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1 file changed

+70
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‎src/hyperparams.cc‎

Lines changed: 70 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -98,32 +98,46 @@ void SimParam::LoadParams(const std::string& filename) {
9898
output_csv_interval = 12 * 60 / dt_step;
9999
}
100100

101-
load_double("volume_relaxation_rate_cytoplasm_apoptotic_cells", volume_relaxation_rate_cytoplasm_apoptotic_cells);
102-
load_double("volume_relaxation_rate_nucleus_apoptotic_cells", volume_relaxation_rate_nucleus_apoptotic_cells);
103-
load_double("volume_relaxation_rate_fluid_apoptotic_cells", volume_relaxation_rate_fluid_apoptotic_cells);
101+
load_double("volume_relaxation_rate_cytoplasm_apoptotic_cells",
102+
volume_relaxation_rate_cytoplasm_apoptotic_cells);
103+
load_double("volume_relaxation_rate_nucleus_apoptotic_cells",
104+
volume_relaxation_rate_nucleus_apoptotic_cells);
105+
load_double("volume_relaxation_rate_fluid_apoptotic_cells",
106+
volume_relaxation_rate_fluid_apoptotic_cells);
104107

105108
load_double("time_apoptosis", time_apoptosis);
106-
load_double("reduction_consumption_dead_cells", reduction_consumption_dead_cells);
109+
load_double("reduction_consumption_dead_cells",
110+
reduction_consumption_dead_cells);
107111
load_int("resolution_grid_substances", resolution_grid_substances);
108112

109113
load_double("diffusion_coefficient_oxygen", diffusion_coefficient_oxygen);
110114
load_double("decay_constant_oxygen", decay_constant_oxygen);
111-
load_double("diffusion_coefficient_immunostimulatory_factor", diffusion_coefficient_immunostimulatory_factor);
112-
load_double("decay_constant_immunostimulatory_factor", decay_constant_immunostimulatory_factor);
115+
load_double("diffusion_coefficient_immunostimulatory_factor",
116+
diffusion_coefficient_immunostimulatory_factor);
117+
load_double("decay_constant_immunostimulatory_factor",
118+
decay_constant_immunostimulatory_factor);
113119
load_double("oxygen_reference_level", oxygen_reference_level);
114120
load_double("initial_oxygen_level", initial_oxygen_level);
115121
load_double("oxygen_saturation", oxygen_saturation);
116122

117-
load_double("cell_repulsion_between_tumor_tumor", cell_repulsion_between_tumor_tumor);
118-
load_double("cell_repulsion_between_cart_cart", cell_repulsion_between_cart_cart);
119-
load_double("cell_repulsion_between_cart_tumor", cell_repulsion_between_cart_tumor);
120-
load_double("cell_repulsion_between_tumor_cart", cell_repulsion_between_tumor_cart);
123+
load_double("cell_repulsion_between_tumor_tumor",
124+
cell_repulsion_between_tumor_tumor);
125+
load_double("cell_repulsion_between_cart_cart",
126+
cell_repulsion_between_cart_cart);
127+
load_double("cell_repulsion_between_cart_tumor",
128+
cell_repulsion_between_cart_tumor);
129+
load_double("cell_repulsion_between_tumor_cart",
130+
cell_repulsion_between_tumor_cart);
121131

122132
load_double("max_relative_adhesion_distance", max_relative_adhesion_distance);
123-
load_double("cell_adhesion_between_tumor_tumor", cell_adhesion_between_tumor_tumor);
124-
load_double("cell_adhesion_between_cart_cart", cell_adhesion_between_cart_cart);
125-
load_double("cell_adhesion_between_cart_tumor", cell_adhesion_between_cart_tumor);
126-
load_double("cell_adhesion_between_tumor_cart", cell_adhesion_between_tumor_cart);
133+
load_double("cell_adhesion_between_tumor_tumor",
134+
cell_adhesion_between_tumor_tumor);
135+
load_double("cell_adhesion_between_cart_cart",
136+
cell_adhesion_between_cart_cart);
137+
load_double("cell_adhesion_between_cart_tumor",
138+
cell_adhesion_between_cart_tumor);
139+
load_double("cell_adhesion_between_tumor_cart",
140+
cell_adhesion_between_tumor_cart);
127141
load_double("length_box_mechanics", length_box_mechanics);
128142

129143
if (jfile.contains("dnew")) {
@@ -138,41 +152,59 @@ void SimParam::LoadParams(const std::string& filename) {
138152
dold = -0.5 * dt_mechanics;
139153
}
140154

141-
load_double("rate_secretion_immunostimulatory_factor", rate_secretion_immunostimulatory_factor);
142-
load_double("saturation_density_immunostimulatory_factor", saturation_density_immunostimulatory_factor);
155+
load_double("rate_secretion_immunostimulatory_factor",
156+
rate_secretion_immunostimulatory_factor);
157+
load_double("saturation_density_immunostimulatory_factor",
158+
saturation_density_immunostimulatory_factor);
143159
load_double("oncoprotein_mean", oncoprotein_mean);
144160
load_double("oncoprotein_standard_deviation", oncoprotein_standard_deviation);
145-
load_double("oxygen_saturation_for_proliferation", oxygen_saturation_for_proliferation);
161+
load_double("oxygen_saturation_for_proliferation",
162+
oxygen_saturation_for_proliferation);
146163
load_double("oxygen_limit_for_proliferation", oxygen_limit_for_proliferation);
147164
load_double("oxygen_limit_for_necrosis", oxygen_limit_for_necrosis);
148-
load_double("oxygen_limit_for_necrosis_maximum", oxygen_limit_for_necrosis_maximum);
165+
load_double("oxygen_limit_for_necrosis_maximum",
166+
oxygen_limit_for_necrosis_maximum);
149167
load_double("time_lysis", time_lysis);
150168
load_double("maximum_necrosis_rate", maximum_necrosis_rate);
151169

152-
load_double("default_oxygen_consumption_tumor_cell", default_oxygen_consumption_tumor_cell);
170+
load_double("default_oxygen_consumption_tumor_cell",
171+
default_oxygen_consumption_tumor_cell);
153172
load_double("default_volume_new_tumor_cell", default_volume_new_tumor_cell);
154-
load_double("default_volume_nucleus_tumor_cell", default_volume_nucleus_tumor_cell);
155-
load_double("default_fraction_fluid_tumor_cell", default_fraction_fluid_tumor_cell);
156-
load_double("average_time_transformation_random_rate", average_time_transformation_random_rate);
157-
load_double("standard_deviation_transformation_random_rate", standard_deviation_transformation_random_rate);
173+
load_double("default_volume_nucleus_tumor_cell",
174+
default_volume_nucleus_tumor_cell);
175+
load_double("default_fraction_fluid_tumor_cell",
176+
default_fraction_fluid_tumor_cell);
177+
load_double("average_time_transformation_random_rate",
178+
average_time_transformation_random_rate);
179+
load_double("standard_deviation_transformation_random_rate",
180+
standard_deviation_transformation_random_rate);
158181
load_double("adhesion_time", adhesion_time);
159182
load_double("oncoprotein_limit", oncoprotein_limit);
160183
load_double("oncoprotein_saturation", oncoprotein_saturation);
161184

162185
// Difference between saturation and limit. This is always calculated here
163186
oncoprotein_difference = oncoprotein_saturation - oncoprotein_limit;
164187

165-
load_double("volume_relaxation_rate_alive_tumor_cell_cytoplasm", volume_relaxation_rate_alive_tumor_cell_cytoplasm);
166-
load_double("volume_relaxation_rate_alive_tumor_cell_nucleus", volume_relaxation_rate_alive_tumor_cell_nucleus);
167-
load_double("volume_relaxation_rate_alive_tumor_cell_fluid", volume_relaxation_rate_alive_tumor_cell_fluid);
168-
169-
load_double("volume_relaxation_rate_cytoplasm_necrotic_swelling_tumor_cell", volume_relaxation_rate_cytoplasm_necrotic_swelling_tumor_cell);
170-
load_double("volume_relaxation_rate_nucleus_necrotic_swelling_tumor_cell", volume_relaxation_rate_nucleus_necrotic_swelling_tumor_cell);
171-
load_double("volume_relaxation_rate_fluid_necrotic_swelling_tumor_cell", volume_relaxation_rate_fluid_necrotic_swelling_tumor_cell);
172-
173-
load_double("volume_relaxation_rate_cytoplasm_necrotic_lysed_tumor_cell", volume_relaxation_rate_cytoplasm_necrotic_lysed_tumor_cell);
174-
load_double("volume_relaxation_rate_nucleus_necrotic_lysed_tumor_cell", volume_relaxation_rate_nucleus_necrotic_lysed_tumor_cell);
175-
load_double("volume_relaxation_rate_fluid_necrotic_lysed_tumor_cell", volume_relaxation_rate_fluid_necrotic_lysed_tumor_cell);
188+
load_double("volume_relaxation_rate_alive_tumor_cell_cytoplasm",
189+
volume_relaxation_rate_alive_tumor_cell_cytoplasm);
190+
load_double("volume_relaxation_rate_alive_tumor_cell_nucleus",
191+
volume_relaxation_rate_alive_tumor_cell_nucleus);
192+
load_double("volume_relaxation_rate_alive_tumor_cell_fluid",
193+
volume_relaxation_rate_alive_tumor_cell_fluid);
194+
195+
load_double("volume_relaxation_rate_cytoplasm_necrotic_swelling_tumor_cell",
196+
volume_relaxation_rate_cytoplasm_necrotic_swelling_tumor_cell);
197+
load_double("volume_relaxation_rate_nucleus_necrotic_swelling_tumor_cell",
198+
volume_relaxation_rate_nucleus_necrotic_swelling_tumor_cell);
199+
load_double("volume_relaxation_rate_fluid_necrotic_swelling_tumor_cell",
200+
volume_relaxation_rate_fluid_necrotic_swelling_tumor_cell);
201+
202+
load_double("volume_relaxation_rate_cytoplasm_necrotic_lysed_tumor_cell",
203+
volume_relaxation_rate_cytoplasm_necrotic_lysed_tumor_cell);
204+
load_double("volume_relaxation_rate_nucleus_necrotic_lysed_tumor_cell",
205+
volume_relaxation_rate_nucleus_necrotic_lysed_tumor_cell);
206+
load_double("volume_relaxation_rate_fluid_necrotic_lysed_tumor_cell",
207+
volume_relaxation_rate_fluid_necrotic_lysed_tumor_cell);
176208

177209
load_double("threshold_cancer_cell_type1", threshold_cancer_cell_type1);
178210
load_double("threshold_cancer_cell_type2", threshold_cancer_cell_type2);
@@ -186,13 +218,15 @@ void SimParam::LoadParams(const std::string& filename) {
186218
average_maximum_time_untill_apoptosis_cart = dt_cycle * 10.0 * 24.0 * 60.0;
187219
}
188220

189-
load_double("default_oxygen_consumption_cart", default_oxygen_consumption_cart);
221+
load_double("default_oxygen_consumption_cart",
222+
default_oxygen_consumption_cart);
190223
load_double("default_volume_new_cart_cell", default_volume_new_cart_cell);
191224
load_double("kill_rate_cart", kill_rate_cart);
192225
load_double("adhesion_rate_cart", adhesion_rate_cart);
193226
load_double("max_adhesion_distance_cart", max_adhesion_distance_cart);
194227
load_double("min_adhesion_distance_cart", min_adhesion_distance_cart);
195-
load_double("minimum_distance_from_tumor_to_spawn_cart", minimum_distance_from_tumor_to_spawn_cart);
228+
load_double("minimum_distance_from_tumor_to_spawn_cart",
229+
minimum_distance_from_tumor_to_spawn_cart);
196230
load_double("persistence_time_cart", persistence_time_cart);
197231
load_double("migration_bias_cart", migration_bias_cart);
198232
load_double("migration_speed_cart", migration_speed_cart);

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