move makeBoundary script to python subdirectory.

1 files changed, 364 insertions, 0 deletions

diff --git a/python/makeBoundary b/python/makeBoundary
new file mode 100755
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+++ b/python/makeBoundary
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+#!/usr/bin/env python3
+
+import matplotlib.pyplot as plt
+import numpy as np
+import bisect
+import ast
+import math
+import argparse
+import sys
+
+#TODO: use YAML/ruamel.yaml for configuration file.
+def read_definition(filename):
+    ddict = {}
+    with open(filename, "r") as f:
+        for line in f:
+            items = line.split(': ', 1)
+            if len(items) == 2:
+                ddict[items[0]] = ast.literal_eval(items[1])
+    return ddict
+
+def conveyance(numH, n_co, xregion, zregion, zmin, zmax):
+    p_i = [] # wetted perimeter
+    A_i = [] # area
+    r_h = [] # hydraulic radius
+    h_i = [] # list of heights
+    K_i = [] # conveyance
+    Q_i = [] # discharge
+    x_sub = [[] for i in range(numH)] # list of x values in subregion
+    z_sub = [[] for i in range(numH)] # list of z values in subregion
+    for i in range(numH):
+        h_i.append(zmin + (i+1)*(zmax-zmin)/numH)
+        #print(zregion[zregion < h_i[i]])
+        booleanArray = zregion < h_i[i]
+        #print(booleanArray[i])
+        x_sub[i] += list(xregion[booleanArray])
+        z_sub[i] += list(zregion[booleanArray])
+        for interval in range(len(xregion)-1):
+            if booleanArray[interval+1] != booleanArray[interval]:
+                x_extra = xregion[interval] \
+                    + (h_i[i] - zregion[interval])\
+                    *(xregion[interval+1] - xregion[interval])\
+                    /(zregion[interval+1] - zregion[interval])
+                bisect.insort(x_sub[i], x_extra) # add intercept value
+                ind_x = x_sub[i].index(x_extra)
+                z_sub[i].insert(ind_x, h_i[i])   # add height value
+        #print(z_sub[i])
+
+        dp = 0
+        dA = 0
+        eps = 1e-06
+        for j in range(len(x_sub[i])-1):
+            if (abs(z_sub[i][j+1] - h_i[i]) > eps
+                or abs(z_sub[i][j] - h_i[i]) > eps):
+                dp += np.hypot(x_sub[i][j+1] - x_sub[i][j],
+                               abs(z_sub[i][j+1] - z_sub[i][j]))
+            #print(dp)
+            # calculate area using trapezium rule
+            dA += (h_i[i]
+                   - (z_sub[i][j+1] + z_sub[i][j])/2)\
+                   *(x_sub[i][j+1] - x_sub[i][j])
+            #print('Area =', dA)
+
+        p_i.append(dp)
+        A_i.append(dA)
+
+        r_h.append(A_i[i]/p_i[i])  # ratio of area and wetted perimeter
+        #print('hydraulic radius =', r_h[i])
+        K_i.append(A_i[i]*(1/n_co)*r_h[i]**(2/3)) # conveyance
+        Q_i.append(K_i[i]*slope**0.5)             # discharge
+
+    return p_i, A_i, r_h, h_i, K_i, Q_i
+
+def plot_region(xdata, labelx,
+                ydata1, labely1,
+                ydata2, labely2,
+                ydata3, labely3, titlep):
+    plt.xlabel(labelx)
+    plt.ylabel(labely1)
+    plt.title(titlep)
+    plt.plot(xdata, ydata1)
+    plt.show()
+
+    plt.xlabel(labelx)
+    plt.ylabel(labely2)
+    plt.title(titlep)
+    plt.plot(xdata, ydata2)
+    plt.show()
+
+    plt.xlabel(labelx)
+    plt.ylabel(labely3)
+    plt.title(titlep)
+    plt.plot(xdata, ydata3)
+    plt.show()
+
+def save_bc(outputfile):
+    with open(outputfile, 'w') as f:
+        f.write('{:6} {:>2} {:>2} {:>10}\n'.format('#x', 'c', 'q', 'h'))
+        for ind_z, (xitem, zitem) in enumerate(zip(xin, zin)):
+            panel_x = bisect.bisect(markers, xitem)
+            if csa[ind_z] == 0:
+                # wall boundary condition
+                f.write('{:6.2f} {:>2}\n'.format(xitem, 2))
+            elif panel_x == panel[ind_p]:
+                # imposed discharge within part-filled panel
+                f.write('{:6.2f} {:>2} {:10.6f} {:9.6f}\n'.format(
+                    xitem, btype,
+                    -csa[ind_z]*panel_target_flow/csa_p[panel_x],
+                    h_extra-zitem))
+            else:
+                # imposed discharge within filled panels
+                f.write('{:6.2f} {:>2} {:10.6f} {:9.6f}\n'.format(
+                    xitem, btype,
+                    -csa[ind_z]*Q_i[panel_x][-1]/csa_p[panel_x],
+                    zmax-zitem))
+
+def interp(extra2, max1, min1, max2, min2):
+    # use similar triangles to perform linear interpolation
+    extra1 = min1 + (max1 - min1)*(extra2 - min2)/(max2 - min2)
+    
+    return extra1
+
+# read command line argument:
+parser = argparse.ArgumentParser(
+    description="generate FullSWOF boundary files")
+parser.add_argument("location", help="boundary location")
+args = parser.parse_args()
+
+if args.location == 'top':
+    inputFilename = "boundaryTop.txt"
+    outputFilename = "BCTop.txt"
+elif args.location == 'bottom':
+    inputFilename = "boundaryBottom.txt"
+    outputFilename = "BCBottom.txt"
+elif args.location == 'left':
+    inputFilename = "boundaryLeft.txt"
+    outputFilename = "BCLeft.txt"
+elif args.location == 'right':
+    inputFilename = "boundaryRight.txt"
+    outputFilename = "BCRight.txt"
+
+# read boundary definition file:
+definition_dict = read_definition(inputFilename)
+#for dd in definition_dict:
+#    print(definition_dict[dd])
+btype       = definition_dict["type"]        # boundary type (1--5)
+slope       = abs(definition_dict["slope"])  # slope at top boundary
+target_flow = definition_dict["target_flow"] # imposed discharge
+plotting    = definition_dict["plotting"]    # enable or disable plotting
+n_co        = definition_dict["n_co"]        # Manning's 'n' coefficients
+# TODO: use weighted mean 'n' values.  See
+# http://help.floodmodeller.com/isis/ISIS/River_Section.htm (Eq. 4)
+# Note: weighted mean calculation requires roughness map.
+markers     = definition_dict["markers"]     # distances from corner point
+panel       = definition_dict["panel"]       # panel fill order
+ztol        = definition_dict["ztol"]        # tolerance in overtopping height
+numH        = definition_dict["numH"]        # number of height intervals
+
+
+# print(len(markers))
+
+# with open('./1D_top.txt', "r") as data:
+#     xch, ych, zch = np.loadtxt(data, delimiter=' ', unpack=True)
+
+# Fit with polyfit
+# m, c = np.polyfit(ych, zch, 1)
+# print('gradient =', m, 'intercept =', c)
+
+# read topography:
+with open("./topography.txt", "r") as topo:
+    xtp, ytp, ztp = np.loadtxt(topo, delimiter=' ', unpack=True)
+
+
+xmax  = (xtp[0]+xtp[-1])                   # domain extent in x-direction
+ymax  = (ytp[0]+ytp[-1])                   # domain extent in y-direction
+ncols = int(math.sqrt(len(xtp)*xmax/ymax)) # number of cells in x-direction
+nrows = int(len(xtp)/ncols)                # number of cells in y-direction
+dX    = xmax/ncols                         # cell size
+print('dX =', dX)
+
+#print(ncols, nrows)
+
+# extract slices from height data array.  Note: xyz format uses ncols
+# blocks, with nrows lines per block.
+if args.location == 'top':
+    xin = xtp[nrows-1:len(xtp):nrows]
+    yin = ytp[nrows-1:len(xtp):nrows]
+    zin = ztp[nrows-1:len(xtp):nrows]
+elif args.location == 'bottom':
+    xin = xtp[0:len(xtp):nrows]
+    yin = ytp[0:len(xtp):nrows]
+    zin = ztp[0:len(xtp):nrows]
+elif args.location == 'left':
+    xin = xtp[:nrows]
+    yin = ytp[:nrows]
+    zin = ztp[:nrows]
+elif args.location == 'right':
+    xin = xtp[nrows*(ncols-1):]
+    yin = ytp[nrows*(ncols-1):]
+    zin = ztp[nrows*(ncols-1):]
+    
+
+# print(xin)
+
+num_panels = len(panel) # number of panels across boundary
+
+# convert marker co-ordinates to array indices:
+marker_ind = [0]
+for i in range(len(markers)):
+    marker_ind.append(int(markers[i]/dX))
+if args.location == 'left' or args.location == 'right':
+    marker_ind.append(nrows)
+elif args.location == 'top' or args.location == 'bottom':
+    marker_ind.append(ncols)
+
+
+# print(marker_ind)
+
+xregion = []
+zregion = []
+zmin = []
+for p in range(num_panels):
+    # identify regions:
+    xregion.append(xin[marker_ind[p]:marker_ind[p+1]])
+    zregion.append(zin[marker_ind[p]:marker_ind[p+1]])
+    # identify minimum heights within each panel:
+    zmin.append(zregion[p].min())
+
+# xregion_west = xin[100:281]
+# zregion_west = zin[100:281]
+
+# xregion_east = xin[300:408]
+# zregion_east = zin[300:408]
+
+# print(zregion)
+# print(xin[12:20])
+
+print('zmin =', zmin)
+
+# channel overtopping height (minimum of left bank and right bank heights):
+zmax = min(zregion[panel[0]][0], zregion[panel[0]][-1]) - ztol
+
+print('zmax =', zmax)
+
+#print(h_i)
+
+
+
+p_i = [[] for _ in range(num_panels)]
+A_i = [[] for _ in range(num_panels)]
+r_h = [[] for _ in range(num_panels)]
+h_i = [[] for _ in range(num_panels)]
+K_i = [[] for _ in range(num_panels)]
+Q_i = [[] for _ in range(num_panels)]
+for p in range(num_panels):
+    if p == panel[0]-1 and zregion[p][-1] < zmax:
+        # ensure end node in region to the left of channel is dry:
+        xregion[p] = np.append(xregion[p], xin[marker_ind[p]])
+        zregion[p] = np.append(zregion[p], zin[marker_ind[p]])
+    if p == panel[0]+1 and zregion[p][0] < zmax:
+        # ensure start node in region to the right of channel is dry:
+        xregion[p] = np.insert(xregion[p], 0, xin[marker_ind[p]-1])
+        zregion[p] = np.insert(zregion[p], 0, zin[marker_ind[p]-1])
+    if zmax > zmin[p]:
+        p_i[p], A_i[p], r_h[p], h_i[p], K_i[p], Q_i[p] = conveyance(
+            numH,
+            n_co[p],
+            xregion[p],
+            zregion[p],
+            zmin[p],
+            zmax)
+        if plotting:
+            plot_region(
+                h_i[p]-zmin[p], 'maximum depth / m',
+                r_h[p], 'hydraulic radius / m',
+                K_i[p], r'conveyance / $m^3/s$',
+                Q_i[p], r'discharge / $m^3/s$',
+                'Panel {}'.format(p))
+    else:
+        p_i[p], A_i[p], r_h[p], h_i[p], K_i[p], Q_i[p] = [
+            [0] * numH for _ in range(6)]
+
+# sort list of discharge lists according to panel fill order:
+sortedQ = [Q_i[i] for i in panel]
+# create cumulative discharge list:
+total_flow = np.cumsum([item[-1] for item in sortedQ])
+print('total_flow = ', total_flow)
+# target_flow_west = target_flow - Q_i[-1] - Q_i_east[-1]
+# calculate velocity: note dependence on hydraulic radius
+velocity_channel = Q_i[panel[0]][-1]/A_i[panel[0]][-1]
+# velocity_east    = Q_i_east[-1]/A_i_east[-1]
+
+# print(target_flow_west)
+# find part-filled panel:
+if total_flow[-1] > target_flow:
+    ind_p = bisect.bisect(total_flow, target_flow)
+else:
+    print('Error: imposed discharge is higher than total capacity of panels.')
+    sys.exit()
+
+print('index of part-filled panel:', ind_p)
+
+# calculate target flow in part-filled panel:
+if ind_p == 0:
+    panel_target_flow = target_flow
+else:
+    panel_target_flow = target_flow - total_flow[ind_p-1]
+
+# find insertion point for target flow value:
+ind_q = bisect.bisect(Q_i[panel[ind_p]], panel_target_flow)
+
+print('insertion point =', ind_q)
+
+# find height at target flow by linear interpolation
+h_extra = interp(
+    panel_target_flow,
+    h_i[panel[ind_p]][ind_q],
+    h_i[panel[ind_p]][ind_q-1],
+    Q_i[panel[ind_p]][ind_q],
+    Q_i[panel[ind_p]][ind_q-1])
+
+print('heights:', h_i[panel[ind_p]][ind_q-1], h_extra, h_i[panel[ind_p]][ind_q])
+
+# find area at target flow by linear interpolation
+A_extra = interp(
+    h_extra,
+    A_i[panel[ind_p]][ind_q],
+    A_i[panel[ind_p]][ind_q-1],
+    h_i[panel[ind_p]][ind_q],
+    h_i[panel[ind_p]][ind_q-1])
+    
+print('hydraulic radii:', r_h[panel[ind_p]][ind_q-1], r_h[panel[ind_p]][ind_q])
+
+velocity_panel    = panel_target_flow/A_extra
+print('velocities:', velocity_channel, velocity_panel)
+
+csa = np.zeros(len(xin))             # cross-sectional area of element
+csa_p = np.zeros(num_panels)         # cross-sectional area of panel
+for i, p in enumerate(panel):
+    if i < ind_p:
+        # panels are filled
+        area_sum = 0
+        for m in range(marker_ind[p], marker_ind[p+1]):
+            csa[m] = max(0, (zmax - zin[m])*dX)
+            area_sum += csa[m]
+        csa_p[p] = area_sum
+    elif i == ind_p:
+        # panel is part-filled
+        area_sum = 0
+        for m in range(marker_ind[p], marker_ind[p+1]):
+            csa[m] = max(0, (h_extra - zin[m])*dX)
+            area_sum += csa[m]
+        csa_p[p] = area_sum
+    else:
+        # panel is empty
+        for m in range(marker_ind[p], marker_ind[p+1]):
+            csa[m] = 0
+        csa_p[p] = 0
+
+
+#print('csa_p[0] = {} csa_p[1] = {}'.format(csa_p[0], csa_p[1]))
+#print('A_i_west = {} A_i = {} A_i_east = {}'.format(A_extra, A_i[-1], A_i_east[-1]))
+
+
+save_bc(outputFilename)