarts the run and re-specifies a rigid
+using an {infile} keyword and the appropriate filename.  Note that the
-fix using an {infile} keyword and the appropriate filename.  Note that
+auxiliary file will contain one line for every rigid body, even if the
-the auxiliary file will contain one line for every rigid body, even if
+original file only listed a subset of the rigid bodies.
-the original file only listed a subset of the rigid bodies.
-
-IMPORTANT NOTE: If you are using fix rigid/small and defining a system
-that has no rigid bodies initially, because they will be added
-on-the-fly by commands such as "fix deposit"_fix_deposit.html or "fix
-pour"_fix_pour.html, you may still wish to use the {infile} keyword.
-This is so that restart files written during the simulation will
-output an auxiliary restart file as described above with information
-on the new rigid bodies.  In this case the initial {infile} file
-should use N = 0.
 
 :line
 
@@ -638,9 +642,12 @@ more instructions on how to use the accelerated styles effectively.
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about the {rigid} and {rigid/small} and {rigid/nve}
-fixes are written to "binary restart files"_restart.html.  For style
+fixes are written to "binary restart files"_restart.html.  The
-{rigid/nvt} the state of the Nose/Hoover thermostat is written to
+exception is if the {infile} or {mol} keyword is used, in which case
-"binary restart files"_restart.html.  See the
+an auxiliary file is written out with rigid body information each time
+a restart file is written, as explained above for the {infile}
+keyword.  For style {rigid/nvt} the state of the Nose/Hoover
+thermostat 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.

doc/group.html

@@ -254,9 +254,9 @@ variable        rad equal 18-(step/v_nsteps)*(18-5)
 region          ss sphere 20 20 0 v_rad
 group           mobile dynamic all region ss
 fix             1 mobile nve
-run             $<I>nsteps</I>
+run             ${nsteps}
 group           mobile static
-run	        $<I>nsteps</I> 
+run	        ${nsteps} 
 </PRE>
 <P>IMPORTANT NOTE: All fixes and computes take a group ID as an argument,
 but they do not all allow for use of a dynamic group.  If you get an

doc/group.txt

@@ -250,9 +250,9 @@ variable        rad equal 18-(step/v_nsteps)*(18-5)
 region          ss sphere 20 20 0 v_rad
 group           mobile dynamic all region ss
 fix             1 mobile nve
-run             ${nsteps}
+run             $\{nsteps\}
 group           mobile static
-run	        ${nsteps} :pre
+run	        $\{nsteps\} :pre
 
 IMPORTANT NOTE: All fixes and computes take a group ID as an argument,
 but they do not all allow for use of a dynamic group.  If you get an

doc/molecule.html

@@ -1,5 +1,5 @@
 <HTML>
-<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> 
+<CENTER><<A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> 
 </CENTER>
 
 
@@ -97,9 +97,9 @@ appear if the value(s) are different than the default.
 </UL>
 <P>For <I>mass</I>, <I>com</I>, and <I>inertia</I>, the default is for LAMMPS to
 calculate this quantity itself if needed, assuming the molecules
-consists of a set of point particles.  You typically only need to
+consists of a set of point particles.  You only need to specify these
-specify these values for a rigid body consisting of overlapping
+values for a rigid body consisting of finite-size particles,
-finite-size particles.
+especially if they are overlapping.
 </P>
 <P>The mass and center-of-mass coordinates (Xc,Yc,Zc) are
 self-explanatory.  The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)

doc/molecule.txt

@@ -1,4 +1,4 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
@@ -94,9 +94,9 @@ Ixx Iyy Izz Ixy Ixz Iyz {inertia} = 6 components of inertia tensor of molecule :
 
 For {mass}, {com}, and {inertia}, the default is for LAMMPS to
 calculate this quantity itself if needed, assuming the molecules
-consists of a set of point particles.  You typically only need to
+consists of a set of point particles.  You only need to specify these
-specify these values for a rigid body consisting of overlapping
+values for a rigid body consisting of finite-size particles,
-finite-size particles.
+especially if they are overlapping.
 
 The mass and center-of-mass coordinates (Xc,Yc,Zc) are
 self-explanatory.  The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)