freepaths 2.2.2__tar.gz → 2.3.0__tar.gz

{freepaths-2.2.2 → freepaths-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: freepaths
-Version: 2.2.2
+Version: 2.3.0
 Summary: Phonon Monte Carlo simulator
 Home-page: https://github.com/anufrievroman/freepaths
 Author: Roman Anufriev
@@ -34,9 +34,9 @@ Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 
-# FreePATHS - Free Phonon And Thermal Simulator
+# FreePATHS - Free Phonon And THermal Simulator
 
-This Monte Carlo algorithm simulates trajectories of phonons in 3D models of nanostructures, which consists of a box with holes or pillars of various shapes. The algorithm outputs phonon trajectories, heat fluxes, temperature maps and profiles, the thermal conductivity, scattering maps and statistics and other information. See [documentation](https://anufrievroman.gitbook.io/freepaths/) for the details of the simulation.
+This Monte Carlo algorithm simulates trajectories of phonons or electrons in 3D models of nanostructures, which consists of a box with holes, pillars, or interfaces of various shapes. For phonons, the algorithm outputs heat fluxes, temperature maps and profiles, thermal conductivity, scattering maps and statistics, and other information. For electrons, it outputs electrical conductivity, Seebeck coefficient, electronic thermal conductivity, power factor, and related quantities as a function of Fermi level. See [documentation](https://anufrievroman.gitbook.io/freepaths/) for the details of the simulation.
 
 ![Screenshot](https://github.com/anufrievroman/Monte-Carlo/blob/master/screenshot.png)
 
@@ -54,9 +54,13 @@ FreePATHS is a command line application, so it runs inside Linux, MacOS, or Wind
 
 There are two modes of using the program. Main mode traces a large number of phonons through a structure and collects statistics about their paths. The MFP sampling mode measures phonon mean free paths using a small number of phonons and calculates the thermal conductivity by integrating phonon dispersion. 
 
-### Demo
+### Getting started
 
-If you simply run `freepaths` without specifying an input file, the program will run a demo simulation.
+If you run `freepaths` without any arguments, the program will print a usage summary. To run a demo simulation with default parameters, use the `--demo` flag:
+
+`freepaths --demo`
+
+Example input files are available in the [examples](https://github.com/anufrievroman/freepaths/tree/master/examples) folder.
 
 ### Main mode
 
@@ -73,6 +77,15 @@ See [documentation](https://anufrievroman.gitbook.io/freepaths/examples) for exp
 After the simulation, see the results in a newly created **Results** folder.
 
 
+### Electron mode
+
+FreePATHS can also simulate electron transport. In this mode, electrons are traced through the structure and thermoelectric properties — electrical conductivity, Seebeck coefficient, electronic thermal conductivity, and power factor — are computed as a function of Fermi level. To run in electron mode, add the `-e` flag:
+
+`freepaths -e your_input_file.py`
+
+See the [tutorial](https://anufrievroman.gitbook.io/freepaths/basic-tutorials/electrons-in-holey-membranes) and [theory](https://anufrievroman.gitbook.io/freepaths/theory/electrical-conductivity) for details.
+
+
 ### MFP sampling mode
 
 Alternatively, you can run FreePATHS in the mean free path sampling mode, which is designed to calculate the thermal conductivity by integrating phonon dispersion. To run the program in this mode, it is advised to reduce the number of phonons to about 30 and add `-s` flag in the command:

{freepaths-2.2.2 → freepaths-2.3.0}/README.md

@@ -1,6 +1,6 @@
-# FreePATHS - Free Phonon And Thermal Simulator
+# FreePATHS - Free Phonon And THermal Simulator
 
-This Monte Carlo algorithm simulates trajectories of phonons in 3D models of nanostructures, which consists of a box with holes or pillars of various shapes. The algorithm outputs phonon trajectories, heat fluxes, temperature maps and profiles, the thermal conductivity, scattering maps and statistics and other information. See [documentation](https://anufrievroman.gitbook.io/freepaths/) for the details of the simulation.
+This Monte Carlo algorithm simulates trajectories of phonons or electrons in 3D models of nanostructures, which consists of a box with holes, pillars, or interfaces of various shapes. For phonons, the algorithm outputs heat fluxes, temperature maps and profiles, thermal conductivity, scattering maps and statistics, and other information. For electrons, it outputs electrical conductivity, Seebeck coefficient, electronic thermal conductivity, power factor, and related quantities as a function of Fermi level. See [documentation](https://anufrievroman.gitbook.io/freepaths/) for the details of the simulation.
 
 ![Screenshot](https://github.com/anufrievroman/Monte-Carlo/blob/master/screenshot.png)
 
@@ -18,9 +18,13 @@ FreePATHS is a command line application, so it runs inside Linux, MacOS, or Wind
 
 There are two modes of using the program. Main mode traces a large number of phonons through a structure and collects statistics about their paths. The MFP sampling mode measures phonon mean free paths using a small number of phonons and calculates the thermal conductivity by integrating phonon dispersion. 
 
-### Demo
+### Getting started
 
-If you simply run `freepaths` without specifying an input file, the program will run a demo simulation.
+If you run `freepaths` without any arguments, the program will print a usage summary. To run a demo simulation with default parameters, use the `--demo` flag:
+
+`freepaths --demo`
+
+Example input files are available in the [examples](https://github.com/anufrievroman/freepaths/tree/master/examples) folder.
 
 ### Main mode
 
@@ -37,6 +41,15 @@ See [documentation](https://anufrievroman.gitbook.io/freepaths/examples) for exp
 After the simulation, see the results in a newly created **Results** folder.
 
 
+### Electron mode
+
+FreePATHS can also simulate electron transport. In this mode, electrons are traced through the structure and thermoelectric properties — electrical conductivity, Seebeck coefficient, electronic thermal conductivity, and power factor — are computed as a function of Fermi level. To run in electron mode, add the `-e` flag:
+
+`freepaths -e your_input_file.py`
+
+See the [tutorial](https://anufrievroman.gitbook.io/freepaths/basic-tutorials/electrons-in-holey-membranes) and [theory](https://anufrievroman.gitbook.io/freepaths/theory/electrical-conductivity) for details.
+
+
 ### MFP sampling mode
 
 Alternatively, you can run FreePATHS in the mean free path sampling mode, which is designed to calculate the thermal conductivity by integrating phonon dispersion. To run the program in this mode, it is advised to reduce the number of phonons to about 30 and add `-s` flag in the command:

freepaths-2.3.0/freepaths/__main__.py

@@ -0,0 +1,64 @@
+"""FreePATHS - Free Phonon and THermal Simulator"""
+
+import sys
+import argparse
+import colorama
+from colorama import Fore, Style
+
+from freepaths.particle_types import ParticleType
+
+__version__ = "2.3.0"
+
+colorama.init()
+
+# Parse user arguments:
+parser = argparse.ArgumentParser(
+                prog = 'FreePATHS',
+                description = 'Phonon Monte Carlo simulator',
+                epilog = 'For more information, examples, and tutorials, visit: https://anufrievroman.gitbook.io/freepaths'
+                )
+parser.add_argument('input_file', nargs='?', default=None, help='The input file')
+parser.add_argument("-v", "--version", action="version", version=f"FreePATHS {__version__}")
+parser.add_argument("-s", "--sampling", help="Run in phonon MFP sampling mode", action="store_true")
+parser.add_argument("-e", "--electron", help="Run simulation for electrons", action="store_true")
+parser.add_argument("--demo", help="Run a demo simulation with default parameters", action="store_true")
+args = parser.parse_args()
+
+
+def run():
+    """Run the program depending on the mode"""
+    print(f"\n{Fore.BLUE}FreePATHS v{__version__}{Style.RESET_ALL}")
+
+    if not args.input_file and not args.demo:
+        print("\nUsage:")
+        print(f"  freepaths <input_file>              run phonon simulation")
+        print(f"  freepaths <input_file> -e           run electron simulation")
+        print(f"  freepaths <input_file> -s           run in MFP sampling mode")
+        print(f"  freepaths --demo                    run a demo with default parameters")
+        print(f"  freepaths --version                 show version")
+        print(f"\nExample input files:")
+        print(f"  https://github.com/anufrievroman/freepaths/tree/master/examples")
+        print(f"\nDocumentation:")
+        print(f"  https://anufrievroman.gitbook.io/freepaths")
+        sys.exit(0)
+
+    try:
+        if args.sampling:
+            import freepaths.main_mfp_sampling
+            freepaths.main_mfp_sampling.main(args.input_file, ParticleType.PHONON)
+
+        elif args.electron:
+            import freepaths.main_tracing
+            freepaths.main_tracing.main(args.input_file, ParticleType.ELECTRON)
+
+        else:
+            import freepaths.main_tracing
+            freepaths.main_tracing.main(args.input_file, ParticleType.PHONON)
+
+    except KeyboardInterrupt:
+        print(f"\n{Fore.RED}Simulation interrupted by user.{Style.RESET_ALL}")
+        sys.exit(0)
+
+
+if __name__ == "__main__":
+    run()

{freepaths-2.2.2 → freepaths-2.3.0}/freepaths/config.py

@@ -26,6 +26,7 @@ parser = argparse.ArgumentParser(prog='FreePATHS', description='Monte Carlo simu
 parser.add_argument('input_file', nargs='?', default=None, help='The input file')
 parser.add_argument("-s", "--sampling", help="Run in MFP sampling mode", action="store_true")
 parser.add_argument("-e", "--electron", help="Run with electrons", action="store_true")
+parser.add_argument("--demo", help="Run a demo simulation with default parameters", action="store_true")
 args = parser.parse_args()
 
 
@@ -36,8 +37,6 @@ if args.input_file:
     except FileNotFoundError:
         logging.error("Input file does not exist. Check if you are in the right folder and the file name is correct.")
         sys.exit()
-else:
-    logging.warning("You provided no input file, so we will run a demo simulation:")
 
 
 class Config:
@@ -160,7 +159,7 @@ class Config:
 
         for source in self.particles_sources:
             if source.y > self.length:
-                logging.error("Y coordinate of a source exceeded LENGHT")
+                logging.error("Y coordinate of a source exceeded LENGTH")
                 sys.exit()
 
             if source.y < 0:
@@ -215,7 +214,7 @@ class Config:
             sys.exit()
 
 
-    def check_depricated_parameters(self):
+    def check_deprecated_parameters(self):
         """Check for deprecated parameters and warn about them"""
 
         if 'COLD_SIDE_POSITION' in globals():
@@ -258,5 +257,5 @@ class Config:
 cf = Config()
 cf.convert_to_enums()
 cf.check_parameter_validity()
-cf.check_depricated_parameters()
+cf.check_deprecated_parameters()
 

{freepaths-2.2.2 → freepaths-2.3.0}/freepaths/data.py

@@ -96,7 +96,6 @@ class GeneralData(Data):
         self.interfaces_mode.extend(flight.interfaces_mode)
 
 
-
     def write_into_files(self):
         import os
         if not os.path.exists("Data"):
@@ -142,7 +141,6 @@ class GeneralData(Data):
         }
 
 
-
 class ScatteringData(Data):
     """Statistics of particle scattering events"""
 
@@ -163,12 +161,6 @@ class ScatteringData(Data):
         self.total = np.zeros(cf.number_of_length_segments+1)
         self.interfaces_transmission_specular= np.zeros(cf.number_of_length_segments + 1)
         self.interfaces_transmission_diffuse = np.zeros(cf.number_of_length_segments + 1)
-        self.interfaces_angles = np.zeros(cf.number_of_length_segments + 1)
-        self.interfaces_transmission_factor = np.zeros(cf.number_of_length_segments + 1)
-        self.interfaces_wavelength = np.zeros(cf.number_of_length_segments+1)
-        self.interfaces_frequency = np.zeros(cf.number_of_length_segments+1)
-        self.interfaces_mode = np.zeros(cf.number_of_length_segments+1)
-
 
 
     def save_scattering_events(self, y, scattering_types):
@@ -212,17 +204,15 @@ class ScatteringData(Data):
     def write_into_files(self):
         """Write data into a file"""
         filename = "Data/Scattering events statistics.csv"
-        data = np.vstack((self.wall_diffuse, self.wall_specular, self.top_diffuse, self.top_specular, self.hole_diffuse,
-                        self.hole_specular, self.hot_side, self.internal, self.pillar_diffuse, self.pillar_specular,
-                        self.interfaces_diffuse, self.interfaces_specular,
-                        self.interfaces_transmission_diffuse, self.interfaces_transmission_specular,
-                        self.interfaces_transmission_factor, self.interfaces_angles,
-                        self.interfaces_wavelength, self.interfaces_mode)).T
-        header1 = "Sidewalls diffuse, Sidewalls specular, Top & bottom diffuse, Top & bottom specular, "
-        header2 = "Holes diffuse, Holes specular, Hot side, Internal, Pillars diffuse, Pillars specular"
-        header3 = "Interfaces diffuse, Interfaces specular, Interfaces transmission diffuse, Interfaces transmission specular, " \
-        "Interfaces transmission factor, Interfaces angles, Interfaces wavelength, Interfaces frequency, Interfaces mode"
-        header = header1 + header2 + header3
+        n = cf.number_of_length_segments
+        data = np.vstack((self.wall_diffuse[:n], self.wall_specular[:n], self.top_diffuse[:n], self.top_specular[:n],
+                        self.hole_diffuse[:n], self.hole_specular[:n], self.hot_side[:n], self.internal[:n],
+                        self.pillar_diffuse[:n], self.pillar_specular[:n],
+                        self.interfaces_diffuse[:n], self.interfaces_specular[:n],
+                        self.interfaces_transmission_diffuse[:n], self.interfaces_transmission_specular[:n])).T
+        header = ("Sidewalls diffuse, Sidewalls specular, Top & bottom diffuse, Top & bottom specular, "
+                  "Holes diffuse, Holes specular, Hot side, Internal, Pillars diffuse, Pillars specular, "
+                  "Interfaces diffuse, Interfaces specular, Interfaces transmission diffuse, Interfaces transmission specular")
         np.savetxt(filename, data, fmt='%1.3e', delimiter=",", header=header, encoding='utf-8')
 
     def dump_data(self):
@@ -242,11 +232,6 @@ class ScatteringData(Data):
             'interfaces_specular': self.interfaces_specular,
             'interfaces_transmission_specular': self.interfaces_transmission_specular,
             'interfaces_transmission_diffuse': self.interfaces_transmission_diffuse,
-            'interfaces_angles': self.interfaces_angles,
-            'interfaces_transmission_factor': self.interfaces_transmission_factor,
-            'interfaces_wavelength': self.interfaces_wavelength,
-            'interfaces_frequency': self.interfaces_frequency,
-            'interfaces_mode' : self.interfaces_mode,
             'total': self.total
         }
 
@@ -297,7 +282,6 @@ class TriangleScatteringData(Data):
         }
 
 
-
 class SegmentData(Data):
     """Statistics of events happening in different segments"""
 

{freepaths-2.2.2 → freepaths-2.3.0}/freepaths/default_config.py

@@ -7,29 +7,29 @@ from freepaths.sources import Source
 
 # General parameters:
 OUTPUT_FOLDER_NAME               = "Si nanowire at 300 K"
-NUMBER_OF_PARTICLES              = 5000
+NUMBER_OF_PARTICLES              = 10000
 NUMBER_OF_NODES                  = 400
 T                                = 300
 OUTPUT_SCATTERING_MAP            = False
-OUTPUT_TRAJECTORIES_OF_FIRST     = 50
+OUTPUT_TRAJECTORIES_OF_FIRST     = 20
 OUTPUT_STRUCTURE_COLOR           = "#F0F0F0"
 NUMBER_OF_LENGTH_SEGMENTS        = 10
 LOW_MEMORY_USAGE                 = False
 
 # Time parameters:
-TIMESTEP                         = 1e-12
-NUMBER_OF_TIMESTEPS              = 300000
+TIMESTEP                         = 2e-12
+NUMBER_OF_TIMESTEPS              = 200000
 NUMBER_OF_VIRTUAL_TIMESTEPS      = NUMBER_OF_TIMESTEPS * 3
 NUMBER_OF_TIMEFRAMES             = 8
 NUMBER_OF_STABILIZATION_TIMEFRAMES = 5
 
 # Electron parameters [eV]
 IS_CARRIER_ELECTRON              = True
-ENERGY_UPPER_BOUND               = 3*k*T / electron_volt
+ENERGY_UPPER_BOUND               = 6*k*T / electron_volt
 ENERGY_LOWER_BOUND               = 0
 ENERGY_STEP                      = 5e-3
 
-ELECTRON_MFP                     = 15e-9 # [m]
+ELECTRON_MFP                     = 10e-9 # [m]
 MEAN_MAPPING_CONSTANT            = 5e-6 # [m²]
 
 
@@ -38,8 +38,8 @@ OUTPUT_PATH_ANIMATION            = False
 OUTPUT_ANIMATION_FPS             = 24
 
 # Map & profiles parameters:
-NUMBER_OF_PIXELS_X               = 25
-NUMBER_OF_PIXELS_Y               = 100
+NUMBER_OF_PIXELS_X               = 7
+NUMBER_OF_PIXELS_Y               = 67
 IGNORE_FAULTY_PARTICLES          = False
 
 # Material parameters:
@@ -53,7 +53,7 @@ GRAY_APPROXIMATION_MFP           = None
 
 # System dimensions [m]:
 THICKNESS                        = 150e-9
-WIDTH                            = 500e-9
+WIDTH                            = 200e-9
 LENGTH                           = 2000e-9
 IS_TWO_DIMENSIONAL_MATERIAL      = False
 INCLUDE_RIGHT_SIDEWALL           = True
@@ -88,7 +88,7 @@ INTERFACE_ROUGHNESS              = 0.2e-9
 HOLES                            = []
 PILLARS                          = []
 INTERFACES                       = []
-BULKS                            = [] 
+BULKS                            = []
 
 # Multiprocessing:
 NUMBER_OF_PROCESSES              = 10

{freepaths-2.2.2 → freepaths-2.3.0}/freepaths/flight.py

@@ -54,7 +54,7 @@ class Flight:
         """Mean value of all free flights"""
         try:
             mfp = sum(self.free_paths)/len(self.free_paths)
-        except:
+        except ZeroDivisionError:
             mfp = 0
         return mfp
 

{freepaths-2.2.2 → freepaths-2.3.0}/freepaths/main_mfp_sampling.py

@@ -1,137 +1,135 @@
-"""Module to run thermal conductivity calculations by integrating the phonon dispersion"""
-
-import os
-import numpy as np
-import sys
-import time
-import shutil
-import scipy
-import math
-import logging
-from colorama import Fore, Style
-
-# Modules:
-from freepaths.animation import create_animation
-from freepaths.config import cf
-from freepaths.run_particle import run_particle
-from freepaths.phonon import Phonon
-from freepaths.flight import Flight
-from freepaths.particle_types import ParticleType
-from freepaths.data import ScatteringData, GeneralData, SegmentData, PathData, TriangleScatteringData
-from freepaths.progress import Progress
-from freepaths.materials import Si, SiC, Graphite, Ge
-from freepaths.maps import ScatteringMap, ThermalMaps
-from freepaths.output_info import output_general_information, output_scattering_information, output_parameter_warnings
-from freepaths.output_plots import plot_data
-
-
-def main(input_file, particle_type):
-    """This is the main function, which integrates phonon dispersion to get thermal conductivity"""
-
-    print(f'Mean free path sampling of {Fore.GREEN}{cf.output_folder_name}{Style.RESET_ALL}')
-    start_time = time.time()
-    progress = Progress()
-
-    # Initialize the material:
-    if cf.media == "Si":
-        material = Si(cf.temp, num_points=cf.number_of_particles +1)
-
-# -------- has to be modified fro have only SiGe values and not a mix between Ge and SiGe------------
-    elif cf.media == "Ge":
-        material = Ge(cf.temp, num_points=cf.number_of_particles +1)
-# -------- has to be modified fro have only SiGe values and not a mix between Ge and SiGe------------
-
-    elif cf.media == "SiC":
-        material = SiC(cf.temp, num_points=cf.number_of_particles+1)
-    elif cf.media == "Graphite":
-        material = Graphite(cf.temp, num_points=cf.number_of_particles+1)
-    else:
-        logging.error(f"Material {cf.media} is not supported")
-        sys.exit()
-
-    # Initiate data structures:
-    scatter_stats = ScatteringData()
-    general_stats = GeneralData()
-    segment_stats = SegmentData()
-    places_stats = TriangleScatteringData()
-    path_stats = PathData()
-    scatter_maps = ScatteringMap()
-    thermal_maps = ThermalMaps()
-
-    total_thermal_conductivity = 0.0
-
-    # For each polarization branch:
-    for branch_number in range(3):
-        sys.stdout.write(f"\rIntegrating branch number {branch_number+1}.\n")
-
-        # For each phonon:
-        for index in range(cf.number_of_particles):
-
-            # Wave vector:
-            k_vector = (material.dispersion[index+1, 0] + material.dispersion[index, 0]) / 2
-            d_k_vector = (material.dispersion[index+1, 0] - material.dispersion[index, 0])
-
-            # Initiate a phonon and its flight:
-            phonon = Phonon(material, branch_number, index)
-            flight = Flight(phonon)
-
-            # Run this phonon through the structure:
-            run_particle(phonon, flight, scatter_stats, places_stats, segment_stats, thermal_maps, scatter_maps, material)
-
-            # Heat capacity, Ref. PRB 88 155318 (2013):
-            omega = 2 * math.pi * phonon.f
-            part = scipy.constants.hbar * omega / (scipy.constants.k * cf.temp)
-            c_p = scipy.constants.k * part**2 * math.exp(part) / (math.exp(part) - 1)**2
-
-            # Thermal conductivity, Ref. Phys. Rev. 132 2461 (1963):
-            mean_relax_time = flight.mean_free_path/phonon.speed
-            flight.thermal_conductivity = (1/(6*(math.pi**2)))*c_p*(phonon.speed**2)*mean_relax_time*(k_vector**2)*d_k_vector
-            total_thermal_conductivity += flight.thermal_conductivity
-
-            # Record the properties returned for this phonon:
-            general_stats.save_particle_data(phonon)
-            general_stats.save_flight_data(flight)
-
-            # Record trajectories of the first N phonons:
-            if index < cf.output_trajectories_of_first:
-                path_stats.save_particle_path(flight)
-
-    # Run additional calculations:
-    thermal_maps.calculate_thermal_conductivity()
-    thermal_maps.calculate_weighted_flux()
-    thermal_maps.calculate_heat_flux_modulus()
-
-    # Create the folder if it does not exist and copy input file there:
-    if not os.path.exists("Results/" + cf.output_folder_name):
-        os.makedirs("Results/" + cf.output_folder_name)
-        os.makedirs("Results/" + cf.output_folder_name + '/Data')
-    if input_file:
-        shutil.copy(input_file, "Results/" + cf.output_folder_name)
-    os.chdir("Results/" + cf.output_folder_name)
-
-    # Save data into files:
-    general_stats.write_into_files()
-    scatter_stats.write_into_files()
-    segment_stats.write_into_files()
-    thermal_maps.write_into_files()
-
-    scatter_maps.write_into_files()
-    path_stats.write_into_files()
-
-    # Generate animation of phonon paths:
-    if cf.output_path_animation:
-        create_animation()
-
-    # Analyze and plot the data:
-    sys.stdout.write("\rAnalyzing the data...")
-    plot_data(particle_type, cf, mfp_sampling=True)
-
-    # Output general information:
-    output_general_information(start_time)
-    output_scattering_information(scatter_stats)
-    output_parameter_warnings()
-
-    np.savetxt("Data/Thermal conductivity from MFP.csv", np.array([total_thermal_conductivity]), fmt='%2.4e', header="K [W/mK]", encoding='utf-8')
-    sys.stdout.write(f'\rSee the results in {Fore.GREEN}Results/{cf.output_folder_name}{Style.RESET_ALL}\n')
-    sys.stdout.write(f"\rThermal conductivity = {Fore.GREEN}{total_thermal_conductivity:.5f}{Style.RESET_ALL} W/m·K\n")
-    sys.stdout.write(f"\r{Fore.BLUE}Thank you for using FreePATHS{Style.RESET_ALL}\n\n")
+"""Module to run thermal conductivity calculations by integrating the phonon dispersion"""
+
+import os
+import numpy as np
+import sys
+import time
+import shutil
+import scipy
+import math
+import logging
+from colorama import Fore, Style
+
+# Modules:
+from freepaths.animation import create_animation
+from freepaths.config import cf
+from freepaths.run_particle import run_particle
+from freepaths.phonon import Phonon
+from freepaths.flight import Flight
+from freepaths.particle_types import ParticleType
+from freepaths.data import ScatteringData, GeneralData, SegmentData, PathData, TriangleScatteringData
+from freepaths.progress import Progress
+from freepaths.materials import Si, SiC, Graphite, SiGe
+from freepaths.maps import ScatteringMap, ThermalMaps
+from freepaths.output_info import output_general_information, output_scattering_information, output_parameter_warnings
+from freepaths.output_plots import plot_data
+
+
+def main(input_file, particle_type):
+    """This is the main function, which integrates phonon dispersion to get thermal conductivity"""
+
+    print(f'Mean free path sampling of {Fore.GREEN}{cf.output_folder_name}{Style.RESET_ALL}')
+    start_time = time.time()
+    progress = Progress()
+
+    # Initialize the material:
+    if cf.media == "Si":
+        material = Si(cf.temp, num_points=cf.number_of_particles +1)
+
+    elif cf.media == "SiGe":
+        material = SiGe(cf.temp, num_points=cf.number_of_particles +1)
+
+    elif cf.media == "SiC":
+        material = SiC(cf.temp, num_points=cf.number_of_particles+1)
+    elif cf.media == "Graphite":
+        material = Graphite(cf.temp, num_points=cf.number_of_particles+1)
+    else:
+        logging.error(f"Material {cf.media} is not supported")
+        sys.exit()
+
+    # Initiate data structures:
+    scatter_stats = ScatteringData()
+    general_stats = GeneralData()
+    segment_stats = SegmentData()
+    places_stats = TriangleScatteringData()
+    path_stats = PathData()
+    scatter_maps = ScatteringMap()
+    thermal_maps = ThermalMaps()
+
+    total_thermal_conductivity = 0.0
+
+    # For each polarization branch:
+    for branch_number in range(3):
+        sys.stdout.write(f"\rIntegrating branch number {branch_number+1}.\n")
+
+        # For each phonon:
+        for index in range(cf.number_of_particles):
+
+            # Wave vector:
+            k_vector = (material.dispersion[index+1, 0] + material.dispersion[index, 0]) / 2
+            d_k_vector = (material.dispersion[index+1, 0] - material.dispersion[index, 0])
+
+            # Initiate a phonon and its flight:
+            phonon = Phonon(material, branch_number, index)
+            flight = Flight(phonon)
+
+            # Run this phonon through the structure:
+            run_particle(phonon, flight, scatter_stats, places_stats, segment_stats, thermal_maps, scatter_maps, material)
+
+            # Heat capacity, Ref. PRB 88 155318 (2013):
+            omega = 2 * math.pi * phonon.f
+            part = scipy.constants.hbar * omega / (scipy.constants.k * cf.temp)
+            c_p = scipy.constants.k * part**2 * math.exp(part) / (math.exp(part) - 1)**2
+
+            # Thermal conductivity, Ref. Phys. Rev. 132 2461 (1963):
+            mean_relax_time = flight.mean_free_path/phonon.speed
+            flight.thermal_conductivity = (1/(6*(math.pi**2)))*c_p*(phonon.speed**2)*mean_relax_time*(k_vector**2)*d_k_vector
+            total_thermal_conductivity += flight.thermal_conductivity
+
+            # Record the properties returned for this phonon:
+            general_stats.save_particle_data(phonon)
+            general_stats.save_flight_data(flight)
+
+            # Record trajectories of the first N phonons:
+            if index < cf.output_trajectories_of_first:
+                path_stats.save_particle_path(flight)
+
+    # Run additional calculations:
+    thermal_maps.calculate_thermal_conductivity()
+    thermal_maps.calculate_weighted_flux()
+    thermal_maps.calculate_heat_flux_modulus()
+
+    # Create the folder if it does not exist and copy input file there:
+    if not os.path.exists("Results/" + cf.output_folder_name):
+        os.makedirs("Results/" + cf.output_folder_name)
+        os.makedirs("Results/" + cf.output_folder_name + '/Data')
+    if input_file:
+        shutil.copy(input_file, "Results/" + cf.output_folder_name)
+    os.chdir("Results/" + cf.output_folder_name)
+
+    # Save data into files:
+    general_stats.write_into_files()
+    scatter_stats.write_into_files()
+    segment_stats.write_into_files()
+    thermal_maps.write_into_files()
+
+    scatter_maps.write_into_files()
+    path_stats.write_into_files()
+
+    # Generate animation of phonon paths:
+    if cf.output_path_animation:
+        create_animation()
+
+    # Analyze and plot the data:
+    sys.stdout.write("\rAnalyzing the data...")
+    plot_data(particle_type, cf, mfp_sampling=True)
+
+    # Output general information:
+    output_general_information(start_time)
+    output_scattering_information(scatter_stats)
+    output_parameter_warnings()
+
+    np.savetxt("Data/Thermal conductivity from MFP.csv", np.array([total_thermal_conductivity]), fmt='%2.4e', header="K [W/mK]", encoding='utf-8')
+    sys.stdout.write(f'\rSee the results in {Fore.GREEN}Results/{cf.output_folder_name}{Style.RESET_ALL}\n')
+    sys.stdout.write(f"\rThermal conductivity = {Fore.GREEN}{total_thermal_conductivity:.5f}{Style.RESET_ALL} W/m·K\n")
+    sys.stdout.write(f"\r{Fore.BLUE}Thank you for using FreePATHS{Style.RESET_ALL}\n\n")