Merge pull request #15 from libefp2/satarupa_new

EFP_calcs update

Author: satgupta98

doc/efp_calcs.rst

@@ -42,12 +42,12 @@ Two options exist for accounting for charge-penetration contribution to electros
 energy:
 
 - exponential screening ("smearing") of charges. This is achieved by invoking screening parameters
-  defined in ``SCREEN2`` section of the `.efp` potential (see :ref:`SCREEN`). The charge-penetration energy
-  is not printed separately but included in the electrostatic energy.
+defined in ``SCREEN2`` section of the `.efp` potential (see :ref:`SCREEN`). The charge-penetration energy
+is not printed separately but included in the electrostatic energy.
 - overlap-based screening. This is a separate energy term derived assuming that localized orbitals
-  can be modeled as spherical gaussions (the same approximation is used in the exchange-repulsion term).
-  This calculation will utilize exchange-repulsion parameters (:ref:`FOCK`, :ref:`WF`, :ref:`BASIS`, :ref:`LMOC`).
-  This overlap-based charge-penetration energy is printed as a separate energy term (see examples in :ref:`libefp`).
+can be modeled as spherical gaussions (the same approximation is used in the exchange-repulsion term).
+This calculation will utilize exchange-repulsion parameters (:ref:`FOCK`, :ref:`WF`, :ref:`BASIS`, :ref:`LMOC`).
+This overlap-based charge-penetration energy is printed as a separate energy term (see examples in :ref:`libefp`).
 
 Detailed description of damping functions and their benchmarks are published in
 `Damping functions for electrostatic term <http://dx.doi.org/10.1002/jcc.20520>`_
@@ -85,12 +85,39 @@ the `short-range damping functions paper <http://dx.doi.org/10.1080/002689708027
 by an optional :ref:`POLAB` keyword; smaller values provide stronger screening of polarization energies which might be necessary for fragments
 with large multiple moments (charged or strongly polar species) or large polarizabilities (e.g., large conjugated/aromatic molecules).
 
+.. _disp_energy:
+
 Dispersion term
 ^^^^^^^^^^^^^^^
 
 Dispersion energy term captures the London interaction between the molecules. Formally, it can be expanded in
-series of (1/R) operator as $$E_{disp} = \frac{C_6}{R^6} + \frac{C_8}{R^8} + \frac{C_{10}}{R^{10}} + ...$$.
+series of (1/R) operator as :math:`E_{disp} = \frac{C_6}{R^6} + \frac{C_8}{R^8} + \frac{C_{10}}{R^{10}} + ....`
 In the case of distributed approach where dispersin contributions are computed as a sum of contributions due to
-individual parts of a molecules, the odd terms $\frac{C_7}{R^7}$, $\frac{C_9}{R^9}$ etc are also non-zero.
-The dispersion energy in LibEFP is computed as the first $\frac{C_6}{R^6}$ in the dispersion expansion, using
-distributed dynamic polarizabilities for evaluating $C_6$ coefficient, i.e.,
+individual parts of a molecules, the odd terms :math:`\frac{C_7}{R^7}, \frac{C_9}{R^9}` etc are also non-zero.
+
+The relevant sections of the EFP potential are:
+
+- :ref:`DYN_POINT`
+
+:ref:`DYN_POINT` group section provides coordinates and values of anisotropic dynamic polarizability tensors for computing dispersion energy.
+
+.. _ex_rep:
+
+Exchange Repulsion
+^^^^^^^^^^^^^^^^^^
+
+Exchange repulsion accounts for the antisymmetry of the wave function of the fragments.It is modelled using inter-fragment kinetic and
+overlap integrals, and the Fock matrices of the fragment. 
+
+The relevant sections of the EFP potential are:
+
+- :ref:`BASIS`
+- :ref:`MULTIPLICITY`
+- :ref:`WF`
+- :ref:`FOCK`
+- :ref:`LMOC`
+
+:ref:`BASIS` provides details of the basis set used for calculation of the exchange repulsion energy, :ref:`MULTIPLICITY` contains information
+on the multiplicity of the fragment (LibEFP works only on fragments with multiplicity 1), :ref:`WF` provides the localized wave function of the 
+fragment, while :ref:`FOCK` and :ref:`LMOC` contain information regarding the elements of the Fock matrix of the fragment in the localized basis, and 
+the coordinates of the localized molecular orbital, respectively.