Update potentials.rst

docs/source/potentials.rst

@@ -356,9 +356,9 @@ The vibrational coordinates are
 
 where :math:`a_{ijklmn}` are the expansion parameters. Here, :math:`r_0`, :math:`r_1` and :math:`r_2` are the bond lengths, :math:`\alpha_{1}` and :math:`\alpha_{2}` are the bond angles, :math:`\tau` is the dihedral angle between two bond planes, and :math:`b_i` is a Morse-oscillator parameter.
 
-The expansion has a symmetry adapted form, which is invariant upon interchanging the two equivalent atoms Y\ :sub:`1` and Y\ :sub:`2``, i.e. for :math:`r_1 \leftrightarrow r_2` simultaneously with  :math:`\alpha_1 \leftrightarrow \alpha_2`.  
+The expansion has a symmetry adapted form, which is invariant upon interchanging the two equivalent atoms Y\ :sub:`1` and Y\ :sub:`2``, i.e. for :math:`r_1 \leftrightarrow r_2` simultaneously with  :math:`\alpha_1 \leftrightarrow \alpha_2`.
 
-The TROVE function for this PEF is ``MLpoten_zxy2_morse_cos``, which can be found in the module ``mol_zxy2.f09``. 
+The TROVE function for this PEF is ``MLpoten_zxy2_morse_cos``, which can be found in the module ``mol_zxy2.f09``.
 
 
 ``poten_zxy2_morse_cos`` uses the ``powers`` form for the potential parameters. An input file example for H\ :sub:`2`\ CS is  `H2CS_zxy2_morse_cos_step1.inp <https://raw.githubusercontent.com/Trovemaster/TROVE/develop/docs/source/input/H2CS_zxy2_morse_cos_step1.inp>`_  where this PES is used.
@@ -372,7 +372,7 @@ XY\ :sub:`3` type (pyramidal)
 ``POTEN_XY3_MORBID_10``
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-This PEF is for ammonia (non-rigid) molecules with an umbrella coordinate representing the 1D inversion motion and other 5 are displacements from their equilibrium values, but it can be equally used for rigid molecules like phosphine as well. As all PEFs in TROVE, ``POTEN_XY3_MORBID_10``  is a symmetry adapted to be fully symmetric for all operations (permutations) of the D\ :sub: `3h`\ (M) (and also C\ :sub:`3v`\ (M)) molecular group symmetry. It uses the following coordinates 
+This PEF is for ammonia (non-rigid) molecules with an umbrella coordinate representing the 1D inversion motion and other 5 are displacements from their equilibrium values, but it can be equally used for rigid molecules like phosphine as well. As all PEFs in TROVE, ``POTEN_XY3_MORBID_10``  is a symmetry adapted to be fully symmetric for all operations (permutations) of the D\ :sub: `3h`\ (M) (and also C\ :sub:`3v`\ (M)) molecular group symmetry. It uses the following coordinates
 
 
 .. math::
@@ -384,20 +384,20 @@ This PEF is for ammonia (non-rigid) molecules with an umbrella coordinate repres
      \xi_6 &= \sin\rho_{\rm e}-\sin\rho,
    \end{split}
 
-where :math:`r_i` (\ :math`i=1,2,3,`\ ) are three bond lengths, :math:`\alpha_i` (\ :math`i=1,2,3,`\ ) are three bond angles with :math:`\alpha_i` opposite to :math:`r_i` and :math:`\rho` is an umbrella coordinate defined as an 'average' angle between three bonds and an average symmetry axis as follows:
+where :math:`r_i` (\ :math:`i=1,2,3,`\ ) are three bond lengths, :math:`\alpha_i` (\ :math:`i=1,2,3,`\ ) are three bond angles with :math:`\alpha_i` opposite to :math:`r_i` and :math:`\rho` is an umbrella coordinate defined as an 'average' angle between three bonds and an average symmetry axis as follows:
 
 .. math::
-        
+
    \sin\rho = \frac{2}{\sqrt{3}}\sin\left(\frac{\bar\alpha}{2}\right)
 
-and 
+and
 
 .. math::
 
-     \bar\alpha = \frac{1}{3} (\alpha_1+\alpha_2+\alpha_3). 
+     \bar\alpha = \frac{1}{3} (\alpha_1+\alpha_2+\alpha_3).
 
 
-The corresponding Fortran function is ``MLpoten_xy3_morbid_10``, which can found in ``mol_xy3.f90``.  It uses the ``Coeffs LIST`` form. A TROVE input example  for NH\ :sub:`3` is  `NH3_BYTe_step1.inp <https://raw.githubusercontent.com/Trovemaster/TROVE/develop/docs/source/input/NH3_BYTe_step1.inp>`_ , see [09YuBaYa]_ where this empirical PES was used to compute the BYTe line list for ammonia. 
+The corresponding Fortran function is ``MLpoten_xy3_morbid_10``, which can found in ``mol_xy3.f90``.  It uses the ``Coeffs LIST`` form. A TROVE input example  for NH\ :sub:`3` is  `NH3_BYTe_step1.inp <https://raw.githubusercontent.com/Trovemaster/TROVE/develop/docs/source/input/NH3_BYTe_step1.inp>`_ , see [09YuBaYa]_ where this empirical PES was used to compute the BYTe line list for ammonia.
 
 
 ``POTEN_XY3_MORBID_11``
@@ -421,9 +421,9 @@ This is a similar PES to ``POTEN_XY3_MORBID_10``, but with the structural parame
     FA5          1 -0.25243109949867E+06
     .....
     end
-    
 
-The Fortran function is ``MLpoten_xy3_morbid_11``, which can found in ``mol_xy3.f90``.  A TROVE input example  for NH\ :sub:`3` is  `NH3_BYTe_morbid_11_step1.inp <https://raw.githubusercontent.com/Trovemaster/TROVE/develop/docs/source/input/NH3_BYTe_morbid_11_step1.inp>`_ using the same parameters as in ``NH3_BYTe_step1.inp``. 
+
+The Fortran function is ``MLpoten_xy3_morbid_11``, which can found in ``mol_xy3.f90``.  A TROVE input example  for NH\ :sub:`3` is  `NH3_BYTe_morbid_11_step1.inp <https://raw.githubusercontent.com/Trovemaster/TROVE/develop/docs/source/input/NH3_BYTe_morbid_11_step1.inp>`_ using the same parameters as in ``NH3_BYTe_step1.inp``.