Build Initial Configurations¶

Build atomistic initial configuration of the hexagonal (HII) or bicontinuous cubic (QI) phase. This method implements the methods of:

Build LLC unit cell

usage: build.py [-h] [-phase PHASE] [-b BUILD_MONOMER [BUILD_MONOMER ...]]
                [-o OUT] [-r PORE_RADIUS] [-seed RANDOM_SEED]
                [-box BOX_LENGTHS [BOX_LENGTHS ...]]
                [-angles ANGLES [ANGLES ...]] [-nc NCOLUMNS] [-p P2P]
                [-n NOPORES] [-d DBWL] [-m MONOMERS_PER_COLUMN] [-t TILT]
                [-L CORRELATION_LENGTH] [--no_column_shift] [-Lvar LVAR]
                [-pd PARALLEL_DISPLACED] [-mf MOL_FRAC [MOL_FRAC ...]]
                [-g GRID] [-dens DENSITY] [-c CURVATURE] [-wt WEIGHT_PERCENT]
                [-sol SOLVENT] [-shift SHIFT] [-plot]

Named Arguments¶

`-phase, --phase`
	Liquid crystal phase to build (HII, QI etc.) Default: “gyroid”
`-b, --build_monomer`
	Name of single monomerstructure file (.gro format) used to build full system
`-o, --out`	Name of output .gro file for full system Default: “initial.gro”
`-r, --pore_radius`
	Initial Pore Radius (nm) Default: 0.6
`-seed, --random_seed`
	Random seed for column shift. Set thisto reproduce results Default: False
`-box, --box_lengths`
	Length of box vectors [x y z]
`-angles, --angles`
	Angles betweenbox vectors Default: [90, 90, 60]
`-nc, --ncolumns`
	Number of columns used to build each pore Default: 5
`-p, --p2p`	Initial pore-to-pore distance (nm) Default: 4.5
`-n, --nopores`	Number of pores (only works with 4 currently) Default: 4
`-d, --dbwl`	Distance between vertically stacked monomers(nm) Default: 0.37
`-m, --monomers_per_column`
	Number of monomers to stack in eachcolumn Default: 20
`-t, --tilt`	Tilt angle of monomer with respect to xy plane (degrees) Default: 0
`-L, --correlation_length`
	Length over which distance correlation betweenstacked monomers persists (nm)
`--no_column_shift`
	Do not randomly shift columns Default: True
`-Lvar`	Variance in z position of monomer heads (nm) Default: 0.1
`-pd, --parallel_displaced`
	Angle of wedge formed between lineextending from pore center to monomer and line from pore center to vertically adjacent monomerhead group. Default: 0
`-mf, --mol_frac`
	If using the -random flag, this givesthe relative amount of each monomer to add. List the fractions in the same order as-build_monomer Default: [1.0]
`-g, --grid`	Number of sections to break grid into when approximating the chosen implicit function Default: 50
`-dens, --density`
	Density of system (g/cm3) Default: 1.1
`-c, --curvature`
	> 0 : QI phase (positive mean curvature), < 0, QII phase (negative meancurvature). Determines whether the phase is normal or inverted Default: 1
`-wt, --weight_percent`
	Weight % of monomer in membrane Default: 77.1
`-sol, --solvent`
	Name of solvent mixed with monomer Default: “glycerol”
`-shift, --shift`
	Shift position of head group shift units in the direction opposite of the normal vector at that point Default: 0
`-plot, --plot_grid`
	Plot the grid of points used to defined the BCC surface Default: False