diff --git a/postprocessing/Makefile b/postprocessing/Makefile
index e2937b6..69cb856 100644
--- a/postprocessing/Makefile
+++ b/postprocessing/Makefile
@@ -1,97 +1,97 @@
IDIR =./include
CXX=g++
#CPPFLAGS=-g -I$(IDIR) -I/home/samarth/codes/voronoi/include -std=c++11 -O3 -w -Wall
-CPPFLAGS=-g -I$(IDIR) -O3
-#CPPFLAGS=-I$(IDIR) -O3
+#CPPFLAGS=-g -I$(IDIR) -O3
+CPPFLAGS=-I$(IDIR) -O3
LDFLAGS=-O3
POSTFIX=-L/home/samarth/codes/voronoi/lib/ -lvoro++
SRC_DIR = ./src
OBJ_DIR = ./obj
SRC_FILES = $(wildcard $(SRC_DIR)/*.cpp)
OBJ_FILES = $(patsubst $(SRC_DIR)/%.cpp,$(OBJ_DIR)/%.o,$(SRC_FILES))
BIN_SRC_DIR = ./bin_src
BIN_DIR = ./bin
all: unfold radius_of_gyration sq_vs_q pair_correlation percolation load_bearing_paths lr_iq lbp_brute_force percolation_invA chemical_distance lb_bonds_clusterwise_invA lbp_bfs
#all: psd_test
density_correlation: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o density_correlation.o target/density_correlation.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ density_correlation.o
unfold: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o unfold.o target/unfold.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ unfold.o
radius_of_gyration: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o radius_of_gyration.o target/radius_of_gyration.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ radius_of_gyration.o
sq_vs_q: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o sq_vs_q.o target/sq_vs_q.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ sq_vs_q.o
pair_correlation: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o pair_correlation.o target/pair_correlation.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ pair_correlation.o
psd_test: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o psd_test.o target/psd_test.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ psd_test.o
percolation: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o percolation.o target/percolation.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ percolation.o
load_bearing_paths: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o load_bearing_paths.o target/load_bearing_paths.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ load_bearing_paths.o
lbp_brute_force: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o lbp_brute_force.o target/lbp_brute_force.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ lbp_brute_force.o
percolation_invA: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o percolation_invA.o target/percolation_invA.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ percolation_invA.o
lb_bonds_invA: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o lb_bonds_invA.o target/lb_bonds_invA.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ lb_bonds_invA.o
lb_bonds_clusterwise_invA: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o lb_bonds_clusterwise_invA.o target/lb_bonds_clusterwise_invA.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ lb_bonds_clusterwise_invA.o
lb_bonds_via_cg: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o lb_bonds_via_cg.o target/lb_bonds_via_cg.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ lb_bonds_via_cg.o
chemical_distance: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o chemical_distance.o target/chemical_distance.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ chemical_distance.o
lr_iq: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o lr_iq.o target/lr_iq.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ lr_iq.o
lbp_bfs: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o lbp_bfs.o target/lbp_bfs.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ lbp_bfs.o
$(OBJ_DIR)/%.o: $(SRC_DIR)/%.cpp | $(OBJ_DIR)
$(CXX) $(CPPFLAGS) -c -o $@ $<
$(BIN_DIR):
mkdir $(BIN_DIR)
$(OBJ_DIR):
mkdir $(OBJ_DIR)
clean:
rm *.o
rm -rf $(BIN_DIR)
rm -rf $(OBJ_DIR)
diff --git a/scripts/setup_simulation_rsp_2d.py b/scripts/setup_simulation_rsp_2d.py
new file mode 100755
index 0000000..551b1fa
--- /dev/null
+++ b/scripts/setup_simulation_rsp_2d.py
@@ -0,0 +1,218 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Jun 4 13:56:09 2021
+
+@author: samarth
+"""
+
+import pandas as pd
+import os
+import sys
+from pathlib import Path
+from joblib import Parallel, delayed
+from matplotlib import pyplot as plt
+import numpy as np
+from sklearn.linear_model import LinearRegression
+from random import random, seed
+
+
+def create_dirs(phi, N, seed_pct, dim):
+
+ global D
+
+ D = dim
+
+ global params_dir
+
+ phi_str = format(phi, '.8f')
+
+ params_dir = './'+str(D)+'d/params/phi='+phi_str+'/seed_pct='+str(seed_pct)+'/L='+str(N)+'/'
+ path = Path(params_dir)
+
+ try:
+ path.mkdir(parents=True, exist_ok=True)
+ except OSError:
+ pass
+ else:
+ pass
+
+
+ global results_dir
+
+ results_dir = './'+str(D)+'d/results/phi='+phi_str+'/seed_pct='+str(seed_pct)+'/L='+str(N)+'/'
+ path = Path(results_dir)
+
+ try:
+ path.mkdir(parents=True, exist_ok=True)
+ except OSError:
+ pass
+ else:
+ pass
+
+ global config_files_dir
+
+ config_files_dir = './'+str(D)+'d/config_files/phi='+phi_str+'/seed_pct='+str(seed_pct)+'/L='+str(N)+'/'
+ path = Path(config_files_dir)
+
+ try:
+ path.mkdir(parents=True, exist_ok=True)
+ except OSError:
+ pass
+ else:
+ pass
+
+def run_simulation(phi, L, seed_pct, rng_seed):
+
+ lattice=1
+
+ params_file = params_dir+'params_'+str(rng_seed)+'.csv'
+
+ file = open(params_file, "w")
+
+ file.write("system=random_site_percolation\n")
+ file.write("lattice="+str(lattice)+"\n")
+ file.write("D="+str(D)+"\n")
+ file.write("phi="+str(phi)+"\n")
+ file.write("seed_pct="+str(seed_pct)+"\n")
+
+ for axis in range(D):
+ file.write("x"+str(axis)+"_bc=periodic\n")
+
+ for axis in range(D):
+ file.write("x"+str(axis)+"_L="+str(L)+"\n")
+
+ file.write("rng_seed="+str(rng_seed)+"\n")
+ file.close()
+
+ print("phi = {}, L={},rng_seed={} simulation".format(phi,L,rng_seed))
+
+ config_filename=config_files_dir+str(rng_seed)+'.csv'
+ command = 'simulation '+params_file+' '+config_filename
+ os.system(command)
+
+ print("phi = {}, L={},rng_seed={} lbp".format(phi,L,rng_seed))
+
+ rog_filename=results_dir+'lbp_'+str(rng_seed)+'.csv'
+ command = 'lb_bonds_clusterwise_invA ' + config_filename +' ' + rog_filename
+ os.system(command)
+
+def create_dirs_for_mk_table(dim):
+
+ global D
+
+ D = dim
+
+ global params_dir
+
+
+ params_dir = './mk_table/params/'
+ path = Path(params_dir)
+
+ try:
+ path.mkdir(parents=True, exist_ok=True)
+ except OSError:
+ pass
+ else:
+ pass
+
+
+ global results_dir
+
+ results_dir = './mk_table/results/'
+ path = Path(results_dir)
+
+ try:
+ path.mkdir(parents=True, exist_ok=True)
+ except OSError:
+ pass
+ else:
+ pass
+
+ global config_files_dir
+
+ config_files_dir = './mk_table/config_files/'
+ path = Path(config_files_dir)
+
+ try:
+ path.mkdir(parents=True, exist_ok=True)
+ except OSError:
+ pass
+ else:
+ pass
+
+def run_simulation_for_random_params(phi, L, rng_seed):
+
+ lattice=1
+ x0_bc="periodic"
+ x1_bc="periodic"
+ x2_bc="periodic"
+ alpha=0.5
+ seedMass=1e12
+ seed_pct = 100
+
+
+ params_file = params_dir+'params_'+str(rng_seed)+'.csv'
+ file = open(params_file, "w")
+
+ file.write("system=random_site_percolation\n")
+ file.write("lattice="+str(lattice)+"\n")
+ file.write("aggregation_type=normal\n")
+ file.write("aggregation_condition=mass\n")
+ file.write("bind=normal\n")
+ file.write("movement=brownian\n")
+ file.write("agg_dist_tolerance=0.0\n")
+ file.write("D="+str(D)+"\n")
+ file.write("seed_pct="+str(seed_pct)+"\n")
+ file.write("x0_bc="+str(x0_bc)+"\n")
+ file.write("x1_bc="+str(x1_bc)+"\n")
+ file.write("x2_bc="+str(x2_bc)+"\n")
+ file.write("x0_L="+str(L)+"\n")
+ file.write("x1_L="+str(L)+"\n")
+ file.write("x2_L="+str(L)+"\n")
+ file.write("phi="+str(phi)+"\n")
+ file.write("alpha="+str(alpha)+"\n")
+ file.write("seedMass="+str(seedMass)+"\n")
+ file.write("rng_seed="+str(rng_seed)+"\n")
+ file.close()
+
+ print("phi = {}, N={},rng_seed={} simulation".format(phi,L,rng_seed))
+
+ config_filename=config_files_dir+str(rng_seed)+'.csv'
+ command = 'simulation '+params_file+' '+config_filename
+ os.system(command)
+
+ print("phi = {}, N={},rng_seed={} lbp".format(phi,L,rng_seed))
+
+ rog_filename=results_dir+'lbp_'+str(rng_seed)+'.csv'
+ time_filename=results_dir+'time_'+str(rng_seed)+'.csv'
+ command = 'lb_bonds_clusterwise_invA ' + config_filename +' ' + rog_filename + ' ' + time_filename
+ os.system(command)
+
+#phi=0.15
+seeds=100
+seed_pct=100
+dim = 2
+
+L_range = [1000, 2000, 5000]
+
+phi_min = 0.005
+phi_max = 0.05
+phi_c = 0.5927462
+
+phi_min += phi_c
+phi_max += phi_c
+
+d_phi = 0.1 * (phi_max - phi_min)
+
+phi_range = []
+
+for i in range(10):
+
+ temp_phi = phi_min * np.exp(i * (d_phi))
+ phi_range.append(temp_phi)
+
+for i in phi_range:
+ for L in L_range:
+ create_dirs(i, L, seed_pct, dim)
+ Parallel(n_jobs=10)(delayed(run_simulation)(i, L, seed_pct, rng_seed) for rng_seed in range(seeds))
\ No newline at end of file
diff --git a/simulation_files/Makefile b/simulation_files/Makefile
index ba48253..546e9ef 100644
--- a/simulation_files/Makefile
+++ b/simulation_files/Makefile
@@ -1,34 +1,34 @@
IDIR =./include
CXX=g++
-CPPFLAGS=-g -I$(IDIR) -std=c++11 -O3 -w
-LDFLAGS=-g -I$(IDIR) -std=c++11 -O3 -w
+#CPPFLAGS=-g -I$(IDIR) -std=c++11 -O3 -w
+#LDFLAGS=-g -I$(IDIR) -std=c++11 -O3 -w
-#CPPFLAGS=-I$(IDIR) -std=c++11 -O3 -w
-#LDFLAGS=-I$(IDIR) -std=c++11 -O3 -w
+CPPFLAGS=-I$(IDIR) -std=c++11 -O3 -w
+LDFLAGS=-I$(IDIR) -std=c++11 -O3 -w
SRC_DIR = ./src
OBJ_DIR = ./obj
SRC_FILES = $(wildcard $(SRC_DIR)/*.cpp)
OBJ_FILES = $(patsubst $(SRC_DIR)/%.cpp,$(OBJ_DIR)/%.o,$(SRC_FILES))
BIN_SRC_DIR = ./bin_src
BIN_DIR = ./bin
all: simulation
simulation: $(OBJ_FILES) | $(BIN_DIR)
$(CXX) $(CPPFLAGS) -c -o simulation.o target/simulation.cpp
$(CXX) $(LDFLAGS) -o $(BIN_DIR)/$@ $^ simulation.o
$(OBJ_DIR)/%.o: $(SRC_DIR)/%.cpp | $(OBJ_DIR)
$(CXX) $(CPPFLAGS) -c -o $@ $<
$(BIN_DIR):
mkdir $(BIN_DIR)
$(OBJ_DIR):
mkdir $(OBJ_DIR)
clean:
rm -rf $(OBJ_DIR)
rm *.o
rm -rf $(BIN_DIR)