v_sat = np.sum(np.ones([points_in_calc, points_in_calc, points_in_calc]))
savedata = [time_minutes]
for D_m2s in logD_list:
D3 = [D_m2s]*3
percent_water_remaining = np.zeros_like(time_minutes)
rim_location_microns = np.zeros_like(time_minutes)
idx = 0
for minutes in time_minutes:
time_seconds = minutes * 60.
v, x, y = diff.diffusion3Dnpi(lengths_microns, D3, time_seconds,
plot3=False, points=points_in_calc)
percent_water_remaining[idx] = 100. * (v_sat - np.sum(v)) / v_sat
idx_rim = (np.abs(y[direction][0:points_in_calc/2] - water_fraction)).argmin()
rim_location_microns[idx] = x[direction][idx_rim]
print ''.join(('logD=', '{:.1f}'.format(D_m2s), ', ',
'{:.1f}'.format(minutes), ' minutes done'))
idx = idx + 1
savedata.append(list(rim_location_microns))
savedata.append(logD_list)
# Save data to file
v_sat = np.sum(np.ones([points_in_calc, points_in_calc, points_in_calc]))
volume_mm3 = lengths_microns[0] * lengths_microns[1] * lengths_microns[2] / 1E9
center_microns = lengths_microns[direction] / 2.
cpx_percent_water_remaining = np.zeros_like(time_hours)
cpx_rim_location_microns = np.zeros_like(time_hours)
mid_percent_water_remaining = np.zeros_like(time_hours)
mid_rim_location_microns = np.zeros_like(time_hours)
oli_percent_water_remaining = np.zeros_like(time_hours)
oli_rim_location_microns = np.zeros_like(time_hours)
idx = 0
for hours in time_hours:
time_seconds = hours * 3600.
cpx_v, cpx_x, cpx_y = diff.diffusion3Dnpi(lengths_microns, cpx_log10D_m2s, time_seconds,
plot3=False, points=points_in_calc)
cpx_percent_water_remaining[idx] = 100. * (v_sat - np.sum(cpx_v)) / v_sat
cpx_idx_rim = (np.abs(cpx_y[direction][0:points_in_calc/2] - water_fraction)).argmin()
cpx_rim_location_microns[idx] = cpx_x[direction][cpx_idx_rim]
mid_v, mid_x, mid_y = diff.diffusion3Dnpi(lengths_microns, mid_log10D_m2s, time_seconds,
plot3=False, points=points_in_calc)
mid_percent_water_remaining[idx] = 100. * (v_sat - np.sum(mid_v)) / v_sat
mid_idx_rim = (np.abs(mid_y[direction][0:points_in_calc/2] - water_fraction)).argmin()
mid_rim_location_microns[idx] = mid_x[direction][mid_idx_rim]
oli_v, oli_x, oli_y = diff.diffusion3Dnpi(lengths_microns, oli_log10D_m2s, time_seconds,
plot3=False, points=points_in_calc)
oli_percent_water_remaining[idx] = 100. * (v_sat - np.sum(oli_v)) / v_sat
oli_idx_rim = (np.abs(oli_y[direction][0:points_in_calc/2] - water_fraction)).argmin()
oli_rim_location_microns[idx] = oli_x[direction][oli_idx_rim]
savefolder = '\\Users\\Ferriss\\Documents\\Code\\Python\\'
lengths_microns = [3000.] * 3
logD_list = [-12.5, -12., -11.5, -11., -10.5, -10.]
# 0 to 60 minutes
time_minutes = list(np.arange(0.001, 61., 0.5))
water_fraction = 0.80 # How much does concentration drop to qualify as a rim
direction = 0 # 0=[100]*, 1=[010], 2=[001]
points_in_calc = 300
################## Set up and run calculation ################################
fig, ax, v, x, y = diff.diffusion3Dnpi(lengths_microns, [-20.]*3,
time_seconds=0.000000000001,
plot3=True, points=points_in_calc,
centered=False)
v_sat = np.sum(v)
#%%
savedata = [time_minutes]
for D_m2s in logD_list:
D3 = [D_m2s]*3
percent_water_remaining = np.zeros_like(time_minutes)
rim_location_microns = np.zeros_like(time_minutes)
for idx, minutes in enumerate(time_minutes):
time_seconds = minutes * 60.
center_microns = lengths_microns[direction] / 2.
cpx_percent_water_remaining = np.zeros_like(time_hours)
cpx_rim_location_microns = np.zeros_like(time_hours)
mid_percent_water_remaining = np.zeros_like(time_hours)
mid_rim_location_microns = np.zeros_like(time_hours)
oli_percent_water_remaining = np.zeros_like(time_hours)
oli_rim_location_microns = np.zeros_like(time_hours)
idx = 0
for hours in time_hours:
time_seconds = hours * 3600.
cpx_v, cpx_x, cpx_y = diff.diffusion3Dnpi(lengths_microns,
cpx_log10D_m2s,
time_seconds,
plot3=False,
points=points_in_calc)
cpx_percent_water_remaining[idx] = 100. * (v_sat - np.sum(cpx_v)) / v_sat
cpx_idx_rim = (np.abs(cpx_y[direction][0:points_in_calc / 2] -
water_fraction)).argmin()
cpx_rim_location_microns[idx] = cpx_x[direction][cpx_idx_rim]
mid_v, mid_x, mid_y = diff.diffusion3Dnpi(lengths_microns,
mid_log10D_m2s,
time_seconds,
plot3=False,
points=points_in_calc)
mid_percent_water_remaining[idx] = 100. * (v_sat - np.sum(mid_v)) / v_sat
mid_idx_rim = (np.abs(mid_y[direction][0:points_in_calc / 2] -
water_fraction)).argmin()