APPLE&P
*******

APPLE&P is a polarizable forcefield suitable for many electrolytes and
polymers.

To use the APPLE&P force field, you need a special license for APPLE&P
that you can obtain from SCM.


APPLE&P use cases
=================

APPLE&P has been specifically parametrized to the below list of
molecules. For molecules not on the list, the force field may or may
not be reasonable, and it is advised that you do your own testing.


Organic Molecules
-----------------

* alcohols

* aldehydes

* alkanes, alkenes, alkynes

* amides

* esters

* ethers

* imides

* ketones

* partially fluorinated alkanes

* perfluoroalkanes


Energetic Materials
-------------------

* FOX-7

* HMX

* hydrazines

* hydroxylammonium nitrate (HAN)

* hydroxylethyl hydrazinium nitrate (HEHN)

* PETN

* RDX

* TATB

* TNT


Polymers
--------

Note:

  The automatic atom typing may be very slow for large polymers
  containing the following functional groups:  nitro, isocyanate
  groups, phenyl rings and conjugated rings with carbon and nitrogen
  (i.e. imidazole), amide, imide and azide groups, as well as
  phosphorous groups with multiple oxygen atoms (phosphorous oxoacids
  and derivatives).

* polyimides

* polyamides

* polyesters

* polyethers (e.g., PEO)

* PIB

* PDMS

* PTFE

* polybutadiene

* polyalkanes


Solvents/Additives
------------------

* acetone

* alcohols

* cyclic carbonates (e.g., ethylene carbonate)

* ethers (e.g., dimethoxyethane)

* linear carbonates (e.g., dimethyl carbonate)

* nitriles (e.g., acetonitrile, succinonitrile, adiponitrile)

* partially fluorinated carbonates (e.g., FEC)

* partially fluorinated ethers

* perfluoroethers

* sulfones (cyclic and acyclic)

* water


SEI compounds
-------------

* dilithium dicarbonates

* lithium carbonates

* LiF

* Li₂CO₃


Cations
-------

* ammoniums

* H₃O⁺, hydronium

* hydraziniums

* imidazoliums

* K⁺, potassium

* Li⁺, lithium

* Mg²⁺, magnesium

* morpholiniums

* Na⁺, sodium

* piperidiniums

* pyrrolidiniums

* Zn²⁺, zinc


Anions
------

* B(CN)₄⁻, tetracyanoborate

* BF₄⁻, tetrafluoroborate

* BF₃CF₃⁻, CF₃BF₃⁻, trifluoro(trifluoromethyl)borate

* BF₃CH₃⁻, CH₃BF₃⁻, methyltrifluoroborate

* BOB, bis(oxalate)borate

* C(CN)₃⁻, tricyanomethanide

* CN⁻, cyanide

* CN₇⁻, azidotetrazolate

* CO₃²⁻, carbonate

* F⁻, fluoride

* FSI, bis(fluorosulfonyl)imide

* N₃⁻, azide

* N(CN)₂⁻, dicyanamide

* NO₃⁻, nitrate

* OH⁻, hydroxide

* PF₆⁻, hexafluorophosphate

* SO₃CF₃⁻, triflate

* TFSI, bistriflimide


Electrodes
----------

Note:

  The automatic atom typing may be extremely slow for graphite sheets
  consisting of more than 30-40 atoms.

* graphite

* iridium


APPLE&P potential shapes
========================

In general, APPLE&P uses similar expressions for the potentials, with
some differences. For completeness' sake we list all APPLE&P
potentials below.

See also: Potential shapes force other force fields.

* Bond: the same as the stretch potential above.

   V^\text{bond} = \frac{1}{2} f_c (r-r_0)^2

* Bend: the same as the harmonic angle potential above.

   V^\text{bend} = \frac{1}{2} f_c (\phi-\phi_0)^2

* Torsion: cyclic.

   V^\text{torsion} =  - \sum_{m=1}^n c_m \cos(m \phi)

* Out-of-plane angle: sum of three harmonic terms, each corresponding
  to an angle between the R_ij bond and the (jkl) plane, where j is
  the central atom and i, k, l are permutations of the other three
  atoms.

   V^\text{oop} =  \frac{1}{2} f_c (\phi_1^2 + \phi_2^2 + \phi_3^2)

* Dispersion: mix of the Buckingham and Lennard-Jones potentials.

   V^\text{dispersion} = A e^{-Br} - \frac{C}{r^6} + \frac{D}{r^{12}}

* Electrostatic potential: charge-charge, charge-dipole and dipole-
  dipole. Interaction are excluded for the 1-2 and 1-3 neighbors and
  can be scaled for the 1-4 ones. For each atom, the self-consistent
  induced dipole moment is computed from its polarizability and the
  electric field due to other charges and dipoles. The latter includes
  the Thole damping.

   V^\text{elstat} = \sum_{i>j} {} \frac{q_i q_j}{4 \pi \epsilon_0
   r_{ij}} + \sum_{i} {} \vec{\mu_i} \cdot \vec{E_i}


APPLE&P Python functions
========================

The "scm.appleandp" Python module contains the below functions.

For example usage, see the APPLE&P tutorial

appleandp_packmol(molecules, forcefield_file, **kwargs)

   molecules: list of Molecule
      If they are ions they should have the molecule.properties.charge
      set to the charge

   forcefield_file: str
      The force field file will be written here. It will be
      overwritten if it already exists

   "**kwargs": various options
      See the documentation for the "packmol()" function

   Returns: a PLAMS Molecule created with packmol

   This function differs from the PLAMS implementation of packmol in
   that it also writes out a force field file for use with APPLE&P.
