Coverage for chemreac/util/grid : 94%

# -*- coding: utf-8 -*- 

""" 

chemreac.util.grid 

------------------ 

Grid related utilities for one dimensional grid of arbitrary spacing. 

""" 

from __future__ import print_function, division 

from math import log 

import numpy as np 

from ..units import get_derived_unit, to_unitless 

def generate_grid(x0, xend, N, logx=False, units=None, random=False): 

    length_unit = get_derived_unit(units, 'length') 

    _x0 = to_unitless(x0, length_unit) 

    _xend = to_unitless(xend, length_unit) 

    if logx: 

        low, high = log(_x0), log(_xend) 

    else: 

        low, high = _x0, _xend 

    result = np.linspace(low, high, N+1) 

    if random is False: 

        return result 

    elif random is True: 

        random = 1.0 

    elif random > 1.0 or random <= 0.0: 

        raise ValueError("0 < random <= 1.0, or True => 1.0") 

    result[1:-1] += random*(np.random.random(N-1)-0.5)*(_xend-_x0)/(N+2) 

    return result 

def padded_centers(x, nsidep): 

    """ 

    Parameters 

    ========== 

    x: sequence 

        strictly monotonically increasing sequence of positions of 

        bin separators. 

    nsidep: integer 

        number of padding bins: (nstencil-1)/2 

    """ 

    xc = x[:-1] + np.diff(x)/2 

    return np.concatenate(( 

        2*x[0]-xc[:nsidep][::-1], xc, 2*x[-1]-xc[-nsidep:][::-1] 

    )) 

def pxci_to_bi(nstencil, N): 

    """ 

    Generates a translation list converting x center indicesex starting 

    at 0, which includes padding bins and into bin indices. 

    Parameters 

    ========== 

    nstencil: integer 

        Number of stencil points used 

    N: integer 

        Number of bins 

    Returns 

    ======= 

    list of bin indices. 

    """ 

    nsidep = (nstencil-1)//2 

    return list(range(nsidep)[::-1]) + list(range(N)) + list( 

        range(N-1, N-nsidep-1, -1)) 

def stencil_pxci_lbounds(nstencil, N, lrefl=False, rrefl=False): 

    """ 

    Generates a list of lower bounds in padded centers for each bin index 

    for use in fintie difference scheme. 

    Parameters 

    ---------- 

    nstencil: int 

        Number of stencil points used 

    N: int 

        Number of bins 

    lrefl, rrefl: bool 

        left and right reflective boundaries 

    """ 

    nsidep = (nstencil-1)//2 

    le = 0 if lrefl else nsidep 

    re = 0 if rrefl else nsidep 

    return [max(le, min(N + 2*nsidep - re - nstencil, i)) 

            for i in range(N)]