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tests/__pycache__/ | ||
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*.whl | ||
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testFiles/output/ |
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##--------------------------------------------- | ||
## /Users/jimschaff/.vcell/simdata/temp/SimID_1585623750_0_.functions | ||
##--------------------------------------------- | ||
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subdomain1::J_flux0; (2.0 * (RanC_cyt - RanC_nuc)); ; Volume_VariableType; false | ||
subdomain1::J_r0; ((2.0 * RanC_cyt) - (1000.0 * Ran_cyt * C_cyt)); ; Volume_VariableType; false | ||
subdomain1::KFlux_nm_cyt; 1.0; ; Volume_Region_VariableType; false | ||
subdomain1::KFlux_nm_nuc; 1.0; ; Volume_Region_VariableType; false | ||
subdomain1::RanC_cyt_init_uM; (1.0 + x); ; Volume_VariableType; false | ||
subdomain0_subdomain1_membrane::s2; 0.0; ; Membrane_Region_VariableType; false | ||
subdomain1::Size_cyt; vcRegionVolume('subdomain1'); ; Volume_Region_VariableType; false | ||
subdomain0::Size_EC; vcRegionVolume('subdomain0'); ; Volume_Region_VariableType; false | ||
subdomain1::Size_nm; vcRegionVolume('subdomain1'); ; Volume_Region_VariableType; false | ||
subdomain1::Size_nuc; vcRegionVolume('subdomain1'); ; Volume_Region_VariableType; false | ||
subdomain0_subdomain1_membrane::Size_pm; vcRegionArea('subdomain0_subdomain1_membrane'); ; Membrane_Region_VariableType; false | ||
subdomain0_subdomain1_membrane::sobj_subdomain11_subdomain00_size; vcRegionArea('subdomain0_subdomain1_membrane'); ; Membrane_Region_VariableType; false | ||
subdomain0::vobj_subdomain00_size; vcRegionVolume('subdomain0'); ; Volume_Region_VariableType; false | ||
subdomain1::vobj_subdomain11_size; vcRegionVolume('subdomain1'); ; Volume_Region_VariableType; false | ||
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# Simulation Parameters | ||
SIMULATION_PARAM_BEGIN | ||
SOLVER SUNDIALS_PDE_SOLVER 1.0E-7 1.0E-9 0.1 | ||
BASE_FILE_NAME /Users/jimschaff/.vcell/simdata/temp/SimID_1585623750_0_ | ||
ENDING_TIME 0.01 | ||
TIME_STEP 0.005 | ||
KEEP_EVERY 1 | ||
SIMULATION_PARAM_END | ||
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# Model description: FEATURE name handle boundary_conditions | ||
MODEL_BEGIN | ||
FEATURE subdomain1 1 flux flux flux flux | ||
FEATURE subdomain0 0 flux flux flux flux | ||
MEMBRANE subdomain0_subdomain1_membrane subdomain1 subdomain0 flux flux flux flux | ||
MODEL_END | ||
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# Mesh file | ||
MESH_BEGIN | ||
VCG_FILE SimID_1585623750_0_.vcg | ||
MESH_END | ||
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# Variables : type name domain time_dependent_flag advection_flag grad_flag solve_whole_mesh_flag solve_regions | ||
VARIABLE_BEGIN | ||
VOLUME_PDE C_cyt subdomain1 false false false false subdomain1 | ||
VOLUME_PDE Ran_cyt subdomain1 false false false false subdomain1 | ||
VOLUME_PDE RanC_cyt subdomain1 false false false false subdomain1 | ||
VOLUME_PDE RanC_nuc subdomain1 false false false false subdomain1 | ||
VARIABLE_END | ||
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POST_PROCESSING_BLOCK_BEGIN | ||
POST_PROCESSING_BLOCK_END | ||
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COMPARTMENT_BEGIN subdomain1 | ||
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EQUATION_BEGIN RanC_cyt | ||
INITIAL (1.0 + x); | ||
RATE ( - ((2.0 * RanC_cyt) - (1000.0 * Ran_cyt * C_cyt)) - (2.0 * (RanC_cyt - RanC_nuc))); | ||
DIFFUSION 10.0; | ||
VELOCITY_X 0.0; | ||
VELOCITY_Y 0.0; | ||
BOUNDARY_XM 0.0; | ||
BOUNDARY_XP 0.0; | ||
BOUNDARY_YM 0.0; | ||
BOUNDARY_YP 0.0; | ||
EQUATION_END | ||
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EQUATION_BEGIN Ran_cyt | ||
INITIAL 0.0; | ||
RATE ((2.0 * RanC_cyt) - (1000.0 * Ran_cyt * C_cyt)); | ||
DIFFUSION 10.0; | ||
VELOCITY_X 0.0; | ||
VELOCITY_Y 0.0; | ||
BOUNDARY_XM 0.0; | ||
BOUNDARY_XP 0.0; | ||
BOUNDARY_YM 0.0; | ||
BOUNDARY_YP 0.0; | ||
EQUATION_END | ||
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EQUATION_BEGIN C_cyt | ||
INITIAL 0.0; | ||
RATE ((2.0 * RanC_cyt) - (1000.0 * Ran_cyt * C_cyt)); | ||
DIFFUSION 10.0; | ||
VELOCITY_X 0.0; | ||
VELOCITY_Y 0.0; | ||
BOUNDARY_XM 0.0; | ||
BOUNDARY_XP 0.0; | ||
BOUNDARY_YM 0.0; | ||
BOUNDARY_YP 0.0; | ||
EQUATION_END | ||
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EQUATION_BEGIN RanC_nuc | ||
INITIAL 4.5E-4; | ||
RATE (2.0 * (RanC_cyt - RanC_nuc)); | ||
DIFFUSION 10.0; | ||
VELOCITY_X 0.0; | ||
VELOCITY_Y 0.0; | ||
BOUNDARY_XM 0.0; | ||
BOUNDARY_XP 0.0; | ||
BOUNDARY_YM 0.0; | ||
BOUNDARY_YP 0.0; | ||
EQUATION_END | ||
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COMPARTMENT_END | ||
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COMPARTMENT_BEGIN subdomain0 | ||
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EQUATION_BEGIN C_cyt | ||
INITIAL 0.0; | ||
RATE 0.0; | ||
DIFFUSION 0.0; | ||
VELOCITY_X 0.0; | ||
VELOCITY_Y 0.0; | ||
BOUNDARY_XM 0.0; | ||
BOUNDARY_XP 0.0; | ||
BOUNDARY_YM 0.0; | ||
BOUNDARY_YP 0.0; | ||
EQUATION_END | ||
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EQUATION_BEGIN Ran_cyt | ||
INITIAL 0.0; | ||
RATE 0.0; | ||
DIFFUSION 0.0; | ||
VELOCITY_X 0.0; | ||
VELOCITY_Y 0.0; | ||
BOUNDARY_XM 0.0; | ||
BOUNDARY_XP 0.0; | ||
BOUNDARY_YM 0.0; | ||
BOUNDARY_YP 0.0; | ||
EQUATION_END | ||
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EQUATION_BEGIN RanC_cyt | ||
INITIAL 0.0; | ||
RATE 0.0; | ||
DIFFUSION 0.0; | ||
VELOCITY_X 0.0; | ||
VELOCITY_Y 0.0; | ||
BOUNDARY_XM 0.0; | ||
BOUNDARY_XP 0.0; | ||
BOUNDARY_YM 0.0; | ||
BOUNDARY_YP 0.0; | ||
EQUATION_END | ||
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EQUATION_BEGIN RanC_nuc | ||
INITIAL 0.0; | ||
RATE 0.0; | ||
DIFFUSION 0.0; | ||
VELOCITY_X 0.0; | ||
VELOCITY_Y 0.0; | ||
BOUNDARY_XM 0.0; | ||
BOUNDARY_XP 0.0; | ||
BOUNDARY_YM 0.0; | ||
BOUNDARY_YP 0.0; | ||
EQUATION_END | ||
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COMPARTMENT_END | ||
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MEMBRANE_BEGIN subdomain0_subdomain1_membrane subdomain1 subdomain0 | ||
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JUMP_CONDITION_BEGIN RanC_cyt | ||
FLUX subdomain1 0.0; | ||
JUMP_CONDITION_END | ||
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JUMP_CONDITION_BEGIN Ran_cyt | ||
FLUX subdomain1 0.0; | ||
JUMP_CONDITION_END | ||
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JUMP_CONDITION_BEGIN C_cyt | ||
FLUX subdomain1 0.0; | ||
JUMP_CONDITION_END | ||
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JUMP_CONDITION_BEGIN RanC_nuc | ||
FLUX subdomain1 0.0; | ||
JUMP_CONDITION_END | ||
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MEMBRANE_END | ||
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0 SimID_1585623750_0_0000.sim SimID_1585623750_0_00.zip 0 | ||
1 SimID_1585623750_0_0001.sim SimID_1585623750_0_00.zip 0.005 | ||
2 SimID_1585623750_0_0002.sim SimID_1585623750_0_00.zip 0.01 |
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Version 1.2 | ||
CartesianMesh { | ||
// X Y Z | ||
Size 51 51 1 | ||
Extent 10 10 1 | ||
Origin 0 0 0 | ||
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VolumeRegionsMapSubvolume { | ||
2 | ||
//VolRegID SubvolID Volume | ||
0 0 72.119999999999877 //subdomain0 | ||
1 1 27.879999999999583 //subdomain1 | ||
} | ||
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MembraneRegionsMapVolumeRegion { | ||
1 | ||
//MemRegID VolReg1 VolReg2 Surface | ||
0 1 0 18.471391535623798 | ||
} | ||
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VolumeElementsMapVolumeRegion { | ||
2601 Compressed | ||
789CEDD6D11100100C0451FA6F5A0306397166D84D01EFEF26A51011DDAE76EFBC902B8D8D0C672E | ||
EC4BEBC68EE3506286E6C40DC571289A1175505050FE545E5A4BCDD172182EC5F3C3AC4A39398C91 | ||
444474BF06C24102BA | ||
} | ||
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MembraneElements { | ||
116 | ||
//Indx Vol1 Vol2 Conn0 Conn1 Conn2 Conn3 MemRegID | ||
0 581 530 1 12 -1 -1 0 | ||
1 582 531 2 0 -1 -1 0 | ||
2 583 532 3 1 -1 -1 0 | ||
3 584 533 4 2 -1 -1 0 | ||
4 585 534 5 3 -1 -1 0 | ||
5 586 535 6 4 -1 -1 0 | ||
6 587 536 7 5 -1 -1 0 | ||
7 588 537 8 6 -1 -1 0 | ||
8 589 538 9 7 -1 -1 0 | ||
9 590 539 10 8 -1 -1 0 | ||
10 591 540 14 9 -1 -1 0 | ||
11 630 579 13 17 -1 -1 0 | ||
12 581 580 13 0 -1 -1 0 | ||
13 631 580 12 11 -1 -1 0 | ||
14 591 592 15 10 -1 -1 0 | ||
15 643 592 16 14 -1 -1 0 | ||
16 644 593 19 15 -1 -1 0 | ||
17 630 629 18 11 -1 -1 0 | ||
18 680 629 17 22 -1 -1 0 | ||
19 644 645 20 16 -1 -1 0 | ||
20 696 645 24 19 -1 -1 0 | ||
21 729 678 23 27 -1 -1 0 | ||
22 680 679 23 18 -1 -1 0 | ||
23 730 679 22 21 -1 -1 0 | ||
24 696 697 25 20 -1 -1 0 | ||
25 748 697 26 24 -1 -1 0 | ||
26 749 698 29 25 -1 -1 0 | ||
27 729 728 28 21 -1 -1 0 | ||
28 779 728 27 31 -1 -1 0 | ||
29 749 750 30 26 -1 -1 0 | ||
30 801 750 32 29 -1 -1 0 | ||
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58 1314 1315 60 56 -1 -1 0 | ||
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60 1365 1366 62 58 -1 -1 0 | ||
61 1388 1387 63 59 -1 -1 0 | ||
62 1416 1417 64 60 -1 -1 0 | ||
63 1439 1438 65 61 -1 -1 0 | ||
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66 1518 1519 69 64 -1 -1 0 | ||
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68 1541 1592 71 67 -1 -1 0 | ||
69 1569 1570 70 66 -1 -1 0 | ||
70 1569 1620 69 72 -1 -1 0 | ||
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72 1619 1620 75 70 -1 -1 0 | ||
73 1644 1643 74 71 -1 -1 0 | ||
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84 1799 1850 87 83 -1 -1 0 | ||
85 1821 1822 86 82 -1 -1 0 | ||
86 1821 1872 85 91 -1 -1 0 | ||
87 1851 1850 88 84 -1 -1 0 | ||
88 1851 1902 89 87 -1 -1 0 | ||
89 1852 1903 93 88 -1 -1 0 | ||
90 1870 1921 92 95 -1 -1 0 | ||
91 1871 1872 92 86 -1 -1 0 | ||
92 1871 1922 91 90 -1 -1 0 | ||
93 1904 1903 94 89 -1 -1 0 | ||
94 1904 1955 97 93 -1 -1 0 | ||
95 1920 1921 96 90 -1 -1 0 | ||
96 1920 1971 95 101 -1 -1 0 | ||
97 1956 1955 98 94 -1 -1 0 | ||
98 1956 2007 99 97 -1 -1 0 | ||
99 1957 2008 103 98 -1 -1 0 | ||
100 1969 2020 102 114 -1 -1 0 | ||
101 1970 1971 102 96 -1 -1 0 | ||
102 1970 2021 101 100 -1 -1 0 | ||
103 2009 2008 104 99 -1 -1 0 | ||
104 2009 2060 105 103 -1 -1 0 | ||
105 2010 2061 106 104 -1 -1 0 | ||
106 2011 2062 107 105 -1 -1 0 | ||
107 2012 2063 108 106 -1 -1 0 | ||
108 2013 2064 109 107 -1 -1 0 | ||
109 2014 2065 110 108 -1 -1 0 | ||
110 2015 2066 111 109 -1 -1 0 | ||
111 2016 2067 112 110 -1 -1 0 | ||
112 2017 2068 113 111 -1 -1 0 | ||
113 2018 2069 115 112 -1 -1 0 | ||
114 2019 2020 115 100 -1 -1 0 | ||
115 2019 2070 114 113 -1 -1 0 | ||
} | ||
} |
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