Class DispersionPauli

Class Documentation

class DispersionPauli

To construct a new force object, define the object with.

This class impliments two forces, a repulsive Pauli force and an attractive dispersion force. The sum of these two constitute a force similar to a Lennard-Jones force used in many MD simulations or a van der Waals force used in the AMOEBA model. To use it, simple create a DispersionPauli object by specifying the number of sites and the parameters for all sites. These parameters can be altered after the creation of the force object.

Next, set the global parameters for dispersion dampening, which employs the same functional form used in Grimme et al https://doi.org/10.1002/jcc.21759 for the r^6 attractive term. If no dampening is desired, set both a1 and a2 parameters to zero. As a result, vdw Radii will not affect the dispersion energy, and only C6 coefficeients will matter. Both C6 Nd vds Radii are determined based on the nuclei of each site, and all sites with the same nuclei will use the same parameters.

For the interaction betweena pair of sites, a geometric mixing is employed for the C6 coefficients while the two vdw radii are simply added together. For the Pauli repulsion, exponents are arithmetically averaged while the radii are converted to coefficient pre-factors that are then multipled by each other.

Param num_sites

The number of sites to create

Param nuclei

The integer nuclei of each site

Param exponents

The exponents used for the Pauli repulsion

Param radii

The Pauli radii used for repulsion

Public Functions

DispersionPauli(const int num_sites, const int *nuclei, const double *exponents, const double *radii)

Construct a new DispersionPauli force object.

Parameters

  • num_sites – The number of sites to create

  • nuclei – The integer nuclei of each site

  • exponents – The exponents used for the Pauli repulsion

  • radii – The Pauli radii used for repulsion

~DispersionPauli()
void set_dispersion_params(double s6, double a1, double a2)

Set the dispersion parameters assording to Grimme et alhttps://doi.org/10.1002/jcc.21759.

Parameters

  • s6 – Coefficient that scales the entire energy

  • a1 – multiple of the vdw radii R_ab

  • a2 – additive to a1*R_ab

void get_dispersion_params(double &s6, double &a1, double &a2)

Get the dispersion parameters.

Parameters

  • s6 – Coefficient that scales the entire energy

  • a1 – multiple of the vdw radii R_ab

  • a2 – additive to a1*R_ab

void set_vdw_radii(map_id nuclei2radiiMap)

Set the vdw radii by the nuclei type.

Parameters

nuclei2radiiMap – mapping from nuclei integers to vdw Radii (in bohr)

map_id get_vdw_radii_map()

Get the vdw radii mapping by the nuclei type.

Returns

mapping from nuclei integers to vdw Radii (in bohr)

vec_d get_vdw_radii()

Get the vdw radii used for all sites.

Returns

array of vdw radii in bohr

void set_C6_map(map_id nucleiToC6Map)

Set the C6 coefficients by the nuclei type.

Parameters

nucleiToC6Map – mapping from nuclei integers to C6 coeff

map_id get_C6_map()

Get the C6 coefficient mapping by nuclei type.

Returns

mapping fron nuclei integers to C6 coeff

vec_d get_C6_coeff()

Get the C6 coefficients used for all sites.

Returns

array of C6 coefficients

void set_pauli_radii(vec_d radii_list)

Set the Pauli radii for all sites.

Parameters

radii_list – list of Pauli radii

void set_pauli_radii(int index, double radii)

Set the Pauli radii for an individual site.

Parameters

  • index – the index of the site to change

  • radii – the Pauli radii to assign

vec_d get_pauli_radii()

Get the Pauli radii for all sites.

Returns

array of Pauli radii in bohr

void set_pauli_exp(vec_d exp_list)

Set the Pauli exponents for all sites.

Parameters

exp_list – array of exponents to use

void set_pauli_exp(int index, double exponent)

Set the Pauli exponent for a particular site.

Parameters

  • index – The index of the site to change the exponent of

  • exponent – The value of the exponent to use on this site

vec_d get_pauli_exp()

Get the Pauli exponents used on all sites in the system.

Returns

vec_d Array of Pauli exponents (in inverse bohr)

int get_num_sites()

Get the number sites.

Returns

int

void create_exclusions_from_bonds(const std::vector<std::pair<int, int>> bonds, int bond_cutoff)

Create exclusions based on wht atoms are bonded to each other.

Parameters

  • bonds – A list of index pairs in which each pair declares a bond between those two sites

  • bond_cutoff – Any site this many bonds away are excluded in the interaction calculation

void create_exclusions_from_fragment(const vec_i frag_idx)

Create exclusions from fragments. A fragment is a collection of indicies in which all sites will not interact with each other.

Parameters

frag_idx – An array of indicies

void add_exclusion(const int i, const int j)

Add an exclusion between a pair of sites.

Parameters

  • i – The index of the first site

  • j – The index of the second site

std::set<int> get_exclusions(const int particle1) const

Get a list of sites that are excluded from interacting with the i-th site.

Parameters

particle1 – The site to inquire about exclusions

Returns

std::set<int> a list of site indicies that do not interact with particle1

void set_use_PBC(bool is_periodic)

Turn on or off periodic boundary conditions.

Parameters

is_periodic – If true, use PBC, if false, do not use them

void set_use_PBC(bool is_periodic, const double x, const double y, const double z)

Set the periodic boundaries.

Parameters

  • is_periodic – If true, use PBC, if false, do not use them

  • x – The x-direction of the periodic box

  • y – The y-direction of the periodic box

  • z – The z-direction of the periodic box

bool get_use_PBC()

Inquire if PBC is used or not.

Returns

true PBC is being used

Returns

false PBC is not being used

void initialize()

Clear energy components before a calculation.

double calc_energy(const vec_d &coords)

Calculate the total interaction energy of all sites.

Parameters

coords – A 1D array of positions of the sites

Returns

The interaction energy

double calc_one_pair(const vec_d &pos, DeltaR &deltaR, int i, int j, Energies &energies, std::vector<Vec3> &forces)

Compute the interaction energy of a single pair of sites.

Parameters

  • pos – A 1D array of positions of the sites

  • deltaR – A distance object for the pair of sites

  • i – Index of the first site

  • j – Index of the second site

  • energies – The Energies object that will be updated

  • forces – The forces array that will be updated

Returns

double

Energies calc_one_pair(const vec_d &pos, int i, int j, std::vector<Vec3> &forces)

Compute the interaction energy of a single pair of sites.

Parameters

  • pos – A 1D array of positions of the sites

  • i – Index of the first site

  • j – Index of the second site

  • forces – The forces array that will be updated

Returns

Energies that were computed for the pair

double get_pauli_energy()

Return the total Pauli repulsion energy for the system.

Returns

double

double get_disp_energy()

Return the total dispersion energy for the system.

Returns

double

std::vector<vec_d> get_forces()

Return the forces exerted on each site after an energy computation.

Returns

std::vector<vec_d> An Nx3 array of forces

void set_use_secondary_radii(bool use_radii = true)

Set the use of secondary radii for Pauli repulsion. This is a backup to ensure that two sites never get too close to each other without an enormous energetic cost. The distances used are chosed to be a close to a third of the vdw radii so that the energy cost will be minimal at normal distances. This can redude performance somewhat.

Parameters

use_radii – If true, the backup radii will alos be used

void set_use_two_site_repulsion(bool on_off)

Set the use two site repulsion (experimental only)

Parameters

on_off – Set to true to enable

void set_two_site_distance(double vertical_dist)

Set the two site repulsion distance.

Parameters

vertical_dist – The virtical distance out of the place

void create_repulsion_sites(double vertical_dist, const std::vector<std::pair<int, int>> &bonds)

Create the two-site repulsion sites.

Parameters

  • vertical_dist – The virtical distance out of the place

  • bonds – A list of all bonds