Commit 9e4147c3 authored by gsaxena's avatar gsaxena
Browse files

Two main features:

1. Code does not crash now in Matlab file writing when there are no cells in a sub-domain (earlier it was crashing because we dereference the *all_cells array
in Matlab file writing even when there are no cells - so obviously it crashes).
2. Program displays a m,essage that the total number of voxels in the X-direction are NOT EXACTLY divisible by the total number of MPI processes and it aborts.
parent 7d507970
......@@ -1498,6 +1498,21 @@ void Cartesian_Mesh::resize( double x_start, double x_end, double y_start, doubl
/*--------------------------------------------*/
int local_x_nodes = x_nodes/dims[1];
/*----------------------------------------------------------------*/
/* Here I need to insert a perfect divisibility check and message */
/*----------------------------------------------------------------*/
if(x_nodes % dims[1] != 0)
{
if(world.rank == 0)
{
std::cout<<"Error: Total voxels in X-Direction are NOT perfectly divisible by the total MPI processes"<<std::endl;
std::cout<<"Aborting the program"<<std::endl;
}
MPI_Abort(cart_topo.mpi_cart_comm, -1);
}
int local_y_nodes = y_nodes/dims[0];
int local_z_nodes = z_nodes/dims[2];
......
......@@ -27,6 +27,18 @@ namespace DistPhy
init_comm = MPI_COMM_WORLD;
MPI_Comm_size(init_comm, &size);
MPI_Comm_rank(init_comm, &rank);
if(rank == 0)
{
cout<<" _____ _ _ _____ _ _ __ __ _ ___ __ \n";
cout<<" | __ \\| | (_)/ ____| | | | \\ \\ / / (_) / _ \\/_ |\n";
cout<<" | |__) | |__ _ _ ___ _| | ___| | |_____\\ V / __ _____ _ __ ___ _ ___ _ __ ______| | | || |\n";
cout<<" | ___/| '_ \\| | | / __| | | / _ \\ | |______> < \\ \\ / / _ \\ '__/ __| |/ _ \\| '_ \\______| | | || |\n";
cout<<" | | | | | | |_| \\__ \\ | |___| __/ | | / . \\ \\ V / __/ | \\__ \\ | (_) | | | | | |_| || |\n";
cout<<" |_| |_| |_|\\__, |___/_|\\_____\\___|_|_| /_/ \\_\\ \\_/ \\___|_| |___/_|\\___/|_| |_| \\___(_)_|\n";
cout<<" __/ | \n";
cout<<" |___/ \n";
}
}
......
This diff is collapsed.
<?xml version="1.0" encoding="UTF-8"?>
<!--
/*
###############################################################################
# If you use PhysiCell in your project, please cite PhysiCell and the version #
# number, such as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# See VERSION.txt or call get_PhysiCell_version() to get the current version #
# x.y.z. Call display_citations() to get detailed information on all cite-#
# able software used in your PhysiCell application. #
# #
# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
# as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
# with BioFVM [2] to solve the transport equations. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
# llelized diffusive transport solver for 3-D biological simulations, #
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
###############################################################################
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
# modification, are permitted provided that the following conditions are met: #
# #
# 1. Redistributions of source code must retain the above copyright notice, #
# this list of conditions and the following disclaimer. #
# #
# 2. Redistributions in binary form must reproduce the above copyright #
# notice, this list of conditions and the following disclaimer in the #
# documentation and/or other materials provided with the distribution. #
# #
# 3. Neither the name of the copyright holder nor the names of its #
# contributors may be used to endorse or promote products derived from this #
# software without specific prior written permission. #
# #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
# POSSIBILITY OF SUCH DAMAGE. #
# #
###############################################################################
*/
-->
<!--
<user_details />
-->
<PhysiCell_settings version="devel-version">
<domain>
<!-- <x_min>-2700</x_min> -->
<!-- <x_max>2700</x_max> -->
<!-- <y_min>-600</y_min> -->
<!-- <y_max>600</y_max> -->
<!-- <z_min>-600</z_min> -->
<!-- <z_max>600</z_max> -->
<x_min>-3000</x_min>
<x_max>3000</x_max>
<y_min>-1000</y_min>
<y_max>1000</y_max>
<z_min>-1000</z_min>
<z_max>1000</z_max>
<dx>20</dx>
<dy>20</dy>
<dz>20</dz>
<use_2D>false</use_2D>
</domain>
<overall>
<max_time units="min">8000</max_time> <!-- 1400 -->
<time_units>min</time_units>
<space_units>micron</space_units>
<dt_diffusion units="min">0.02</dt_diffusion>
<dt_mechanics units="min">0.1</dt_mechanics>
<dt_phenotype units="min">2</dt_phenotype>
</overall>
<parallel>
<omp_num_threads>1</omp_num_threads>
</parallel>
<save>
<folder>output</folder> <!-- use . for root -->
<full_data>
<interval units="min">100</interval>
<enable>false</enable>
</full_data>
<SVG>
<interval units="min">100</interval>
<enable>true</enable>
</SVG>
<legacy_data>
<enable>false</enable>
</legacy_data>
</save>
<microenvironment_setup>
<variable name="oxygen" units="mmHg" ID="0">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">100000.0</diffusion_coefficient>
<decay_rate units="1/min">.1</decay_rate>
</physical_parameter_set>
<initial_condition units="mmHg">38.0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="true">38.0</Dirichlet_boundary_condition>
</variable>
<variable name="tnf" units="TNF/um^3" ID="1">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">1200.0</diffusion_coefficient>
<decay_rate units="1/min">.0275</decay_rate>
</physical_parameter_set>
<initial_condition units="molecules/voxel">0.0</initial_condition>
<Dirichlet_boundary_condition units="molecules/voxel" enabled="false">0.0</Dirichlet_boundary_condition>
</variable>
<options>
<calculate_gradients>true</calculate_gradients>
<track_internalized_substrates_in_each_agent>true</track_internalized_substrates_in_each_agent>
<!-- not yet supported -->
<initial_condition type="matlab" enabled="false">
<filename>./config/initial.mat</filename>
</initial_condition>
<!-- not yet supported -->
<dirichlet_nodes type="matlab" enabled="false">
<filename>./config/dirichlet.mat</filename>
</dirichlet_nodes>
</options>
</microenvironment_setup>
<cell_definitions>
<cell_definition name="default" ID="0">
<phenotype>
<cycle code="5" name="live_cells_cycle_model">
<!-- using higher than normal significant digits to match divisions in default code -->
<phase_transition_rates units="1/min">
<!-- Cycle duration -->
<rate start_index="0" end_index="0" fixed_duration="false">0.00075</rate>
</phase_transition_rates>
</cycle>
<death>
<model code="100" name="apoptosis">
<death_rate units="1/min">5.31667e-05</death_rate>
<phase_durations units="min">
<duration index="0" fixed_duration="true">516</duration>
</phase_durations>
<!--
<phase_transition_rates units="1/min">
<rate start_index="0" end_index="1" fixed_duration="false">0.00193798</rate>
</phase_transition_rates> -->
<parameters>
<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</parameters>
</model>
<model code="101" name="necrosis">
<rate units="1/min">0.0</rate>
<phase_durations units="min">
<duration index="0" fixed_duration="true">0</duration>
<duration index="1" fixed_duration="true">86400</duration>
</phase_durations>
<!--
<transition_rates units="1/min">
<rate start_index="0" end_index="1" fixed_duration="false">9e9</rate>
<rate start_index="1" end_index="2" fixed_duration="true">1.15741e-5</rate>
</transition_rates>
-->
<parameters>
<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</parameters>
</model>
</death>
<secretion>
<substrate name="oxygen">
<secretion_rate units="1/min">0</secretion_rate>
<secretion_target units="substrate density">38</secretion_target>
<uptake_rate units="1/min">10</uptake_rate>
<net_export_rate units="total substrate/min">0</net_export_rate>
</substrate>
<substrate name="tnf">
<secretion_rate units="1/min">0</secretion_rate>
<secretion_target units="substrate density">0</secretion_target>
<uptake_rate units="1/min">0</uptake_rate>
<net_export_rate units="total substrate/min">0</net_export_rate>
</substrate>
</secretion>
<molecular />
<intracellular type="maboss">
<bnd_filename>./config/TNF_nodes.bnd</bnd_filename>
<cfg_filename>./config/TNF_conf.cfg</cfg_filename>
<time_step>10</time_step>
</intracellular>
</phenotype>
<custom_data>
<!-- Time steps for maboss update-->
<next_physiboss_run units="dimensionless">10.</next_physiboss_run>
<!-- Molecular model internal variables-->
<TNFR_binding_rate type="double" units="1/min" description="TNF receptor binding rate">0.243</TNFR_binding_rate> <!-- 0.243 -->
<TNFR_endocytosis_rate type="double" units="1/min" description="TNF receptor-TNF endocytosis rate">0.128</TNFR_endocytosis_rate>
<TNFR_recycling_rate type="double" units="1/min" description="TNF receptor recycling">0.293</TNFR_recycling_rate>
<TNFR_activation_threshold type="double" units="" description="TNFR threshold to update booleano model input">0.5</TNFR_activation_threshold>
<TNFR_receptors_per_cell type="double" units="dimensionless" description="number of TNFR receptors per cell">1.0</TNFR_receptors_per_cell>
<TNF_net_production_rate type="double" units="TNF/cell/min" description="The total TNF produced by the cell when NFkB is active">0</TNF_net_production_rate> <!-- 0.5 ng/mL -->
<!-- Auxiliary variables used to monitorize simulation-->
<tnf_node units="dimensionless">0</tnf_node>
<fadd_node units="dimensionless">0</fadd_node>
<nfkb_node units="dimensionless">0</nfkb_node>
<external_tnf units="TNF/um^3">0</external_tnf>
</custom_data>
</cell_definition>
</cell_definitions>
<user_parameters>
<random_seed type="int" units="dimensionless">0</random_seed>
<!-- example parameters from the template -->
<!-- init file -->
<init_cells_filename type="string" units="">./config/init_1M_rectangle.txt</init_cells_filename>
<!-- <bnd_file type="string" units="">./config/boolean_network/TNF_nodes.bnd</bnd_file>
<cfg_file type="string" units="">./config/boolean_network/TNF_conf.cfg</cfg_file>
<maboss_time_step type="double" units="dimensionless">10.</maboss_time_step> -->
<time_add_tnf type="int" units="min">50</time_add_tnf> <!-- 150 -->
<duration_add_tnf type="int" units="min">10</duration_add_tnf> <!-- 10 -->
<concentration_tnf type="double" units="TNF/um^3"> 0.0 </concentration_tnf> <!-- 0.5 ng/mL -->
<time_remove_tnf type="int" units="min">100000</time_remove_tnf> <!-- 8000 -->
<membrane_length type="int" units=""> 170 </membrane_length> <!-- 470 -->
<update_pc_parameters_O2_based type="bool" units="">false</update_pc_parameters_O2_based>
</user_parameters>
</PhysiCell_settings>
<?xml version="1.0" encoding="UTF-8"?>
<!--
/*
###############################################################################
# If you use PhysiCell in your project, please cite PhysiCell and the version #
# number, such as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1]. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# See VERSION.txt or call get_PhysiCell_version() to get the current version #
# x.y.z. Call display_citations() to get detailed information on all cite-#
# able software used in your PhysiCell application. #
# #
# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM #
# as below: #
# #
# We implemented and solved the model using PhysiCell (Version x.y.z) [1], #
# with BioFVM [2] to solve the transport equations. #
# #
# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, #
# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- #
# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 #
# DOI: 10.1371/journal.pcbi.1005991 #
# #
# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- #
# llelized diffusive transport solver for 3-D biological simulations, #
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
###############################################################################
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2018, Paul Macklin and the PhysiCell Project #
# All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
# modification, are permitted provided that the following conditions are met: #
# #
# 1. Redistributions of source code must retain the above copyright notice, #
# this list of conditions and the following disclaimer. #
# #
# 2. Redistributions in binary form must reproduce the above copyright #
# notice, this list of conditions and the following disclaimer in the #
# documentation and/or other materials provided with the distribution. #
# #
# 3. Neither the name of the copyright holder nor the names of its #
# contributors may be used to endorse or promote products derived from this #
# software without specific prior written permission. #
# #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" #
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE #
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE #
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE #
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR #
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF #
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS #
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN #
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) #
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE #
# POSSIBILITY OF SUCH DAMAGE. #
# #
###############################################################################
*/
-->
<!--
<user_details />
-->
<PhysiCell_settings version="devel-version">
<domain>
<x_min>-1000</x_min>
<x_max>1000</x_max>
<y_min>-1000</y_min>
<y_max>1000</y_max>
<z_min>-1000</z_min>
<z_max>1000</z_max>
<dx>20</dx>
<dy>20</dy>
<dz>20</dz>
<use_2D>false</use_2D>
</domain>
<overall>
<max_time units="min">3600</max_time> <!-- 1400 -->
<time_units>min</time_units>
<space_units>micron</space_units>
<dt_diffusion units="min">0.02</dt_diffusion>
<dt_mechanics units="min">0.1</dt_mechanics>
<dt_phenotype units="min">2</dt_phenotype>
</overall>
<parallel>
<omp_num_threads>1</omp_num_threads>
</parallel>
<save>
<folder>output</folder> <!-- use . for root -->
<full_data>
<interval units="min">100</interval>
<enable>true</enable>
</full_data>
<SVG>
<interval units="min">100</interval>
<enable>true</enable>
</SVG>
<legacy_data>
<enable>true</enable>
</legacy_data>
</save>
<microenvironment_setup>
<variable name="oxygen" units="mmHg" ID="0">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">100000.0</diffusion_coefficient>
<decay_rate units="1/min">.1</decay_rate>
</physical_parameter_set>
<initial_condition units="mmHg">38.0</initial_condition>
<Dirichlet_boundary_condition units="mmHg" enabled="true">38.0</Dirichlet_boundary_condition>
</variable>
<variable name="tnf" units="TNF/um^3" ID="1">
<physical_parameter_set>
<diffusion_coefficient units="micron^2/min">1200.0</diffusion_coefficient>
<decay_rate units="1/min">.0275</decay_rate>
</physical_parameter_set>
<initial_condition units="molecules/voxel">0.0</initial_condition>
<Dirichlet_boundary_condition units="molecules/voxel" enabled="false">0.0</Dirichlet_boundary_condition>
</variable>
<options>
<calculate_gradients>true</calculate_gradients>
<track_internalized_substrates_in_each_agent>true</track_internalized_substrates_in_each_agent>
<!-- not yet supported -->
<initial_condition type="matlab" enabled="false">
<filename>./config/initial.mat</filename>
</initial_condition>
<!-- not yet supported -->
<dirichlet_nodes type="matlab" enabled="false">
<filename>./config/dirichlet.mat</filename>
</dirichlet_nodes>
</options>
</microenvironment_setup>
<cell_definitions>
<cell_definition name="default" ID="0">
<phenotype>
<cycle code="5" name="live_cells_cycle_model">
<!-- using higher than normal significant digits to match divisions in default code -->
<phase_transition_rates units="1/min">
<!-- Cycle duration -->
<rate start_index="0" end_index="0" fixed_duration="false">0.00075</rate>
</phase_transition_rates>
</cycle>
<death>
<model code="100" name="apoptosis">
<death_rate units="1/min">5.31667e-05</death_rate>
<phase_durations units="min">
<duration index="0" fixed_duration="true">516</duration>
</phase_durations>
<!--
<phase_transition_rates units="1/min">
<rate start_index="0" end_index="1" fixed_duration="false">0.00193798</rate>
</phase_transition_rates> ok -->
<parameters>
<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</parameters>
</model>
<model code="101" name="necrosis">
<rate units="1/min">0.0</rate>
<phase_durations units="min">
<duration index="0" fixed_duration="true">0</duration>
<duration index="1" fixed_duration="true">86400</duration>
</phase_durations>
<!--
<transition_rates units="1/min">
<rate start_index="0" end_index="1" fixed_duration="false">9e9</rate>
<rate start_index="1" end_index="2" fixed_duration="true">1.15741e-5</rate>
</transition_rates>
-->
<parameters>
<unlysed_fluid_change_rate units="1/min">0.05</unlysed_fluid_change_rate>
<lysed_fluid_change_rate units="1/min">0</lysed_fluid_change_rate>
<cytoplasmic_biomass_change_rate units="1/min">1.66667e-02</cytoplasmic_biomass_change_rate>
<nuclear_biomass_change_rate units="1/min">5.83333e-03</nuclear_biomass_change_rate>
<calcification_rate units="1/min">0</calcification_rate>
<relative_rupture_volume units="dimensionless">2.0</relative_rupture_volume>
</parameters>
</model>
</death>
<secretion>
<substrate name="oxygen">
<secretion_rate units="1/min">0</secretion_rate>
<secretion_target units="substrate density">38</secretion_target>
<uptake_rate units="1/min">10</uptake_rate>
<net_export_rate units="total substrate/min">0</net_export_rate>
</substrate>
<substrate name="tnf">
<secretion_rate units="1/min">0</secretion_rate>
<secretion_target units="substrate density">0</secretion_target>
<uptake_rate units="1/min">0</uptake_rate>
<net_export_rate units="total substrate/min">0</net_export_rate>
</substrate>
</secretion>
<molecular />
<intracellular type="maboss">
<bnd_filename>./config/TNF_nodes.bnd</bnd_filename>
<cfg_filename>./config/TNF_conf.cfg</cfg_filename>
<time_step>10</time_step>
</intracellular>
</phenotype>
<custom_data>
<!-- Time steps for maboss update-->
<next_physiboss_run units="dimensionless">10.</next_physiboss_run>
<!-- Molecular model internal variables-->
<TNFR_binding_rate type="double" units="1/min" description="TNF receptor binding rate">0.243</TNFR_binding_rate> <!-- 0.243 -->
<TNFR_endocytosis_rate type="double" units="1/min" description="TNF receptor-TNF endocytosis rate">0.128</TNFR_endocytosis_rate>
<TNFR_recycling_rate type="double" units="1/min" description="TNF receptor recycling">0.293</TNFR_recycling_rate>
<TNFR_activation_threshold type="double" units="" description="TNFR threshold to update booleano model input">0.5</TNFR_activation_threshold>
<TNFR_receptors_per_cell type="double" units="dimensionless" description="number of TNFR receptors per cell">1.0</TNFR_receptors_per_cell>
<TNF_net_production_rate type="double" units="TNF/cell/min" description="The total TNF produced by the cell when NFkB is active">0</TNF_net_production_rate> <!-- 0.5 ng/mL -->
<!-- Auxiliary variables used to monitorize simulation-->
<tnf_node units="dimensionless">0</tnf_node>
<fadd_node units="dimensionless">0</fadd_node>
<nfkb_node units="dimensionless">0</nfkb_node>
<external_tnf units="TNF/um^3">0</external_tnf>
</custom_data>
</cell_definition>
</cell_definitions>
<user_parameters>
<random_seed type="int" units="dimensionless">0</random_seed>
<!-- example parameters from the template -->
<!-- init file -->
<init_cells_filename type="string" units="">./config/init.txt</init_cells_filename>
<!-- <bnd_file type="string" units="">./config/boolean_network/TNF_nodes.bnd</bnd_file>
<cfg_file type="string" units="">./config/boolean_network/TNF_conf.cfg</cfg_file>
<maboss_time_step type="double" units="dimensionless">10.</maboss_time_step> -->
<time_add_tnf type="int" units="min">50</time_add_tnf> <!-- 150 -->
<duration_add_tnf type="int" units="min">10</duration_add_tnf> <!-- 10 -->
<concentration_tnf type="double" units="TNF/um^3"> 0.05 </concentration_tnf> <!-- 0.5 ng/mL -->
<time_remove_tnf type="int" units="min">100000</time_remove_tnf> <!-- 8000 -->
<membrane_length type="int" units=""> 850 </membrane_length> <!-- 470 -->
<update_pc_parameters_O2_based type="bool" units="">false</update_pc_parameters_O2_based>
</user_parameters>
</PhysiCell_settings>
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$time_scale = 0.05;
discrete_time = 0;