/MultiPhysics/CoupledDiffusionDiffusion/MonolithicSchemeTestAnalytic/src/MonolithicSchemeTestAnalyticExample.f90

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  1. !> \file
    2. 

  2. !> \authors Andrew Cookson
    3. 

  3. !> \brief This is an example program to solve coupled multi-compartment diffusion equations in monolithic scheme using openCMISS calls.
    4. 

  4. !>
    5. 

  5. !> \section LICENSE
    6. 

  6. !>
    7. 

  7. !> Version: MPL 1.1/GPL 2.0/LGPL 2.1
    8. 

  8. !>
    9. 

  9. !> The contents of this file are subject to the Mozilla Public License
    10. 

  10. !> Version 1.1 (the "License"); you may not use this file except in
    11. 

  11. !> compliance with the License. You may obtain a copy of the License at
    12. 

  12. !> http://www.mozilla.org/MPL/
    13. 

  13. !>
    14. 

  14. !> Software distributed under the License is distributed on an "AS IS"
    15. 

  15. !> basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
    16. 

  16. !> License for the specific language governing rights and limitations
    17. 

  17. !> under the License.
    18. 

  18. !>
    19. 

  19. !> The Original Code is OpenCMISS
    20. 

  20. !>
    21. 

  21. !> The Initial Developer of the Original Code is University of Auckland,
    22. 

  22. !> Auckland, New Zealand and University of Oxford, Oxford, United
    23. 

  23. !> Kingdom. Portions created by the University of Auckland and University
    24. 

  24. !> of Oxford are Copyright (C) 2007 by the University of Auckland and
    25. 

  25. !> the University of Oxford. All Rights Reserved.
    26. 

  26. !>
    27. 

  27. !> Contributor(s):
    28. 

  28. !>
    29. 

  29. !> Alternatively, the contents of this file may be used under the terms of
    30. 

  30. !> either the GNU General Public License Version 2 or later (the "GPL"), or
    31. 

  31. !> the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
    32. 

  32. !> in which case the provisions of the GPL or the LGPL are applicable instead
    33. 

  33. !> of those above. If you wish to allow use of your version of this file only
    34. 

  34. !> under the terms of either the GPL or the LGPL, and not to allow others to
    35. 

  35. !> use your version of this file under the terms of the MPL, indicate your
    36. 

  36. !> decision by deleting the provisions above and replace them with the notice
    37. 

  37. !> and other provisions required by the GPL or the LGPL. If you do not delete
    38. 

  38. !> the provisions above, a recipient may use your version of this file under
    39. 

  39. !> the terms of any one of the MPL, the GPL or the LGPL.
    40. 

  40. !>
    41. 

  41. 

  42. !> \example MultiPhysics/CoupledDiffusionDiffusion/MonolithicSchemeTest/src/MonolithicSchemeTestExample.f90
    43. 

  43. !! Example program to solve coupled MonolithicSchemeTest equations using OpenCMISS calls.
    44. 

  44. !! \par Latest Builds:
    45. 

  45. !! \li <a href='http://autotest.bioeng.auckland.ac.nz/opencmiss-build/logs_x86_64-linux/MultiPhysics/CoupledDiffusionDiffusion/MonolithicSchemeTest/build-intel'>Linux Intel Build</a>
    46. 

  46. !! \li <a href='http://autotest.bioeng.auckland.ac.nz/opencmiss-build/logs_x86_64-linux/MultiPhysics/CoupledDiffusionDiffusion/MonolithicSchemeTest/build-intel'>Linux GNU Build</a>
    47. 

  47. !!
    48. 

  48. !<
    49. 

  49. 

  50. ! ! 
    51. 

  51. ! !  This example considers a volume coupled multi-compartment diffusion model, as a means of testing the monolithic assembly of
    52. 

  52. ! !  such a system of equations, for use in more complicated problem in future.
    53. 

  53. ! !  This example will initially couple together three diffusion equations, with the transfer between each equation being proportional to
    54. 

  54. ! !  the concentration difference between each equation.
    55. 

  55. 

  56. !> Main program
    57. 

  57. 

  58. PROGRAM MONOLITHICSCHEMETESTFIELDMLEXAMPLE
    59. 

  59. 

  60.   !
    61. 

  61.   !================================================================================================================================
    62. 

  62.   !
    63. 

  63. 

  64.   !PROGRAM LIBRARIES
    65. 

  65. 

  66.   USE OPENCMISS
    67. 

  67.   USE FIELDML_OUTPUT_ROUTINES
    68. 

  68.   USE FIELDML_UTIL_ROUTINES
    69. 

  69.   USE FIELDML_API
    70. 

  70.   USE FLUID_MECHANICS_IO_ROUTINES
    71. 

  71.   USE MPI
    72. 

  72. 

  73. #ifdef WIN32
    74. 

  74.   USE IFQWINCMISS
    75. 

  75. #endif
    76. 

  76. 

  77.   !
    78. 

  78.   !================================================================================================================================
    79. 

  79.   !
    80. 

  80. 

  81.   !PROGRAM VARIABLES AND TYPES
    82. 

  82. 

  83.   IMPLICIT NONE
    84. 

  84. 

  85.   !Test program parameters
    86. 

  86. 

  87.   REAL(CMISSDP), PARAMETER :: HEIGHT=1.0_CMISSDP
    88. 

  88.   REAL(CMISSDP), PARAMETER :: WIDTH=1.0_CMISSDP
    89. 

  89.   REAL(CMISSDP), PARAMETER :: LENGTH=3.0_CMISSDP
    90. 

  90. 

  91.   INTEGER(CMISSIntg), PARAMETER :: CoordinateSystemUserNumber=1
    92. 

  92.   INTEGER(CMISSIntg), PARAMETER :: RegionUserNumber=2
    93. 

  93.   INTEGER(CMISSIntg), PARAMETER :: MeshUserNumber=3
    94. 

  94.   INTEGER(CMISSIntg), PARAMETER :: DecompositionUserNumber=4
    95. 

  95.   INTEGER(CMISSIntg), PARAMETER :: GeometricFieldUserNumber=5
    96. 

  96.   INTEGER(CMISSIntg), PARAMETER :: DependentFieldUserNumber=6
    97. 

  97.   INTEGER(CMISSIntg), PARAMETER :: GeneratedMeshUserNumber=9
    98. 

  98.   INTEGER(CMISSIntg) :: MaterialsFieldUserNumberDiffusion
    99. 

  99. !   INTEGER(CMISSIntg), PARAMETER :: MaterialsFieldUserNumberDiffusionTwo=10
    100. 

  100. !   INTEGER(CMISSIntg), PARAMETER :: MaterialsFieldUserNumberDiffusionThree=11
    101. 

  101.   INTEGER(CMISSIntg) :: SourceFieldUserNumberDiffusion
    102. 

  102. !   INTEGER(CMISSIntg), PARAMETER :: SourceFieldUserNumberDiffusionTwo=16
    103. 

  103. !   INTEGER(CMISSIntg), PARAMETER :: SourceFieldUserNumberDiffusionThree=17
    104. 

  104.   INTEGER(CMISSIntg) :: EquationsSetUserNumberDiffusion
    105. 

  105.   INTEGER(CMISSIntg) :: AnalyticFieldUserNumberDiffusion
    106. 

  106. !   INTEGER(CMISSIntg), PARAMETER :: EquationsSetUserNumberDiffusionTwo=13
    107. 

  107. !   INTEGER(CMISSIntg), PARAMETER :: EquationsSetUserNumberDiffusionThree=14
    108. 

  108.   INTEGER(CMISSIntg), PARAMETER :: ProblemUserNumber=20
    109. 

  109. !!!!!!!!!!!!!!!!!!!EQUATIONS FIELD PARAMETERS
    110. 

  110.   INTEGER(CMISSIntg), PARAMETER :: EquationsFieldDiffusionOne=33
    111. 

  111.   INTEGER(CMISSIntg), PARAMETER :: EquationsFieldDiffusionTwo=34
    112. 

  112.   INTEGER(CMISSIntg), PARAMETER :: EquationsFieldDiffusionThree=35
    113. 

  113. 

  114. 

  115. 

  116. 

  117. 

  118.   INTEGER(CMISSIntg) :: EquationsSetFieldUserNumberDiffusion
    119. 

  119.   INTEGER(CMISSIntg) :: icompartment,Ncompartments,num_var
    120. 

  120. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    121. 

  121.   INTEGER(CMISSIntg), PARAMETER :: DomainUserNumber=1
    122. 

  122.   INTEGER(CMISSIntg), PARAMETER :: NumberOfUserDomains=1
    123. 

  123.   INTEGER(CMISSIntg), PARAMETER :: SolverDiffusionUserNumber=1
    124. 

  124.   !Program types
    125. 

  125. 

  126.   TYPE(EXPORT_CONTAINER):: CM
    127. 

  127. 

  128.   !Program variables
    129. 

  129.   INTEGER(CMISSIntg) :: NUMBER_GLOBAL_X_ELEMENTS,NUMBER_GLOBAL_Y_ELEMENTS,NUMBER_GLOBAL_Z_ELEMENTS
    130. 

  130.   INTEGER(CMISSIntg) :: NUMBER_OF_DOMAINS
    131. 

  131. 

  132.   INTEGER(CMISSIntg) :: MPI_IERROR
    133. 

  133. 

  134.   INTEGER(CMISSIntg) :: NUMBER_OF_DIMENSIONS
    135. 

  135. 

  136.   INTEGER(CMISSIntg) :: NUMBER_OF_COMPARTMENTS
    137. 

  137.   
    138. 

  138.   INTEGER(CMISSIntg) :: BASIS_TYPE
    139. 

  139.   INTEGER(CMISSIntg) :: BASIS_NUMBER_GEOMETRY
    140. 

  140.   INTEGER(CMISSIntg) :: BASIS_NUMBER_CONC_ONE
    141. 

  141.   INTEGER(CMISSIntg) :: BASIS_NUMBER_CONC_TWO
    142. 

  142.   INTEGER(CMISSIntg) :: BASIS_NUMBER_CONC_THREE
    143. 

  143.   INTEGER(CMISSIntg) :: BASIS_XI_GAUSS_GEOMETRY
    144. 

  144.   INTEGER(CMISSIntg) :: BASIS_XI_GAUSS_CONC_ONE
    145. 

  145.   INTEGER(CMISSIntg) :: BASIS_XI_GAUSS_CONC_TWO
    146. 

  146.   INTEGER(CMISSIntg) :: BASIS_XI_GAUSS_CONC_THREE
    147. 

  147.   INTEGER(CMISSIntg) :: BASIS_XI_INTERPOLATION_GEOMETRY
    148. 

  148.   INTEGER(CMISSIntg) :: BASIS_XI_INTERPOLATION_CONC_ONE
    149. 

  149.   INTEGER(CMISSIntg) :: BASIS_XI_INTERPOLATION_CONC_TWO
    150. 

  150.   INTEGER(CMISSIntg) :: BASIS_XI_INTERPOLATION_CONC_THREE
    151. 

  151.   INTEGER(CMISSIntg) :: MESH_NUMBER_OF_COMPONENTS,MESH_NUMBER_OF_ALL_COMPONENTS
    152. 

  152.   INTEGER(CMISSIntg) :: MESH_COMPONENT_NUMBER_GEOMETRY
    153. 

  153.   INTEGER(CMISSIntg) :: MESH_COMPONENT_NUMBER_CONC_ONE
    154. 

  154.   INTEGER(CMISSIntg) :: MESH_COMPONENT_NUMBER_CONC_TWO
    155. 

  155.   INTEGER(CMISSIntg) :: MESH_COMPONENT_NUMBER_CONC_THREE
    156. 

  156.   INTEGER(CMISSIntg) :: NUMBER_OF_NODES_GEOMETRY
    157. 

  157.   INTEGER(CMISSIntg) :: NUMBER_OF_NODES_CONC_ONE
    158. 

  158.   INTEGER(CMISSIntg) :: NUMBER_OF_NODES_CONC_TWO
    159. 

  159.   INTEGER(CMISSIntg) :: NUMBER_OF_NODES_CONC_THREE
    160. 

  160.   INTEGER(CMISSIntg) :: NUMBER_OF_ELEMENT_NODES_GEOMETRY
    161. 

  161.   INTEGER(CMISSIntg) :: NUMBER_OF_ELEMENT_NODES_CONC_ONE
    162. 

  162.   INTEGER(CMISSIntg) :: NUMBER_OF_ELEMENT_NODES_CONC_TWO
    163. 

  163.   INTEGER(CMISSIntg) :: NUMBER_OF_ELEMENT_NODES_CONC_THREE
    164. 

  164.   INTEGER(CMISSIntg) :: TOTAL_NUMBER_OF_NODES,TOTAL_NUMBER_OF_ALL_NODES
    165. 

  165.   INTEGER(CMISSIntg) :: TOTAL_NUMBER_OF_ELEMENTS
    166. 

  166.   INTEGER(CMISSIntg) :: MAXIMUM_ITERATIONS
    167. 

  167.   INTEGER(CMISSIntg) :: RESTART_VALUE
    168. 

  168.   INTEGER(CMISSIntg) :: NUMBER_OF_FIXED_WALL_NODES_DIFFUSION_ONE
    169. 

  169.   INTEGER(CMISSIntg) :: NUMBER_OF_INLET_WALL_NODES_DIFFUSION_ONE
    170. 

  170.   INTEGER(CMISSIntg) :: NUMBER_OF_FIXED_WALL_NODES_DIFFUSION_TWO
    171. 

  171.   INTEGER(CMISSIntg) :: NUMBER_OF_INLET_WALL_NODES_DIFFUSION_TWO
    172. 

  172.   INTEGER(CMISSIntg) :: NUMBER_OF_FIXED_WALL_NODES_DIFFUSION_THREE
    173. 

  173.   INTEGER(CMISSIntg) :: NUMBER_OF_INLET_WALL_NODES_DIFFUSION_THREE
    174. 

  174.   INTEGER(CMISSIntg) :: EQUATIONS_DIFFUSION_OUTPUT
    175. 

  175.   INTEGER(CMISSIntg) :: EQUATIONS_DIFFUSION_TWO_OUTPUT
    176. 

  176.   INTEGER(CMISSIntg) :: EQUATIONS_DIFFUSION_THREE_OUTPUT
    177. 

  177.   INTEGER(CMISSIntg) :: COMPONENT_NUMBER
    178. 

  178.   INTEGER(CMISSIntg) :: NODE_NUMBER
    179. 

  179.   INTEGER(CMISSIntg) :: ELEMENT_NUMBER
    180. 

  180.   INTEGER(CMISSIntg) :: NODE_COUNTER
    181. 

  181.   INTEGER(CMISSIntg) :: CONDITION
    182. 

  182. 

  183.   INTEGER(CMISSIntg) :: LINEAR_SOLVER_DIFFUSION_OUTPUT_FREQUENCY
    184. 

  184.   INTEGER(CMISSIntg) :: LINEAR_SOLVER_DIFFUSION_OUTPUT_TYPE
    185. 

  185. 

  186. 

  187.   REAL(CMISSDP) :: DOMAIN_X1, DOMAIN_X2, DOMAIN_Y1, DOMAIN_Y2, DOMAIN_Z1, DOMAIN_Z2
    188. 

  188.   REAL(CMISSDP) :: GEOMETRY_TOLERANCE
    189. 

  189. 

  190.   INTEGER, ALLOCATABLE, DIMENSION(:):: FIXED_WALL_NODES_DIFFUSION_ONE
    191. 

  191.   INTEGER, ALLOCATABLE, DIMENSION(:):: INLET_WALL_NODES_DIFFUSION_ONE
    192. 

  192.   INTEGER, ALLOCATABLE, DIMENSION(:):: FIXED_WALL_NODES_DIFFUSION_TWO
    193. 

  193.   INTEGER, ALLOCATABLE, DIMENSION(:):: INLET_WALL_NODES_DIFFUSION_TWO
    194. 

  194.   INTEGER, ALLOCATABLE, DIMENSION(:):: FIXED_WALL_NODES_DIFFUSION_THREE
    195. 

  195.   INTEGER, ALLOCATABLE, DIMENSION(:):: INLET_WALL_NODES_DIFFUSION_THREE
    196. 

  196. 

  197.   REAL(CMISSDP) :: INITIAL_FIELD_DIFFUSION_ONE
    198. 

  198.   REAL(CMISSDP) :: INITIAL_FIELD_DIFFUSION_TWO
    199. 

  199.   REAL(CMISSDP) :: INITIAL_FIELD_DIFFUSION_THREE
    200. 

  200.   REAL(CMISSDP) :: BOUNDARY_CONDITIONS_DIFFUSION_ONE
    201. 

  201.   REAL(CMISSDP) :: BOUNDARY_CONDITIONS_DIFFUSION_TWO
    202. 

  202.   REAL(CMISSDP) :: BOUNDARY_CONDITIONS_DIFFUSION_THREE
    203. 

  203.   REAL(CMISSDP) :: DIVERGENCE_TOLERANCE
    204. 

  204.   REAL(CMISSDP) :: RELATIVE_TOLERANCE
    205. 

  205.   REAL(CMISSDP) :: ABSOLUTE_TOLERANCE
    206. 

  206.   REAL(CMISSDP) :: LINESEARCH_ALPHA
    207. 

  207.   REAL(CMISSDP) :: VALUE
    208. 

  208. 

  209.   REAL(CMISSDP) :: LINEAR_SOLVER_DIFFUSION_START_TIME
    210. 

  210.   REAL(CMISSDP) :: LINEAR_SOLVER_DIFFUSION_STOP_TIME
    211. 

  211.   REAL(CMISSDP) :: LINEAR_SOLVER_DIFFUSION_TIME_INCREMENT
    212. 

  212. 

  213.   LOGICAL :: EXPORT_FIELD_IO
    214. 

  214.   LOGICAL :: LINEAR_SOLVER_DIFFUSION_DIRECT_FLAG
    215. 

  215.   LOGICAL :: INLET_WALL_NODES_DIFFUSION_ONE_FLAG
    216. 

  216.   LOGICAL :: INLET_WALL_NODES_DIFFUSION_TWO_FLAG
    217. 

  217.   LOGICAL :: INLET_WALL_NODES_DIFFUSION_THREE_FLAG
    218. 

  218.   !CMISS variables
    219. 

  219.   CHARACTER(C_CHAR), PARAMETER :: NUL=C_NULL_CHAR
    220. 

  220.   !Regions
    221. 

  221.   TYPE(CMISSRegionType) :: Region
    222. 

  222.   TYPE(CMISSRegionType) :: WorldRegion
    223. 

  223.   !Coordinate systems
    224. 

  224.   TYPE(CMISSCoordinateSystemType) :: CoordinateSystem
    225. 

  225.   TYPE(CMISSCoordinateSystemType) :: WorldCoordinateSystem
    226. 

  226.   !Basis
    227. 

  227.   TYPE(CMISSBasisType) :: BasisGeometry
    228. 

  228.   TYPE(CMISSBasisType) :: BasisConcOne
    229. 

  229.   TYPE(CMISSBasisType) :: BasisConcTwo
    230. 

  230.   TYPE(CMISSBasisType) :: BasisConcThree
    231. 

  231.   
    232. 

  232.   !TYPE(CMISSBasisType), ALLOCATABLE, DIMENSION(:) :: BasicConc
    233. 

  233. 

  234.   !Nodes
    235. 

  235.   TYPE(CMISSNodesType) :: Nodes
    236. 

  236.   !Elements
    237. 

  237.   TYPE(CMISSMeshElementsType) :: MeshElementsGeometry
    238. 

  238.   TYPE(CMISSMeshElementsType) :: MeshElementsConcOne
    239. 

  239.   TYPE(CMISSMeshElementsType) :: MeshElementsConcTwo
    240. 

  240.   TYPE(CMISSMeshElementsType) :: MeshElementsConcThree
    241. 

  241. 

  242.   TYPE(CMISSMeshElementsType), ALLOCATABLE, DIMENSION(:) :: MeshElementsConc
    243. 

  243.   !Meshes
    244. 

  244.   TYPE(CMISSMeshType) :: Mesh
    245. 

  245.   !Decompositions
    246. 

  246.   TYPE(CMISSDecompositionType) :: Decomposition
    247. 

  247.   !Fields
    248. 

  248.   TYPE(CMISSFieldsType) :: Fields
    249. 

  249.   TYPE(CMISSGeneratedMeshType) :: GeneratedMesh  
    250. 

  250.   !Field types
    251. 

  251.   TYPE(CMISSFieldType) :: GeometricField
    252. 

  252.   TYPE(CMISSFieldType) :: DependentField
    253. 

  253.   TYPE(CMISSFieldType), ALLOCATABLE, DIMENSION(:) :: MaterialsFieldDiffusion
    254. 

  254.   TYPE(CMISSFieldType), ALLOCATABLE, DIMENSION(:) :: SourceFieldDiffusion
    255. 

  255.   TYPE(CMISSFieldType), ALLOCATABLE, DIMENSION(:) :: AnalyticFieldDiffusion
    256. 

  256.   TYPE(CMISSBoundaryConditionsType) :: BoundaryConditionsDiffusion
    257. 

  257.   TYPE(CMISSEquationsSetType), ALLOCATABLE, DIMENSION(:) :: EquationsSetDiffusion
    258. 

  258.   TYPE(CMISSEquationsType), ALLOCATABLE, DIMENSION(:) :: EquationsDiffusion
    259. 

  259.   TYPE(CMISSFieldType), ALLOCATABLE, DIMENSION(:) :: EquationsSetFieldDiffusion
    260. 

  260.   !Problems
    261. 

  261.   TYPE(CMISSProblemType) :: Problem
    262. 

  262.   !Control loops
    263. 

  263.   TYPE(CMISSControlLoopType) :: ControlLoop
    264. 

  264.   !Solvers
    265. 

  265.   TYPE(CMISSSolverType) :: SolverDiffusion
    266. 

  266.   TYPE(CMISSSolverType) :: LinearSolverDiffusion
    267. 

  267.   !Solver equations
    268. 

  268.   TYPE(CMISSSolverEquationsType) :: SolverEquationsDiffusion
    269. 

  269. 

  270. #ifdef WIN32
    271. 

  271.   !Quickwin type
    272. 

  272.   LOGICAL :: QUICKWIN_STATUS=.FALSE.
    273. 

  273.   TYPE(WINDOWCONFIG) :: QUICKWIN_WINDOW_CONFIG
    274. 

  274. #endif
    275. 

  275.   
    276. 

  276.   !Generic CMISS variables
    277. 

  277.   INTEGER(CMISSIntg) :: NumberOfComputationalNodes,ComputationalNodeNumber
    278. 

  278.   INTEGER(CMISSIntg) :: EquationsSetIndex
    279. 

  279.   INTEGER(CMISSIntg) :: EquationsSetIndexTwo
    280. 

  280.   INTEGER(CMISSIntg) :: EquationsSetIndexThree
    281. 

  281.   INTEGER(CMISSIntg) :: Err
    282. 

  282. 

  283. 

  284.   !Array containing the field variable types that will be used (for ease of incorporating inside a loop)
    285. 

  285.   INTEGER(CMISSIntg), ALLOCATABLE, DIMENSION(:) :: VariableTypes
    286. 

  286.   REAL(CMISSDP), ALLOCATABLE, DIMENSION(:,:) :: CouplingCoeffs
    287. 

  287. 

  288.   INTEGER(CMISSIntg) :: DIAG_LEVEL_LIST(5)
    289. 

  289. !   CHARACTER(LEN=255) :: DIAG_ROUTINE_LIST(8) !,TIMING_ROUTINE_LIST(1)
    290. 

  290.   CHARACTER(LEN=255) :: DIAG_ROUTINE_LIST(1) !,TIMING_ROUTINE_LIST(1)
    291. 

  291.  
    292. 

  292.   INTEGER(CMISSIntg) :: TotalNumberOfSolidNodes
    293. 

  293. !   INTEGER(CMISSIntg) :: NumberOfSolidMeshComponents
    294. 

  294.   !
    295. 

  295.   !--------------------------------------------------------------------------------------------------------------------------------
    296. 

  296.   !
    297. 

  297. 

  298. 

  299.   !FieldML variables
    300. 

  300.   CHARACTER(KIND=C_CHAR,LEN=*), PARAMETER :: outputDirectory = ""
    301. 

  301.   CHARACTER(KIND=C_CHAR,LEN=*), PARAMETER :: outputFilename = "MonolithicMultiCompDiffusion.xml"
    302. 

  302.   CHARACTER(KIND=C_CHAR,LEN=*), PARAMETER :: basename = "monolithic_multicomp_diffusion"
    303. 

  303. 

  304.   TYPE(FieldmlInfoType) :: fieldmlInfo
    305. 

  305. 

  306. 

  307. 

  308. 

  309. #ifdef WIN32
    310. 

  310.   !Initialise QuickWin
    311. 

  311.   QUICKWIN_WINDOW_CONFIG%TITLE="General Output" !Window title
    312. 

  312.   QUICKWIN_WINDOW_CONFIG%NUMTEXTROWS=-1 !Max possible number of rows
    313. 

  313.   QUICKWIN_WINDOW_CONFIG%MODE=QWIN$SCROLLDOWN
    314. 

  314.   !Set the window parameters
    315. 

  315.   QUICKWIN_STATUS=SETWINDOWCONFIG(QUICKWIN_WINDOW_CONFIG)
    316. 

  316.   !If attempt fails set with system estimated values
    317. 

  317.   IF(.NOT.QUICKWIN_STATUS) QUICKWIN_STATUS=SETWINDOWCONFIG(QUICKWIN_WINDOW_CONFIG)
    318. 

  318. #endif
    319. 

  319. 

  320.   !
    321. 

  321.   !================================================================================================================================
    322. 

  322.   !
    323. 

  323.   !INITIALISE OPENCMISS
    324. 

  324.   CALL CMISSInitialise(WorldCoordinateSystem,WorldRegion,Err)
    325. 

  325.   !CALL CMISSErrorHandlingModeSet(CMISS_ERRORS_TRAP_ERROR,Err)
    326. 

  326.   !
    327. 

  327.   !================================================================================================================================
    328. 

  328.   !
    329. 

  329.   !PROBLEM CONTROL PANEL
    330. 

  330.   !Import cmHeart mesh information
    331. 

  331.   CALL FLUID_MECHANICS_IO_READ_CMHEART(CM,Err)  
    332. 

  332.   BASIS_NUMBER_GEOMETRY=CM%ID_M
    333. 

  333.   BASIS_NUMBER_CONC_ONE=CM%ID_V !USE THE V COMPONENT OF CMHEART INPUT FOR CONCENTRATION ONE
    334. 

  334.   BASIS_NUMBER_CONC_TWO=CM%ID_P !USE THE p COMPONENT OF CMHEART INPUT FOR CONCENTRATION TWO
    335. 

  335.   NUMBER_OF_DIMENSIONS=CM%D
    336. 

  336.   BASIS_TYPE=CM%IT_T
    337. 

  337.   BASIS_XI_INTERPOLATION_GEOMETRY=CM%IT_M
    338. 

  338. !   BASIS_XI_INTERPOLATION_GEOMETRY=2
    339. 

  339.   BASIS_XI_INTERPOLATION_CONC_ONE=CM%IT_V
    340. 

  340.   BASIS_XI_INTERPOLATION_CONC_TWO=CM%IT_P
    341. 

  341.   NUMBER_OF_NODES_GEOMETRY=CM%N_M
    342. 

  342.   NUMBER_OF_NODES_CONC_ONE=CM%N_V
    343. 

  343.   NUMBER_OF_NODES_CONC_TWO=CM%N_P
    344. 

  344.   TOTAL_NUMBER_OF_NODES=CM%N_T
    345. 

  345.   TOTAL_NUMBER_OF_ELEMENTS=CM%E_T
    346. 

  346.   NUMBER_OF_ELEMENT_NODES_GEOMETRY=CM%EN_M
    347. 

  347.   NUMBER_OF_ELEMENT_NODES_CONC_ONE=CM%EN_V
    348. 

  348.   NUMBER_OF_ELEMENT_NODES_CONC_TWO=CM%EN_P
    349. 

  349. !   !Set domain dimensions
    350. 

  350. !   DOMAIN_X1 =  0.0_CMISSDP
    351. 

  351. !   DOMAIN_X2 =  1.0_CMISSDP
    352. 

  352. !   DOMAIN_Y1 =  0.0_CMISSDP
    353. 

  353. !   DOMAIN_Y2 =  1.0_CMISSDP
    354. 

  354. !   DOMAIN_Z1 =  0.0_CMISSDP
    355. 

  355. !   DOMAIN_Z2 =  1.0_CMISSDP
    356. 

  356. !   !Set geometric tolerance
    357. 

  357. !   GEOMETRY_TOLERANCE = 1.0E-12_CMISSDP
    358. 

  358. !   !Set initial values
    359. 

  359. !   INITIAL_FIELD_DIFFUSION_ONE=1.0_CMISSDP
    360. 

  360. !   INITIAL_FIELD_DIFFUSION_TWO=1.0_CMISSDP
    361. 

  361. !   INITIAL_FIELD_DIFFUSION_THREE=1.0_CMISSDP
    362. 

  362. !   !Set initial boundary conditions
    363. 

  363. !   INLET_WALL_NODES_DIFFUSION_ONE_FLAG=.TRUE.
    364. 

  364. !   IF(INLET_WALL_NODES_DIFFUSION_ONE_FLAG) THEN
    365. 

  365. !     NUMBER_OF_INLET_WALL_NODES_DIFFUSION_ONE=36
    366. 

  366. !     ALLOCATE(INLET_WALL_NODES_DIFFUSION_ONE(NUMBER_OF_INLET_WALL_NODES_DIFFUSION_ONE))
    367. 

  367. !     INLET_WALL_NODES_DIFFUSION_ONE=(/191,155,119,83,23,21,192,156,120,84,24,22,&
    368. 

  368. !      & 198,162,126,90,36,35,204,168,132,96,48,47,210,174,138,102,60,59,216,180,144,108,72,71/)
    369. 

  369. !     !Set initial boundary conditions
    370. 

  370. !     BOUNDARY_CONDITIONS_DIFFUSION_ONE=1.0_CMISSDP
    371. 

  371. !   ENDIF  !Set material parameters
    372. 

  372. ! 
    373. 

  373. !   INLET_WALL_NODES_DIFFUSION_TWO_FLAG=.TRUE.
    374. 

  374. !   IF(INLET_WALL_NODES_DIFFUSION_TWO_FLAG) THEN
    375. 

  375. !     NUMBER_OF_INLET_WALL_NODES_DIFFUSION_TWO=36
    376. 

  376. !     ALLOCATE(INLET_WALL_NODES_DIFFUSION_TWO(NUMBER_OF_INLET_WALL_NODES_DIFFUSION_TWO))
    377. 

  377. !     INLET_WALL_NODES_DIFFUSION_TWO=(/191,155,119,83,23,21,192,156,120,84,24,22,&
    378. 

  378. !      & 198,162,126,90,36,35,204,168,132,96,48,47,210,174,138,102,60,59,216,180,144,108,72,71/)
    379. 

  379. !     !Set initial boundary conditions
    380. 

  380. !     BOUNDARY_CONDITIONS_DIFFUSION_TWO=1.0_CMISSDP
    381. 

  381. !   ENDIF  !Set material parameters
    382. 

  382. ! 
    383. 

  383. !   INLET_WALL_NODES_DIFFUSION_THREE_FLAG=.TRUE.
    384. 

  384. !   IF(INLET_WALL_NODES_DIFFUSION_THREE_FLAG) THEN
    385. 

  385. !     NUMBER_OF_INLET_WALL_NODES_DIFFUSION_THREE=36
    386. 

  386. !     ALLOCATE(INLET_WALL_NODES_DIFFUSION_THREE(NUMBER_OF_INLET_WALL_NODES_DIFFUSION_THREE))
    387. 

  387. !     INLET_WALL_NODES_DIFFUSION_THREE=(/191,155,119,83,23,21,192,156,120,84,24,22,&
    388. 

  388. !      & 198,162,126,90,36,35,204,168,132,96,48,47,210,174,138,102,60,59,216,180,144,108,72,71/)
    389. 

  389. !     !Set initial boundary conditions
    390. 

  390. !     BOUNDARY_CONDITIONS_DIFFUSION_THREE=1.0_CMISSDP
    391. 

  391. !   ENDIF  !Set material parameters
    392. 

  392. 

  393.   !Get the computational nodes information
    394. 

  394.   CALL CMISSComputationalNumberOfNodesGet(NumberOfComputationalNodes,Err)
    395. 

  395.   CALL CMISSComputationalNodeNumberGet(ComputationalNodeNumber,Err)
    396. 

  396. 

  397.   NUMBER_GLOBAL_X_ELEMENTS=40
    398. 

  398.   NUMBER_GLOBAL_Y_ELEMENTS=40
    399. 

  399.   NUMBER_GLOBAL_Z_ELEMENTS=0
    400. 

  400. 

  401.   IF(NUMBER_GLOBAL_Z_ELEMENTS==0)THEN
    402. 

  402.     NUMBER_OF_DIMENSIONS=2
    403. 

  403.   ELSE
    404. 

  404.     NUMBER_OF_DIMENSIONS=3
    405. 

  405.   ENDIF
    406. 

  406.   NUMBER_OF_DOMAINS=NumberOfComputationalNodes
    407. 

  407. 

  408.   !Set all diganostic levels on for testing
    409. 

  409. 

  410.   CALL MPI_BCAST(NUMBER_GLOBAL_X_ELEMENTS,1,MPI_INTEGER,0,MPI_COMM_WORLD,MPI_IERROR)
    411. 

  411.   CALL MPI_BCAST(NUMBER_GLOBAL_Y_ELEMENTS,1,MPI_INTEGER,0,MPI_COMM_WORLD,MPI_IERROR)
    412. 

  412.   CALL MPI_BCAST(NUMBER_GLOBAL_Z_ELEMENTS,1,MPI_INTEGER,0,MPI_COMM_WORLD,MPI_IERROR)
    413. 

  413.   CALL MPI_BCAST(NUMBER_OF_DOMAINS,1,MPI_INTEGER,0,MPI_COMM_WORLD,MPI_IERROR)
    414. 

  414. 

  415. 

  416. 

  417. 

  418.   !Set material parameters
    419. 

  419.   !Set number of Gauss points (Mind that also material field may be interpolated)
    420. 

  420.   BASIS_XI_GAUSS_GEOMETRY=3 !4
    421. 

  421.   BASIS_XI_GAUSS_CONC_ONE=3 !4
    422. 

  422.   BASIS_XI_GAUSS_CONC_TWO=3 !4
    423. 

  423.   !Set output parameter
    424. 

  424.   !(NoOutput/ProgressOutput/TimingOutput/SolverOutput/SolverMatrixOutput)
    425. 

  425.   LINEAR_SOLVER_DIFFUSION_OUTPUT_TYPE=CMISS_SOLVER_MATRIX_OUTPUT
    426. 

  426.   !LINEAR_SOLVER_DIFFUSION_OUTPUT_TYPE=CMISS_SOLVER_NO_OUTPUT
    427. 

  427.   !(NoOutput/TimingOutput/MatrixOutput/ElementOutput)
    428. 

  428.   EQUATIONS_DIFFUSION_OUTPUT=CMISS_EQUATIONS_MATRIX_OUTPUT
    429. 

  429.   !EQUATIONS_DIFFUSION_OUTPUT=CMISS_EQUATIONS_NO_OUTPUT
    430. 

  430.   EQUATIONS_DIFFUSION_TWO_OUTPUT=CMISS_EQUATIONS_NO_OUTPUT
    431. 

  431.   EQUATIONS_DIFFUSION_THREE_OUTPUT=CMISS_EQUATIONS_NO_OUTPUT
    432. 

  432.   !Set time parameter
    433. 

  433.   LINEAR_SOLVER_DIFFUSION_START_TIME=0.0_CMISSDP
    434. 

  434.   LINEAR_SOLVER_DIFFUSION_STOP_TIME=0.3000001_CMISSDP 
    435. 

  435.   LINEAR_SOLVER_DIFFUSION_TIME_INCREMENT=0.005_CMISSDP
    436. 

  436.   !Set result output parameter
    437. 

  437.   LINEAR_SOLVER_DIFFUSION_OUTPUT_FREQUENCY=1
    438. 

  438.   !Set solver parameters
    439. 

  439.   LINEAR_SOLVER_DIFFUSION_DIRECT_FLAG=.FALSE.
    440. 

  440. 

  441.   RELATIVE_TOLERANCE=1.0E-10_CMISSDP !default: 1.0E-05_CMISSDP
    442. 

  442.   ABSOLUTE_TOLERANCE=1.0E-10_CMISSDP !default: 1.0E-10_CMISSDP
    443. 

  443.   DIVERGENCE_TOLERANCE=1.0E5_CMISSDP !default: 1.0E5
    444. 

  444.   MAXIMUM_ITERATIONS=10000_CMISSIntg !default: 100000
    445. 

  445.   RESTART_VALUE=30_CMISSIntg !default: 30
    446. 

  446.   LINESEARCH_ALPHA=1.0_CMISSDP
    447. 

  447. 

  448. 

  449.   icompartment =1_CMISSIntg
    450. 

  450.   Ncompartments=2_CMISSIntg
    451. 

  451.   !
    452. 

  452.   !================================================================================================================================
    453. 

  453.   !
    454. 

  454. 

  455.   !Set diagnostics
    456. 

  456. 

  457.    !DIAG_LEVEL_LIST(1)=1
    458. 

  458. !   DIAG_LEVEL_LIST(2)=2
    459. 

  459. !   DIAG_LEVEL_LIST(3)=3
    460. 

  460. !   DIAG_LEVEL_LIST(4)=4
    461. 

  461. !   DIAG_LEVEL_LIST(5)=5
    462. 

  462. 

  463. !   DIAG_ROUTINE_LIST(1)="DIFFUSION_EQUATION_FINITE_ELEMENT_CALCULATE"
    464. 

  464. !   DIAG_ROUTINE_LIST(2)="PROBLEM_SOLVER_EQUATIONS_SOLVE"
    465. 

  465.    !DIAG_ROUTINE_LIST(1)="SOLVER_DYNAMIC_CREATE_FINISH"
    466. 

  466. 

  467.   !CMISS_ALL_DIAG_TYPE/CMISS_IN_DIAG_TYPE/CMISS_FROM_DIAG_TYPE
    468. 

  468.    !CALL CMISSDiagnosticsSetOn(CMISS_IN_DIAG_TYPE,DIAG_LEVEL_LIST,"Diagnostics",DIAG_ROUTINE_LIST,Err)
    469. 

  469. 

  470.   !CMISS_ALL_TIMING_TYPE/CMISS_IN_TIMING_TYPE/CMISS_FROM_TIMING_TYPE
    471. 

  471.   !TIMING_ROUTINE_LIST(1)="PROBLEM_FINITE_ELEMENT_CALCULATE"
    472. 

  472.   !CALL TIMING_SET_ON(IN_TIMING_TYPE,.TRUE.,"",TIMING_ROUTINE_LIST,ERR,ERROR,*999)
    473. 

  473. 

  474.   !ALLOCATE THE ARRAYS
    475. 

  475.   ALLOCATE (EquationsSetDiffusion(Ncompartments))
    476. 

  476.   ALLOCATE (EquationsSetFieldDiffusion(Ncompartments))
    477. 

  477.   ALLOCATE (MaterialsFieldDiffusion(Ncompartments))
    478. 

  478.   ALLOCATE (SourceFieldDiffusion(Ncompartments))
    479. 

  479.   ALLOCATE (EquationsDiffusion(Ncompartments))
    480. 

  480.   ALLOCATE (AnalyticFieldDiffusion(Ncompartments))
    481. 

  481. 

  482. !
    483. 

  483.   !================================================================================================================================
    484. 

  484.   !
    485. 

  485.   !COORDINATE SYSTEM
    486. 

  486.   !Start the creation of a new RC coordinate system
    487. 

  487.   CALL CMISSCoordinateSystem_Initialise(CoordinateSystem,Err)
    488. 

  488.   CALL CMISSCoordinateSystem_CreateStart(CoordinateSystemUserNumber,CoordinateSystem,Err)
    489. 

  489.   !Set the coordinate system dimension
    490. 

  490.   CALL CMISSCoordinateSystem_DimensionSet(CoordinateSystem,NUMBER_OF_DIMENSIONS,Err)
    491. 

  491.   !Finish the creation of the coordinate system
    492. 

  492.   CALL CMISSCoordinateSystem_CreateFinish(CoordinateSystem,Err)
    493. 

  493.   !
    494. 

  494.   !================================================================================================================================
    495. 

  495.   !
    496. 

  496.   !REGION
    497. 

  497.   !For a volume-coupled problem, both concentrations are based in the same region
    498. 

  498.   !Start the creation of a new region
    499. 

  499.   CALL CMISSRegion_Initialise(Region,Err)
    500. 

  500.   CALL CMISSRegion_CreateStart(RegionUserNumber,WorldRegion,Region,Err)
    501. 

  501.   !Set the regions coordinate system as defined above
    502. 

  502.   CALL CMISSRegion_CoordinateSystemSet(Region,CoordinateSystem,Err)
    503. 

  503.   !Finish the creation of the region
    504. 

  504.   CALL CMISSRegion_CreateFinish(Region,Err)
    505. 

  505.   !
    506. 

  506.   !================================================================================================================================
    507. 

  507.   !
    508. 

  508.   !BASES
    509. 

  509.   !Start the creation of new bases: Geometry
    510. 

  510.   MESH_NUMBER_OF_COMPONENTS=1
    511. 

  511.   CALL CMISSBasis_Initialise(BasisGeometry,Err)
    512. 

  512.   CALL CMISSBasis_CreateStart(BASIS_NUMBER_GEOMETRY,BasisGeometry,Err)
    513. 

  513.   !Set the basis type (Lagrange/Simplex)
    514. 

  514.   CALL CMISSBasis_TypeSet(BasisGeometry,BASIS_TYPE,Err)
    515. 

  515.   !Set the basis xi number
    516. 

  516.   CALL CMISSBasis_NumberOfXiSet(BasisGeometry,NUMBER_OF_DIMENSIONS,Err)
    517. 

  517.   !Set the basis xi interpolation and number of Gauss points
    518. 

  518.   IF(NUMBER_OF_DIMENSIONS==2) THEN
    519. 

  519.     CALL CMISSBasis_InterpolationXiSet(BasisGeometry,(/BASIS_XI_INTERPOLATION_GEOMETRY,BASIS_XI_INTERPOLATION_GEOMETRY/),Err)
    520. 

  520.     CALL CMISSBasis_QuadratureNumberOfGaussXiSet(BasisGeometry,(/BASIS_XI_GAUSS_GEOMETRY,BASIS_XI_GAUSS_GEOMETRY/),Err)
    521. 

  521.   ELSE IF(NUMBER_OF_DIMENSIONS==3) THEN
    522. 

  522.     CALL CMISSBasis_InterpolationXiSet(BasisGeometry,(/BASIS_XI_INTERPOLATION_GEOMETRY,BASIS_XI_INTERPOLATION_GEOMETRY, & 
    523. 

  523.       & BASIS_XI_INTERPOLATION_GEOMETRY/),Err)                         
    524. 

  524.     CALL CMISSBasis_QuadratureNumberOfGaussXiSet(BasisGeometry,(/BASIS_XI_GAUSS_GEOMETRY,BASIS_XI_GAUSS_GEOMETRY, &
    525. 

  525.       & BASIS_XI_GAUSS_GEOMETRY/),Err)
    526. 

  526.   ENDIF
    527. 

  527.   !Finish the creation of the basis
    528. 

  528.   CALL CMISSBasis_CreateFinish(BasisGeometry,Err)
    529. 

  529.   !
    530. 

  530.   !Start the creation of another basis: Concentration_One
    531. 

  531. !  IF(BASIS_XI_INTERPOLATION_CONC_ONE==BASIS_XI_INTERPOLATION_GEOMETRY) THEN
    532. 

  532.     BasisConcOne=BasisGeometry
    533. 

  533. !  ELSE
    534. 

  534. !     MESH_NUMBER_OF_COMPONENTS=MESH_NUMBER_OF_COMPONENTS+1
    535. 

  535. !     !Initialise a new velocity basis
    536. 

  536. !     CALL CMISSBasis_Initialise(BasisConcOne,Err)
    537. 

  537. !     !Start the creation of a basis
    538. 

  538. !     CALL CMISSBasis_CreateStart(BASIS_NUMBER_CONC_ONE,BasisConcOne,Err)
    539. 

  539. !     !Set the basis type (Lagrange/Simplex)
    540. 

  540. !     CALL CMISSBasis_TypeSet(BasisConcOne,BASIS_TYPE,Err)
    541. 

  541. !     !Set the basis xi number
    542. 

  542. !     CALL CMISSBasis_NumberOfXiSet(BasisConcOne,NUMBER_OF_DIMENSIONS,Err)
    543. 

  543. !     !Set the basis xi interpolation and number of Gauss points
    544. 

  544. !     IF(NUMBER_OF_DIMENSIONS==2) THEN
    545. 

  545. !       CALL CMISSBasis_InterpolationXiSet(BasisConcOne,(/BASIS_XI_INTERPOLATION_CONC_ONE,BASIS_XI_INTERPOLATION_CONC_ONE/),Err)
    546. 

  546. !       CALL CMISSBasis_QuadratureNumberOfGaussXiSet(BasisConcOne,(/BASIS_XI_GAUSS_CONC_ONE,BASIS_XI_GAUSS_CONC_ONE/),Err)
    547. 

  547. !     ELSE IF(NUMBER_OF_DIMENSIONS==3) THEN
    548. 

  548. !       CALL CMISSBasis_InterpolationXiSet(BasisConcOne,(/BASIS_XI_INTERPOLATION_CONC_ONE,BASIS_XI_INTERPOLATION_CONC_ONE, & 
    549. 

  549. !         & BASIS_XI_INTERPOLATION_CONC_ONE/),Err)                         
    550. 

  550. !       CALL CMISSBasis_QuadratureNumberOfGaussXiSet(BasisConcOne,(/BASIS_XI_GAUSS_CONC_ONE,BASIS_XI_GAUSS_CONC_ONE, & 
    551. 

  551. !         & BASIS_XI_GAUSS_CONC_ONE/),Err)
    552. 

  552. !     ENDIF
    553. 

  553. !     !Finish the creation of the basis
    554. 

  554. !     CALL CMISSBasis_CreateFinish(BasisConcOne,Err)
    555. 

  555. !   ENDIF
    556. 

  556.   !
    557. 

  557.   !Start the creation of another basis: Concentration_Two
    558. 

  558. !  IF(BASIS_XI_INTERPOLATION_CONC_TWO==BASIS_XI_INTERPOLATION_GEOMETRY) THEN
    559. 

  559.     BasisConcTwo=BasisGeometry
    560. 

  560. !  ELSE IF(BASIS_XI_INTERPOLATION_CONC_TWO==BASIS_XI_INTERPOLATION_CONC_ONE) THEN
    561. 

  561. !     BasisConcTwo=BasisConcOne
    562. 

  562. !   ELSE
    563. 

  563. !     MESH_NUMBER_OF_COMPONENTS=MESH_NUMBER_OF_COMPONENTS+1
    564. 

  564. !     !Initialise a new concentration basis
    565. 

  565. !     CALL CMISSBasis_Initialise(BasisConcTwo,Err)
    566. 

  566. !     !Start the creation of a basis
    567. 

  567. !     CALL CMISSBasis_CreateStart(BASIS_NUMBER_CONC_TWO,BasisConcTwo,Err)
    568. 

  568. !     !Set the basis type (Lagrange/Simplex)
    569. 

  569. !     CALL CMISSBasis_TypeSet(BasisConcTwo,BASIS_TYPE,Err)
    570. 

  570. !     !Set the basis xi number
    571. 

  571. !     CALL CMISSBasis_NumberOfXiSet(BasisConcTwo,NUMBER_OF_DIMENSIONS,Err)
    572. 

  572. !     !Set the basis xi interpolation and number of Gauss points
    573. 

  573. !     IF(NUMBER_OF_DIMENSIONS==2) THEN
    574. 

  574. !       CALL CMISSBasis_InterpolationXiSet(BasisConcTwo,(/BASIS_XI_INTERPOLATION_CONC_TWO,BASIS_XI_INTERPOLATION_CONC_TWO/),Err)
    575. 

  575. !       CALL CMISSBasis_QuadratureNumberOfGaussXiSet(BasisConcTwo,(/BASIS_XI_GAUSS_CONC_TWO,BASIS_XI_GAUSS_CONC_TWO/),Err)
    576. 

  576. !     ELSE IF(NUMBER_OF_DIMENSIONS==3) THEN
    577. 

  577. !       CALL CMISSBasis_InterpolationXiSet(BasisConcTwo,(/BASIS_XI_INTERPOLATION_CONC_TWO,BASIS_XI_INTERPOLATION_CONC_TWO, & 
    578. 

  578. !         & BASIS_XI_INTERPOLATION_CONC_TWO/),Err)                         
    579. 

  579. !       CALL CMISSBasis_QuadratureNumberOfGaussXiSet(BasisConcTwo,(/BASIS_XI_GAUSS_CONC_TWO,BASIS_XI_GAUSS_CONC_TWO, & 
    580. 

  580. !         & BASIS_XI_GAUSS_CONC_TWO/),Err)
    581. 

  581. !     ENDIF
    582. 

  582. !     !Finish the creation of the basis
    583. 

  583. !     CALL CMISSBasis_CreateFinish(BasisConcTwo,Err)
    584. 

  584. !   ENDIF
    585. 

  585. 

  586.     BasisConcThree=BasisGeometry
    587. 

  587.   !
    588. 

  588.   !================================================================================================================================
    589. 

  589.   !
    590. 

  590. !   !MESH
    591. 

  591. !   !All types of physics utilize the same "mesh", but may be represented on individual mesh components.
    592. 

  592. !   TotalNumberOfSolidNodes = NUMBER_OF_NODES_GEOMETRY
    593. 

  593. !   TOTAL_NUMBER_OF_ALL_NODES = TOTAL_NUMBER_OF_NODES + TotalNumberOfSolidNodes
    594. 

  594. !   MESH_NUMBER_OF_ALL_COMPONENTS = MESH_NUMBER_OF_COMPONENTS
    595. 

  595. ! 
    596. 

  596. !   !Start the creation of mesh nodes
    597. 

  597. !   CALL CMISSNodes_Initialise(Nodes,Err)
    598. 

  598. !   CALL CMISSNodes_CreateStart(Region,TOTAL_NUMBER_OF_ALL_NODES,Nodes,Err)
    599. 

  599. !   CALL CMISSNodes_CreateFinish(Nodes,Err)
    600. 

  600. !   !Start the creation of the mesh
    601. 

  601. !   CALL CMISSMesh_Initialise(Mesh,Err)
    602. 

  602. !   CALL CMISSMesh_CreateStart(MeshUserNumber,Region,NUMBER_OF_DIMENSIONS,Mesh,Err)
    603. 

  603. !   !Set number of mesh elements
    604. 

  604. !   CALL CMISSMesh_NumberOfElementsSet(Mesh,TOTAL_NUMBER_OF_ELEMENTS,Err)
    605. 

  605. !   !Set number of mesh components
    606. 

  606. !   CALL CMISSMesh_NumberOfComponentsSet(Mesh,MESH_NUMBER_OF_ALL_COMPONENTS,Err)
    607. 

  607. !   !
    608. 

  608. !   CALL CMISSMeshElements_Initialise(MeshElementsGeometry,Err)
    609. 

  609. !   CALL CMISSMeshElements_Initialise(MeshElementsConcOne,Err)
    610. 

  610. !   CALL CMISSMeshElements_Initialise(MeshElementsConcTwo,Err)
    611. 

  611. !   CALL CMISSMeshElements_Initialise(MeshElementsConcThree,Err)
    612. 

  612.   MESH_COMPONENT_NUMBER_GEOMETRY=1
    613. 

  613.   MESH_COMPONENT_NUMBER_CONC_ONE=1
    614. 

  614.   MESH_COMPONENT_NUMBER_CONC_TWO=1
    615. 

  615.   MESH_COMPONENT_NUMBER_CONC_THREE=1
    616. 

  616. !   !Specify spatial mesh component
    617. 

  617. !   CALL CMISSMeshElements_CreateStart(Mesh,MESH_COMPONENT_NUMBER_GEOMETRY,BasisGeometry,MeshElementsGeometry,Err)
    618. 

  618. !   DO ELEMENT_NUMBER=1,TOTAL_NUMBER_OF_ELEMENTS
    619. 

  619. !     CALL CMISSMeshElements_NodesSet(MeshElementsGeometry,ELEMENT_NUMBER,CM%M(ELEMENT_NUMBER,1:NUMBER_OF_ELEMENT_NODES_GEOMETRY),Err)
    620. 

  620. !   ENDDO
    621. 

  621. !   CALL CMISSMeshElements_CreateFinish(MeshElementsGeometry,Err)
    622. 

  622. !   !Specify concentration one mesh component
    623. 

  623. ! ! !  IF(BASIS_XI_INTERPOLATION_CONC_ONE==BASIS_XI_INTERPOLATION_GEOMETRY) THEN
    624. 

  624. !      MeshElementsConcOne=MeshElementsGeometry
    625. 

  625. ! ! !   ELSE
    626. 

  626. ! ! !     MESH_COMPONENT_NUMBER_CONC_ONE=MESH_COMPONENT_NUMBER_GEOMETRY+1
    627. 

  627. ! !      CALL CMISSMeshElements_CreateStart(Mesh,MESH_COMPONENT_NUMBER_CONC_ONE,BasisConcOne,MeshElementsConcOne,Err)
    628. 

  628. ! ! !     DO ELEMENT_NUMBER=1,TOTAL_NUMBER_OF_ELEMENTS
    629. 

  629. ! ! !       CALL CMISSMeshElements_NodesSet(MeshElementsConcOne,ELEMENT_NUMBER,CM%V(ELEMENT_NUMBER, & 
    630. 

  630. ! ! !         & 1:NUMBER_OF_ELEMENT_NODES_CONC_ONE),Err)
    631. 

  631. ! ! !     ENDDO
    632. 

  632. !  !    CALL CMISSMeshElements_CreateFinish(MeshElementsConcOne,Err)
    633. 

  633. ! ! !  ENDIF
    634. 

  634. ! !   !Specify concentration two mesh component
    635. 

  635. ! ! !  IF(BASIS_XI_INTERPOLATION_CONC_TWO==BASIS_XI_INTERPOLATION_GEOMETRY) THEN
    636. 

  636. !      MeshElementsConcTwo=MeshElementsGeometry
    637. 

  637. ! ! !    MESH_COMPONENT_NUMBER_CONC_TWO=MESH_COMPONENT_NUMBER_GEOMETRY
    638. 

  638. ! ! !  ELSE IF(BASIS_XI_INTERPOLATION_CONC_TWO==BASIS_XI_INTERPOLATION_CONC_ONE) THEN
    639. 

  639. ! ! !    MeshElementsConcTwo=MeshElementsConcOne
    640. 

  640. ! ! !    MESH_COMPONENT_NUMBER_CONC_TWO=MESH_COMPONENT_NUMBER_CONC_ONE
    641. 

  641. ! ! !  ELSE
    642. 

  642. ! ! !    MESH_COMPONENT_NUMBER_CONC_TWO=MESH_COMPONENT_NUMBER_CONC_ONE+1
    643. 

  643. ! !     CALL CMISSMeshElements_CreateStart(Mesh,MESH_COMPONENT_NUMBER_CONC_TWO,BasisConcTwo,MeshElementsConcTwo,Err)
    644. 

  644. ! ! !    DO ELEMENT_NUMBER=1,TOTAL_NUMBER_OF_ELEMENTS
    645. 

  645. ! ! !      CALL CMISSMeshElements_NodesSet(MeshElementsConcTwo,ELEMENT_NUMBER,CM%P(ELEMENT_NUMBER, & 
    646. 

  646. ! ! !        & 1:NUMBER_OF_ELEMENT_NODES_CONC_TWO),Err)
    647. 

  647. ! ! !    ENDDO
    648. 

  648. ! !     CALL CMISSMeshElements_CreateFinish(MeshElementsConcTwo,Err)
    649. 

  649. ! !  ! ENDIF
    650. 

  650. ! !   !Specify concentration three mesh component
    651. 

  651. ! ! !  IF(BASIS_XI_INTERPOLATION_CONC_THREE==BASIS_XI_INTERPOLATION_GEOMETRY) THEN
    652. 

  652. !      MeshElementsConcThree=MeshElementsGeometry
    653. 

  653. ! ! !    MESH_COMPONENT_NUMBER_CONC_THREE=MESH_COMPONENT_NUMBER_GEOMETRY
    654. 

  654. ! ! !   ELSE IF(BASIS_XI_INTERPOLATION_CONC_THREE==BASIS_XI_INTERPOLATION_CONC_ONE) THEN
    655. 

  655. ! ! !     MeshElementsConcThree=MeshElementsConcOne
    656. 

  656. ! ! !    MESH_COMPONENT_NUMBER_CONC_THREE=MESH_COMPONENT_NUMBER_CONC_ONE
    657. 

  657. ! ! !  ELSE
    658. 

  658. ! ! !    MESH_COMPONENT_NUMBER_CONC_TWO=MESH_COMPONENT_NUMBER_CONC_ONE+1
    659. 

  659. ! !     CALL CMISSMeshElements_CreateStart(Mesh,MESH_COMPONENT_NUMBER_CONC_THREE,BasisConcThree,MeshElementsConcThree,Err)
    660. 

  660. ! ! !    DO ELEMENT_NUMBER=1,TOTAL_NUMBER_OF_ELEMENTS
    661. 

  661. ! ! !      CALL CMISSMeshElements_NodesSet(MeshElementsConcTwo,ELEMENT_NUMBER,CM%P(ELEMENT_NUMBER, & 
    662. 

  662. ! ! !        & 1:NUMBER_OF_ELEMENT_NODES_CONC_TWO),Err)
    663. 

  663. ! ! !    ENDDO
    664. 

  664. ! !     CALL CMISSMeshElements_CreateFinish(MeshElementsConcThree,Err)
    665. 

  665. ! ! !  ENDIF
    666. 

  666. ! 
    667. 

  667. !   !Finish the creation of the mesh
    668. 

  668. !   CALL CMISSMesh_CreateFinish(Mesh,Err)
    669. 

  669. 

  670.   !Start the creation of a generated mesh in the region
    671. 

  671.   CALL CMISSGeneratedMesh_Initialise(GeneratedMesh,Err)
    672. 

  672.   CALL CMISSGeneratedMesh_CreateStart(GeneratedMeshUserNumber,Region,GeneratedMesh,Err)
    673. 

  673.   !Set up a regular x*y*z mesh
    674. 

  674.   CALL CMISSGeneratedMesh_TypeSet(GeneratedMesh,CMISS_GENERATED_MESH_REGULAR_MESH_TYPE,Err)
    675. 

  675.   !Set the default basis
    676. 

  676.   CALL CMISSGeneratedMesh_BasisSet(GeneratedMesh,BasisGeometry,Err)   
    677. 

  677.   !Define the mesh on the region
    678. 

  678.   IF(NUMBER_GLOBAL_Z_ELEMENTS==0) THEN
    679. 

  679.     CALL CMISSGeneratedMesh_ExtentSet(GeneratedMesh,(/WIDTH,HEIGHT/),Err)
    680. 

  680.     CALL CMISSGeneratedMesh_NumberOfElementsSet(GeneratedMesh,(/NUMBER_GLOBAL_X_ELEMENTS,NUMBER_GLOBAL_Y_ELEMENTS/),Err)
    681. 

  681.   ELSE
    682. 

  682.     CALL CMISSGeneratedMesh_ExtentSet(GeneratedMesh,(/WIDTH,HEIGHT,LENGTH/),Err)
    683. 

  683.     CALL CMISSGeneratedMesh_NumberOfElementsSet(GeneratedMesh,(/NUMBER_GLOBAL_X_ELEMENTS,NUMBER_GLOBAL_Y_ELEMENTS, &
    684. 

  684.       & NUMBER_GLOBAL_Z_ELEMENTS/),Err)
    685. 

  685.   ENDIF
    686. 

  686.   !Finish the creation of a generated mesh in the region
    687. 

  687.   CALL CMISSMesh_Initialise(Mesh,Err)
    688. 

  688.   CALL CMISSGeneratedMesh_CreateFinish(GeneratedMesh,MeshUserNumber,Mesh,Err)
    689. 

  689. 

  690.   !
    691. 

  691.   !================================================================================================================================
    692. 

  692.   !
    693. 

  693.   !GEOMETRIC FIELD
    694. 

  694.   !Create a decomposition:
    695. 

  695.   !All mesh components share the same decomposition
    696. 

  696.   CALL CMISSDecomposition_Initialise(Decomposition,Err)
    697. 

  697.   CALL CMISSDecomposition_CreateStart(DecompositionUserNumber,Mesh,Decomposition,Err)
    698. 

  698.   !Set the decomposition to be a general decomposition with the specified number of domains
    699. 

  699.   CALL CMISSDecomposition_TypeSet(Decomposition,CMISS_DECOMPOSITION_CALCULATED_TYPE,Err)
    700. 

  700.   CALL CMISSDecomposition_NumberOfDomainsSet(Decomposition,NumberOfUserDomains,Err)
    701. 

  701.   !Finish the decomposition
    702. 

  702.   CALL CMISSDecomposition_CreateFinish(Decomposition,Err)
    703. 

  703. 

  704.   !Start to create a default (geometric) field on the region
    705. 

  705.   CALL CMISSField_Initialise(GeometricField,Err)
    706. 

  706.   CALL CMISSField_CreateStart(GeometricFieldUserNumber,Region,GeometricField,Err)
    707. 

  707.   !Set the field type
    708. 

  708.   CALL CMISSField_TypeSet(GeometricField,CMISS_FIELD_GEOMETRIC_TYPE,Err)
    709. 

  709.   !Set the decomposition to use
    710. 

  710.   CALL CMISSField_MeshDecompositionSet(GeometricField,Decomposition,Err)
    711. 

  711.   !Set the scaling to use
    712. 

  712.   CALL CMISSField_ScalingTypeSet(GeometricField,CMISS_FIELD_NO_SCALING,Err)
    713. 

  713. 

  714.   DO COMPONENT_NUMBER=1,NUMBER_OF_DIMENSIONS
    715. 

  715.     CALL CMISSField_ComponentMeshComponentSet(GeometricField,CMISS_FIELD_U_VARIABLE_TYPE,COMPONENT_NUMBER, & 
    716. 

  716.       & MESH_COMPONENT_NUMBER_GEOMETRY,Err)
    717. 

  717.   ENDDO
    718. 

  718.   !Finish creating the field
    719. 

  719.   CALL CMISSField_CreateFinish(GeometricField,Err)
    720. 

  720. 

  721.   !Update the geometric field parameters
    722. 

  722.   CALL CMISSGeneratedMesh_GeometricParametersCalculate(GeneratedMesh,GeometricField,Err)
    723. 

  723.   !Update the geometric field parameters
    724. 

  724. !   DO NODE_NUMBER=1,NUMBER_OF_NODES_GEOMETRY
    725. 

  725. !     DO COMPONENT_NUMBER=1,NUMBER_OF_DIMENSIONS
    726. 

  726. !       VALUE=CM%N(NODE_NUMBER,COMPONENT_NUMBER)
    727. 

  727. !       CALL CMISSField_ParameterSetUpdateNode(GeometricField,CMISS_FIELD_U_VARIABLE_TYPE,CMISS_FIELD_VALUES_SET_TYPE, & 
    728. 

  728. !         & CMISS_NO_GLOBAL_DERIV,NODE_NUMBER,COMPONENT_NUMBER,VALUE,Err)
    729. 

  729. !     ENDDO
    730. 

  730. !   ENDDO
    731. 

  731. !   CALL CMISSField_ParameterSetUpdateStart(GeometricField,CMISS_FIELD_U_VARIABLE_TYPE,CMISS_FIELD_VALUES_SET_TYPE,Err)
    732. 

  732. !   CALL CMISSField_ParameterSetUpdateFinish(GeometricField,CMISS_FIELD_U_VARIABLE_TYPE,CMISS_FIELD_VALUES_SET_TYPE,Err)
    733. 

  733.   !
    734. 

  734.   !================================================================================================================================
    735. 

  735.   !
    736. 

  736.   !EQUATIONS SETS - USING NEW ARGUMENTS TO ALLOW FOR MULTI-COMPARTMENT MODELS
    737. 

  737.   DO icompartment = 1,Ncompartments
    738. 

  738. 

  739.     EquationsSetFieldUserNumberDiffusion = 100_CMISSIntg+icompartment
    740. 

  740.     EquationsSetUserNumberDiffusion = 200_CMISSIntg+icompartment
    741. 

  741.     CALL CMISSField_Initialise(EquationsSetFieldDiffusion(icompartment),Err)
    742. 

  742.     CALL CMISSEquationsSet_Initialise(EquationsSetDiffusion(icompartment),Err)
    743. 

  743.     CALL CMISSEquationsSet_CreateStart(EquationsSetUserNumberDiffusion,Region,GeometricField,&
    744. 

  744.          & CMISS_EQUATIONS_SET_CLASSICAL_FIELD_CLASS, &
    745. 

  745.          & CMISS_EQUATIONS_SET_DIFFUSION_EQUATION_TYPE,CMISS_EQUATIONS_SET_MULTI_COMP_TRANSPORT_DIFFUSION_SUBTYPE,&
    746. 

  746.          & EquationsSetFieldUserNumberDiffusion,EquationsSetFieldDiffusion(icompartment),EquationsSetDiffusion(icompartment),&
    747. 

  747.          & Err)
    748. 

  748.     !Finish creating the equations set
    749. 

  749.     CALL CMISSEquationsSet_CreateFinish(EquationsSetDiffusion(icompartment),Err)
    750. 

  750.     CALL CMISSField_ParameterSetUpdateConstant(RegionUserNumber,EquationsSetFielduserNumberDiffusion,CMISS_FIELD_U_VARIABLE_TYPE, &
    751. 

  751.       & CMISS_FIELD_VALUES_SET_TYPE,1,icompartment,Err)
    752. 

  752.     CALL CMISSField_ParameterSetUpdateConstant(EquationsSetFieldDiffusion(icompartment),CMISS_FIELD_U_VARIABLE_TYPE, &
    753. 

  753.       & CMISS_FIELD_VALUES_SET_TYPE,2,Ncompartments,Err)
    754. 

  754.   END DO 
    755. 

  755. 

  756.   !-------------------------------------------------------------------------------------
    757. 

  757.   ! DEPENDENT FIELD: Shared
    758. 

  758.   CALL CMISSField_Initialise(DependentField,Err)
    759. 

  759.   CALL CMISSField_CreateStart(DependentFieldUserNumber,Region,DependentField,Err)
    760. 

  760.   CALL CMISSField_TypeSet(DependentField,CMISS_FIELD_GENERAL_TYPE,Err)  
    761. 

  761.   CALL CMISSField_MeshDecompositionSet(DependentField,Decomposition,Err)
    762. 

  762.   CALL CMISSField_GeometricFieldSet(DependentField,GeometricField,Err) 
    763. 

  763.   CALL CMISSField_DependentTypeSet(DependentField,CMISS_FIELD_DEPENDENT_TYPE,Err) 
    764. 

  764.   !Create 2N number of variables
    765. 

  765.   CALL CMISSField_NumberOfVariablesSet(DependentField,2*Ncompartments,Err) 
    766. 

  766.   !create two variables for each compartment
    767. 

  767.   ALLOCATE(VariableTypes(2*Ncompartments))
    768. 

  768.   DO num_var=1,Ncompartments
    769. 

  769.      VariableTypes(2*num_var-1)=CMISS_FIELD_U_VARIABLE_TYPE+(CMISS_FIELD_NUMBER_OF_VARIABLE_SUBTYPES*(num_var-1))
    770. 

  770.      VariableTypes(2*num_var)=CMISS_FIELD_DELUDELN_VARIABLE_TYPE+(CMISS_FIELD_NUMBER_OF_VARIABLE_SUBTYPES*(num_var-1))
    771. 

  771.   ENDDO
    772. 

  772.   CALL CMISSField_VariableTypesSet(DependentField,VariableTypes,Err) 
    773. 

  773.   !loop over the number of compartments
    774. 

  774.   DO icompartment=1,2*Ncompartments
    775. 

  775.     !set dimension type
    776. 

  776.     CALL CMISSField_DimensionSet(DependentField,VariableTypes(icompartment), &
    777. 

  777.        & CMISS_FIELD_SCALAR_DIMENSION_TYPE,Err)
    778. 

  778.     CALL CMISSField_NumberOfComponentsSet(DependentField,VariableTypes(icompartment),1,Err)
    779. 

  779.     CALL CMISSField_ComponentMeshComponentSet(DependentField,VariableTypes(icompartment),1, & 
    780. 

  780.        & MESH_COMPONENT_NUMBER_CONC_ONE,Err)
    781. 

  781.   ENDDO
    782. 

  782.   CALL CMISSField_CreateFinish(DependentField,Err)
    783. 

  783.   
    784. 

  784.   DO icompartment = 1,Ncompartments
    785. 

  785.     CALL CMISSEquationsSet_DependentCreateStart(EquationsSetDiffusion(icompartment),DependentFieldUserNumber,&
    786. 

  786.       & DependentField,Err)
    787. 

  787.     CALL CMISSEquationsSet_DependentCreateFinish(EquationsSetDiffusion(icompartment),Err)
    788. 

  788.   ENDDO
    789. 

  789. 

  790. !   !Set the mesh component to be used by the field components.
    791. 

  791. ! !   DO COMPONENT_NUMBER=1,NUMBER_OF_DIMENSIONS
    792. 

  792. ! !     CALL CMISSField_ComponentMeshComponentSet(DependentFieldDiffusionTwo,CMISS_FIELD_U_VARIABLE_TYPE,COMPONENT_NUMBER, & 
    793. 

  793. ! !       & MESH_COMPONENT_NUMBER_CONC_TWO,Err)
    794. 

  794. ! !     CALL CMISSField_ComponentMeshComponentSet(DependentFieldDiffusionTwo,CMISS_FIELD_DELUDELN_VARIABLE_TYPE,COMPONENT_NUMBER, & 
    795. 

  795. ! !       & MESH_COMPONENT_NUMBER_CONC_TWO,Err)
    796. 

  796. ! !   ENDDO
    797. 

  797. !   !Set the mesh component to be used by the field components.
    798. 

  798. ! !   DO COMPONENT_NUMBER=1,NUMBER_OF_DIMENSIONS
    799. 

  799. ! !     CALL CMISSField_ComponentMeshComponentSet(DependentFieldDiffusionTwo,CMISS_FIELD_U_VARIABLE_TYPE,COMPONENT_NUMBER, & 
    800. 

  800. ! !       & MESH_COMPONENT_NUMBER_CONC_TWO,Err)
    801. 

  801. ! !     CALL CMISSField_ComponentMeshComponentSet(DependentFieldDiffusionTwo,CMISS_FIELD_DELUDELN_VARIABLE_TYPE,COMPONENT_NUMBER, & 
    802. 

  802. ! !       & MESH_COMPONENT_NUMBER_CONC_TWO,Err)
    803. 

  803. ! !   ENDDO
    804. 

  804. !   !Set the mesh component to be used by the field components.
    805. 

  805. ! !   DO COMPONENT_NUMBER=1,NUMBER_OF_DIMENSIONS
    806. 

  806. ! !     CALL CMISSField_ComponentMeshComponentSet(DependentFieldDiffusionTwo,CMISS_FIELD_U_VARIABLE_TYPE,COMPONENT_NUMBER, & 
    807. 

  807. ! !       & MESH_COMPONENT_NUMBER_CONC_TWO,Err)
    808. 

  808. ! !     CALL CMISSField_ComponentMeshComponentSet(DependentFieldDiffusionTwo,CMISS_FIELD_DELUDELN_VARIABLE_TYPE,COMPONENT_NUMBER, & 
    809. 

  809. ! !       & MESH_COMPONENT_NUMBER_CONC_TWO,Err)
    810. 

  810. ! !   ENDDO
    811. 

  811. !   !Finish the equations set dependent field variables
    812. 

  812. 

  813.   !-------------------------------------------------------------------------------------
    814. 

  814.   ! INITIALISE DEPENDENT FIELDS
    815. 

  815. !   !Initialise dependent field (concentration one components)
    816. 

  816. !   CALL CMISSField_ComponentValuesInitialise(DependentField,CMISS_FIELD_U_VARIABLE_TYPE,CMISS_FIELD_VALUES_SET_TYPE, & 
    817. 

  817. !     & 1,1.0_CMISSDP,Err)
    818. 

  818. 

  819. !   !Initialise dependent field (concentration two components)
    820. 

  820. !   CALL CMISSField_ComponentValuesInitialise(DependentField,CMISS_FIELD_U2_VARIABLE_TYPE,CMISS_FIELD_VALUES_SET_TYPE, & 
    821. 

  821. !     & 1,INITIAL_FIELD_DIFFUSION_TWO,Err)
    822. 

  822. 

  823. !   !Initialise dependent field (concentration three components)
    824. 

  824. !   CALL CMISSField_ComponentValuesInitialise(DependentField,CMISS_FIELD_U3_VARIABLE_TYPE,CMISS_FIELD_VALUES_SET_TYPE, & 
    825. 

  825. !     & 1,INITIAL_FIELD_DIFFUSION_THREE,Err)
    826. 

  826. 

  827. 

  828.   !
    829. 

  829.   !================================================================================================================================
    830. 

  830.   !
    831. 

  831.   ALLOCATE(CouplingCoeffs(Ncompartments,Ncompartments))
    832. 

  832.   IF(Ncompartments==2)THEN
    833. 

  833. !     CouplingCoeffs(1,1)=1.0E-01_CMISSDP
    834. 

  834. ! !     CouplingCoeffs(1,2)=-1.0E-04_CMISSDP
    835. 

  835. ! !     CouplingCoeffs(2,1)=-1.0E-04_CMISSDP
    836. 

  836. !     CouplingCoeffs(1,2)=1.0E-01_CMISSDP
    837. 

  837. !     CouplingCoeffs(2,1)=1.0E-01_CMISSDP
    838. 

  838. !     CouplingCoeffs(2,2)=1.0E-01_CMISSDP
    839. 

  839.     CouplingCoeffs(1,1)=1.0E-01_CMISSDP
    840. 

  840.     CouplingCoeffs(1,2)=1.0E-01_CMISSDP
    841. 

  841.     CouplingCoeffs(2,1)=1.0E-01_CMISSDP
    842. 

  842.     CouplingCoeffs(2,2)=1.0E-01_CMISSDP
    843. 

  843.   ELSE IF(Ncompartments==3)THEN
    844. 

  844.     CouplingCoeffs(1,1)=1.0E-02_CMISSDP
    845. 

  845.     CouplingCoeffs(1,2)=1.0E-02_CMISSDP
    846. 

  846.     CouplingCoeffs(1,3)=0.0E-02_CMISSDP
    847. 

  847.     CouplingCoeffs(2,1)=1.0E-02_CMISSDP
    848. 

  848.     CouplingCoeffs(2,2)=2.0E-02_CMISSDP
    849. 

  849.     CouplingCoeffs(2,3)=1.0E-02_CMISSDP
    850. 

  850.     CouplingCoeffs(3,1)=0.0E-02_CMISSDP
    851. 

  851.     CouplingCoeffs(3,2)=1.0E-02_CMISSDP
    852. 

  852.     CouplingCoeffs(3,3)=1.0E-02_CMISSDP
    853. 

  853.   ELSE IF(Ncompartments==4)THEN
    854. 

  854.     CouplingCoeffs(1,1)=0.0E-02_CMISSDP
    855. 

  855.     CouplingCoeffs(1,2)=0.0E-02_CMISSDP
    856. 

  856.     CouplingCoeffs(1,3)=0.0E-02_CMISSDP
    857. 

  857.     CouplingCoeffs(1,4)=0.0E-02_CMISSDP
    858. 

  858.     CouplingCoeffs(2,1)=0.0E-02_CMISSDP
    859. 

  859.     CouplingCoeffs(2,2)=0.0E-02_CMISSDP
    860. 

  860.     CouplingCoeffs(2,3)=0.0E-02_CMISSDP
    861. 

  861.     CouplingCoeffs(2,4)=0.0E-02_CMISSDP
    862. 

  862.     CouplingCoeffs(3,1)=0.0E-02_CMISSDP
    863. 

  863.     CouplingCoeffs(3,2)=0.0E-02_CMISSDP
    864. 

  864.     CouplingCoeffs(3,3)=0.0E-02_CMISSDP
    865. 

  865.     CouplingCoeffs(3,4)=0.0E-02_CMISSDP
    866. 

  866.     CouplingCoeffs(4,1)=0.0E-02_CMISSDP
    867. 

  867.     CouplingCoeffs(4,2)=0.0E-02_CMISSDP
    868. 

  868.     CouplingCoeffs(4,3)=0.0E-02_CMISSDP
    869. 

  869.     CouplingCoeffs(4,4)=0.0E-02_CMISSDP
    870. 

  870.   ELSE IF(Ncompartments==5)THEN
    871. 

  871.     CouplingCoeffs(1,1)=0.0E-02_CMISSDP
    872. 

  872.     CouplingCoeffs(1,2)=0.0E-02_CMISSDP
    873. 

  873.     CouplingCoeffs(1,3)=0.0E-02_CMISSDP
    874. 

  874.     CouplingCoeffs(1,4)=0.0E-02_CMISSDP
    875. 

  875.     CouplingCoeffs(1,5)=0.0E-02_CMISSDP
    876. 

  876.     CouplingCoeffs(2,1)=0.0E-02_CMISSDP
    877. 

  877.     CouplingCoeffs(2,2)=0.0E-02_CMISSDP
    878. 

  878.     CouplingCoeffs(2,3)=0.0E-02_CMISSDP
    879. 

  879.     CouplingCoeffs(2,4)=0.0E-02_CMISSDP
    880. 

  880.     CouplingCoeffs(2,5)=0.0E-02_CMISSDP
    881. 

  881.     CouplingCoeffs(3,1)=0.0E-02_CMISSDP
    882. 

  882.     CouplingCoeffs(3,2)=0.0E-02_CMISSDP
    883. 

  883.     CouplingCoeffs(3,3)=0.0E-02_CMISSDP
    884. 

  884.     CouplingCoeffs(3,4)=0.0E-02_CMISSDP
    885. 

  885.     CouplingCoeffs(3,5)=0.0E-02_CMISSDP
    886. 

  886.     CouplingCoeffs(4,1)=0.0E-02_CMISSDP
    887. 

  887.     CouplingCoeffs(4,2)=0.0E-02_CMISSDP
    888. 

  888.     CouplingCoeffs(4,3)=0.0E-02_CMISSDP
    889. 

  889.     CouplingCoeffs(4,4)=0.0E-02_CMISSDP
    890. 

  890.     CouplingCoeffs(4,5)=0.0E-02_CMISSDP
    891. 

  891.     CouplingCoeffs(5,1)=0.0E-02_CMISSDP
    892. 

  892.     CouplingCoeffs(5,2)=0.0E-02_CMISSDP
    893. 

  893.     CouplingCoeffs(5,3)=0.0E-02_CMISSDP
    894. 

  894.     CouplingCoeffs(5,4)=0.0E-02_CMISSDP
    895. 

  895.     CouplingCoeffs(5,5)=0.0E-02_CMISSDP
    896. 

  896.   ELSE
    897. 

  897.     write(*,*) "Can't initialise coupling coefficients array."
    898. 

  898.   ENDIF
    899. 

  899.   !MATERIALS FIELDS - create the materials field
    900. 

  900.   !Auto-created field contains a U variable type to store the diffusion coefficient(s)
    901. 

  901.   !It also contains a V variable type to store the coupling coefficients 
    902. 

  902.   DO icompartment = 1,Ncompartments
    903. 

  903.     MaterialsFieldUserNumberDiffusion = 400+icompartment
    904. 

  904.     CALL CMISSField_Initialise(MaterialsFieldDiffusion(icompartment),Err)
    905. 

  905.     CALL CMISSEquationsSet_MaterialsCreateStart(EquationsSetDiffusion(icompartment),MaterialsFieldUserNumberDiffusion,&
    906. 

  906.          & MaterialsFieldDiffusion(icompartment),Err)
    907. 

  907.     CALL CMISSEquationsSet_MaterialsCreateFinish(EquationsSetDiffusion(icompartment),Err)
    908. 

  908.   END DO
    909. 

  909.   !Initialise the coupling coefficients
    910. 

  910.   !Need to devise a neater way of specifying these components - e.g. specify only the upper diagonal components, and then automatically fill out the rest
    911. 

  911. 

  912. 

  913.   DO icompartment = 1, Ncompartments
    914. 

  914.     DO COMPONENT_NUMBER=1, Ncompartments
    915. 

  915. !       CALL CMISSField_ComponentValuesInitialise(MaterialsFieldDiffusion(icompartment),CMISS_FIELD_V_VARIABLE_TYPE, &
    916. 

  916. !          & CMISS_FIELD_VALUES_SET_TYPE,COMPONENT_NUMBER,CouplingCoeffs(icompartment,COMPONENT_NUMBER),Err)
    917. 

  917.         CALL CMISSField_ParameterSetUpdateConstant(MaterialsFieldDiffusion(icompartment),CMISS_FIELD_V_VARIABLE_TYPE, &
    918. 

  918.           & CMISS_FIELD_VALUES_SET_TYPE,COMPONENT_NUMBER,CouplingCoeffs(icompartment,COMPONENT_NUMBER),Err)
    919. 

  919.     END DO
    920. 

  920.   END DO
    921. 

  921. 

  922. !   CALL CMISSField_ComponentValuesInitialise(MaterialsFieldDiffusionOne,CMISS_FIELD_U_VARIABLE_TYPE,CMISS_FIELD_VALUES_SET_TYPE, & 
    923. 

  923. !     & MaterialsFieldUserNumberDiffusionOne,POROSITY_PARAM_MAT_PROPERTIES,Err)
    924. 

  924. !   CALL CMISSField_ComponentValuesInitialise(MaterialsFieldDiffusionTwo,CMISS_FIELD_U_VARIABLE_TYPE,CMISS_FIELD_VALUES_SET_TYPE, & 
    925. 

  925. !     & MaterialsFieldUserNumberMatPropertiesPermOverVis,PERM_OVER_VIS_PARAM_MAT_PROPERTIES,Err)
    926. 

  926. 

  927.   !
    928. 

  928.   !================================================================================================================================
    929. 

  929.   !
    930. 

  930. 

  931.   !SOURCE FIELDS
    932. 

  932. 

  933.    !create the equations set source field variables for both equations sets 
    934. 

  934.   DO icompartment = 1,Ncompartments
    935. 

  935.     SourceFieldUserNumberDiffusion=700_CMISSIntg+icompartment
    936. 

  936.     CALL CMISSField_Initialise(SourceFieldDiffusion(icompartment),Err)
    937. 

  937.     CALL CMISSEquationsSet_SourceCreateStart(EquationsSetDiffusion(icompartment),SourceFieldUserNumberDiffusion,&
    938. 

  938.          & SourceFieldDiffusion(icompartment),Err)
    939. 

  939.     CALL CMISSEquationsSet_SourceCreateFinish(EquationsSetDiffusion(icompartment),Err)
    940. 

  940.   END DO 
    941. 

  941. 

  942.   !Create the equations set analytic field variables
    943. 

  943.   DO icompartment = 1,Ncompartments
    944. 

  944.     AnalyticFieldUserNumberDiffusion=900_CMISSIntg+icompartment
    945. 

  945.     CALL CMISSField_Initialise(AnalyticFieldDiffusion(icompartment),Err)
    946. 

  946. 

  947.     CALL CMISSEquationsSet_AnalyticCreateStart(EquationsSetDiffusion(icompartment), &
    948. 

  948.       & CMISS_EQUATIONS_SET_MULTI_COMP_DIFFUSION_TWO_COMP_TWO_DIM,&
    949. 

  949.       & AnalyticFieldUserNumberDiffusion,AnalyticFieldDiffusion(icompartment),Err)
    950. 

  950.   
    951. 

  951.     !Finish the equations set analytic field variables
    952. 

  952.     CALL CMISSEquationsSet_AnalyticCreateFinish(EquationsSetDiffusion(icompartment),Err)
    953. 

  953.   END DO 
    954. 

  954. 

  955.   !
    956. 

  956.   !================================================================================================================================
    957. 

  957.   !
    958. 

  958. 

  959.   !EQUATIONS
    960. 

  960.   DO icompartment=1,Ncompartments
    961. 

  961.     CALL CMISSEquations_Initialise(EquationsDiffusion(icompartment),Err)
    962. 

  962.     CALL CMISSEquationsSet_EquationsCreateStart(EquationsSetDiffusion(icompartment),EquationsDiffusion(icompartment),Err)
    963. 

  963.     CALL CMISSEquations_SparsityTypeSet(EquationsDiffusion(icompartment),CMISS_EQUATIONS_SPARSE_MATRICES,Err)
    964. 

  964.     CALL CMISSEquations_OutputTypeSet(EquationsDiffusion(icompartment),EQUATIONS_DIFFUSION_OUTPUT,Err)
    965. 

  965.     CALL CMISSEquationsSet_EquationsCreateFinish(EquationsSetDiffusion(icompartment),Err)
    966. 

  966.   ENDDO
    967. 

  967.   !
    968. 

  968.   !================================================================================================================================
    969. 

  969.   !
    970. 

  970.   !PROBLEMS
    971. 

  971. 

  972.   !Start the creation of a problem.
    973. 

  973.   CALL CMISSProblem_Initialise(Problem,Err)
    974. 

  974.   CALL CMISSControlLoop_Initialise(ControlLoop,Err)
    975. 

  975.   CALL CMISSProblem_CreateStart(ProblemUserNumber,Problem,Err)
    976. 

  976.   !Set the problem to be a coupled diffusion-diffusion problem
    977. 

  977.   CALL CMISSProblem_SpecificationSet(Problem,CMISS_PROBLEM_MULTI_PHYSICS_CLASS,CMISS_PROBLEM_MULTI_COMPARTMENT_TRANSPORT_TYPE, &
    978. 

  978.     & CMISS_PROBLEM_STANDARD_MULTI_COMPARTMENT_TRANSPORT_SUBTYPE,Err)
    979. 

  979.   !Finish the creation of a problem.
    980. 

  980.   CALL CMISSProblem_CreateFinish(Problem,Err)
    981. 

  981.   !Start the creation of the problem control loop
    982. 

  982.   CALL CMISSProblem_ControlLoopCreateStart(Problem,Err)
    983. 

  983.   !Get the control loop
    984. 

  984.   CALL CMISSProblem_ControlLoopGet(Problem,CMISS_CONTROL_LOOP_NODE,ControlLoop,Err)
    985. 

  985.   !Set the times
    986. 

  986.   CALL CMISSControlLoop_TimesSet(ControlLoop,LINEAR_SOLVER_DIFFUSION_START_TIME,&
    987. 

  987.     & LINEAR_SOLVER_DIFFUSION_STOP_TIME,LINEAR_SOLVER_DIFFUSION_TIME_INCREMENT,Err)
    988. 

  988.   !Set the output timing
    989. 

  989.   CALL CMISSControlLoop_TimeOutputSet(ControlLoop,LINEAR_SOLVER_DIFFUSION_OUTPUT_FREQUENCY,Err)
    990. 

  990.   !Finish creating the problem control loop
    991. 

  991.   CALL CMISSProblem_ControlLoopCreateFinish(Problem,Err)
    992. 

  992. 

  993.   !
    994. 

  994.   !================================================================================================================================
    995. 

  995.   !
    996. 

  996.   !SOLVERS
    997. 

  997. 

  998.   !Start the creation of the problem solvers
    999. 

  999.   CALL CMISSSolver_Initialise(SolverDiffusion,Err)
    1000. 

  1000.   CALL CMISSSolver_Initialise(LinearSolverDiffusion,Err)
    1001. 

  1001.   CALL CMISSProblem_SolversCreateStart(Problem,Err)
    1002. 

  1002. 

  1003.   CALL CMISSProblem_SolverGet(Problem,CMISS_CONTROL_LOOP_NODE,SolverDiffusionUserNumber,SolverDiffusion,Err)
    1004. 

  1004.   !Set the output type
    1005. 

  1005.   CALL CMISSSolver_OutputTypeSet(SolverDiffusion,LINEAR_SOLVER_DIFFUSION_OUTPUT_TYPE,Err)
    1006. 

  1006.   !Set the solver settings
    1007. 

  1007. !  IF(LINEAR_SOLVER_DIFFUSION_ONE_DIRECT_FLAG) THEN
    1008. 

  1008. !    CALL CMISSSolver_LinearTypeSet(LinearSolverDiffusionOne,CMISS_SOLVER_LINEAR_DIRECT_SOLVE_TYPE,Err)
    1009. 

  1009. !    CALL CMISSSolver_LibraryTypeSet(LinearSolverDiffusionOne,CMISS_SOLVER_MUMPS_LIBRARY,Err)
    1010. 

  1010. !  ELSE
    1011. 

  1011. !    CALL CMISSSolver_LinearTypeSet(LinearSolverDiffusionOne,CMISS_SOLVER_LINEAR_ITERATIVE_SOLVE_TYPE,Err)
    1012. 

  1012.    CALL CMISSSolver_DynamicLinearSolverGet(SolverDiffusion,LinearSolverDiffusion,Err)
    1013. 

  1013.     CALL CMISSSolver_LinearIterativeMaximumIterationsSet(LinearSolverDiffusion,MAXIMUM_ITERATIONS,Err)
    1014. 

  1014. !    CALL CMISSSolver_LinearIterativeDivergenceToleranceSet(LinearSolverDiffusionOne,DIVERGENCE_TOLERANCE,Err)
    1015. 

  1015. !    CALL CMISSSolver_LinearIterativeRelativeToleranceSet(LinearSolverDiffusionOne,RELATIVE_TOLERANCE,Err)
    1016. 

  1016. !    CALL CMISSSolver_LinearIterativeAbsoluteToleranceSet(LinearSolverDiffusionOne,ABSOLUTE_TOLERANCE,Err)
    1017. 

  1017. !    CALL CMISSSolver_LinearIterativeGMRESRestartSet(LinearSolverDiffusionOne,RESTART_VALUE,Err)
    1018. 

  1018. !  ENDIF
    1019. 

  1019.   !Finish the creation of the problem solver
    1020. 

  1020.   CALL CMISSProblem_SolversCreateFinish(Problem,Err)
    1021. 

  1021. 

  1022.   !
    1023. 

  1023.   !================================================================================================================================
    1024. 

  1024.   !
    1025. 

  1025.   !SOLVER EQUATIONS
    1026. 

  1026.   !Start the creation of the problem solver equations
    1027. 

  1027.   CALL CMISSSolver_Initialise(SolverDiffusion,Err)
    1028. 

  1028.   CALL CMISSSolverEquations_Initialise(SolverEquationsDiffusion,Err)
    1029. 

  1029.   CALL CMISSProblem_SolverEquationsCreateStart(Problem,Err)
    1030. 

  1030.   !
    1031. 

  1031.   CALL CMISSProblem_SolverGet(Problem,CMISS_CONTROL_LOOP_NODE,SolverDiffusionUserNumber,SolverDiffusion,Err)
    1032. 

  1032.   CALL CMISSSolver_SolverEquationsGet(SolverDiffusion,SolverEquationsDiffusion,Err)
    1033. 

  1033.   CALL CMISSSolverEquations_SparsityTypeSet(SolverEquationsDiffusion,CMISS_SOLVER_SPARSE_MATRICES,Er…
    1034.