git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15171 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/src/Section_commands.txt

@@ -576,6 +576,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
+"spring/chunk"_fix_spring_chunk.html,
 "spring/rg"_fix_spring_rg.html,
 "spring/self"_fix_spring_self.html,
 "srd"_fix_srd.html,

doc/src/fix.txt

@@ -264,6 +264,7 @@ of "this page"_Section_commands.html#cmd_5.
 "setforce"_fix_setforce.html - set the force on each atom
 "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
 "spring"_fix_spring.html - apply harmonic spring force to group of atoms
+"spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms
 "spring/rg"_fix_spring_rg.html - spring on radius of gyration of \
      group of atoms
 "spring/self"_fix_spring_self.html - spring from each atom to its origin

doc/src/fix_rigid.txt

@@ -188,11 +188,12 @@ Each rigid 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.
 
-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 using the {mol} keyword in conjunction with
-another fix that is adding rigid bodies on-the-fly, such as "fix
-deposit"_fix_deposit.html or "fix pour"_fix_pour.html.
+NOTE: With fix rigid/small, which requires that {bodystyle} be
+specified as {molecule}, you can define a system that has no rigid
+bodies initially.  This is useful when you are using the {mol} keyword
+in conjunction with another fix that is adding rigid bodies on-the-fly
+as molecules, 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

doc/src/fix_spring_chunk.txt

@@ -0,0 +1,82 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix spring/chunk command :h3
+
+[Syntax:]
+
+fix ID group-ID spring/chunk K chunkID comID :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+spring/chunk = style name of this fix command
+K = spring constant for each chunk (force/distance units)
+chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command
+comID = ID of "compute com/chunk"_compute_com_chunk.html command :ul
+
+[Examples:]
+
+fix restrain all spring/chunk 100 chunkID comID :pre
+
+[Description:]
+
+Apply a spring force to the center-of-mass (COM) of chunks of atoms as
+defined by the "compute chunk/atom"_compute_chunk_atom.html command.
+Chunks can be molecules or spatial bins or other groupings of atoms.
+This is a way of tethering each chunk to its initial COM coordinates.
+
+The {chunkID} is the ID of a compute chunk/atom command defined in the
+input script.  It is used to define the chunks.  The {comID} is the ID
+of a compute com/chunk command defined in the input script.  It is
+used to compute the COMs of each chunk.
+
+At the beginning of the first "run"_run.html or
+"minimize"_miminize.html command after this fix is defined, the
+initial COM of each chunk is calculated and stored as R0c, where C is
+the chunk number.  Thereafter, at every timestep (or minimization
+iteration), the current COM of each chunk is calculated as Rc.  A
+restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each
+atom in each chunk where {K} is the specified spring constant, Mi is
+the mass of the atom, and Mc is the total mass of all atoms in the
+chunk.  Note that {K} thus represents the spring constant for the
+total force on each chunk of atoms, not for a spring applied to each
+atom.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html. 
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy stored in all the springs to the system's potential
+energy as part of "thermodynamic output"_thermo_style.html.
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Section_howto.html#howto_15.  The scalar is the
+energy of all the springs, i.e. 0.5 * K * r^2 per-spring.
+
+The scalar value calculated by this fix is "extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
+
+NOTE: If you want the spring energies to be included in the total
+potential energy of the system (the quantity being minimized), you
+MUST enable the "fix_modify"_fix_modify.html {energy} option for this
+fix.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html,
+"fix spring/rg"_fix_spring_rg.html
+
+[Default:] none