diff --git a/sample_projects/biorobots/config/PhysiCell_settings.xml b/sample_projects/biorobots/config/PhysiCell_settings.xml index 2d5f7e46b..e005c6f71 100644 --- a/sample_projects/biorobots/config/PhysiCell_settings.xml +++ b/sample_projects/biorobots/config/PhysiCell_settings.xml @@ -1,557 +1,553 @@ - - -1000 - 1000 - -1000 - 1000 - -10 - 10 - 20 - 20 - 20 - true - - - - 2880 - min - micron - - 0.01 - 0.1 - 6 - - - - 6 - - - - output - - 2 - true - - - - 2 - true - - - - false - - - - - false - true - true - - - - - - 1000 - 0.1 - - 0 - 0 - - 0 - 0 - 0 - 0 - 0 - 0 - + + + + config + rules.csv + + + + + + -1000 + 1000 + -1000 + 1000 + -10 + 10 + 20 + 20 + 20 + true + + + + 2880 + min + micron + 0.01 + 0.1 + 6 + + + + 6 + + + + output + + 2 + true + + + 2 + true + + director signal + + + + + + + false + + + + + false + true + true + 0 + + + + + + 1000 + 0.1 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + - - - - 1000 - 0.4 - - 0 - 0 - - 0 - 0 - 0 - 0 - 0 - 0 - + + + 1000 + 0.4 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + - - - true - true - - - ./config/initial.mat - - - - ./config/dirichlet.mat - - - - - - - - - - 0.0 - - - - - - 0 - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - - - 0.0 - - 0 - 86400 - - - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 - - - - - - 2494 - 0.75 - 540 - 0.05 - 0.0045 - 0.0055 - 0 - 0 - 2.0 - - - - 0.4 - 10.0 - 1.25 - - 1.0 - 1.0 - 1.0 - - - 1.8 - 15.12 - - 4.0 - 10.0 - 0.5 - 10.0 - 0.0 - - - - 1 - 1 - .5 - - false - true - - false - director signal - 1 - - - false - false - - 0.0 - 0.0 - - - - - - - - 9.9 - 1 - 0 - 0 - - - 0.0 - 1 - 0.0 - 0.0 - - - - - 0 - - 0.0 - 0.0 - 0.0 - - - - 0.0 - 0.0 - 0.0 - - - 1 - - 0.0 - 0.0 - 0.0 - - - - - - - 0.0 - 0.0 - 0.0 - - - - - - 0 - - - - - - - - 0.0 - - - - - - 0 - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - - - 0.0 - - 0 - 86400 - - - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 - - - - - - 2494 - 0.75 - 540 - 0.05 - 0.0045 - 0.0055 - 0 - 0 - 2.0 - - - - 0.4 - 10.0 - 1.25 - - 1.0 - 1.0 - 1.0 - - - 1.8 - 15.12 - - 4.0 - 10.0 - 0.5 - 10.0 - 0.0 - - - - 1 - 1 - .5 - - false - true - - false - director signal - 1 - - - false - false - - 0.0 - 0.0 - - - - - - - - 0 - 1 - 0 - 0 - - - 9.9 - 1 - 0.0 - 0.0 - - - - - 0 - - 0.0 - 0.0 - 0.0 - - - - 0.0 - 0.0 - 0.0 - - - 1 - - 0.0 - 0.0 - 0.0 - - - - - - - 0.0 - 0.0 - 0.0 - - - - - - 1 - - - - - - - - 0.0 - - - - - - 0 - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - - - 0.0 - - 0 - 86400 - - - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 - - - - - - 2494 - 0.75 - 540 - 0.05 - 0.0045 - 0.0055 - 0 - 0 - 2.0 - - - - 0.4 - 10.0 - 1.25 - - 1.0 - 1.0 - 1.0 - - - 1.8 - 15.12 - - 4.0 - 10.0 - 0.5 - 10.0 - 0.0 - - - - 5 - 5 - .5 - - true - true - - false - director signal - 1 - - - true - false - - 0.0 - 1 - - - - - - - - 0 - 1 - 0 - 0 - - - 0.0 - 1 - 0.0 - 0.0 - - - - - 0 - - 0.0 - 0.0 - 0.0 - - - - 0.0 - 0.0 - 0.0 - - - 1 - - 0.0 - 0.0 - 0.0 - - - - - - - 0.0 - 0.0 - 0.0 - - - - - - 1 - - - - - - - - ./config - cells.csv - - - - - 0 + + true + true + + ./config/initial.mat + + + ./config/dirichlet.mat + + + + + + + + + + 0.0 + + + + + 0 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 0.0 + + 0 + 86400 + + + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 + + + + + 2494 + 0.75 + 540 + 0.05 + 0.0045 + 0.0055 + 0 + 0 + 2.0 + + + 0.4 + 10.0 + 1.25 + + 1.0 + 1.0 + 1.0 + + + 1.8 + 15.12 + + 0.5 + 10.0 + 0.0 + 12 + + + 1 + 1 + .5 + + false + true + + false + director signal + 1 + + + false + false + + 0.0 + 0.0 + + + + + + + 9.9 + 1 + 0 + 0 + + + 0.0 + 1 + 0.0 + 0.0 + + + + 0 + 0 + 0 + + 0.0 + 0.0 + 0.0 + + + 0.0 + 0.0 + 0.0 + + 1 + 0.1 + + 0.0 + 0.0 + 0.0 + + + + + 0.0 + 0.0 + 0.0 + + + + 0.0 + 0.0 + + + + 0 + + + + + + + + + 0.0 + + + + + 0 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 0.0 + + 0 + 86400 + + + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 + + + + + 2494 + 0.75 + 540 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0.0 + 0.0 + + + + + 0.0 + 0.0 + 0.0 + + + + 0.0 + 0.0 + + + + 1 + + + + + + + + + ./config + cells.csv + + + + 0 red blue @@ -564,5 +560,4 @@ 1 0.5 - \ No newline at end of file diff --git a/sample_projects/cancer_biorobots/config/PhysiCell_settings.xml b/sample_projects/cancer_biorobots/config/PhysiCell_settings.xml index 5263677a6..fd9e9221a 100644 --- a/sample_projects/cancer_biorobots/config/PhysiCell_settings.xml +++ b/sample_projects/cancer_biorobots/config/PhysiCell_settings.xml @@ -1,5 +1,14 @@ + + + + config + rules.csv + + + + -750 750 @@ -35,6 +44,12 @@ 60 true + + oxygen + + + + false @@ -45,6 +60,7 @@ false true true + 0 @@ -70,7 +86,7 @@ 0.1 0 - 0 + 0 0 0 @@ -86,7 +102,7 @@ .15625 0 - 0 + 0 0 0 @@ -138,12 +154,12 @@ 86400 - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 @@ -171,11 +187,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 10.0 0.0 + 12 1 @@ -221,7 +236,9 @@ - 0 + 0 + 0 + 0 0 0.0 @@ -232,7 +249,8 @@ 0.0 0.0 - 1 + 1 + 0.1 0 0.0 @@ -246,6 +264,10 @@ 0.0 + + 0.0 + 0.0 + 0 @@ -262,6 +284,8 @@ 0.0 0.0 + + @@ -292,12 +316,12 @@ 86400 - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 @@ -325,11 +349,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 10.0 0.0 + 12 1 @@ -375,7 +398,9 @@ - 0 + 0 + 0 + 0 0.0 0.0 @@ -386,7 +411,8 @@ 0.0 0.0 - 1 + 1 + 0.1 0.0 0.0 @@ -400,6 +426,10 @@ 0.0 + + 0.0 + 0.0 + 1 @@ -416,6 +446,8 @@ 0.0 0.0 + + @@ -446,12 +478,12 @@ 86400 - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 @@ -479,11 +511,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 10.0 0.0 + 12 2 @@ -529,7 +560,9 @@ - 0 + 0 + 0 + 0 0.0 0.0 @@ -540,7 +573,8 @@ 0.0 0.0 - 1 + 1 + 0.1 0.0 0.0 @@ -554,6 +588,10 @@ 0.0 + + 0.0 + 0.0 + 0 @@ -570,6 +608,8 @@ 0.5 0.5 + + @@ -581,7 +621,6 @@ - 0 0 10080 3 diff --git a/sample_projects/custom_division/config/PhysiCell_settings.xml b/sample_projects/custom_division/config/PhysiCell_settings.xml index 33ff1fb6c..c05d6a672 100644 --- a/sample_projects/custom_division/config/PhysiCell_settings.xml +++ b/sample_projects/custom_division/config/PhysiCell_settings.xml @@ -50,6 +50,7 @@ false true false + 0 @@ -146,6 +147,7 @@ 0.01 0.0 0.0 + 12 1 @@ -177,7 +179,9 @@ - 0 + 0 + 0 + 0 0.0 0 @@ -186,7 +190,8 @@ 0.0 0 - 1 + 1 + 0.1 0.0 0 @@ -198,10 +203,16 @@ 0 + + 0.0 + 0.0 + 1.0 + + @@ -267,6 +278,7 @@ 0.01 0.0 0.0 + 12 0.05 @@ -298,7 +310,9 @@ - 0 + 0 + 0 + 0 0 0 @@ -307,7 +321,8 @@ 0 0 - 1 + 1 + 0.1 0 0 @@ -319,10 +334,16 @@ 0 + + 0.0 + 0.0 + 1.0 + + @@ -343,7 +364,6 @@ - 0 0 - + \ No newline at end of file diff --git a/sample_projects/heterogeneity/config/PhysiCell_settings.xml b/sample_projects/heterogeneity/config/PhysiCell_settings.xml index 9bd89bc01..2cefeefa9 100644 --- a/sample_projects/heterogeneity/config/PhysiCell_settings.xml +++ b/sample_projects/heterogeneity/config/PhysiCell_settings.xml @@ -1,229 +1,234 @@ - - -1000 - 1000 - -1000 - 1000 - -10 - 10 - 20 - 20 - 20 - true - - - - 64800 - min - micron - - 0.01 - 0.1 - 6 - - - - 6 - - - - output - - 60 - true - - - - 60 - true - - - - false - - - - - false - true - false - - - - - - 100000.0 - 0.1 - - 38 - 38 - - 38 - 38 - 38 - 38 - 38 - 38 - - - - - true - true - - - ./config/initial.mat - - - - ./config/dirichlet.mat - - - - - - - - - - 0.00072 - - + + + + config + rules.csv + + + - - - 5.31667e-05 - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - - - 0.0 - - 0 - 86400 - - - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 - - - + + -1000 + 1000 + -1000 + 1000 + -10 + 10 + 20 + 20 + 20 + true + - - 2494 - 0.75 - 540 - 0.05 - 0.0045 - 0.0055 - 0 - 0 - 2.0 - + + 64800 + min + micron + 0.01 + 0.1 + 6 + - - 0.4 - 10.0 - 1.25 - - 1 - - - 1.8 - 15.12 - - 4.0 - 10.0 - 0.01 - 0.0 - 0.0 - + + 6 + - - 1 - 1 - .5 - - false - true - - false + + output + + 60 + true + + + 60 + true + oxygen - 1 - - - false - false - - 0.0 - - 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--git a/sample_projects/interactions/config/PhysiCell_settings.xml b/sample_projects/interactions/config/PhysiCell_settings.xml index 05f09bfc9..c702bb526 100644 --- a/sample_projects/interactions/config/PhysiCell_settings.xml +++ b/sample_projects/interactions/config/PhysiCell_settings.xml @@ -1,1529 +1,1566 @@ - - -400 - 400 - -400 - 400 - -10 - 10 - 20 - 20 - 20 - true - - - - 10080 - min - micron - - 0.01 - 0.1 - 6 - - - - 6 - - - - output - - 180 - true - - - - 30 - true - - - - false - - - - - false - true - false - false - - - - - - 100000.0 - 0.1 - - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - + + + + config + rules.csv + + + + + + -400 + 400 + -400 + 400 + -10 + 10 + 20 + 20 + 20 + true + + + + 10080 + min + micron + 0.01 + 0.1 + 6 + + + + 6 + + + + output + + 180 + true + + + 180 + true + + resource + + + + + + + false + + + + + false + true + false + false + 0 + + + + + + 100000.0 + 0.1 + + 1 + 1 + + 1 + 1 + 1 + 1 + 1 + 1 + - - - - 100 - 0.1 - - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - + + + 100 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- - false - true - - - - - - 100000.0 - 0.1 - - 38 - 0 - - 38 - 10 - 10 - 38 - 0 - 0 - - - - - 10 - .1 - - 0 - 0 - - 0 - 0 - 0 - 0 - 0 - 0 - - - - - 10 - 0.1 - - 0 - 0 - - 0 - 0 - 0 - 0 - 0 - 0 - - - - true - true - - ./config/initial.mat - - - ./config/dirichlet.mat - - - - - - - - - - 0.000 - - - - - 5.31667e-05 - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - - - 2.80E-03 - - 0 - 86400 - - - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 - - - - - 2494 - 0.75 - 540 - 0.05 - 0.0045 - 0.0055 - 0 - 0 - 2.0 - - - 0.4 - 10.0 - 1.25 - - 1 - - - 1.8 - 15.12 - - 4.0 - 10.0 - 0.01 - 0.0 - 0.0 - - - 1 - 1 - .5 - - false - true - - false - oxygen - 1 - - - false - false - - 0.0 - 0.0 - 0.0 - - - - - - - 0 - 1 - 10 - 0 - - - 0.0 - 1 - 0.0 - 0.0 - - - 0.0 - 1 - 0.0 - 0.0 - - - - 0 - - 0 - 0 - - - 0 - 0 - - 1 - - 0 - 0 - - - - - 0 - 0 - - - - - 1.0 - - - - - - - ./config - cells.csv - - - - - - - ./config - cell_rules_v2.csv - - - - - - - - 0 - 0 - - \ No newline at end of file diff --git a/sample_projects/rules_sample/config/PhysiCell_settings.xml b/sample_projects/rules_sample/config/PhysiCell_settings.xml index c4c65b93b..79972ef99 100644 --- a/sample_projects/rules_sample/config/PhysiCell_settings.xml +++ b/sample_projects/rules_sample/config/PhysiCell_settings.xml @@ -35,6 +35,12 @@ 60 true + + oxygen + + + + false @@ -45,6 +51,7 @@ false true false + 0 @@ -209,11 +216,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 0.0 0.0 + 12 0.1 @@ -273,7 +279,9 @@ - 0 + 0 + 0 + 0 0 0.0 @@ -290,7 +298,8 @@ 0.0 0.0 - 1 + 1 + 0.1 0 0.0 @@ -310,10 +319,16 @@ 0.0 + + 0.0 + 0.0 + 1.0 + + @@ -380,11 +395,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 0.0 0.0 + 12 1.0 @@ -444,7 +458,9 @@ - 0.01 + 0.01 + 0.01 + 0.01 0.0 0.0 @@ -461,7 +477,8 @@ 0.0 0.0 - 1.0 + 1.0 + 0.1 0.0 0.0 @@ -481,10 +498,16 @@ 0.0 + + 0.0 + 0.0 + 0.0 + + @@ -551,11 +574,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 0.0 0.0 + 12 1.0 @@ -615,7 +637,9 @@ - 0.01 + 0.01 + 0.01 + 0.01 0.0 0.0 @@ -632,7 +656,8 @@ 0.0 0.0 - 1.0 + 1.0 + 0.1 0.0 0.0 @@ -652,10 +677,16 @@ 0.0 + + 0.0 + 0.0 + 0.0 + + @@ -722,11 +753,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 0.0 0.0 + 12 1.0 @@ -786,7 +816,9 @@ - 0.01 + 0.01 + 0.01 + 0.01 0.0 0.0 @@ -803,7 +835,8 @@ 0.0 0.0 - 1.0 + 1.0 + 0.1 0.0 0.0 @@ -823,10 +856,16 @@ 0.0 + + 0.0 + 0.0 + 0.0 + + @@ -893,11 +932,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 0.0 0.0 + 12 0.1 @@ -957,7 +995,9 @@ - 0 + 0 + 0 + 0 0.0 0.0 @@ -974,7 +1014,8 @@ 0.0 0.0 - 1.0 + 1.0 + 0.1 0.0 0.0 @@ -994,10 +1035,16 @@ 0.0 + + 0.0 + 0.0 + 0.0 + + @@ -1064,11 +1111,10 @@ 1.8 15.12 - 4.0 - 10.0 0.01 0.0 0.0 + 12 0.01 @@ -1128,7 +1174,9 @@ - 0 + 0 + 0 + 0 0.0 0.0 @@ -1145,7 +1193,8 @@ 0.0 0.0 - 1.0 + 1.0 + 0.1 0.0 0.0 @@ -1165,10 +1214,16 @@ 0.0 + + 0.0 + 0.0 + 0.0 + + @@ -1190,7 +1245,6 @@ - 0 0 - + \ No newline at end of file diff --git a/sample_projects/template/config/PhysiCell_settings.xml b/sample_projects/template/config/PhysiCell_settings.xml index eeb0b79d1..d22bc606c 100644 --- a/sample_projects/template/config/PhysiCell_settings.xml +++ b/sample_projects/template/config/PhysiCell_settings.xml @@ -1,356 +1,238 @@ - - + - + + -500 + 500 + -500 + 500 + -10 + 10 + 20 + 20 + 20 + true + - - - -500 - 500 - -500 - 500 - -10 - 10 - 20 - 20 - 20 - true - - - - 7200 - min - micron - - 0.01 - 0.1 - 6 - - - - 6 - - - - output + + 7200 + min + micron + 0.01 + 0.1 + 6 + + + + 6 + - - 60 - true - - - - 60 - true - + + output + + 60 + true + + + 60 + true + substrate YlOrRd 0 1 - - - - false - - - - - false - true - false - - - - - - - 100000.0 - 10 - - 0 - 0 - - - - - - true - true - - - ./config/initial.mat - - - - ./config/dirichlet.mat - - - - - - - - - + + + false + + - - - - - - - 300.0 - 480 - 240 - 60 - - - - - - 5.31667e-05 - - - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - - - - 0.0 - - - - - 0 - 86400 - - - - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 - - - - - - 2494 - 0.75 - 540 - - 0.05 - 0.0045 - 0.0055 - - 0 - 0 - - 2.0 - - - - 0.4 - 10.0 - 1.25 - - 1 - - - 1.8 - 15.12 - - 4.0 - 10.0 - 0.01 - 0.0 - 0.0 - 12 - - - - 1 - 1 - .5 - - - false - true - - false - substrate - 1 - - - - - - - 0 - 1 - 0 - 0 - - + + false + true + false + 0 + - - 0 - - 0 - - - 0 - - 1 - - 0 - - - - - 0 - - + + + + 100000.0 + 10 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + + + + true + true + + ./config/initial.mat + + + ./config/dirichlet.mat + + + + + + + + + 300.030003 + 480.076812 + 239.980802 + 59.998800 + + + + + 5.31667e-05 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 0.0 + + 0 + 86400 + + + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 + + + + + 2494 + 0.75 + 540 + 0.05 + 0.0045 + 0.0055 + 0 + 0 + 2.0 + + + 0.4 + 10.0 + 1.25 + + 1 + + + 1.8 + 15.12 + + 0.01 + 0.0 + 0.0 + 12 + + + 1 + 1 + .5 + + false + true + + false + substrate + 1 + + + false + false + + 0.0 + + + + + + + 0 + 1 + 0 + 0 + + + + 0 + 0 + 0 + + 0 + + + 0 + + 1 + 0.1 + + 0 + + + + + 0 + + + + 0.0 + 0.0 + + + + 1.0 + + + + Volume + 4 + 2 + 100000 + + + apoptosis + 1e-6 + 1e-2 + + + + - - - - 1.0 - + + + ./config + cells.csv + + - - - Volume - 4 - 2 - 100000 - - - apoptosis - 1e-6 - 1e-2 - - - - - - - - - ./config - cells.csv - - - @@ -360,14 +242,8 @@ - - - 0 - - - - - 5 - - - + + + 5 + + \ No newline at end of file diff --git a/sample_projects/virus_macrophage/config/PhysiCell_settings.xml b/sample_projects/virus_macrophage/config/PhysiCell_settings.xml index 9c47fed12..5e3be1a7c 100644 --- a/sample_projects/virus_macrophage/config/PhysiCell_settings.xml +++ b/sample_projects/virus_macrophage/config/PhysiCell_settings.xml @@ -1,422 +1,423 @@ - - + - + + + + config + rules.csv + + + - - - -500 - 500 - -500 - 500 - -10 - 10 - 20 - 20 - 20 - true - - - - 2880 - min - micron - - 0.01 - 0.1 - 6 - - - - 8 - - - - output + + -500 + 500 + -500 + 500 + -10 + 10 + 20 + 20 + 20 + true + - - 60 - true - - - - 10 - true - - - - false - - - - - false - true - false - + + 2880 + min + micron + 0.01 + 0.1 + 6 + - - - - 1e3 - 0 - - 0 - 0 - - - - - 1e4 - 1 - - 0 - 0 - - - - true - true - - - ./config/initial.mat - - - - ./config/dirichlet.mat - - - - - - - - - - 0 - 0.00208333 - 0.00416667 - 0.0166667 - - - - - - 0 - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - + + 8 + - - 0.0 - - - - - 0 - 86400 - - - - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 - - - + + output + + 60 + true + + + 10 + true + + virus + + + + + + + false + + - - 2494 - 0.75 - 540 - - 0.05 - 0.0045 - 0.0055 - - 0 - 0 - - 2.0 - - - - 0.4 - 10.0 - 1.25 - - - 1.8 - 15.12 - - - - - 1 - 1 - .75 - - - false - true - - false - virus - 1 - - - - - - - 0 - 1 - 10 - 0 - - - - 0 - 1 - 0 - 0 - - - - - - 0.15 - - 1 - 100 - - 10 - 1 + + false + true + false + 0 + - 1 - 0.01 - - - - - - - - 0 - 0.00208333 - 0.00416667 - 0.0166667 - - - - - - 0 - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - + + + + 1e3 + 0 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + + + + + 1e4 + 1 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + + + + true 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diff --git a/sample_projects/worm/config/PhysiCell_settings.xml b/sample_projects/worm/config/PhysiCell_settings.xml index 6cdee6e31..1c7ced5f9 100644 --- a/sample_projects/worm/config/PhysiCell_settings.xml +++ b/sample_projects/worm/config/PhysiCell_settings.xml @@ -1,299 +1,242 @@ - - - - - - - -500 - 500 - -500 - 500 - -10 - 10 - 20 - 20 - 20 - true - - - - 3000 - min - micron - - 0.01 - 0.1 - 6 - - - - 6 - - - - output - - 360 - true - - - - 3 - true - - - - false - - - - - false - true - true - + + + + config + rules.csv + + + - - - - 100000.0 - 10 - - 0 - 0 - - - - true - true - - - ./config/initial.mat - - - - ./config/dirichlet.mat - - - - - - - - - + + -500 + 500 + -500 + 500 + -10 + 10 + 20 + 20 + 20 + true + - - - - 0.0 - 0.00208333 - 0.00416667 - 0.0166667 - - - - - - 0 - - - 516 - - - 0.05 - 0 - 1.66667e-02 - 5.83333e-03 - 0 - 2.0 - - + + 3000 + min + micron + 0.01 + 0.1 + 6 + - - 0.0 - - 0 - 86400 - - - - 1.11667e-2 - 8.33333e-4 - 5.33333e-5 - 2.16667e-3 - 0 - 2.0 - - - + + 6 + - - 2494 - 0.75 - 540 - - 0.05 - 0.0045 - 0.0055 - - 0 - 0 - - 2.0 - - - - 0.4 - 10.0 - 1.25 - - - 1.8 - 15.12 - - - - - 1 - 1 - .5 - - - true - true - - true - signal - 1 - - - - - - - 10 - 1 - 0 - 0 - - + + output + + 360 + true + + + 3 + true + + signal + + + + + + + false + + + + + false + true + true + 0 + - - - - 2 - - 1 - 1 - 0.1 - - - - - - - ./config - cells.csv - - - - - 0 - - - - - 250 - 0.03 + + + + 100000.0 + 10 + + 0 + 0 + + + true + true + + ./config/initial.mat + + + ./config/dirichlet.mat + + + - - -1 - 0.75 - 0.5 - 60 + + + + + + 0.0 + 0.00208333 + 0.00416667 + 0.0166667 + + + + + 0 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 0.0 + + 0 + 86400 + + + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 + + + + + 2494 + 0.75 + 540 + 0.05 + 0.0045 + 0.0055 + 0 + 0 + 2.0 + + + 0.4 + 10.0 + 1.25 + + 1.0 + + + 1.8 + 15.12 + + 0.01 + 0.0 + 0.0 + 12 + + + 1 + 1 + .5 + + true + true + + true + signal + 1 + + + false + false + + 0.0 + + + 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