-
Notifications
You must be signed in to change notification settings - Fork 3
/
DetailedModel_onewell_optimized.py
982 lines (728 loc) · 29.2 KB
/
DetailedModel_onewell_optimized.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 6 19:05:58 2020
@author: yuchen
"""
import flopy
import flopy.utils.binaryfile as bf
import numpy as np
from osgeo import gdal
import matplotlib.pyplot as plt
import pandas as pd
#========== Plot Functions ==============================
def Get_Conc(Times, units):
ucnobj = bf.UcnFile('MT3D001.UCN')
times = ucnobj.get_times()
concList = []
for i in Times:
concList.append('conc_%dd'%(i))
conc_dict = {}
for index, item in enumerate(concList):
conc_dict[item] = ucnobj.get_data(totim=Times[index])
density = 1500
if units == 'g':
cF = ((0.001/density)*prsity*1000) # conversion factor to convert from kg m**3 to mug L
else:
cF = 10**6
for k in conc_dict.keys():
conc_dict[k] = [cF*x for x in conc_dict[k]]
return conc_dict
def Plot_Conc_Break_Down():
ucnobj = flopy.utils.UcnFile('MT3D001.UCN')
times = ucnobj.get_times()
conc = ucnobj.get_alldata()
obs1_data = conc[:,:,obs1_row,obs1_col][:,0] # Observation at high recharge cell
obs2_data = conc[:,:,obs2_row,obs2_col][:,0] # Observation well 2
obs3_data = conc[:,:,obs3_row,obs3_col][:,0]
obs4_data = conc[:,:,obsSpill_row,obsSpill_col][:,0] # Observation at extraction well
fig = plt.figure(figsize = (50,10))
ax = fig.add_subplot(1,1,1)
# Panel 1 (Concentration time series)
ax.plot(times,obs1_data,'-^',c='r',label='obs1',
markersize=mS, linewidth=lW)
ax.plot(times,obs2_data,'-s',c='k',label='Obs2',
markersize=mS, linewidth=lW)
ax.plot(times,obs3_data,'-o',c='b',label='Obs3',
markersize=mS, linewidth=lW)
ax.plot(times,obs4_data,'-o',c='g',label='spill point',
markersize=mS, linewidth=lW)
ax.grid()
ax.set_xlim(0,sum(perlen))
ax.set_ylim(0.001,10**5)
ax.set_yscale('log')
ax.set_xlabel('Elapsed time [days]')
ax.set_ylabel('Concentration [g L$^-$$^1$]')
ax.set_title('Contaminant concentration',loc='left')
ax.legend(loc='upper right')
return None
def Concentration_Plan_View(conc_dict, units, Times):
fig = plt.figure(figsize=(14,10))
ax1 = fig.add_subplot(2, 2, 1)
# flopy plot object
pmv = flopy.plot.PlotMapView(model=mf, layer=0)
# plot grid
lc = pmv.plot_grid() # grid
# plot concentration
cmap = plt.get_cmap('jet')
if units == 'g':
cmin = 0
cmax = 0.1
else:
cmin = 0
cmax = 20000
cs = pmv.plot_array(conc_dict['conc_%dd'%(Times[0])],
cmap=cmap,vmin=cmin,vmax=cmax) # concentration colourmap
cbar = plt.colorbar(cs,format='%.0e') # colour bar
if units == 'g':
cbar.ax.set_ylabel('C [$\mu$g g$^-$$^1$]')
else:
cbar.ax.set_ylabel('C [$\mu$g L$^-$$^1$]')
# plot the spill site location
ax1.plot(obsSpill_xcoord, obsSpill_ycoord,'o',c='r',label='Spill site',
markersize=mS)
#ax1.plot(w2_xcoord,w2_ycoord,'x',c='r')
# ax1.plot(w3_xcoord,w3_ycoord,'x',c='r')
# ax1.plot(w4_xcoord,w4_ycoord,'x',c='r')
# ax1.plot(w5_xcoord,w5_ycoord,'x',c='r')
# ax1.plot(w6_xcoord,w6_ycoord,'x',c='r')
# ax1.plot(w7_xcoord,w7_ycoord,'x',c='r')
# setting labels
ax1.set_xlabel('X-coordinate [m]')
ax1.set_ylabel('Y-coordinate [m]')
ax1.set_xlim(obsSpill_xcoord-50,obsSpill_xcoord+100)
ax1.set_ylim(obsSpill_ycoord-80,obsSpill_ycoord+60)
tday = Times[0]
titleText = "Plan view: Concentration at t = %i" % tday+' days'
ax1.set_title(titleText,loc='left')
#fig = plt.figure(figsize=(14,10))
ax2 = fig.add_subplot(2, 2, 2)
# flopy plot object
pmv = flopy.plot.PlotMapView(model=mf, layer=0)
# plot grid
lc = pmv.plot_grid() # grid
# plot concentration
cmap = plt.get_cmap('jet')
if units == 'g':
cmin = 0
cmax = 0.1
else:
cmin = 0
cmax = 20000
cs = pmv.plot_array(conc_dict['conc_%dd'%(Times[1])],
cmap=cmap,vmin=cmin,vmax=cmax) # concentration colourmap
cbar = plt.colorbar(cs,format='%.0e') # colour bar
if units == 'g':
cbar.ax.set_ylabel('C [$\mu$g g$^-$$^1$]')
else:
cbar.ax.set_ylabel('C [$\mu$g L$^-$$^1$]')
# plot the spill site location
ax2.plot(obsSpill_xcoord, obsSpill_ycoord,'o',c='r',label='Spill site',
markersize=mS)
#ax2.plot(w2_xcoord,w2_ycoord,'x',c='r')
# ax2.plot(w3_xcoord,w3_ycoord,'x',c='r')
# ax2.plot(w4_xcoord,w4_ycoord,'x',c='r')
# ax2.plot(w5_xcoord,w5_ycoord,'x',c='r')
# ax2.plot(w6_xcoord,w6_ycoord,'x',c='r')
# ax2.plot(w7_xcoord,w7_ycoord,'x',c='r')
# setting labels
ax2.set_xlabel('X-coordinate [m]')
ax2.set_ylabel('Y-coordinate [m]')
ax2.set_xlim(obsSpill_xcoord-50,obsSpill_xcoord+100)
ax2.set_ylim(obsSpill_ycoord-80,obsSpill_ycoord+60)
tday = Times[1]
titleText = "Plan view: Concentration at t = %i" % tday+' days'
ax2.set_title(titleText,loc='right')
#fig = plt.figure(figsize=(14,10))
ax3 = fig.add_subplot(2, 2, 3)
# flopy plot object
pmv = flopy.plot.PlotMapView(model=mf, layer=0)
# plot grid
lc = pmv.plot_grid() # grid
# plot concentration
cmap = plt.get_cmap('jet')
if units == 'g':
cmin = 0
cmax = 0.1
else:
cmin = 0
cmax = 20000
cs = pmv.plot_array(conc_dict['conc_%dd'%(Times[2])],
cmap=cmap,vmin=cmin,vmax=cmax) # concentration colourmap
cbar = plt.colorbar(cs,format='%.0e') # colour bar
if units == 'g':
cbar.ax.set_ylabel('C [$\mu$g g$^-$$^1$]')
else:
cbar.ax.set_ylabel('C [$\mu$g L$^-$$^1$]')
# plot the spill site location
ax3.plot(obsSpill_xcoord, obsSpill_ycoord,'o',c='r',label='Spill site',
markersize=mS)
#ax3.plot(w2_xcoord,w2_ycoord,'x',c='r')
# ax3.plot(w3_xcoord,w3_ycoord,'x',c='r')
# ax3.plot(w4_xcoord,w4_ycoord,'x',c='r')
# ax3.plot(w5_xcoord,w5_ycoord,'x',c='r')
# ax3.plot(w6_xcoord,w6_ycoord,'x',c='r')
# ax3.plot(w7_xcoord,w7_ycoord,'x',c='r')
# setting labels
ax3.set_xlabel('X-coordinate [m]')
ax3.set_ylabel('Y-coordinate [m]')
ax3.set_xlim(obsSpill_xcoord-50,obsSpill_xcoord+100)
ax3.set_ylim(obsSpill_ycoord-85,obsSpill_ycoord+60)
tday = Times[2]
titleText = "Plan view: Concentration at t = %i" % tday+' days'
ax3.set_title(titleText,loc='left')
#fig = plt.figure(figsize=(14,10))
ax4 = fig.add_subplot(2, 2, 4)
# flopy plot object
pmv = flopy.plot.PlotMapView(model=mf, layer=0)
# plot grid
lc = pmv.plot_grid() # grid
# plot concentration
cmap = plt.get_cmap('jet')
if units == 'g':
cmin = 0
cmax = 0.1
else:
cmin = 0
cmax = 20000
cs = pmv.plot_array(conc_dict['conc_%dd'%(Times[3])],
cmap=cmap,vmin=cmin,vmax=cmax) # concentration colourmap
cbar = plt.colorbar(cs,format='%.0e') # colour bar
if units == 'g':
cbar.ax.set_ylabel('C [$\mu$g g$^-$$^1$]')
else:
cbar.ax.set_ylabel('C [$\mu$g L$^-$$^1$]')
# plot the spill site location
ax4.plot(obsSpill_xcoord, obsSpill_ycoord,'o',c='r',label='Spill site',
markersize=mS)
#ax4.plot(w2_xcoord,w2_ycoord,'x',c='r')
# ax4.plot(w3_xcoord,w3_ycoord,'x',c='r')
# ax4.plot(w4_xcoord,w4_ycoord,'x',c='r')
# ax4.plot(w5_xcoord,w5_ycoord,'x',c='r')
# ax4.plot(w6_xcoord,w6_ycoord,'x',c='r')
# ax4.plot(w7_xcoord,w7_ycoord,'x',c='r')
# setting labels
ax4.set_xlabel('X-coordinate [m]')
ax4.set_ylabel('Y-coordinate [m]')
ax4.set_xlim(obsSpill_xcoord-50,obsSpill_xcoord+100)
ax4.set_ylim(obsSpill_ycoord-85,obsSpill_ycoord+60)
tday = Times[3]
titleText = "Plan view: Concentration at t = %i" % tday+' days'
ax4.set_title(titleText,loc='right')
plt.tight_layout()
return None
def Concentration_Cross_View(units):
fig = plt.figure(figsize=(14,10))
ax1 = fig.add_subplot(2, 2, 1)
hds = bf.HeadFile(modelname + '.hds')
times = hds.get_times()
head = hds.get_data(totim=times[-1])
modelxsect = flopy.plot.PlotCrossSection(model=mf, line={'Row': obsSpill_row})
cmap = plt.get_cmap('jet')
if units == 'g':
cmin = 0
cmax = 0.1
else:
cmin = 0
cmax = 50
hvc = modelxsect.plot_array(np.array(conc_dict['conc_%dd'%(Times[0])]),
cmap=cmap,vmin=cmin,vmax=cmax,head=head)
cbar = plt.colorbar(hvc) # colour bar
if units == 'g':
cbar.ax.set_ylabel('C [$\mu$g g$^-$$^1$]')
else:
cbar.ax.set_ylabel('C [$\mu$g L$^-$$^1$]')
ax1.grid()
#ax3.set_xlim(-10,375)
ax1.set_ylim(-8.8,3.2)
ax1.set_xlabel('X-coordinate [m]')
ax1.set_ylabel('Elevation [m]')
tday = Times[0]
titleText = "Vertical section: Concentration at t = %i" % tday+' days'
ax1.set_title(titleText,loc='left')
ax2 = fig.add_subplot(2, 2, 2)
hds = bf.HeadFile(modelname + '.hds')
times = hds.get_times()
head = hds.get_data(totim=times[-1])
modelxsect = flopy.plot.PlotCrossSection(model=mf, line={'Row': obsSpill_row})
cmap = plt.get_cmap('jet')
hvc = modelxsect.plot_array(np.array(conc_dict['conc_%dd'%(Times[1])]),
cmap=cmap,vmin=cmin,vmax=cmax,head=head)
cbar = plt.colorbar(hvc) # colour bar
if units == 'g':
cbar.ax.set_ylabel('C [$\mu$g g$^-$$^1$]')
else:
cbar.ax.set_ylabel('C [$\mu$g L$^-$$^1$]')
ax2.grid()
#ax4.set_xlim(-10,375)
ax2.set_ylim(-8.8,3.2)
ax2.set_xlabel('X-coordinate [m]')
ax2.set_ylabel('Elevation [m]')
tday = Times[1]
titleText = "Vertical section: Concentration at t = %i" % tday+' days'
ax2.set_title(titleText,loc='right')
ax3 = fig.add_subplot(2, 2, 3)
hds = bf.HeadFile(modelname + '.hds')
times = hds.get_times()
head = hds.get_data(totim=times[-1])
modelxsect = flopy.plot.PlotCrossSection(model=mf, line={'Row': obsSpill_row})
cmap = plt.get_cmap('jet')
hvc = modelxsect.plot_array(np.array(conc_dict['conc_%dd'%(Times[2])]),
cmap=cmap,vmin=cmin,vmax=cmax,head=head)
cbar = plt.colorbar(hvc) # colour bar
if units == 'g':
cbar.ax.set_ylabel('C [$\mu$g g$^-$$^1$]')
else:
cbar.ax.set_ylabel('C [$\mu$g L$^-$$^1$]')
ax3.grid()
#ax4.set_xlim(-10,375)
ax3.set_ylim(-8.8,3.2)
ax3.set_xlabel('X-coordinate [m]')
ax3.set_ylabel('Elevation [m]')
tday = Times[2]
titleText = "Vertical section: Concentration at t = %i" % tday+' days'
ax3.set_title(titleText,loc='left')
ax4 = fig.add_subplot(2, 2, 4)
hds = bf.HeadFile(modelname + '.hds')
times = hds.get_times()
head = hds.get_data(totim=times[-1])
modelxsect = flopy.plot.PlotCrossSection(model=mf, line={'Row': obsSpill_row})
cmap = plt.get_cmap('jet')
hvc = modelxsect.plot_array(np.array(conc_dict['conc_%dd'%(Times[3])]),
cmap=cmap,vmin=cmin,vmax=cmax,head=head)
cbar = plt.colorbar(hvc) # colour bar
if units == 'g':
cbar.ax.set_ylabel('C [$\mu$g g$^-$$^1$]')
else:
cbar.ax.set_ylabel('C [$\mu$g L$^-$$^1$]')
ax4.grid()
#ax4.set_xlim(-10,375)
ax4.set_ylim(-8.8,3.2)
ax4.set_xlabel('X-coordinate [m]')
ax4.set_ylabel('Elevation [m]')
tday = Times[3]
titleText = "Vertical section: Concentration at t = %i" % tday+' days'
ax4.set_title(titleText,loc='right')
plt.tight_layout()
return None
def Plot_Map():
# Plan view
fig = plt.figure(figsize=(10,12))
ax = fig.add_subplot(1, 1, 1)
hds = bf.HeadFile(modelname+'.hds')
times = hds.get_times()
head = hds.get_data(totim=times[-1])
levels = np.linspace(-1, 1, 10)
#levels = np.linspace(-1, 3, 16)
cbb = bf.CellBudgetFile(modelname+'.cbc') # read budget file
kstpkper_list = cbb.get_kstpkper()
# cbb.textlist to get a list of data texts
frf = cbb.get_data(text='FLOW RIGHT FACE', totim=times[-1])[0]
fff = cbb.get_data(text='FLOW FRONT FACE', totim=times[-1])[0]
# flopy plot object
pmv = flopy.plot.PlotMapView(model=mf, layer=0)
# plot grid
lc = pmv.plot_grid() # grid
# plot contour
cs = pmv.contour_array(head, levels=levels) # head contour
plt.clabel(cs, fontsize=fS, fmt='%1.3f') # contour label
# plot discharge quiver
quiver = pmv.plot_discharge(frf, fff, head=head)
# plot ibound
qm = pmv.plot_ibound()
#plot well locations
plt.plot(obsSpill_xcoord,obsSpill_ycoord,'o',markersize=mS,label='WEL')
## plot high rechare zone
#r3_pt = ((r3_col+0.5)*delr, Ly - ((r3_row + 0.5)#*delc))
#plt.plot(r3_xcoord,r3_ycoord,'cs',markersize=mS,#label='High recharge')
# Specifying and plotting observation points
plt.plot(obs2_xcoord,obs2_ycoord,'kx',markersize=mS,marker='v',label='Obs2')
plt.plot(obs1_xcoord,obs1_ycoord,'cs',markersize=mS,marker='x',label='Obs1')
plt.plot(obs3_xcoord,obs3_ycoord,'cs',markersize=mS,marker='*',label='Obs3')
#plt.plot(obs2_xcoord,obs2_ycoord,'kx',markersize=mS,label='Obs')
# setting labels
ax.set_xlabel('X-coordinate [m]')
ax.set_ylabel('Y-coordinate [m]')
ax.set_title('Plan view - Flow field',loc='left')
ax.legend(loc='upper left')
plt.show()
return None
def Time_Series_Plot():
fig = plt.figure(figsize=(50,10))
ax1 = fig.add_subplot(3,1,1)
hds = bf.HeadFile(modelname + '.hds')
times = hds.get_times()
head = hds.get_data(totim=times[-1])
head_all = hds.get_alldata()
lyr = 0 # Defines layer to use when plotting
# h_obs1 = head_all[:,lyr,obs1_row,obs1_col]
# h_obs3 = head_all[:,lyr,obs3_row,obs3_col]
# h_obs2 = head_all[:,lyr,obs2_row,obs2_col]
# h_obs4 = head_all[:,lyr,obs4_row,obs4_col]
h_Spill = head_all[:,lyr,obsSpill_row,obsSpill_col]
# ax1.plot(times,h_obs1,'-',c='c',label='Obs 1',
# markersize=mS, linewidth=lW)
# ax1.plot(times,h_obs2,'-',c='y',label='Obs 2',
# markersize=mS, linewidth=lW)
# ax1.plot(times,h_obs3,'-',c='r',label='Obs 3',
# markersize=mS, linewidth=lW)
ax1.plot(times,h_Spill,'-',c='b',label='Spill site',
markersize=mS, linewidth=lW)
# ax1.plot(times,h_obs4,'-',c='k',label='Obs 4',
# markersize=mS, linewidth=lW)
ax1.grid()
#ax1.set_xlim(0,nper)
#ax1.set_ylim(0,0.06)
#ax1.set_ylim(0.00001,1000)
#ax1.set_yscale('log')
ax1.set_xlabel('Elapsed time [days]')
ax1.set_ylabel('Hydraulic head [m]')
titleText = 'Hydraulic heads: Layer %i' % lyr
ax1.set_title(titleText,loc='left')
ax1.legend(loc='upper right')
ax2 = fig.add_subplot(3,1,2)
hds = bf.HeadFile(modelname + '.hds')
times = hds.get_times()
head = hds.get_data(totim=times[-1])
head_all = hds.get_alldata()
lyr = 1 # Defines layer to use when plotting
# h_obs1 = head_all[:,lyr,obs1_row,obs1_col]
# h_obs2 = head_all[:,lyr,obs2_row,obs2_col]
# h_obs3 = head_all[:,lyr,obs3_row,obs3_col]
#h_Spill = head_all[:,lyr,obsSpill_row,obsSpill_col]
h_Spill = head_all[:,lyr,obsSpill_row,obsSpill_col]
#h_obs4 = head_all[:,lyr,obs4_row,obs4_col]
# ax2.plot(times,h_obs1,'-',c='c',label='Obs 1',
# markersize=mS, linewidth=lW)
# ax2.plot(times,h_obs2,'-',c='y',label='Obs 2',
# markersize=mS, linewidth=lW)
# ax2.plot(times,h_obs3,'-',c='r',label='Obs 3',
# markersize=mS, linewidth=lW)
ax2.plot(times,h_Spill,'-',c='b',label='Spill site',
markersize=mS, linewidth=lW)
# ax2.plot(times,h_obs4,'-',c='k',label='Obs 4',
# markersize=mS, linewidth=lW)
ax2.grid()
#TODO: change
#ax2.set_xlim(0,nper)
#ax2.set_ylim(0,0.06)
#ax2.set_ylim(0.00001,1000)
#ax2.set_yscale('log')
ax2.set_xlabel('Elapsed time [days]')
ax2.set_ylabel('Hydraulic head [m]')
titleText = 'Hydraulic heads: Layer %i' % lyr
ax2.set_title(titleText,loc='left')
ax2.legend(loc='upper right')
ax3 = fig.add_subplot(3,1,3)
hds = bf.HeadFile(modelname + '.hds')
times = hds.get_times()
head = hds.get_data(totim=times[-1])
head_all = hds.get_alldata()
lyr = 2 # Defines layer to use when plotting
# h_obs1 = head_all[:,lyr,obs1_row,obs1_col]
# h_obs2 = head_all[:,lyr,obs2_row,obs2_col]
# h_obs3 = head_all[:,lyr,obs3_row,obs3_col]
#h_Spill = head_all[:,lyr,obsSpill_row,obsSpill_col]
h_Spill = head_all[:,lyr,obsSpill_row,obsSpill_col]
#h_obs4 = head_all[:,lyr,obs4_row,obs4_col]
# ax3.plot(times,h_obs1,'-',c='c',label='Obs 1',
# markersize=mS, linewidth=lW)
# ax3.plot(times,h_obs2,'-',c='y',label='Obs 2',
# markersize=mS, linewidth=lW)
# ax3.plot(times,h_obs3,'-',c='r',label='Obs 3',
# markersize=mS, linewidth=lW)
ax3.plot(times,h_Spill,'-',c='b',label='Spill site',
markersize=mS, linewidth=lW)
# ax3.plot(times,h_obs4,'-',c='k',label='Obs 4',
# markersize=mS, linewidth=lW)
ax3.grid()
#ax3.set_xlim(0,nper)
#ax3.set_ylim(0,0.06)
#ax3.set_ylim(0.00001,1000)
#ax3.set_yscale('log')
ax3.set_xlabel('Elapsed time [days]')
ax3.set_ylabel('Hydraulic head [m]')
titleText = 'Hydraulic heads: Layer %i' % lyr
ax3.set_title(titleText,loc='left')
ax3.legend(loc='upper right')
# preventing overlap
plt.tight_layout()
return None
# The file path
Merged = '/Users/yuchenli/Documents/UQ/CIVL4140/pymake-master/examples/MT3DMS_model/Test_flopy/resoluted.tif'
SpillSite = '/Users/yuchenli/Documents/UQ/CIVL4140/pymake-master/examples/MT3DMS_model/Test_flopy/resolutedspillsite.tif'
MF2005_exeLocation = '/Users/yuchenli/Documents/UQ/CIVL4140/pymake-master/examples/mf2005'
MT3DMS_exeLocation = '/Users/yuchenli/Documents/UQ/CIVL4140/pymake-master/examples/mt3dms'
modelname = 'Simple'
mf = flopy.modflow.Modflow(
modelname,
exe_name=MF2005_exeLocation
)
# Get the data from tiff files
demDs = gdal.Open(Merged)
spillSite = gdal.Open(SpillSite)
geot = demDs.GetGeoTransform()
demData = demDs.GetRasterBand(1).ReadAsArray()
spillData = spillSite.GetRasterBand(1).ReadAsArray()
demNd = demDs.GetRasterBand(1).GetNoDataValue()
# Modle Domain
nlay = 3
nrow = demDs.RasterYSize
ncol = demDs.RasterXSize
ztop = np.zeros((nrow, ncol), dtype = np.float32)+3
zbotm = np.zeros((nlay, nrow, ncol), dtype = np.float32)
zbotm[0,:,:] = -1.5 # upper layer, sand
zbotm[1,:,:] = -1.5-0.3 # middle layer, clay
zbotm[2,:,:] = -7 # lower layer, silt and clay
delr = geot[1]
delc = geot[1]
itmuni = 4 # Days
lenuni = 2 # M
# # =============Get the ibound way 1 ===============
# ibound = np.zeros(demData.shape, dtype=np.int32)
# ibound[demData == 255] = -1 #constant head
# ibound[demData == 0] = 1 #active
## ==============Get the ibound way 2 ===============
#import pandas as pd
ibound=pd.read_csv('/Users/yuchenli/Documents/UQ/CIVL4140/pymake-master/examples/MT3DMS_model/Test_flopy/ibound.csv'
,header=None,sep=',').values
#np.savetxt("/Users/yuchen/Desktop/ibound.csv", ibound, delimiter=',')
# Get the constant head
# 2: drainage, 3: coast 4: link
# strt = np.zeros(demData.shape, dtype=np.int32)
# strt[demData == 255] = 0 # constant head = 0
strt = pd.read_csv('/Users/yuchenli/Documents/UQ/CIVL4140/pymake-master/examples/MT3DMS_model/Test_flopy/StrtMask.csv'
,header=None,sep=',').values
strt[strt == 2] = -0.5
strt[strt == 3] = 1.46
strt[strt == 4] = 0
# Simulation time, stress period
nper = 5 # Number of stress periods #385
# =============== rainfall data and number of days ================
RainfallAVG = pd.read_csv('/Users/yuchenli/Documents/UQ/CIVL4140/pymake-master/examples/MT3DMS_model/Test_flopy/RainfallAVG.csv')
Mdata = RainfallAVG['Date'].values
#Mdata = Mdata.apply(lambda x:x[:2]).tolist()
#Mdata = pd.Series(Mdata, dtype='int').to_numpy()
perlen = Mdata[:nper]
nstp = Mdata[:nper]
periodType = RainfallAVG['Type'].values[:nper]
periodType[0] = True
# periodType = [False]*nper
# Creat the discretization object
dis = flopy.modflow.ModflowDis(
mf, nlay=nlay, nrow=nrow, ncol=ncol, nper=nper,
perlen=perlen, nstp=nstp, steady=periodType,
delr=delr, delc=delc, top=ztop, botm=zbotm,
itmuni=itmuni, lenuni=lenuni
)
# Create BAS object
bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)
# Hydraulic conducticity of each layer
K_horiz = np.zeros((nlay, nrow, ncol), dtype=np.float32)
K_vert = np.zeros((nlay,nrow,ncol), dtype=np.float32)
K_horiz[0,:,:] = 0.01*29.7*24
K_horiz[1,:,:] = 0.01*0.2*24
K_horiz[2,:,:] = 0.01*0.02*24
K_vert[0,:,:] = 0.01*29.7*24
K_vert[1,:,:] = 0.01*0.2*24
K_vert[2,:,:] = 0.01*0.02*24
sy = np.zeros((nlay,nrow,ncol),dtype=np.float32)+0.1
ss = np.zeros((nlay,nrow,ncol),dtype=np.float32)+1e-4
scoefbool = False
laytyp = [1,1,1] # Sets layer type: 1=uncofnined; 0=confined
laywet = [1,1,1] # 0 = wetting inactive, not 0 = active wetting
layvka = [0, 0, 0] # 0 = Kv values, >0 or <0 = ratio Kh to Kv
# Create LPF object
lpf = flopy.modflow.ModflowLpf(mf, hk=K_horiz, vka=K_vert,
laytyp=laytyp, layvka=layvka, laywet=laywet,
sy=sy, ss=ss, ipakcb=53)
nrchop=3
rain_Data = RainfallAVG['Rain'] #rainfall for each month
rchF = 0.12 # Recharge factor - % rainfall that becomes recharge
n = nper
recharge = [[] for _ in range(n)]
for i in range (nper):
recharge[i] = np.ones((nrow,ncol),dtype=np.float32)*rchF*(
rain_Data[i]/1000)# /Mdata[i]
rech_StressPeriod_dat = {}
for i in range(nper):
rech_StressPeriod_dat[i] = [recharge[i]]
# Create recharge object
rch = flopy.modflow.ModflowRch(mf, nrchop=nrchop, ipakcb=None,
rech=rech_StressPeriod_dat, irch=0,
extension='rch', unitnumber=None,
filenames=None)
# Well stress period
cord = ibound.shape
obsSpill_xcoord = 144
obsSpill_ycoord = 264 # botm->top
obsSpill_col = int(np.round(obsSpill_xcoord/delc))
obsSpill_row = int(np.round((cord[0]*delr-obsSpill_ycoord)/delr)) # top->botm
w_pumping_rate = 0.00275/30 #m^3/day
w_sp = [0, obsSpill_row, obsSpill_col, w_pumping_rate] # lay, row, col index, pumping rate
# w2_pumping_rate = -10
# w2_xcoord = 175
# w2_ycoord = 250
# w2_row = int(np.round((cord[0]*delr-w2_ycoord)/delr))
# w2_col = int(np.round(w2_xcoord/delc))
# w2_sp = [0,w2_row,w2_col,w2_pumping_rate]
# w3_pumping_rate = -3
# w3_xcoord = 180
# w3_ycoord = 260
# w3_row = int(np.round((cord[0]*delr-w3_ycoord)/delr))
# w3_col = int(np.round(w3_xcoord/delc))
# w3_sp = [0,w3_row,w3_col,w3_pumping_rate]
# w4_pumping_rate = -3
# w4_xcoord = 170
# w4_ycoord = 237.5
# w4_row = int(np.round((cord[0]*delr-w4_ycoord)/delr))
# w4_col = int(np.round(w4_xcoord/delc))
# w4_sp = [0,w4_row,w4_col,w4_pumping_rate]
# w5_pumping_rate = -3
# w5_xcoord = 125
# w5_ycoord = 275
# w5_row = int(np.round((cord[0]*delr-w5_ycoord)/delr))
# w5_col = int(np.round(w5_xcoord/delc))
# w5_sp = [0,w5_row,w5_col,w5_pumping_rate]
# w6_pumping_rate = -3
# w6_xcoord = 140
# w6_ycoord = 280
# w6_row = int(np.round((cord[0]*delr-w5_ycoord)/delr))
# w6_col = int(np.round(w5_xcoord/delc))
# w6_sp = [0,w6_row,w6_col,w6_pumping_rate]
# w7_pumping_rate = -3
# w7_xcoord = 125
# w7_ycoord = 260
# w7_row = int(np.round((cord[0]*delr-w5_ycoord)/delr))
# w7_col = int(np.round(w5_xcoord/delc))
# w7_sp = [0,w7_row,w7_col,w7_pumping_rate]
# stress_period_data = {0: [w_sp, w2_sp,
# w3_sp, w4_sp, w5_sp, w6_sp, w7_sp]} # define well stress period {period, well info dictionary}
stress_period_data = {0: [w_sp]} # define well stress period {period, well info dictionary}
# stress_period_data = {0: [w_sp,w2_sp]}
# Well package
wel = flopy.modflow.ModflowWel(mf, stress_period_data=stress_period_data)
# OC package
sp_data = {}
for kper in range(nper):
for kstp in range(nstp[kper]):
sp_data[(kper, kstp)] = ['save head','save drawdown','save budget',
'print head','print budget']
# Create Output Control (OC) package
oc = flopy.modflow.ModflowOc(mf, stress_period_data=sp_data, compact=True)
# Solver
pcg = flopy.modflow.mfpcg.ModflowPcg(mf, mxiter=1000, iter1=500, npcond=1,
hclose=1e-05, rclose=1e-05, relax=1.0,
nbpol=0, iprpcg=0, mutpcg=3, damp=1.0,
dampt=1.0, ihcofadd=0, extension='pcg',
unitnumber=None, filenames=None)
# Link to the MT3DMS LMT package
lmt = flopy.modflow.ModflowLmt(mf, output_file_name='mt3d_link.ftl')
# Check model for basic errors
chk = mf.check(verbose=True,level=1)
# Write the MODFLOW model input files
mf.write_input()
# Run the MODFLOW model
success, buff = mf.run_model(report=True)
if not success:
raise Exception('MODFLOW did not terminate normally.')
# Creat MT3DMS object
mt = flopy.mt3d.Mt3dms(modflowmodel=mf,
modelname=modelname,
exe_name=MT3DMS_exeLocation,
ftlfilename='mt3d_link.ftl')
prsity=0.39
# Boundary types: 0=inactive, <0=constant conc, >0=active cell | same as ibound
#icbund_array = np.ones((nlay, nrow, ncol), dtype=np.float32)
# icbund_array = np.zeros(demData.shape, dtype=np.int32)
# icbund_array[demData == 255] = -1 #constant head
# icbund_array[demData == 0] = 1 #active
icbund_array = ibound
# Starting concentration
sconc_array = np.zeros((nlay, nrow, ncol), dtype=np.float32)
# Specifying initial concentration at spill location
sconc_array[0, obsSpill_row, obsSpill_col] = 1056.2 #initial C upper layer
# Set up BTN package
nper=nper #Number of stress periods
perlen=perlen #length of stress period
nstp=nstp #Number of timesteps in each stress period
tsmult=1.0 # Time step multiplier
dt0=0 #Transport step size
ttsmax=0 #maximum transport step size
nprs=-1 #options: >0 save at "timprs", 0=only end step saved, <0 save at transport step
btn = flopy.mt3d.Mt3dBtn(mt, prsity=0.3, icbund=icbund_array,
sconc=sconc_array, ncomp=1, perlen=perlen, nper=nper,
nstp=nstp, tsmult=tsmult, nprs=nprs,
nprobs = 10, cinact = -1, chkmas=True)
# advection package
adv = flopy.mt3d.Mt3dAdv(mt, mixelm=-1, percel=0.75)
alpha = 10 # Longitudinal dispersivity [l] (alpha)
ratio_ht = 0.1 # Ratio of horizontal to transverse dipsersivity
ratio_hv = 0.1 # Ratio of horizontal to vertical dipsersivity
DmCoeff = 2.5e-5 # Molecular diffusion coefficient [L2/T]
dsp = flopy.mt3d.Mt3dDsp(mt, al=alpha, trpt=ratio_ht, trpv=ratio_ht,
dmcoef=DmCoeff)
# source/sink package
ssm_data = {}
itype = flopy.mt3d.Mt3dSsm.itype_dict()
# Format is [layer, row column, concentration, input type 'WEL' = well package]
C_in = 100
ssm_data[0] = [(0, obsSpill_row, obsSpill_col, C_in, 1)]
ssm = flopy.mt3d.Mt3dSsm(mt, stress_period_data=ssm_data)
# ===== Matrix solver package =============================================
gcg = flopy.mt3d.Mt3dGcg(mt, cclose=1e-6)
# ===== Write MT3DMS input ================================================
mt.write_input()
# ===== Run MT3DMS ========================================================
mt.run_model()
# 4.1 ===== Setting plot formatting (global settings - applies to all plots) ==
mS = 12 # Used to set marker size
lW = 3 # Used to set linewidth
fS = 18 # Used to set font size
plt.rcParams['font.family'] = 'Times New Roman' # Globally sets the font type
plt.rc('font',size=fS)
plt.rc('axes',titlesize=fS)
plt.rc('axes',labelsize=fS)
plt.rc('xtick',labelsize=fS)
plt.rc('ytick',labelsize=fS)
plt.rc('legend',fontsize=fS)
plt.rc('figure',titlesize=fS)
# Specifying and plotting observation points
obs1_xcoord = 150
obs1_ycoord = 250
obs1_col = int(np.round(obs1_xcoord/delc))
obs1_row = int(np.round((cord[0]*5-obs1_ycoord)/delr))
obs2_xcoord = 160
obs2_ycoord = 240
obs2_col = int(np.round(obs2_xcoord/delc))
obs2_row = int(np.round((cord[0]*5-obs2_ycoord)/delr))
obs3_xcoord = 180
obs3_ycoord = 220
obs3_col = int(np.round(obs3_xcoord/delc))
obs3_row = int(np.round((cord[0]*5-obs3_ycoord)/delr))
# obs4_xcoord = 125
# obs4_ycoord = 130
# obs4_col = int(np.round(obs4_xcoord/delc))
# obs4_row = int(np.round((cord[0]*5-obs4_ycoord)/delr))
units = 'L'
Times = [30, 80, 100, sum(perlen)]
conc_dict = Get_Conc(Times, units)
Plot_Map()
#Time_Series_Plot()
Concentration_Plan_View(conc_dict, units, Times)
#Concentration_Cross_View(units)
#Plot_Conc_Break_Down()
# a = conc_dict['conc_%dd'%10195][0]
# np.savetxt("conc_1_L_onewel_2.csv", a, delimiter=',')
# b = conc_dict['conc_%dd'%(10196)][0]
# np.savetxt('conc_1_L_2015NOV_onewel.csv',b, delimiter=',')
# cF = 10**6
# ucnobj = bf.UcnFile('MT3D001.UCN')
# c = ucnobj.get_data(totim=8432)[0]
# c = [cF*x for x in c]
# np.savetxt('conc_day_8432.csv', c, delimiter=',')
# cF = 10**6
# ucnobj = bf.UcnFile('MT3D001.UCN')
# a = ucnobj.get_data(totim=7000)[0]
# a = [cF*x for x in a]
# np.savetxt('conc_day_7000.csv', a, delimiter=',')