Implementing gradient in different directions

anufrievroman · May 11, 2023 · 81eb823 · 81eb823
1 parent 34f6b43
commit 81eb823
Show file tree

Hide file tree

Showing 22 changed files with 3,487 additions and 50 deletions.
diff --git a/examples/animated_corrugated_nanowire.py b/examples/animated_corrugated_nanowire.py
@@ -16,7 +16,6 @@
 OUTPUT_SCATTERING_MAP          = False
 OUTPUT_RAW_THERMAL_MAP         = True
 NUMBER_OF_LENGTH_SEGMENTS      = 10
-HOT_SIDE_ANGLE_DISTRIBUTION    = 'random'
 
 
 # Animation parameters:

diff --git a/examples/anisotropy_study_horizontal.py b/examples/anisotropy_study_horizontal.py
@@ -0,0 +1,74 @@
+"""Config file to simulate a membrane with a staggered lattice of rectangular slits"""
+
+import numpy as np
+
+
+# General parameters:
+OUTPUT_FOLDER_NAME             = 'Anisotropy study horizontal'
+NUMBER_OF_PHONONS              = 1000
+NUMBER_OF_TIMESTEPS            = 30000
+NUMBER_OF_NODES                = 400
+TIMESTEP                       = 1e-12
+T                              = 4.0
+
+# Map & profiles parameters:
+NUMBER_OF_PIXELS_X             = 100
+NUMBER_OF_PIXELS_Y             = 100
+NUMBER_OF_TIMEFRAMES           = 6
+
+# Material parameters:
+MEDIA                          = 'Si'
+SPECIFIC_HEAT_CAPACITY         = 0.0176  # [J/kg/K] for Si at 4 K
+
+
+# System dimensions [m]:
+THICKNESS                      = 150e-9
+WIDTH                          = 1300e-9
+LENGTH                         = 1300e-9
+
+# STRUCTURE:
+
+#      ---->
+#-------------------
+#
+# H               C
+#
+#-------------------
+
+INCLUDE_RIGHT_SIDEWALL         = False
+INCLUDE_LEFT_SIDEWALL          = False
+INCLUDE_TOP_SIDEWALL           = True
+INCLUDE_BOTTOM_SIDEWALL        = True
+
+# Hot and cold sides [m]:
+COLD_SIDE_POSITION             = 'right'
+HOT_SIDE_POSITION              = 'left'
+HOT_SIDE_X                     = -WIDTH/2
+HOT_SIDE_Y                     = LENGTH/2
+HOT_SIDE_WIDTH_X               = 0
+HOT_SIDE_WIDTH_Y               = LENGTH
+HOT_SIDE_ANGLE_DISTRIBUTION    = 'random_right'
+
+
+# Hole array parameters [m]:
+INCLUDE_HOLES                  = True
+CIRCULAR_HOLE_DIAMETER         = 0
+RECTANGULAR_HOLE_SIDE_X        = 200e-9
+RECTANGULAR_HOLE_SIDE_Y        = 100e-9
+PERIOD_X                       = 300e-9
+PERIOD_Y                       = 300e-9
+
+
+# Staggered attice of holes:
+FIRST_HOLE_COORDINATE = 200e-9
+NUMBER_OF_PERIODS_X = 4
+NUMBER_OF_PERIODS_Y = 4
+HOLE_COORDINATES = np.zeros((NUMBER_OF_PERIODS_X * NUMBER_OF_PERIODS_Y, 3))
+HOLE_SHAPES = ['rectangle' for x in range(HOLE_COORDINATES.shape[0])]
+hole_number = 0
+for i in range(NUMBER_OF_PERIODS_Y):
+    for j in range(NUMBER_OF_PERIODS_X):
+        HOLE_COORDINATES[hole_number, 0] = -(NUMBER_OF_PERIODS_X - 1) * PERIOD_X / 2 + j * PERIOD_X
+        HOLE_COORDINATES[hole_number, 1] = FIRST_HOLE_COORDINATE + i * PERIOD_Y
+        HOLE_COORDINATES[hole_number, 2] = 0
+        hole_number += 1
diff --git a/examples/anisotropy_study_vertical.py b/examples/anisotropy_study_vertical.py
@@ -0,0 +1,74 @@
+"""Config file to simulate a membrane with a staggered lattice of rectangular slits
+Here we impose thermal gradient in vertical direction"""
+
+import numpy as np
+
+
+# General parameters:
+OUTPUT_FOLDER_NAME             = 'Anisotropy study vertical'
+NUMBER_OF_PHONONS              = 1000
+NUMBER_OF_TIMESTEPS            = 30000
+NUMBER_OF_NODES                = 400
+TIMESTEP                       = 1e-12
+T                              = 4.0
+
+# Map & profiles parameters:
+NUMBER_OF_PIXELS_X             = 100
+NUMBER_OF_PIXELS_Y             = 100
+NUMBER_OF_TIMEFRAMES           = 6
+
+# Material parameters:
+MEDIA                          = 'Si'
+SPECIFIC_HEAT_CAPACITY         = 0.0176  # [J/kg/K] for Si at 4 K
+
+
+# System dimensions [m]:
+THICKNESS                      = 150e-9
+WIDTH                          = 1300e-9
+LENGTH                         = 1300e-9
+
+# STRUCTURE:
+
+# |    C    |   
+# |         |  ^
+# |         |  |
+# |         |  |
+# |    H    | 
+
+INCLUDE_RIGHT_SIDEWALL         = True
+INCLUDE_LEFT_SIDEWALL          = True
+INCLUDE_TOP_SIDEWALL           = False
+INCLUDE_BOTTOM_SIDEWALL        = False
+
+# Hot and cold sides [m]:
+COLD_SIDE_POSITION             = 'top'
+HOT_SIDE_POSITION              = 'bottom'
+HOT_SIDE_X                     = 0
+HOT_SIDE_Y                     = 0
+HOT_SIDE_WIDTH_X               = WIDTH
+HOT_SIDE_WIDTH_Y               = 0
+HOT_SIDE_ANGLE_DISTRIBUTION    = 'random_up'
+
+# Hole array parameters [m]:
+INCLUDE_HOLES                  = True
+CIRCULAR_HOLE_DIAMETER         = 0
+RECTANGULAR_HOLE_SIDE_X        = 200e-9
+RECTANGULAR_HOLE_SIDE_Y        = 100e-9
+PERIOD_X                       = 300e-9
+PERIOD_Y                       = 300e-9
+
+
+# Staggered attice of holes:
+FIRST_HOLE_COORDINATE = 200e-9
+NUMBER_OF_PERIODS_X = 4
+NUMBER_OF_PERIODS_Y = 4
+HOLE_COORDINATES = np.zeros((NUMBER_OF_PERIODS_X * NUMBER_OF_PERIODS_Y, 3))
+HOLE_SHAPES = ['rectangle' for x in range(HOLE_COORDINATES.shape[0])]
+hole_number = 0
+for i in range(NUMBER_OF_PERIODS_Y):
+    for j in range(NUMBER_OF_PERIODS_X):
+        HOLE_COORDINATES[hole_number, 0] = -(NUMBER_OF_PERIODS_X - 1) * PERIOD_X / 2 + j * PERIOD_X
+        HOLE_COORDINATES[hole_number, 1] = FIRST_HOLE_COORDINATE + i * PERIOD_Y
+        HOLE_COORDINATES[hole_number, 2] = 0
+        hole_number += 1
+
diff --git a/examples/fishbone_nanowire.py b/examples/fishbone_nanowire.py
@@ -14,7 +14,6 @@
 OUTPUT_RAW_THERMAL_MAP         = True
 OUTPUT_TRAJECTORIES_OF_FIRST   = 30
 NUMBER_OF_LENGTH_SEGMENTS      = 10
-HOT_SIDE_ANGLE_DISTRIBUTION    = 'random'
 
 
 # Map & profiles parameters:

diff --git a/examples/parabolic_lens_focusing.py b/examples/parabolic_lens_focusing.py
@@ -13,7 +13,6 @@
 OUTPUT_RAW_THERMAL_MAP         = True
 OUTPUT_TRAJECTORIES_OF_FIRST   = 30
 NUMBER_OF_LENGTH_SEGMENTS      = 10
-HOT_SIDE_ANGLE_DISTRIBUTION    = 'directional'
 
 
 # Map & profiles parameters:
@@ -43,6 +42,7 @@
 COLD_SIDE_POSITION             = 'top'
 HOT_SIDE_X                     = 0.0
 HOT_SIDE_WIDTH_X               = WIDTH
+HOT_SIDE_ANGLE_DISTRIBUTION    = 'directional'
 
 # Roughness [m]:
 SIDE_WALL_ROUGHNESS            = 2e-9

diff --git a/examples/phononic_crystal.py b/examples/phononic_crystal.py
@@ -15,7 +15,6 @@
 OUTPUT_RAW_THERMAL_MAP         = True
 OUTPUT_TRAJECTORIES_OF_FIRST   = 30
 NUMBER_OF_LENGTH_SEGMENTS      = 10
-HOT_SIDE_ANGLE_DISTRIBUTION    = 'random'
 
 
 # Map & profiles parameters:

diff --git a/examples/simple_nanowire.py b/examples/simple_nanowire.py
@@ -15,7 +15,6 @@
 OUTPUT_RAW_THERMAL_MAP         = True
 OUTPUT_TRAJECTORIES_OF_FIRST   = 30
 NUMBER_OF_LENGTH_SEGMENTS      = 10
-HOT_SIDE_ANGLE_DISTRIBUTION    = 'random'
 
 
 # Map & profiles parameters:

diff --git a/examples/slits_array.py b/examples/slits_array.py
@@ -15,7 +15,6 @@
 OUTPUT_RAW_THERMAL_MAP         = True
 OUTPUT_TRAJECTORIES_OF_FIRST   = 30
 NUMBER_OF_LENGTH_SEGMENTS      = 10
-HOT_SIDE_ANGLE_DISTRIBUTION    = 'random'
 
 
 # Map & profiles parameters:

diff --git a/examples/triangles_array.py b/examples/triangles_array.py
@@ -15,7 +15,6 @@
 OUTPUT_RAW_THERMAL_MAP         = True
 OUTPUT_TRAJECTORIES_OF_FIRST   = 30
 NUMBER_OF_LENGTH_SEGMENTS      = 10
-HOT_SIDE_ANGLE_DISTRIBUTION    = 'random'
 
 
 # Map & profiles parameters:

diff --git a/freepaths/__main__.py b/freepaths/__main__.py
@@ -5,13 +5,13 @@
 import freepaths.main_tracing
 import freepaths.main_mfp_sampling
 
-__version__ = "1.2.2"
+__version__ = "1.3"
 
 # Parse user arguments:
 parser = argparse.ArgumentParser(
                 prog = 'FreePATHS',
                 description = 'Monte Carlo simulator',
-                epilog = 'For more information, visit: https://github.com/anufrievroman/freepaths'
+                epilog = 'For more information, visit: https://anufrievroman.gitbook.io/freepaths'
                 )
 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")

diff --git a/freepaths/animation.py b/freepaths/animation.py
@@ -80,9 +80,18 @@ def generate_animation_xy():
     filenames = os.listdir("Frames/")
     for filename in filenames:
         images.append(imageio.imread(f"Frames/{filename}"))
+
+    # Create a GIF file:
     imageio.mimsave("Animated paths XY.gif", images,
                     fps=cf.output_animation_fps, subrectangles=True)
 
+    # Create an MP4 file:
+    # writer = imageio.get_writer('Animated paths XY.mp4', fps=cf.output_animation_fps)
+
+    # for im in images:
+        # writer.append_data(imageio.imread(im))
+    # writer.close()
+
 
 def delete_frames():
     """Delete frames after creating the animation"""

diff --git a/freepaths/animation__.py b/freepaths/animation__.py
@@ -0,0 +1,97 @@
+"""Module that creates animations from recorded phonon paths"""
+
+import sys
+import os
+import shutil
+import imageio
+import numpy as np
+import matplotlib.pyplot as plt
+
+from freepaths.config import cf
+from freepaths.output_structure import draw_structure
+
+
+def generate_frames_xy():
+    """Generate animation frames with phonon paths"""
+
+    data = np.genfromtxt("Data/Phonon paths.csv",
+                         unpack=False,
+                         delimiter=',',
+                         skip_header=1,
+                         encoding='utf-8')
+
+    # Create XY plots for each timestep where all phonon shown at the same time:
+    number_of_steps = np.shape(data)[0]
+    number_of_phonons = np.shape(data)[1]//3
+
+    for step in range(1, number_of_steps):
+        fig, ax = plt.subplots()
+
+        # Draw the structure:
+        patches = draw_structure(cf)
+        for patch in patches:
+            ax.add_patch(patch)
+
+        # Draw the paths:
+        for phonon_num in range(number_of_phonons):
+            x_coords = np.trim_zeros(data[:, 3 * phonon_num], trim='b')
+            y_coords = np.trim_zeros(data[:, 3 * phonon_num + 1], trim='b')
+            ax.plot(x_coords[:step], y_coords[:step], linewidth=0.5)
+
+        # Plot settings:
+        ax.set_xlim([-0.55*cf.width*1e6, 0.55*cf.width*1e6])
+        ax.set_ylim([0, cf.length*1e6])
+        ax.set_aspect('equal')
+        ax.axis('off')
+        for spine in ['top', 'right', 'left', 'bottom']:
+            ax.spines[spine].set_visible(False)
+        fig.savefig(f"Frames/frame_{step:0>6}.png", dpi=600, bbox_inches="tight")
+        plt.close(fig)
+
+        # Progress:
+        sys.stdout.write(f"\rAnimation: {step}/{number_of_steps - 1} frames")
+
+    # Create XY plots for each step for each phonon one by one:
+    # cmap = plt.get_cmap("tab10")
+    # frame_number = 0
+    # number_of_phonons = np.shape(data)[1]//3
+    # for phonon_num in range(number_of_phonons):
+        # x_coords = np.trim_zeros(data[:, 3 * phonon_num], trim='b')
+        # y_coords = np.trim_zeros(data[:, 3 * phonon_num + 1], trim='b')
+        # steps = np.shape(x_coords)[0]
+        # for step in range(1, steps):
+            # fig, ax = plt.subplots()
+            # ax.plot(x_coords[:step], y_coords[:step], color=cmap(phonon_num), linewidth=0.5)
+            # ax.axis('off')
+            # for spine in ['top', 'right', 'left', 'bottom']:
+                # ax.spines[spine].set_visible(False)
+            # ax.set_xlim([-0.55*cf.width*1e6, 0.55*cf.width*1e6])
+            # ax.set_ylim([0, cf.length*1e6])
+            # ax.set_aspect('equal')
+            # fig.savefig(f"Frames/frame_{frame_number:0>6}.png", dpi=600, bbox_inches="tight")
+            # plt.close(fig)
+            # frame_number += 1
+
+
+def generate_animation_xy():
+    """Generate animation of phonon path in XY plane"""
+    sys.stdout.write(f"\rAnimation: creating animation file")
+    images = []
+    filenames = os.listdir("Frames/")
+    for filename in filenames:
+        images.append(imageio.imread(f"Frames/{filename}"))
+    imageio.mimsave("Animated paths XY.gif", images,
+                    fps=cf.output_animation_fps, subrectangles=True)
+
+
+def delete_frames():
+    """Delete frames after creating the animation"""
+    folder_path = "Frames/"
+    shutil.rmtree(folder_path)
+
+
+def create_animation():
+    """Main function that creates the animation"""
+    generate_frames_xy()
+    generate_animation_xy()
+    delete_frames()