DispersionPauli

class AmberFD.DispersionPauli(*args)

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.

To construct a new force object, define the object with

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

__init__(*args)

Methods

`__init__`(*args)
`add_exclusion`(i, j)	Add an exclusion between a pair of sites
`calc_energy`(coords)	Calculate the total interaction energy of all sites
`calc_one_pair`(*args)	Overload 1:
`create_exclusions_from_bonds`(bonds, bond_cutoff)	Create exclusions based on wht atoms are bonded to each other
`create_exclusions_from_fragment`(frag_idx)	Create exclusions from fragments.
`create_repulsion_sites`(vertical_dist, bonds)	Create the two-site repulsion sites
`get_C6_coeff`()	Get the C6 coefficients used for all sites
`get_C6_map`()	Get the C6 coefficient mapping by nuclei type
`get_disp_energy`()	Return the total dispersion energy for the system
`get_dispersion_params`()	Get the dispersion parameters
`get_exclusions`(particle1)	Get a list of sites that are excluded from interacting with the i-th site
`get_forces`()	Return the forces exerted on each site after an energy computation
`get_num_sites`()	Get the number sites
`get_pauli_energy`()	Return the total Pauli repulsion energy for the system
`get_pauli_exp`()	Get the Pauli exponents used on all sites in the system
`get_pauli_radii`()	Get the Pauli radii for all sites
`get_use_PBC`()	Inquire if PBC is used or not
`get_vdw_radii`()	Get the vdw radii used for all sites
`get_vdw_radii_map`()	Get the vdw radii mapping by the nuclei type
`initialize`()	Clear energy components before a calculation
`set_C6_map`(nucleiToC6Map)	Set the C6 coefficients by the nuclei type
`set_dispersion_params`(s6, a1, a2)	Set the dispersion parameters assording to Grimme et alhttps://doi.org/10.1002/jcc.21759
`set_pauli_exp`(*args)	Overload 1:
`set_pauli_radii`(*args)	Overload 1:
`set_two_site_distance`(vertical_dist)	Set the two site repulsion distance
`set_use_PBC`(*args)	Overload 1:
`set_use_secondary_radii`([use_radii])	Set the use of secondary radii for Pauli repulsion.
`set_use_two_site_repulsion`(on_off)	Set the use two site repulsion (experimental only)
`set_vdw_radii`(nuclei2radiiMap)	Set the vdw radii by the nuclei type

Attributes

thisown

The membership flag

property thisown: The membership flag

set_dispersion_params(s6, a1, a2)

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

Parameters

s6 (float) – Coefficient that scales the entire energy
a1 (float) – multiple of the vdw radii R_ab
a2 (float) – additive to a1*R_ab

get_dispersion_params()

Get the dispersion parameters

Parameters

s6 (float) – Coefficient that scales the entire energy
a1 (float) – multiple of the vdw radii R_ab
a2 (float) – additive to a1*R_ab

set_vdw_radii(nuclei2radiiMap)

Set the vdw radii by the nuclei type

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

get_vdw_radii_map()

Get the vdw radii mapping by the nuclei type

Return type: map_id
Returns: mapping from nuclei integers to vdw Radii (in bohr)

get_vdw_radii()

Get the vdw radii used for all sites

Return type: vec_d
Returns: array of vdw radii in bohr

set_C6_map(nucleiToC6Map)

Set the C6 coefficients by the nuclei type

Parameters: nucleiToC6Map (map_id) – mapping from nuclei integers to C6 coeff

get_C6_map()

Get the C6 coefficient mapping by nuclei type

Return type: map_id
Returns: mapping fron nuclei integers to C6 coeff

get_C6_coeff()

Get the C6 coefficients used for all sites

Return type: vec_d
Returns: array of C6 coefficients

set_pauli_radii(*args)

Overload 1:

Set the Pauli radii for all sites

Parameters: radii_list (vec_d) – list of Pauli radii

Overload 2:

Set the Pauli radii for an individual site

Parameters

index (int) – the index of the site to change
radii (float) – the Pauli radii to assign

get_pauli_radii()

Get the Pauli radii for all sites

Return type: vec_d
Returns: array of Pauli radii in bohr

set_pauli_exp(*args)

Overload 1:

Set the Pauli exponents for all sites

Parameters: exp_list (vec_d) – array of exponents to use

Overload 2:

Set the Pauli exponent for a particular site

Parameters

index (int) – The index of the site to change the exponent of
exponent (float) – The value of the exponent to use on this site

get_pauli_exp()

Get the Pauli exponents used on all sites in the system

Return type: vec_d
Returns: vec_d Array of Pauli exponents (in inverse bohr)

get_num_sites()

Get the number sites

Return type: int
Returns: int

create_exclusions_from_bonds(bonds, bond_cutoff)

Create exclusions based on wht atoms are bonded to each other

Parameters

bonds (std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >) – A list of index pairs in which each pair declares a bond between those two sites
bond_cutoff (int) – Any site this many bonds away are excluded in the interaction calculation

create_exclusions_from_fragment(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 (vec_i) – An array of indicies

add_exclusion(i, j)

Add an exclusion between a pair of sites

Parameters

i (int) – The index of the first site
j (int) – The index of the second site

get_exclusions(particle1)

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

Parameters: particle1 (int) – The site to inquire about exclusions
Return type: std::set< int,std::less< int >,std::allocator< int > >
Returns: std::set<int> a list of site indicies that do not interact with particle1

set_use_PBC(*args)

Overload 1:

Turn on or off periodic boundary conditions

Parameters: is_periodic (boolean) – If true, use PBC, if false, do not use them

Overload 2:

Set the periodic boundaries

Parameters

is_periodic (boolean) – If true, use PBC, if false, do not use them
x (float) – The x-direction of the periodic box
y (float) – The y-direction of the periodic box
z (float) – The z-direction of the periodic box

get_use_PBC()

Inquire if PBC is used or not

Return type: boolean
Returns: true PBC is being used
Return type: boolean
Returns: false PBC is not being used

initialize(): Clear energy components before a calculation

calc_energy(coords)

Calculate the total interaction energy of all sites

Parameters: coords (vec_d) – A 1D array of positions of the sites
Return type: float
Returns: The interaction energy

calc_one_pair(*args)

Overload 1:

Compute the interaction energy of a single pair of sites

Parameters

pos (vec_d) – A 1D array of positions of the sites
deltaR (DeltaR) – A distance object for the pair of sites
i (int) – Index of the first site
j (int) – Index of the second site
energies (Energies) – The Energies object that will be updated
forces (std::vector< Vec3,std::allocator< Vec3 > >) – The forces array that will be updated

Return type

float

Returns

double

Overload 2:

Compute the interaction energy of a single pair of sites

Parameters

pos (vec_d) – A 1D array of positions of the sites
i (int) – Index of the first site
j (int) – Index of the second site
forces (std::vector< Vec3,std::allocator< Vec3 > >) – The forces array that will be updated

Return type

Energies

Returns

Energies that were computed for the pair

get_pauli_energy()

Return the total Pauli repulsion energy for the system

Return type: float
Returns: double

get_disp_energy()

Return the total dispersion energy for the system

Return type: float
Returns: double

get_forces()

Return the forces exerted on each site after an energy computation

Return type: std::vector< vec_d,std::allocator< vec_d > >
Returns: std::vector<vec_d> An Nx3 array of forces

set_use_secondary_radii(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 (boolean) – If true, the backup radii will alos be used

set_use_two_site_repulsion(on_off)

Set the use two site repulsion (experimental only)

Parameters: on_off (boolean) – Set to true to enable

set_two_site_distance(vertical_dist)

Set the two site repulsion distance

Parameters: vertical_dist (float) – The virtical distance out of the place

create_repulsion_sites(vertical_dist, bonds)

Create the two-site repulsion sites

Parameters

vertical_dist (float) – The virtical distance out of the place
bonds (std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >) – A list of all bonds