Index

_

__eq__() (mocafe.angie.base_classes.BaseCell method) __floordiv__() (mocafe.angie.af_sourcing.ConstantSourcesField method) (mocafe.angie.tipcells.TipCellsField method) (mocafe.expressions.EllipseField method) (mocafe.expressions.EllipsoidField method) (mocafe.expressions.PythonFunctionField method) (mocafe.expressions.SmoothCircle method)

__hash__() (mocafe.angie.base_classes.BaseCell method)

A

activate_tip_cell() (mocafe.angie.tipcells.TipCellManager method) add_tip_cell() (mocafe.angie.tipcells.TipCellsField method) angiogenesis_form() (in module mocafe.angie.forms)

angiogenesis_form_no_proliferation() (in module mocafe.angie.forms) angiogenic_factor_form() (in module mocafe.angie.forms) apply_sources() (mocafe.angie.af_sourcing.SourcesManager method) as_dataframe() (mocafe.fenut.parameters.Parameters method)

B

BaseCell (class in mocafe.angie.base_classes)

BestSolverFinder (class in mocafe.fenut.solvers) build_local_box() (in module mocafe.fenut.fenut)

C

cahn_hillard_form() (in module mocafe.angie.forms) clock_check() (mocafe.angie.base_classes.ClockChecker method) ClockChecker (class in mocafe.angie.base_classes) comm (in module mocafe.fenut.log) (in module mocafe.fenut.mansimdata) (in module mocafe.fenut.solvers)

compute_phi_c() (mocafe.angie.tipcells.TipCellsField method) compute_tip_cell_velocity() (mocafe.angie.tipcells.TipCellManager method) confgure_root_logger_with_standard_settings() (in module mocafe.fenut.log) ConstantSourcesField (class in mocafe.angie.af_sourcing)

D

DebugAdapter (class in mocafe.fenut.log) default_data_folder_name (in module mocafe.fenut.mansimdata) default_debug_log_file (in module mocafe.fenut.log) default_debug_log_folder (in module mocafe.fenut.log) default_info_log_file (in module mocafe.fenut.log)

default_info_log_folder (in module mocafe.fenut.log) default_main_log_folder (in module mocafe.fenut.log) default_runtime_folder_name (in module mocafe.fenut.mansimdata) default_saved_sim_folder_name (in module mocafe.fenut.mansimdata) df_dphi() (in module mocafe.litforms.prostate_cancer) divide_in_chunks() (in module mocafe.fenut.fenut)

E

EllipseField (class in mocafe.expressions) EllipsoidField (class in mocafe.expressions) estimate_cancer_area() (in module mocafe.math) estimate_capillaries_area() (in module mocafe.math) eval() (mocafe.angie.af_sourcing.ConstantSourcesField method) (mocafe.angie.tipcells.TipCellsField method) (mocafe.expressions.EllipseField method) (mocafe.expressions.EllipsoidField method) (mocafe.expressions.PythonFunctionField method) (mocafe.expressions.SmoothCircle method) (mocafe.expressions.SmoothCircularTumor method)

F

F() (mocafe.fenut.solvers.PETScProblem method) (mocafe.fenut.solvers.SNESProblem method) fibonacci_sphere() (in module mocafe.angie.base_classes) find_qucker_snes_solver() (mocafe.fenut.solvers.BestSolverFinder method)

find_quicker_gmres_pc() (mocafe.fenut.solvers.BestSolverFinder method) flatten_list_of_lists() (in module mocafe.fenut.fenut) from_dict() (in module mocafe.fenut.parameters) from_ods_sheet() (in module mocafe.fenut.parameters)

G

get_dimension() (mocafe.angie.base_classes.BaseCell method) get_distance() (mocafe.angie.base_classes.BaseCell method) get_global_source_cells() (mocafe.angie.af_sourcing.SourceMap method) get_global_tip_cells_list() (mocafe.angie.tipcells.TipCellManager method) get_latest_tip_cell_function() (mocafe.angie.tipcells.TipCellManager method)

get_local_source_cells() (mocafe.angie.af_sourcing.SourceMap method) get_mixed_function_space() (in module mocafe.fenut.fenut) get_position() (mocafe.angie.base_classes.BaseCell method) get_radius() (mocafe.angie.tipcells.TipCell method) get_value() (mocafe.fenut.parameters.Parameters method)

I

InfoCsvAdapter (class in mocafe.fenut.log) is_in_local_box() (in module mocafe.fenut.fenut) is_parameter() (mocafe.fenut.parameters.Parameters method)

is_point_inside() (mocafe.angie.tipcells.TipCell method) is_point_inside_mesh() (in module mocafe.fenut.fenut) is_value_present() (mocafe.fenut.parameters.Parameters method)

J

J() (mocafe.fenut.solvers.PETScProblem method) (mocafe.fenut.solvers.SNESProblem method)

L

load_parameters() (in module mocafe.fenut.fenut)

load_tip_cells_from_json() (in module mocafe.angie.tipcells) log_header (in module mocafe.fenut.log)

M

main() (in module mocafe.__main__) mocafe module mocafe.__main__ module mocafe.angie module mocafe.angie.af_sourcing module mocafe.angie.base_classes module mocafe.angie.forms module mocafe.angie.tipcells module mocafe.expressions module mocafe.fenut module mocafe.fenut.fenut module mocafe.fenut.log module mocafe.fenut.mansimdata module mocafe.fenut.parameters module mocafe.fenut.solvers module

mocafe.litforms module mocafe.litforms.prostate_cancer module mocafe.litforms.xu16 module mocafe.math module module mocafe mocafe.__main__ mocafe.angie mocafe.angie.af_sourcing mocafe.angie.base_classes mocafe.angie.forms mocafe.angie.tipcells mocafe.expressions mocafe.fenut mocafe.fenut.fenut mocafe.fenut.log mocafe.fenut.mansimdata mocafe.fenut.parameters mocafe.fenut.solvers mocafe.litforms mocafe.litforms.prostate_cancer mocafe.litforms.xu16 mocafe.math move() (mocafe.angie.tipcells.TipCell method) move_tip_cells() (mocafe.angie.tipcells.TipCellManager method)

P

Parameters (class in mocafe.fenut.parameters) PETScNewtonSolver (class in mocafe.fenut.solvers) PETScProblem (class in mocafe.fenut.solvers) process() (mocafe.fenut.log.DebugAdapter method) (mocafe.fenut.log.InfoCsvAdapter method)

prostate_cancer_chem_potential() (in module mocafe.litforms.prostate_cancer) prostate_cancer_form() (in module mocafe.litforms.prostate_cancer) prostate_cancer_nutrient_form() (in module mocafe.litforms.prostate_cancer) PythonFunctionField (class in mocafe.expressions)

R

RandomSourceMap (class in mocafe.angie.af_sourcing) rank (in module mocafe.fenut.log) (in module mocafe.fenut.mansimdata) (in module mocafe.fenut.solvers)

remove_global_source() (mocafe.angie.af_sourcing.SourceMap method) remove_sources_near_vessels() (mocafe.angie.af_sourcing.SourcesManager method) revert_tip_cells() (mocafe.angie.tipcells.TipCellManager method)

S

save_incremental_tip_cells() (mocafe.angie.tipcells.TipCellManager method) save_sim_info() (in module mocafe.fenut.mansimdata) save_tip_cells() (mocafe.angie.tipcells.TipCellManager method) set_value() (mocafe.fenut.parameters.Parameters method) setup_data_folder() (in module mocafe.fenut.mansimdata) setup_pvd_files() (in module mocafe.fenut.fenut) setup_xdmf_files() (in module mocafe.fenut.fenut) shf() (in module mocafe.math) sigmoid() (in module mocafe.math)

sim_info_file (in module mocafe.fenut.mansimdata) SmoothCircle (class in mocafe.expressions) SmoothCircularTumor (class in mocafe.expressions) SNESProblem (class in mocafe.fenut.solvers) solver_setup() (mocafe.fenut.solvers.PETScNewtonSolver method) SourceCell (class in mocafe.angie.af_sourcing) SourceMap (class in mocafe.angie.af_sourcing) sources_in_circle_points() (in module mocafe.angie.af_sourcing) SourcesManager (class in mocafe.angie.af_sourcing)

T

test_sim_name (in module mocafe.fenut.mansimdata) TipCell (class in mocafe.angie.tipcells)

TipCellManager (class in mocafe.angie.tipcells) TipCellsField (class in mocafe.angie.tipcells)

V

value_shape() (mocafe.angie.af_sourcing.ConstantSourcesField method) (mocafe.angie.tipcells.TipCellsField method) (mocafe.expressions.EllipseField method) (mocafe.expressions.EllipsoidField method) (mocafe.expressions.PythonFunctionField method) (mocafe.expressions.SmoothCircle method)

vascular_proliferation_form() (in module mocafe.angie.forms)

X

xu2016_nutrient_form() (in module mocafe.litforms.xu16)

xu_2016_cancer_form() (in module mocafe.litforms.xu16)