fix errors in fix amoeba/pitorsion doc page

doc/src/fix_amoeba_bitorsion.rst

@@ -35,7 +35,11 @@ the implementation of AMOEBA and HIPPO in LAMMPS.
 
 Bitorsion interactions add additional potential energy contributions
 to pairs of overlapping phi-psi dihedrals of amino-acids, which are
-important to properly represent their conformational behavior.
+important to properly represent their conformational behavior.  Each
+bitorsion interaction is thus defined for a 5-tuple of atoms
+:math:`IJKLM` with bonds between successive atoms in the list,
+i.e. two overlapping dihedral interactions for atoms :math:`IJKL` and
+:math:`JKLM`.
 
 The examples/amoeba directory has a sample input script and data file
 for ubiquitin, which illustrates use of the fix amoeba/bitorsion
@@ -68,14 +72,15 @@ lines:
           [...]
           N       3     314     315     317      318    330
 
-The first column is an index from 1 to :math:`N` to enumerate the bitorsion
-5-atom tuples; it is ignored by LAMMPS.  The second column is the
-*type* of the interaction; it is an index into the bitorsion force
-field file.  The remaining 5 columns are the atom IDs of the atoms in
-the two 4-atom dihedrals that overlap to create the bitorsion 5-body
-interaction.  Note that the *bitorsions* and *BiTorsions* keywords for
-the header and body sections match those specified in the
-:doc:`read_data <read_data>` command following the data file name.
+The first column is an index from 1 to :math:`N` to enumerate the
+bitorsion 5-atom tuples; it is ignored by LAMMPS.  The second column
+is the *type* of the interaction; it is an index into the bitorsion
+force field file.  The remaining 5 columns are the atom IDs of the
+atoms (in order) for the 5-tuple :math:`IJKLM`, as described above.
+
+Note that the *bitorsions* and *BiTorsions* keywords for the header
+and body sections match those specified in the :doc:`read_data
+<read_data>` command following the data file name.
 
 The data file should be generated by using the
 tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS

doc/src/fix_amoeba_pitorsion.rst

@@ -57,7 +57,7 @@ should have two lines like these in its header section:
    M pitorsion types
    N pitorsions
 
-where :math:`N` is the number of pitorsion 5-body interactions and :math:`M` is
+where :math:`N` is the number of pitorsion 6-body interactions and :math:`M` is
 the number of pitorsion types.  It should also have two sections in the body
 of the data file like these with :math:`M` and :math:`N` lines each:
 
@@ -79,16 +79,15 @@ of the data file like these with :math:`M` and :math:`N` lines each:
           [...]
           N       3     314     315     317      318    330
 
-For PiTorsion Coeffs, the first column is an index from 1 to :math:`M` to
-enumerate the pitorsion types.  The second column is the single
+For PiTorsion Coeffs, the first column is an index from 1 to :math:`M`
+to enumerate the pitorsion types.  The second column is the single
 prefactor coefficient needed for each type.
 
-For PiTorsions, the first column is an index from 1 to :math:`N` to enumerate
-the pitorsion 5-atom tuples; it is ignored by LAMMPS.  The second
-column is the "type" of the interaction; it is an index into the
-PiTorsion Coeffs.  The remaining 5 columns are the atom IDs of the
-atoms in the two 4-atom dihedrals that overlap to create the pitorsion
-5-body interaction.
+For PiTorsions, the first column is an index from 1 to :math:`N` to
+enumerate the pitorsion 6-atom tuples; it is ignored by LAMMPS.  The
+second column is the "type" of the interaction; it is an index into
+the PiTorsion Coeffs.  The remaining 6 columns are the atom IDs of the
+atoms (in order) for the 6-tuple :math:`IJKLMN`, as described above.
 
 Note that the *pitorsion types* and *pitorsions* and *PiTorsion
 Coeffs* and *PiTorsions* keywords for the header and body sections of

tools/tinker/tinker2lmp.py

@@ -923,7 +923,7 @@ def bitorsions(self):
   elif (c3,c2,c1) in ubdict:
     ublist.append((atom3,atom2,atom1))
 
-# create pitorslist = list of 6-body interactions
+# create pitorsionlist = list of 6-body interactions
 # based on central bond, each bond atom is bonded to exactly 2 other atoms
 # avoid double counting by requiring atom1 < atom2
 # NOTE: need more info on how to order the 6 atoms for Tinker to compute on
@@ -962,7 +962,7 @@ def bitorsions(self):
 
       pitorsionlist.append((atom3,atom4,atom1,atom2,atom5,atom6))
 
-# create bitorslist = list of 5-body interactions
+# create bitorsionlist = list of 5-body interactions
 # generate topology via double loop over neighbors of central atom3
 #   additional double loop over bonds of atom2 and bonds of atom4
 # avoid double counting the reverse bitorsion by use of btdict dictionary