External forces and constraints

Constraints or external forces such as the presence of a external field or surface can be modeled by using the "field" argument in the input file. The "field" argument accepts a file containing the list of constraints as an argument. Each constraint is specified in a single line and has the general syntax

<constraint name> <x1> <x2> ...... <xn> 

where <x1>, <x2>,....,<xn> are the constraint parameters. Currently the following constraints have been implemented:

Point constraint

The interface can be harmonically pinned at a site R = (x,y) by using the following localized potential

H_{pin}[h(x,y)] = \frac{\gamma}{2} h^{2}(x,y) \exp \left[ - \left( \frac{r-R}{l/4} \right)^{2} \right]

The harmonic pin is specified in the field file by the following syntax:

harmonicpin x y z k l

Where each pinning site requires the following parameters:

Parameter	Type	Units	Comments
x	float	nm	x location of pinning site
y	float	nm	y location of pinning site
z	float	nm	height at pinning site
k	float	kJ/mol/nm	Pinning force constant
z	float	nm	L / number of grid points

Self-Assembled Monolayer Surface

The presence of a SAM surface can be modeled by setting up smeared interaction force between the surface and the interface. Such a smeared potential depends only on the z coordinate. The details of the SAM surface potential are explained in the Supporting Information section of [Patel et al., Proc. Natl. Acad. Sci. USA, 108, 17678-17683 (2011)] (http://dx.doi.org/10.1073/pnas.1110703108)

The SAM surface potential is specified in the field file using the following syntax:

samsurface zsurf sig_head eps_head rho_head sig_tail eps_tail rho_tail (lambda xi R_0 rho_l) 

Parameter	Type	Units	Comments
sig_head	float	nm	Head group LJ sigma
eps_head	float	kJ/mol	Head group LJ epsilon
rho_head	float	#/nm**2	Head group surface density
sig_tail	float	nm	Tail group LJ sigma
eps_tail	float	kJ/mol	Tail group LJ epsilon
rho_tail	float	#/nm**3	Tail group volume density
lambda	float		Surface attraction scaling parameter
x_i	float	nm	Depth of tail groups
R_0	float	nm
rho_l	float	#/nm**3	Density of liquid phase