forked from dladd/CardiacCalcium_FiniteElement
/
CardiacEcc.py
executable file
·625 lines (543 loc) · 24.3 KB
/
CardiacEcc.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
#!/usr/bin/env python
'''
Author: David Ladd
Brief: Main program file to simulate calcium release from RyR clusters using OpenCMISS
Copyright 2019 David Ladd, University of Melbourne
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
'''
import numpy as np
import pandas as pd
from scipy.io import loadmat
import gc
import time
import requests
import shutil
import os
from opencmiss.iron import iron
from mpi4py import MPI
# C l a s s e s a n d F u n c t i o n s
# ----------------------------------------------------
class numberIncrementor:
"""Simple incrementor for unique integer user numbers"""
def __init__(self):
self.__value = 0
def getInc(self):
self.__value += 1
return self.__value
def download_file(local_file, targetDir):
"""Download the local_file from the URL"""
resourceLinks = {
"Combined_8Sarc_1319kNodes_node.h5" : "https://melbourne.figshare.com/ndownloader/files/15045695",
"Combined_8Sarc_1319kNodes_elem.h5" : "https://melbourne.figshare.com/ndownloader/files/15045677",
"Combined_8Sarc_1436kNodes_elem.h5" : "https://melbourne.figshare.com/ndownloader/files/15045683",
"Combined_8Sarc_1436kNodes_node.h5" : "https://melbourne.figshare.com/ndownloader/files/15045701",
"Cyto_8Sarc_1319kNodes_elem.h5" : "https://melbourne.figshare.com/ndownloader/files/15045707",
"Cyto_8Sarc_1319kNodes_node.h5" : "https://melbourne.figshare.com/ndownloader/files/15045710",
"Cyto_8Sarc_1436kNodes_elem" : "https://melbourne.figshare.com/ndownloader/files/15045713",
"Cyto_8Sarc_1436kNodes_node.h5" : "https://melbourne.figshare.com/ndownloader/files/15045716",
"Cyto_8Sarc_1319kNodes_spherical_ryr_kie_wh0.05.FixedNnd_offset05_N50_1umSpacing_tausimnum_1.mat" : "https://melbourne.figshare.com/ndownloader/files/15045719",
"Cyto_8Sarc_1436kNodes_spherical_ryr_kie_wh0.05.FixedNnd_offset05_N123_tausimnum_1.mat" : "https://melbourne.figshare.com/ndownloader/files/15045722"
}
url = resourceLinks[local_file]
r = requests.get(url, stream=True)
with open(targetDir + local_file, 'wb') as f:
shutil.copyfileobj(r.raw, f)
"""
======================================================
C O N T R O L P A N E L
======================================================
"""
# Solve time (ms)
startTime = 0.0
endTime = 30.00001
pdeTimestep = 0.1
odeTimestep = 0.0001
outputFrequency = 10
# Input and output directories
inputDir = './input/'
outputDir = './output/'
# Specify model type
lowRyrDensity = True
mitochondria = False
# The CellML model file to use to describe the calcium source terms
cellmlFile = inputDir + 'ryrNtroponinNfluo3_wryrscaling_wtimelag_wtimecourse.xml'
iCa = 2.0e-15
# Initial conditions
initCa = 0.1
initF = 22.92
initFCa = 2.08
initCaM = 23.529
initCaMCa = 0.471
initATP = 454.682
initATPCa = 0.318
initCaTnC = 10.0
# Diffusion parameters
diffCa = [0.22, 0.22, 0.22]
diffF = [0.042, 0.042, 0.042]
diffFCa = [0.042, 0.042, 0.042]
diffCaM = [0.025, 0.025, 0.025]
diffCaMCa = [0.025, 0.025, 0.025]
diffATP = [0.14, 0.14, 0.14]
diffATPCa = [0.14, 0.14, 0.14]
"""
======================================================
"""
# Get the computational node information
numberOfComputationalNodes = iron.ComputationalNumberOfNodesGet()
computationalNodeNumber = iron.ComputationalNodeNumberGet()
userNumber = numberIncrementor()
comm = MPI.COMM_WORLD
# G e t m e s h r e s o u r c e s
# -----------------------------------
if mitochondria:
meshName = 'Cyto_'
else:
meshName = 'Combined_'
if lowRyrDensity:
meshName = meshName + '8Sarc_1319kNodes_'
ryrName = 'Cyto_8Sarc_1319kNodes_spherical_ryr_kie_wh0.05.FixedNnd_offset05_N50_1umSpacing_tausimnum_1.mat'
else:
meshName = meshName + '8Sarc_1436kNodes_'
ryrName = 'Cyto_8Sarc_1436kNodes_spherical_ryr_kie_wh0.05.FixedNnd_offset05_N123_tausimnum_1.mat'
# Download node file if it doesn't already exist
fileName = meshName + 'node.h5'
nodeFile = inputDir + fileName
if computationalNodeNumber == 0:
print('Checking for node file...')
if not os.path.exists(nodeFile):
print('Downloading node file to input directory...')
download_file(fileName, inputDir)
# Download elem file if it doesn't already exist
fileName = meshName + 'elem.h5'
elemFile = inputDir + fileName
if computationalNodeNumber == 0:
print('Checking for element file...')
if not os.path.exists(elemFile):
print('Downloading element file to input directory...')
download_file(fileName, inputDir)
# Download ryr file if it doesn't already exist
ryrFile = inputDir + ryrName
if computationalNodeNumber == 0:
print('Checking for RyR file...')
if not os.path.exists(ryrFile):
print('Downloading RyR file to input directory...')
download_file(ryrName, inputDir)
# O u t p u t d i r e c t o r y
# -------------------------------
if computationalNodeNumber == 0:
try:
os.makedirs(outputDir)
except OSError as e:
if e.errno != 17:
raise
# Let rank 0 catch up if it has been busy downloading
comm.Barrier()
# P r o b l e m S e t u p
# ----------------------------------------------------
if computationalNodeNumber == 0:
print('Setting up problem...')
# Set up 3D RC coordinate system
coordinateSystem = iron.CoordinateSystem()
coordinateSystem.CreateStart(userNumber.getInc())
coordinateSystem.dimension = 3
coordinateSystem.CreateFinish()
# Create world region
region = iron.Region()
region.CreateStart(userNumber.getInc(), iron.WorldRegion)
region.label = "Region"
region.coordinateSystem = coordinateSystem
region.CreateFinish()
# Create basis
basis = iron.Basis()
basis.CreateStart(userNumber.getInc())
basis.numberOfXi = 3
basis.type = iron.BasisTypes.SIMPLEX
basis.interpolationXi = [iron.BasisInterpolationSpecifications.LINEAR_SIMPLEX]*3
basis.CreateFinish()
# M e s h S e t u p
# ----------------------------------------------------
# Open and close the node store to get the number of nodes
if computationalNodeNumber == 0:
print('Setting up mesh...')
store = pd.HDFStore(nodeFile, 'r')
df = store['Node_Coordinates']
numberOfNodes = df.shape[0]
store.close()
nodes = iron.Nodes()
nodes.CreateStart(region, numberOfNodes)
nodes.CreateFinish()
# Open the elem store
store = pd.HDFStore(elemFile, 'r')
df = store['Element_Node_Map']
numberOfElements = df.shape[0]
mesh = iron.Mesh()
mesh.CreateStart(userNumber.getInc(), region, 3)
mesh.NumberOfElementsSet(numberOfElements)
mesh.NumberOfComponentsSet(1)
# Load in element dataframe
meshElements = iron.MeshElements()
meshElements.CreateStart(mesh, 1, basis)
elementNumber = 0
start = time.time()
for elementNodes in df.itertuples(index=False, name=None):
elementNumber += 1
meshElements.NodesSet(elementNumber, elementNodes[:4])
end = time.time()
if computationalNodeNumber == 0:
print('Number of Nodes: ' + str(numberOfNodes))
print('Number of Elements: ' + str(numberOfElements))
print('Element read time: ' + str(end - start))
print('Finalising mesh...')
meshElements.CreateFinish()
mesh.CreateFinish()
# Destroy element dataframe and collect garbage to free up memory
store.close()
gc.collect()
# Decompose mesh accross computational nodes
if computationalNodeNumber == 0:
print('Decomposing mesh...')
decomposition = iron.Decomposition()
decomposition.CreateStart(userNumber.getInc(), mesh)
decomposition.type = iron.DecompositionTypes.CALCULATED
decomposition.NumberOfDomainsSet(numberOfComputationalNodes)
decomposition.CalculateFacesSet(False)
decomposition.CreateFinish()
# G e o m e t r i c F i e l d
# ----------------------------------------------------
if computationalNodeNumber == 0:
print('Setting up geometric field...')
geometricField = iron.Field()
geometricField.CreateStart(userNumber.getInc(), region)
geometricField.MeshDecompositionSet(decomposition)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 2, 1)
geometricField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 3, 1)
geometricField.VariableLabelSet(iron.FieldVariableTypes.U, "Geometry")
geometricField.CreateFinish()
# Load in node df
store = pd.HDFStore(nodeFile, 'r')
df = store['Node_Coordinates']
start = time.time()
for node in range(numberOfNodes):
nodeDomain = decomposition.NodeDomainGet(node+1, 1)
if nodeDomain == computationalNodeNumber:
for component in range(3):
geometricField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1, node+1, component+1, df.iat[node, component])
end = time.time()
if computationalNodeNumber == 0:
print('Node read time: ' + str(end - start))
print('Updating nodal fields')
geometricField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
geometricField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
# destroy node df and garbage collect
store.close()
del df
gc.collect()
df = pd.DataFrame()
# E q u a t i o n s S e t s
# ----------------------------------------------------
if computationalNodeNumber == 0:
print('Setting up equations sets...')
equationsSetSpecification = [iron.EquationsSetClasses.CLASSICAL_FIELD,
iron.EquationsSetTypes.REACTION_DIFFUSION_EQUATION,
iron.EquationsSetSubtypes.CELLML_REAC_SPLIT_REAC_DIFF]
equationLabels = ['Ca', 'F', 'FCa', 'CaM', 'CaMCa', 'ATP', 'ATPCa']
dependentInit = [initCa, initF, initFCa, initCaM, initCaMCa, initATP, initATPCa]
materialsDiff = [diffCa, diffF, diffFCa, diffCaM, diffCaMCa, diffATP, diffATPCa]
equationsSets = []
dependentFields = []
materialsFields = []
sourceFields = []
# M a i n b u f f e r i n g e q u a t i o n s
# -------------------------------------------------
i = 0
for label in equationLabels:
if computationalNodeNumber == 0:
print('...' + label)
# Equations set
equationsSets.append(iron.EquationsSet())
equationsSetField = iron.Field()
equationsSets[i].CreateStart(userNumber.getInc(), region, geometricField, equationsSetSpecification,
userNumber.getInc(), equationsSetField)
equationsSets[i].CreateFinish()
# Dependent
dependentFields.append(iron.Field())
equationsSets[i].DependentCreateStart(userNumber.getInc(), dependentFields[i])
dependentFields[i].LabelSet(label)
equationsSets[i].DependentCreateFinish()
dependentFields[i].ComponentValuesInitialiseDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1,
dependentInit[i])
# Materials
materialsFields.append(iron.Field())
equationsSets[i].MaterialsCreateStart(userNumber.getInc(), materialsFields[i])
materialsFields[i].LabelSet(label + '_Materials')
equationsSets[i].MaterialsCreateFinish()
for c in range(3):
materialsFields[i].ComponentValuesInitialiseDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES,
c+1, materialsDiff[i][c])
materialsFields[i].ComponentValuesInitialiseDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 4, 1.0)
# Source
sourceFields.append(iron.Field())
equationsSets[i].SourceCreateStart(userNumber.getInc(), sourceFields[i])
sourceFields[i].VariableLabelSet(iron.FieldVariableTypes.U, 'i' + label)
equationsSets[i].SourceCreateFinish()
if label == 'Ca':
sourceFields[i].ComponentValuesInitialiseDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, iCa)
else:
sourceFields[i].ComponentValuesInitialiseDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, 0.0)
i += 1
# T r o p o n i n C
# -------------------
CaTnCField = iron.Field()
CaTnCField.CreateStart(userNumber.getInc(), region)
CaTnCField.TypeSet(iron.FieldTypes.GENERAL)
CaTnCField.MeshDecompositionSet(decomposition)
CaTnCField.GeometricFieldSet(geometricField)
CaTnCField.NumberOfVariablesSet(1)
CaTnCField.VariableTypesSet([iron.FieldVariableTypes.U])
CaTnCField.DataTypeSet(iron.FieldVariableTypes.U, iron.FieldDataTypes.DP)
CaTnCField.DimensionSet(iron.FieldVariableTypes.U, iron.FieldDimensionTypes.SCALAR)
CaTnCField.NumberOfComponentsSet(iron.FieldVariableTypes.U, 1)
CaTnCField.LabelSet('CaTnC')
CaTnCField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
CaTnCField.ComponentInterpolationSet(iron.FieldVariableTypes.U, 1, iron.FieldInterpolationTypes.NODE_BASED)
CaTnCField.CreateFinish()
CaTnCField.ComponentValuesInitialiseDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, initCaTnC)
# R y R D e n s i t y a n d T i m e l a g
# -----------------------------------------------
RyRDensityField = iron.Field()
RyRDensityField.CreateStart(userNumber.getInc(), region)
RyRDensityField.TypeSet(iron.FieldTypes.GENERAL)
RyRDensityField.MeshDecompositionSet(decomposition)
RyRDensityField.GeometricFieldSet(geometricField)
RyRDensityField.NumberOfVariablesSet(1)
RyRDensityField.VariableTypesSet([iron.FieldVariableTypes.U])
RyRDensityField.DataTypeSet(iron.FieldVariableTypes.U, iron.FieldDataTypes.DP)
RyRDensityField.DimensionSet(iron.FieldVariableTypes.U, iron.FieldDimensionTypes.SCALAR)
RyRDensityField.NumberOfComponentsSet(iron.FieldVariableTypes.U, 1)
RyRDensityField.LabelSet('RyRDensity')
RyRDensityField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
RyRDensityField.ComponentInterpolationSet(iron.FieldVariableTypes.U, 1, iron.FieldInterpolationTypes.NODE_BASED)
RyRDensityField.CreateFinish()
RyRDensityField.ComponentValuesInitialiseDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, 0.0)
RyRTimelagField = iron.Field()
RyRTimelagField.CreateStart(userNumber.getInc(), region)
RyRTimelagField.TypeSet(iron.FieldTypes.GENERAL)
RyRTimelagField.MeshDecompositionSet(decomposition)
RyRTimelagField.GeometricFieldSet(geometricField)
RyRTimelagField.NumberOfVariablesSet(1)
RyRTimelagField.VariableTypesSet([iron.FieldVariableTypes.U])
RyRTimelagField.DataTypeSet(iron.FieldVariableTypes.U, iron.FieldDataTypes.DP)
RyRTimelagField.DimensionSet(iron.FieldVariableTypes.U, iron.FieldDimensionTypes.SCALAR)
RyRTimelagField.NumberOfComponentsSet(iron.FieldVariableTypes.U, 1)
RyRTimelagField.LabelSet('RyRTimelag')
RyRTimelagField.ComponentMeshComponentSet(iron.FieldVariableTypes.U, 1, 1)
RyRTimelagField.ComponentInterpolationSet(iron.FieldVariableTypes.U, 1, iron.FieldInterpolationTypes.NODE_BASED)
RyRTimelagField.CreateFinish()
RyRTimelagField.ComponentValuesInitialiseDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, 0.0)
ryrData = loadmat(ryrFile)
for ryrNodeIdx in range(len(ryrData['nonzeroNodes'])):
nodeNumber = np.asscalar(ryrData['nonzeroNodes'][ryrNodeIdx])
nodeDomain = decomposition.NodeDomainGet(nodeNumber, 1)
if nodeDomain == computationalNodeNumber:
RyRDensityField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, 1, nodeNumber, 1,
np.asscalar(ryrData['nonzeroIntensities'][ryrNodeIdx]))
RyRTimelagField.ParameterSetUpdateNodeDP(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES, 1, 1, nodeNumber, 1,
np.asscalar(ryrData['nonzeroTimelags'][ryrNodeIdx]))
RyRDensityField.ParameterSetUpdateStart(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
RyRDensityField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
RyRTimelagField.ParameterSetUpdateStart(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
RyRTimelagField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U, iron.FieldParameterSetTypes.VALUES)
del ryrData
gc.collect()
# C e l l M L
# -----------
if computationalNodeNumber == 0:
print('Setting up CellML model and variable mapping...')
cellmlModelIndex = 1
cellml = iron.CellML()
cellml.CreateStart(userNumber.getInc(), region)
cellml.ModelImport(cellmlFile)
known = ["CRU/iCa",
"CRU/ryrDensity",
"CRU/timelag"]
for var in known:
cellml.VariableSetAsKnown(cellmlModelIndex, var)
wanted = ["CRU/Jryr",
"FluoBuffer/Jfluo",
"TnCBuffer/Jtnc",
"ATPBuffer/JATP",
"CaMBuffer/JCaM"]
for var in wanted:
cellml.VariableSetAsWanted(cellmlModelIndex, var)
cellml.CreateFinish()
# Field mapping
cellml.FieldMapsCreateStart()
fieldToCellmlMaps = [(dependentFields[equationLabels.index('Ca')], "CRU/Ca_free"),
(sourceFields[equationLabels.index('Ca')], "CRU/iCa"),
(RyRDensityField, "CRU/ryrDensity"),
(RyRTimelagField, "CRU/timelag"),
(dependentFields[equationLabels.index('F')], "FluoBuffer/Fluo_free"),
(dependentFields[equationLabels.index('FCa')], "FluoBuffer/FluoCa"),
(CaTnCField, "TnCBuffer/CaTnC"),
(dependentFields[equationLabels.index('CaM')], "CaMBuffer/CaM_free"),
(dependentFields[equationLabels.index('CaMCa')], "CaMBuffer/CaMCa"),
(dependentFields[equationLabels.index('ATP')], "ATPBuffer/ATP_free"),
(dependentFields[equationLabels.index('ATPCa')], "ATPBuffer/ATPCa")]
for pair in fieldToCellmlMaps:
cellml.CreateFieldToCellMLMap(pair[0],
iron.FieldVariableTypes.U, 1,
iron.FieldParameterSetTypes.VALUES,
cellmlModelIndex,
pair[1],
iron.FieldParameterSetTypes.VALUES)
cellml.CreateCellMLToFieldMap(cellmlModelIndex,
pair[1],
iron.FieldParameterSetTypes.VALUES,
pair[0],
iron.FieldVariableTypes.U, 1,
iron.FieldParameterSetTypes.VALUES)
cellml.FieldMapsCreateFinish()
# Models field
cellmlModelsField = iron.Field()
cellml.ModelsFieldCreateStart(userNumber.getInc(), cellmlModelsField)
cellml.ModelsFieldCreateFinish()
cellmlModelsField.ComponentValuesInitialiseIntg(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES,
1, 1)
cellmlModelsField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
cellmlModelsField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
# State field
cellmlStateField = iron.Field()
cellml.StateFieldCreateStart(userNumber.getInc(), cellmlStateField)
cellml.StateFieldCreateFinish()
cellmlStateField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
cellmlStateField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
# Intermediate field
cellmlIntermediateField = iron.Field()
cellml.IntermediateFieldCreateStart(userNumber.getInc(), cellmlIntermediateField)
cellml.IntermediateFieldCreateFinish()
cellmlIntermediateField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
cellmlIntermediateField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
# Parameters field
cellmlParametersField = iron.Field()
cellml.ParametersFieldCreateStart(userNumber.getInc(), cellmlParametersField)
cellml.ParametersFieldCreateFinish()
cellmlParametersField.ParameterSetUpdateStart(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
cellmlParametersField.ParameterSetUpdateFinish(iron.FieldVariableTypes.U,
iron.FieldParameterSetTypes.VALUES)
# E q u a t i o n s
# -----------------
if computationalNodeNumber == 0:
print('Setting up equations for each buffer...')
for equationsSet in equationsSets:
equations = iron.Equations()
equationsSet.EquationsCreateStart(equations)
equations.SparsityTypeSet(iron.EquationsSparsityTypes.SPARSE)
equations.OutputTypeSet(iron.EquationsOutputTypes.NONE)
equationsSet.EquationsCreateFinish()
# P r o b l e m
# -------------
if computationalNodeNumber == 0:
print('Setting up problem...')
problemSpecification = [iron.ProblemClasses.CLASSICAL_FIELD,
iron.ProblemTypes.REACTION_DIFFUSION_EQUATION,
iron.ProblemSubtypes.CELLML_REAC_INTEG_REAC_DIFF_STRANG_SPLIT]
problem = iron.Problem()
problem.CreateStart(userNumber.getInc(), problemSpecification)
problem.CreateFinish()
problem.ControlLoopCreateStart()
controlLoop = iron.ControlLoop()
problem.ControlLoopGet([iron.ControlLoopIdentifiers.NODE], controlLoop)
controlLoop.TimesSet(startTime, endTime, pdeTimestep)
controlLoop.TimeOutputSet(outputFrequency)
controlLoop.OutputTypeSet(iron.ControlLoopOutputTypes.NONE)
problem.ControlLoopCreateFinish()
# S o l v e r s
# -------------
problem.SolversCreateStart()
# CellML solver
solver = iron.Solver()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 1, solver)
solver.DAESolverTypeSet(iron.DAESolverTypes.EULER)
solver.DAETimeStepSet(odeTimestep)
solver.OutputTypeSet(iron.SolverOutputTypes.NONE)
# PDE solver
solver = iron.Solver()
linearSolver = iron.Solver()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 2, solver)
solver.DynamicThetaSet([1.0])
solver.OutputTypeSet(iron.SolverOutputTypes.NONE)
solver.DynamicLinearSolverGet(linearSolver)
linearSolver.LinearIterativeMaximumIterations = 1000
linearSolver.linearIterativeAbsoluteTolerance = 1.0e-10
linearSolver.linearIterativeRelativeTolerance = 1.0e-8
# CellML solver
solver = iron.Solver()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 3, solver)
solver.DAESolverTypeSet(iron.DAESolverTypes.EULER)
solver.DAETimeStepSet(odeTimestep)
solver.OutputTypeSet(iron.SolverOutputTypes.NONE)
problem.SolversCreateFinish()
# C e l l M L e n v i r o n m e n t
# -----------------------------------
problem.CellMLEquationsCreateStart()
for solverIndex in (1, 3):
solver = iron.Solver()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], solverIndex, solver)
cellmlEquations = iron.CellMLEquations()
solver.CellMLEquationsGet(cellmlEquations)
cellmlEquations.CellMLAdd(cellml)
problem.CellMLEquationsCreateFinish()
# P D E S o l v e r e q u a t i o n s
# ---------------------------------------
problem.SolverEquationsCreateStart()
solver = iron.Solver()
problem.SolverGet([iron.ControlLoopIdentifiers.NODE], 2, solver)
solverEquations = iron.SolverEquations()
solver.SolverEquationsGet(solverEquations)
solverEquations.SparsityTypeSet(iron.SolverEquationsSparsityTypes.SPARSE)
for equationsSet in equationsSets:
solverEquations.EquationsSetAdd(equationsSet)
problem.SolverEquationsCreateFinish()
# B o u n d a r y C o n d i t i o n s
# -------------------------------------
# Don't need to set BCs- source terms from the CellML model
# will be injecting Ca into the domain. Sarcolemma and mitochondrial
# boundaries will default to a no flux condition.
if computationalNodeNumber == 0:
print('Setting up boundary conditions...')
boundaryConditions = iron.BoundaryConditions()
solverEquations.BoundaryConditionsCreateStart(boundaryConditions)
solverEquations.BoundaryConditionsCreateFinish()
# S o l v e p r o b le m
# -------------------------
gc.collect()
if computationalNodeNumber == 0:
print('Solving problem...')
start = time.time()
problem.Solve()
end = time.time()
if computationalNodeNumber == 0:
print('Success!')
print('Solve time: ' + str(end - start))
iron.Finalise()