The inefficient overlap removal algorithm has been removed from the project

Author: egor-demidov

CMakeLists.txt

@@ -49,7 +49,7 @@ add_compile_definitions("COMPILER_STRING=\"${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_
 add_compile_definitions("SYSTEM_STRING=\"${CMAKE_SYSTEM_NAME} ${CMAKE_SYSTEM_VERSION}\"")
 
 set(CMAKE_UTIL_SOURCES src/random_engine.cpp src/writer.cpp src/energy.cpp src/reader.cpp
-        src/break_neck.cpp src/remove_overlap.cpp src/aggregate_stats.cpp
+        src/break_neck.cpp src/aggregate_stats.cpp
         src/parameter_loader.cpp src/io_common.cpp deps/tinyxml2/tinyxml2.cpp)
 
 add_executable(aggregate_deposition src/aggregate_deposition.cpp ${CMAKE_UTIL_SOURCES})

src/afm_breaking_necks.cpp

@@ -21,7 +21,6 @@
 #include "reader.h"
 #include "writer.h"
 #include "break_neck.h"
-#include "remove_overlap.h"
 #include "io_common.h"
 #include "random_engine.h"
 
@@ -96,8 +95,6 @@ int main(int argc, const char ** argv) {
     const size_t neighbor_list_update_period = get_integer_parameter(parameter_store, "neighbor_update_period");
     // Side length of the square substrate
     const double substrate_size = get_real_parameter(parameter_store, "substrate_size");
-    // Number of overlap reduction iterations to be performed upon loading an aggregate
-    const long n_overlap_iter = get_integer_parameter(parameter_store, "n_overlap_iter");
     // AFM tip indentation/retraction velocity
     const double v_afm = get_real_parameter(parameter_store, "v_afm");
     // Time when AFM tip reverses its motion
@@ -247,8 +244,6 @@ int main(int argc, const char ** argv) {
     }
     std::cout << "Loaded an aggregate of size " << x0.size() << std::endl;
 
-    remove_overlap(x0, r_part, d_crit, n_overlap_iter);
-
     // Randomly pick the monomer that will be indented
     seed_random_engine(rng_seed);
     std::uniform_int_distribution<long> dist(0, x0.size() - 1);

src/afm_necking_fraction.cpp

@@ -21,7 +21,6 @@
 #include "reader.h"
 #include "writer.h"
 #include "break_neck.h"
-#include "remove_overlap.h"
 #include "io_common.h"
 #include "random_engine.h"
 
@@ -96,8 +95,6 @@ int main(int argc, const char ** argv) {
     const size_t neighbor_list_update_period = get_integer_parameter(parameter_store, "neighbor_update_period");
     // Side length of the square substrate
     const double substrate_size = get_real_parameter(parameter_store, "substrate_size");
-    // Number of overlap reduction iterations to be performed upon loading an aggregate
-    const long n_overlap_iter = get_integer_parameter(parameter_store, "n_overlap_iter");
     // AFM tip indentation/retraction velocity
     const double v_afm = get_real_parameter(parameter_store, "v_afm");
     // Time when AFM tip reverses its motion
@@ -255,8 +252,6 @@ int main(int argc, const char ** argv) {
     }
     std::cout << "Loaded an aggregate of size " << x0.size() << std::endl;
 
-    remove_overlap(x0, r_part, d_crit, n_overlap_iter);
-
     // Randomly pick the monomer that will be indented
     seed_random_engine(rng_seed);
     std::uniform_int_distribution<long> dist(0, x0.size() - 1);

src/aggregate_deposition.cpp

@@ -17,7 +17,6 @@
 #include "aggregate.h"
 #include "writer.h"
 #include "energy.h"
-#include "remove_overlap.h"
 #include "io_common.h"
 
 using aggregate_model_t = aggregate<Eigen::Vector3d, double>;
@@ -75,7 +74,6 @@ int main(int argc, const char ** argv) {
     const double rot_x = get_real_parameter(parameter_store, "rot_x");
     const double rot_y = get_real_parameter(parameter_store, "rot_y");
     const double rot_z = get_real_parameter(parameter_store, "rot_z");
-    const long n_overlap_iter = get_integer_parameter(parameter_store, "n_overlap_iter");
 
     // General parameters
     const double rho = get_real_parameter(parameter_store, "rho");
@@ -154,7 +152,6 @@ int main(int argc, const char ** argv) {
     }
     std::cout << "Loaded an aggregate of size " << x0.size() << std::endl;
 
-    remove_overlap(x0, r_part, d_crit, n_overlap_iter);
 
     Eigen::Vector3d center_of_mass = Eigen::Vector3d::Zero();
     for (auto const & x : x0) {

src/aggregation.cpp

@@ -24,7 +24,6 @@
 #include "writer.h"
 #include "reader.h"
 #include "break_neck.h"
-#include "remove_overlap.h"
 #include "aggregate_stats.h"
 #include "io_common.h"
 #include "parameter_loader.h"

src/anchored_restructuring.cpp

@@ -23,7 +23,6 @@
 #include "writer.h"
 #include "reader.h"
 #include "break_neck.h"
-#include "remove_overlap.h"
 #include "aggregate_stats.h"
 #include "io_common.h"
 #include "parameter_loader.h"
@@ -62,7 +61,6 @@ int main(int argc, const char ** argv) {
     const long n_dumps = get_integer_parameter(parameter_store, "n_dumps");
     const long dump_period = n_steps / n_dumps;
     const long neighbor_update_period = get_integer_parameter(parameter_store, "neighbor_update_period");
-    const long n_overlap_iter = get_integer_parameter(parameter_store, "n_overlap_iter");
     const long rng_seed = get_integer_parameter(parameter_store, "rng_seed");
     const double substrate_size = get_real_parameter(parameter_store, "substrate_size");
 
@@ -144,7 +142,6 @@ int main(int argc, const char ** argv) {
     std::vector<Eigen::Vector3d> x0, v0, theta0, omega0;
 
     x0 = load_aggregate(parameter_store);
-    remove_overlap(x0, r_part, d_crit, n_overlap_iter);
 
     if (x0.size() == 0) {
         std::cerr << "Loaded an empty aggregate" << std::endl;

src/mechanics_testing.cpp

@@ -23,7 +23,6 @@
 #include "writer.h"
 #include "reader.h"
 #include "break_neck.h"
-#include "remove_overlap.h"
 #include "aggregate_stats.h"
 #include "io_common.h"
 #include "parameter_loader.h"

src/remove_overlap.cpp

@@ -23,7 +23,6 @@
 #include "writer.h"
 #include "reader.h"
 #include "break_neck.h"
-#include "remove_overlap.h"
 #include "aggregate_stats.h"
 #include "io_common.h"
 #include "parameter_loader.h"
@@ -124,7 +123,6 @@ int main(int argc, const char ** argv) {
     std::vector<Eigen::Vector3d> x0, v0, theta0, omega0;
 
     x0 = load_aggregate(parameter_store);
-    remove_overlap(x0, r_part, d_crit, n_overlap_iter);
 
     if (x0.size() == 0) {
         std::cerr << "Loaded an empty aggregate" << std::endl;

src/remove_overlap.h

@@ -20,7 +20,6 @@
 #include "writer.h"
 #include "reader.h"
 #include "break_neck.h"
-#include "remove_overlap.h"
 #include "aggregate_stats.h"
 #include "io_common.h"
 #include "parameter_loader.h"
@@ -62,7 +61,6 @@ static constexpr double rho = 1700;
 static constexpr double t_tot = 5e-08;
 static constexpr double e_crit = 5e-19;
 static constexpr long n_dumps = 500;
-static constexpr long n_overlap_iter = 10000;
 static constexpr long neighbor_update_period = 20;
 static constexpr long rng_seed = 0;