Examples for the fix ilves bond and angle constraint solver.

fix ilves enforces rigid bond lengths (and, via an A-C "virtual bond", rigid
angles) using the ILVES algorithm.  These inputs mirror the standard LAMMPS
peptide and rhodopsin benchmarks so the results can be compared directly with
the equivalent fix shake / fix rattle runs.

Each fix ilves run gives the same dynamics on any number of MPI ranks (to the
solver tolerance) and prints per-type constraint statistics every N steps.

Basic example
-------------
  mol.dimer   -- molecule template for a rigid diatomic (dumbbell)
  in.dimer    -- a Lennard-Jones fluid of rigid dimers whose bonds are held
                 rigid by fix ilves; demonstrates the basic usage and the
                 per-bond-type constraint statistics output

Peptide (solvated protein, CHARMM force field, data.peptide)
------------------------------------------------------------
  in.peptide-ilves    -- constrain the bonds involving hydrogen atoms of the protein
                         and the O-H bonds + H-O-H angle of every water using ILVES
  in.peptide-fixed    -- same constraints but fixed number of 3 Newton iterations
  in.peptide-allbonds -- constrain all protein bonds plus the rigid waters
  in.peptide-mix      -- fix ilves on the protein, fix shake on the water,
                         showing the two can be combined on disjoint atoms
  in.peptide-shake    -- reference run using fix shake (for comparison)
  in.peptide-rattle   -- reference run using fix rattle (for comparison)

Rhodopsin (membrane protein benchmark, bench/data.rhodo)
--------------------------------------------------------
  in.rhodo-ilves      -- constrain all bond with hydrogen atoms + water using ILVES
  in.rhodo-shake      -- reference run using fix shake (for comparison)
  in.rhodo-allbonds   -- constrain hydrogen bonds and selected heavy-atom bond
                         types as well with ILVES

COVID (COVID main protease in water, adapted from ILVES paper)
--------------------------------------------------------------

  in.covid            -- constrain waters with fix shake and protein with fix ilves

Polymelt (long chains of constrained LJ beads)
----------------------------------------------
  in.polymelt        -- constrain all bonds of the chains using ILVES

Near-linear angles (coarse-grain polymer chains, data.cg-polymers)
-----------------------------------------------------------------
  in.cg-polymers      -- chains whose backbone angles have a 180 degree
                         equilibrium.  The A-C "virtual bond" of an angle is
                         rank-deficient near 180 degrees, so this uses
                         "linearangle skip 165": the backbone bonds are held
                         rigid by fix ilves while the (intentionally soft)
                         backbone angle is left to the cosine/squared
                         angle_style.

The data.peptide and data.rhodo files are symbolic links to the data files of
the standard examples/peptide and bench benchmarks.

Run with, e.g.:
  lmp -in in.peptide-ilves              # serial
  mpirun -np 4 lmp -in in.peptide-ilves # 4 MPI ranks (same dynamics)
